diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index ac6bfee64a4d6460e1a02df3626eb4b309629590..2a95c9633b399b2087b9fcafbc5da2df0844166d 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -1,7 +1,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@

LAMMPS Documentation :c,h3 -22 Feb 2018 version :c,h4 +16 Mar 2018 version :c,h4 Version info: :h4 diff --git a/doc/src/PDF/colvars-refman-lammps.pdf b/doc/src/PDF/colvars-refman-lammps.pdf index daa1393269b953d569aff9846a135480dcdd42c7..2d28758819a9a7a0dac700cd4a8239f51257b8e1 100644 Binary files a/doc/src/PDF/colvars-refman-lammps.pdf and b/doc/src/PDF/colvars-refman-lammps.pdf differ diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt index affcae1e5494fdd02d5849298cb7f50dc760c186..6473c346dce1acbdf9a220d4149c6925de0c0cc3 100644 --- a/doc/src/Section_start.txt +++ b/doc/src/Section_start.txt @@ -803,6 +803,10 @@ currently installed. For those that are installed, it will list any files that are different in the src directory and package sub-directory. +Typing "make package-installed" or "make pi" will list which packages are +currently installed, without listing the status of packages that are not +installed. + Typing "make package-update" or "make pu" will overwrite src files with files from the package sub-directories if the package is installed. It should be used after a patch has been applied, since diff --git a/doc/src/pair_meam.txt b/doc/src/pair_meam.txt index 62fa59f406064301bcd0eea5fd106e18e0ee1041..c7449428bd05aa010182dc17cb2f9206b69e5303 100644 --- a/doc/src/pair_meam.txt +++ b/doc/src/pair_meam.txt @@ -77,7 +77,7 @@ See the "pair_coeff"_pair_coeff.html doc page for alternate ways to specify the path for the potential files. As an example, the potentials/library.meam file has generic MEAM -settings for a variety of elements. The potentials/sic.meam file has +settings for a variety of elements. The potentials/SiC.meam file has specific parameter settings for a Si and C alloy system. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si, and the 4th to be C, you would use the following pair_coeff command: @@ -105,6 +105,15 @@ This can be used when a {meam} potential is used as part of the {hybrid} pair style. The NULL values are placeholders for atom types that will be used with other potentials. +NOTE: If the 2nd filename is NULL, the element names between the two +filenames can appear in any order, e.g. "Si C" or "C Si" in the +example above. However, if the 2nd filename is not NULL (as in the +example above), it contains settings that are Fortran-indexed for the +elements that preceed it. Thus you need to insure you list the +elements between the filenames in an order consistent with how the +values in the 2nd filename are indexed. See details below on the +syntax for settings in the 2nd file. + The MEAM library file provided with LAMMPS has the name potentials/library.meam. It is the "meamf" file used by other MD codes. Aside from blank and comment lines (start with #) which can @@ -164,7 +173,15 @@ keyword(I) = value keyword(I,J) = value keyword(I,J,K) = value :pre -The recognized keywords are as follows: +The indices I, J, K correspond to the elements selected from the +MEAM library file numbered in the order of how those elements were +selected starting from 1. Thus for the example given below + +pair_coeff * * library.meam Si C sic.meam Si Si Si C :pre + +an index of 1 would refer to Si and an index of 2 to C. + +The recognized keywords for the parameter file are as follows: Ec, alpha, rho0, delta, lattce, attrac, repuls, nn2, Cmin, Cmax, rc, delr, augt1, gsmooth_factor, re diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt index 4ea60163b2214c35c0328975f33c97664c19635d..fd297e36c121e1efb8f631c95c182a51587a60c0 100644 --- a/doc/src/read_data.txt +++ b/doc/src/read_data.txt @@ -15,10 +15,11 @@ read_data file keyword args ... :pre file = name of data file to read in :ulb,l zero or more keyword/arg pairs may be appended :l keyword = {add} or {offset} or {shift} or {extra/atom/types} or {extra/bond/types} or {extra/angle/types} or {extra/dihedral/types} or {extra/improper/types} or {extra/bond/per/atom} or {extra/angle/per/atom} or {extra/dihedral/per/atom} or {extra/improper/per/atom} or {group} or {nocoeff} or {fix} :l - {add} arg = {append} or {Nstart} or {merge} - append = add new atoms with IDs appended to current IDs - Nstart = add new atoms with IDs starting with Nstart - merge = add new atoms with their IDs unchanged + {add} arg = {append} or {IDoffset} or {IDoffset MOLoffset} or {merge} + append = add new atoms with atom IDs appended to current IDs + IDoffset = add new atoms with atom IDs having IDoffset added + MOLoffset = add new atoms with molecule IDs having MOLoffset added (only when molecule IDs are enabled) + merge = add new atoms with their atom IDs (and molecule IDs) unchanged {offset} args = toff boff aoff doff ioff toff = offset to add to atom types boff = offset to add to bond types @@ -120,20 +121,26 @@ boundary, then the atoms may become far apart if the box size grows. This will separate the atoms in the bond, which can lead to "lost" bond atoms or bad dynamics. -The three choices for the {add} argument affect how the IDs of atoms -in the data file are treated. If {append} is specified, atoms in the -data file are added to the current system, with their atom IDs reset -so that an atomID = M in the data file becomes atomID = N+M, where N -is the largest atom ID in the current system. This rule is applied to -all occurrences of atom IDs in the data file, e.g. in the Velocity or -Bonds section. If {Nstart} is specified, then {Nstart} is a numeric -value is given, e.g. 1000, so that an atomID = M in the data file -becomes atomID = 1000+M. If {merge} is specified, the data file atoms +The three choices for the {add} argument affect how the atom IDs and +molecule IDs of atoms in the data file are treated. If {append} is +specified, atoms in the data file are added to the current system, +with their atom IDs reset so that an atomID = M in the data file +becomes atomID = N+M, where N is the largest atom ID in the current +system. This rule is applied to all occurrences of atom IDs in the +data file, e.g. in the Velocity or Bonds section. This is also done +for molecule IDs, if the atom style does support molecule IDs or +they are enabled via fix property/atom. If {IDoffset} is specified, +then {IDoffset} is a numeric value is given, e.g. 1000, so that an +atomID = M in the data file becomes atomID = 1000+M. For systems +with enabled molecule IDs, another numerical argument {MOLoffset} +is required representing the equivalent offset for molecule IDs. +If {merge} is specified, the data file atoms are added to the current system without changing their IDs. They are assumed to merge (without duplication) with the currently defined atoms. It is up to you to insure there are no multiply defined atom IDs, as LAMMPS only performs an incomplete check that this is the case -by insuring the resulting max atomID >= the number of atoms. +by insuring the resulting max atomID >= the number of atoms. For +molecule IDs, there is no check done at all. The {offset} and {shift} keywords can only be used if the {add} keyword is also specified. diff --git a/examples/reax/AB/log.5Oct16.AB.g++.4 b/examples/reax/AB/log.5Oct16.AB.g++.4 deleted file mode 100644 index cfc4476ef58a1ed94168c277db5e48ff5ce3fb70..0000000000000000000000000000000000000000 --- a/examples/reax/AB/log.5Oct16.AB.g++.4 +++ /dev/null @@ -1,70 +0,0 @@ -LAMMPS (5 Oct 2016) -# REAX potential for Nitroamines system -# ..... - -units real - -atom_style charge -read_data data.AB - orthogonal box = (0 0 0) to (25 25 25) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 104 atoms - -pair_style reax/c lmp_control -pair_coeff * * ffield.reax.AB H B N -Reading potential file ffield.reax.AB with DATE: 2011-02-18 - -neighbor 2 bin -neigh_modify every 10 delay 0 check no - -fix 1 all nve -fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq -fix 3 all temp/berendsen 500.0 500.0 100.0 - -timestep 0.25 - -#dump 1 all atom 30 dump.reax.ab - -run 3000 -Neighbor list info ... - 2 neighbor list requests - update every 10 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12 - ghost atom cutoff = 12 - binsize = 6 -> bins = 5 5 5 -Memory usage per processor = 12.622 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -8505.1816 0 -8505.1816 -673.36566 - 3000 496.56561 -8405.3755 0 -8252.9182 472.58916 -Loop time of 7.23109 on 4 procs for 3000 steps with 104 atoms - -Performance: 8.961 ns/day, 2.678 hours/ns, 414.875 timesteps/s -99.4% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 5.705 | 5.7262 | 5.7504 | 0.7 | 79.19 -Neigh | 0.14367 | 0.15976 | 0.16805 | 2.4 | 2.21 -Comm | 0.053353 | 0.077311 | 0.097821 | 5.7 | 1.07 -Output | 1.812e-05 | 1.9848e-05 | 2.408e-05 | 0.1 | 0.00 -Modify | 1.2559 | 1.2647 | 1.2818 | 0.9 | 17.49 -Other | | 0.003126 | | | 0.04 - -Nlocal: 26 ave 35 max 13 min -Histogram: 1 0 0 0 0 1 0 0 1 1 -Nghost: 421 ave 450 max 377 min -Histogram: 1 0 0 0 0 1 0 0 1 1 -Neighs: 847.25 ave 1149 max 444 min -Histogram: 1 0 0 0 1 0 0 0 1 1 - -Total # of neighbors = 3389 -Ave neighs/atom = 32.5865 -Neighbor list builds = 300 -Dangerous builds not checked - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:07 diff --git a/examples/reax/AB/log.5Oct16.AB.g++.1 b/examples/reax/AB/log.8Mar18.AB.g++.1 similarity index 50% rename from examples/reax/AB/log.5Oct16.AB.g++.1 rename to examples/reax/AB/log.8Mar18.AB.g++.1 index df7d20d8bcebb00be7dddd8c207ee8944c8ac472..065b1a1e677fa07d1ad71fc1dbab4d32a2a375b9 100644 --- a/examples/reax/AB/log.5Oct16.AB.g++.1 +++ b/examples/reax/AB/log.8Mar18.AB.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (8 Mar 2018) + using 1 OpenMP thread(s) per MPI task # REAX potential for Nitroamines system # ..... @@ -28,43 +29,53 @@ timestep 0.25 run 3000 Neighbor list info ... - 2 neighbor list requests update every 10 steps, delay 0 steps, check no max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 - binsize = 6 -> bins = 5 5 5 -Memory usage per processor = 18.4119 Mbytes + binsize = 6, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reax/c, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: half/ghost/bin/3d/newtoff + bin: standard + (2) fix qeq/reax, perpetual, copy from (1) + attributes: half, newton off, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 19.3 | 19.3 | 19.3 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8505.1816 0 -8505.1816 -673.36566 - 3000 499.30579 -8405.1387 0 -8251.8401 -94.844317 -Loop time of 12.5114 on 1 procs for 3000 steps with 104 atoms + 3000 478.18595 -8398.4168 0 -8251.6025 1452.6935 +Loop time of 14.3573 on 1 procs for 3000 steps with 104 atoms -Performance: 5.179 ns/day, 4.634 hours/ns, 239.782 timesteps/s -99.3% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 4.513 ns/day, 5.318 hours/ns, 208.952 timesteps/s +96.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 11.137 | 11.137 | 11.137 | 0.0 | 89.01 -Neigh | 0.29816 | 0.29816 | 0.29816 | 0.0 | 2.38 -Comm | 0.016993 | 0.016993 | 0.016993 | 0.0 | 0.14 -Output | 1.1921e-05 | 1.1921e-05 | 1.1921e-05 | 0.0 | 0.00 -Modify | 1.0552 | 1.0552 | 1.0552 | 0.0 | 8.43 -Other | | 0.004142 | | | 0.03 +Pair | 12.709 | 12.709 | 12.709 | 0.0 | 88.52 +Neigh | 0.36804 | 0.36804 | 0.36804 | 0.0 | 2.56 +Comm | 0.022419 | 0.022419 | 0.022419 | 0.0 | 0.16 +Output | 2.8133e-05 | 2.8133e-05 | 2.8133e-05 | 0.0 | 0.00 +Modify | 1.2513 | 1.2513 | 1.2513 | 0.0 | 8.72 +Other | | 0.006263 | | | 0.04 Nlocal: 104 ave 104 max 104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 694 ave 694 max 694 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 2927 ave 2927 max 2927 min +Neighs: 2866 ave 2866 max 2866 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 2927 -Ave neighs/atom = 28.1442 +Total # of neighbors = 2866 +Ave neighs/atom = 27.5577 Neighbor list builds = 300 Dangerous builds not checked Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:12 +Total wall time: 0:00:14 diff --git a/examples/reax/AB/log.8Mar18.AB.g++.4 b/examples/reax/AB/log.8Mar18.AB.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..1e02ec5725e4bdcdb6402e6c73147d9f47b0006b --- /dev/null +++ b/examples/reax/AB/log.8Mar18.AB.g++.4 @@ -0,0 +1,81 @@ +LAMMPS (8 Mar 2018) + using 1 OpenMP thread(s) per MPI task +# REAX potential for Nitroamines system +# ..... + +units real + +atom_style charge +read_data data.AB + orthogonal box = (0 0 0) to (25 25 25) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 104 atoms + +pair_style reax/c lmp_control +pair_coeff * * ffield.reax.AB H B N +Reading potential file ffield.reax.AB with DATE: 2011-02-18 + +neighbor 2 bin +neigh_modify every 10 delay 0 check no + +fix 1 all nve +fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq +fix 3 all temp/berendsen 500.0 500.0 100.0 + +timestep 0.25 + +#dump 1 all atom 30 dump.reax.ab + +run 3000 +Neighbor list info ... + update every 10 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reax/c, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: half/ghost/bin/3d/newtoff + bin: standard + (2) fix qeq/reax, perpetual, copy from (1) + attributes: half, newton off, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 12.38 | 13.22 | 13.64 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -8505.1816 0 -8505.1816 -673.36566 + 3000 555.17702 -8426.5541 0 -8256.1017 219.26856 +Loop time of 9.03521 on 4 procs for 3000 steps with 104 atoms + +Performance: 7.172 ns/day, 3.346 hours/ns, 332.034 timesteps/s +94.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7.0347 | 7.0652 | 7.1049 | 1.0 | 78.20 +Neigh | 0.18481 | 0.20727 | 0.22108 | 3.0 | 2.29 +Comm | 0.075175 | 0.11496 | 0.14517 | 7.4 | 1.27 +Output | 2.2888e-05 | 2.569e-05 | 3.1948e-05 | 0.0 | 0.00 +Modify | 1.6286 | 1.6421 | 1.6649 | 1.1 | 18.17 +Other | | 0.005646 | | | 0.06 + +Nlocal: 26 ave 35 max 13 min +Histogram: 1 0 0 0 0 1 0 0 1 1 +Nghost: 420.25 ave 454 max 370 min +Histogram: 1 0 0 0 0 1 0 0 1 1 +Neighs: 862.5 ave 1178 max 444 min +Histogram: 1 0 0 0 1 0 0 0 1 1 + +Total # of neighbors = 3450 +Ave neighs/atom = 33.1731 +Neighbor list builds = 300 +Dangerous builds not checked + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:09 diff --git a/examples/reax/AuO/log.5Oct16.AuO.g++.1 b/examples/reax/AuO/log.8Mar18.AuO.g++.1 similarity index 52% rename from examples/reax/AuO/log.5Oct16.AuO.g++.1 rename to examples/reax/AuO/log.8Mar18.AuO.g++.1 index 7ae86b9d60c413b7c23b946d5b20c5fff7c99363..3c609ac0238cabb2dad613fbcfcbfdece3e30340 100644 --- a/examples/reax/AuO/log.5Oct16.AuO.g++.1 +++ b/examples/reax/AuO/log.8Mar18.AuO.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (8 Mar 2018) + using 1 OpenMP thread(s) per MPI task # REAX potential for AuO system # ..... @@ -28,30 +29,40 @@ timestep 0.25 run 100 Neighbor list info ... - 2 neighbor list requests update every 10 steps, delay 0 steps, check no max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 - binsize = 6 -> bins = 5 4 5 -Memory usage per processor = 144.382 Mbytes + binsize = 6, bins = 5 4 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reax/c, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: half/ghost/bin/3d/newtoff + bin: standard + (2) fix qeq/reax, perpetual, copy from (1) + attributes: half, newton off, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 157.6 | 157.6 | 157.6 Mbytes Step Temp E_pair E_mol TotEng Press - 0 0 -72201.743 0 -72201.743 -166.1947 - 100 69.043346 -72076.31 0 -71878.943 22702.308 -Loop time of 17.7559 on 1 procs for 100 steps with 960 atoms + 0 0 -72201.743 0 -72201.743 -166.19482 + 100 69.043331 -72076.309 0 -71878.942 22702.89 +Loop time of 18.4369 on 1 procs for 100 steps with 960 atoms -Performance: 0.122 ns/day, 197.288 hours/ns, 5.632 timesteps/s -99.8% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.117 ns/day, 204.854 hours/ns, 5.424 timesteps/s +98.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 15.102 | 15.102 | 15.102 | 0.0 | 85.05 -Neigh | 0.49358 | 0.49358 | 0.49358 | 0.0 | 2.78 -Comm | 0.0067561 | 0.0067561 | 0.0067561 | 0.0 | 0.04 -Output | 1.502e-05 | 1.502e-05 | 1.502e-05 | 0.0 | 0.00 -Modify | 2.1525 | 2.1525 | 2.1525 | 0.0 | 12.12 -Other | | 0.001267 | | | 0.01 +Pair | 15.373 | 15.373 | 15.373 | 0.0 | 83.38 +Neigh | 0.58774 | 0.58774 | 0.58774 | 0.0 | 3.19 +Comm | 0.0079026 | 0.0079026 | 0.0079026 | 0.0 | 0.04 +Output | 3.171e-05 | 3.171e-05 | 3.171e-05 | 0.0 | 0.00 +Modify | 2.4665 | 2.4665 | 2.4665 | 0.0 | 13.38 +Other | | 0.001366 | | | 0.01 Nlocal: 960 ave 960 max 960 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/reax/AuO/log.5Oct16.AuO.g++.4 b/examples/reax/AuO/log.8Mar18.AuO.g++.4 similarity index 51% rename from examples/reax/AuO/log.5Oct16.AuO.g++.4 rename to examples/reax/AuO/log.8Mar18.AuO.g++.4 index 01f29738f26cfe56a2bc313f0b8babd3b4b33ace..ed98e1f2f4d8dedb41476be50afd34b26fa8c010 100644 --- a/examples/reax/AuO/log.5Oct16.AuO.g++.4 +++ b/examples/reax/AuO/log.8Mar18.AuO.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (8 Mar 2018) + using 1 OpenMP thread(s) per MPI task # REAX potential for AuO system # ..... @@ -28,30 +29,40 @@ timestep 0.25 run 100 Neighbor list info ... - 2 neighbor list requests update every 10 steps, delay 0 steps, check no max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 - binsize = 6 -> bins = 5 4 5 -Memory usage per processor = 80.1039 Mbytes + binsize = 6, bins = 5 4 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reax/c, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: half/ghost/bin/3d/newtoff + bin: standard + (2) fix qeq/reax, perpetual, copy from (1) + attributes: half, newton off, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 87.17 | 87.17 | 87.17 Mbytes Step Temp E_pair E_mol TotEng Press - 0 0 -72201.743 0 -72201.743 -166.20356 - 100 69.043372 -72076.31 0 -71878.943 22701.855 -Loop time of 7.66838 on 4 procs for 100 steps with 960 atoms + 0 0 -72201.743 0 -72201.743 -166.2027 + 100 69.043379 -72076.31 0 -71878.943 22701.771 +Loop time of 8.44797 on 4 procs for 100 steps with 960 atoms -Performance: 0.282 ns/day, 85.204 hours/ns, 13.041 timesteps/s -99.7% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.256 ns/day, 93.866 hours/ns, 11.837 timesteps/s +96.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 6.7833 | 6.7864 | 6.7951 | 0.2 | 88.50 -Neigh | 0.2412 | 0.24206 | 0.24396 | 0.2 | 3.16 -Comm | 0.010402 | 0.019419 | 0.022561 | 3.7 | 0.25 -Output | 2.0981e-05 | 2.3007e-05 | 2.9087e-05 | 0.1 | 0.00 -Modify | 0.61733 | 0.61964 | 0.62064 | 0.2 | 8.08 -Other | | 0.0007888 | | | 0.01 +Pair | 7.3702 | 7.3757 | 7.3879 | 0.3 | 87.31 +Neigh | 0.28875 | 0.29449 | 0.29747 | 0.6 | 3.49 +Comm | 0.015008 | 0.027055 | 0.032681 | 4.3 | 0.32 +Output | 2.4319e-05 | 2.8551e-05 | 3.8624e-05 | 0.0 | 0.00 +Modify | 0.74721 | 0.74985 | 0.75539 | 0.4 | 8.88 +Other | | 0.0008975 | | | 0.01 Nlocal: 240 ave 240 max 240 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -67,4 +78,4 @@ Dangerous builds not checked Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:07 +Total wall time: 0:00:08 diff --git a/examples/reax/CHO/log.5Oct16.CHO.g++.1 b/examples/reax/CHO/log.8Mar18.CHO.g++.1 similarity index 53% rename from examples/reax/CHO/log.5Oct16.CHO.g++.1 rename to examples/reax/CHO/log.8Mar18.CHO.g++.1 index 2e346f75853ec2dd8f8979a04dd63e56f26f5c85..305ccbf3a01ba39f11550937ca67bd668d8c59a5 100644 --- a/examples/reax/CHO/log.5Oct16.CHO.g++.1 +++ b/examples/reax/CHO/log.8Mar18.CHO.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (8 Mar 2018) + using 1 OpenMP thread(s) per MPI task # REAX potential for CHO system # ..... @@ -28,30 +29,40 @@ timestep 0.25 run 3000 Neighbor list info ... - 2 neighbor list requests update every 10 steps, delay 0 steps, check no max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 - binsize = 6 -> bins = 5 5 5 -Memory usage per processor = 17.7936 Mbytes + binsize = 6, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reax/c, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: half/ghost/bin/3d/newtoff + bin: standard + (2) fix qeq/reax, perpetual, copy from (1) + attributes: half, newton off, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 18.68 | 18.68 | 18.68 Mbytes Step Temp E_pair E_mol TotEng Press - 0 0 -10226.557 0 -10226.557 -106.09789 - 3000 548.72503 -10170.457 0 -10000.349 34.314945 -Loop time of 11.5678 on 1 procs for 3000 steps with 105 atoms + 0 0 -10226.557 0 -10226.557 -106.09755 + 3000 548.5116 -10170.389 0 -10000.348 40.372297 +Loop time of 12.6046 on 1 procs for 3000 steps with 105 atoms -Performance: 5.602 ns/day, 4.284 hours/ns, 259.340 timesteps/s -99.3% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 5.141 ns/day, 4.668 hours/ns, 238.008 timesteps/s +98.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 10.111 | 10.111 | 10.111 | 0.0 | 87.41 -Neigh | 0.27992 | 0.27992 | 0.27992 | 0.0 | 2.42 -Comm | 0.01603 | 0.01603 | 0.01603 | 0.0 | 0.14 -Output | 1.2159e-05 | 1.2159e-05 | 1.2159e-05 | 0.0 | 0.00 -Modify | 1.1563 | 1.1563 | 1.1563 | 0.0 | 10.00 -Other | | 0.004084 | | | 0.04 +Pair | 10.931 | 10.931 | 10.931 | 0.0 | 86.72 +Neigh | 0.33107 | 0.33107 | 0.33107 | 0.0 | 2.63 +Comm | 0.017975 | 0.017975 | 0.017975 | 0.0 | 0.14 +Output | 2.0742e-05 | 2.0742e-05 | 2.0742e-05 | 0.0 | 0.00 +Modify | 1.3197 | 1.3197 | 1.3197 | 0.0 | 10.47 +Other | | 0.005059 | | | 0.04 Nlocal: 105 ave 105 max 105 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -67,4 +78,4 @@ Dangerous builds not checked Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:11 +Total wall time: 0:00:12 diff --git a/examples/reax/CHO/log.5Oct16.CHO.g++.4 b/examples/reax/CHO/log.8Mar18.CHO.g++.4 similarity index 51% rename from examples/reax/CHO/log.5Oct16.CHO.g++.4 rename to examples/reax/CHO/log.8Mar18.CHO.g++.4 index 3536b912281186df6d4be7c6df34e2ee044d19ba..2bc19dc789e8b9fa2f1a7d2c595eb07a23aeb7c2 100644 --- a/examples/reax/CHO/log.5Oct16.CHO.g++.4 +++ b/examples/reax/CHO/log.8Mar18.CHO.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (8 Mar 2018) + using 1 OpenMP thread(s) per MPI task # REAX potential for CHO system # ..... @@ -28,30 +29,40 @@ timestep 0.25 run 3000 Neighbor list info ... - 2 neighbor list requests update every 10 steps, delay 0 steps, check no max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 - binsize = 6 -> bins = 5 5 5 -Memory usage per processor = 12.9938 Mbytes + binsize = 6, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reax/c, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: half/ghost/bin/3d/newtoff + bin: standard + (2) fix qeq/reax, perpetual, copy from (1) + attributes: half, newton off, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 11.75 | 12.85 | 13.81 Mbytes Step Temp E_pair E_mol TotEng Press - 0 0 -10226.557 0 -10226.557 -106.0974 - 3000 547.91377 -10170.194 0 -10000.338 61.118402 -Loop time of 6.51546 on 4 procs for 3000 steps with 105 atoms + 0 0 -10226.557 0 -10226.557 -106.09745 + 3000 548.30567 -10170.323 0 -10000.346 47.794514 +Loop time of 7.42367 on 4 procs for 3000 steps with 105 atoms -Performance: 9.946 ns/day, 2.413 hours/ns, 460.443 timesteps/s -99.1% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 8.729 ns/day, 2.750 hours/ns, 404.113 timesteps/s +97.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 4.9869 | 5.0615 | 5.1246 | 2.3 | 77.68 -Neigh | 0.12213 | 0.14723 | 0.17304 | 5.5 | 2.26 -Comm | 0.05189 | 0.11582 | 0.18932 | 15.4 | 1.78 -Output | 1.812e-05 | 2.0564e-05 | 2.5988e-05 | 0.1 | 0.00 -Modify | 1.1626 | 1.1878 | 1.2122 | 1.9 | 18.23 -Other | | 0.003059 | | | 0.05 +Pair | 5.3058 | 5.4086 | 5.4922 | 3.1 | 72.86 +Neigh | 0.14791 | 0.17866 | 0.2106 | 6.5 | 2.41 +Comm | 0.080185 | 0.16666 | 0.26933 | 17.7 | 2.24 +Output | 2.5988e-05 | 2.8491e-05 | 3.4571e-05 | 0.0 | 0.00 +Modify | 1.6364 | 1.6658 | 1.6941 | 2.0 | 22.44 +Other | | 0.003964 | | | 0.05 Nlocal: 26.25 ave 45 max 6 min Histogram: 1 0 1 0 0 0 0 0 1 1 @@ -67,4 +78,4 @@ Dangerous builds not checked Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:06 +Total wall time: 0:00:07 diff --git a/examples/reax/FC/log.5Oct16.FC.g++.1 b/examples/reax/FC/log.8Mar18.FC.g++.1 similarity index 67% rename from examples/reax/FC/log.5Oct16.FC.g++.1 rename to examples/reax/FC/log.8Mar18.FC.g++.1 index e669c3916986242889bfb3174b52b1ee376febd8..1e2f723966330025b4a997ff6de0c351de9e1992 100644 --- a/examples/reax/FC/log.5Oct16.FC.g++.1 +++ b/examples/reax/FC/log.8Mar18.FC.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (8 Mar 2018) + using 1 OpenMP thread(s) per MPI task # REAX potential for Nitroamines system # ..... @@ -29,13 +30,23 @@ thermo 1 dump 4 all xyz 5000 dumpnpt.xyz run 10 Neighbor list info ... - 2 neighbor list requests update every 10 steps, delay 0 steps, check no max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 - binsize = 6 -> bins = 28 27 17 -Memory usage per processor = 440.212 Mbytes + binsize = 6, bins = 28 27 17 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reax/c, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: half/ghost/bin/3d/newtoff + bin: standard + (2) fix qeq/reax, perpetual, copy from (1) + attributes: half, newton off, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 470 | 470 | 470 Mbytes Step Temp E_pair TotEng Press 0 0 -808525.04 -808525.04 58194.694 1 4.9935726 -808803.89 -808546.69 58205.825 @@ -48,20 +59,20 @@ Step Temp E_pair TotEng Press 8 320.17692 -826387.27 -809896.43 58886.877 9 404.17073 -831129.48 -810312.5 59064.551 10 497.02486 -836425.19 -810825.72 59260.714 -Loop time of 20.3094 on 1 procs for 10 steps with 17280 atoms +Loop time of 21.5054 on 1 procs for 10 steps with 17280 atoms -Performance: 0.009 ns/day, 2820.746 hours/ns, 0.492 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.008 ns/day, 2986.857 hours/ns, 0.465 timesteps/s +98.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 18.124 | 18.124 | 18.124 | 0.0 | 89.24 -Neigh | 0.072459 | 0.072459 | 0.072459 | 0.0 | 0.36 -Comm | 0.00077629 | 0.00077629 | 0.00077629 | 0.0 | 0.00 -Output | 0.00075412 | 0.00075412 | 0.00075412 | 0.0 | 0.00 -Modify | 2.1109 | 2.1109 | 2.1109 | 0.0 | 10.39 -Other | | 0.0005426 | | | 0.00 +Pair | 19.008 | 19.008 | 19.008 | 0.0 | 88.39 +Neigh | 0.084401 | 0.084401 | 0.084401 | 0.0 | 0.39 +Comm | 0.00080419 | 0.00080419 | 0.00080419 | 0.0 | 0.00 +Output | 0.00095367 | 0.00095367 | 0.00095367 | 0.0 | 0.00 +Modify | 2.4109 | 2.4109 | 2.4109 | 0.0 | 11.21 +Other | | 0.0004592 | | | 0.00 Nlocal: 17280 ave 17280 max 17280 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -85,7 +96,7 @@ timestep 0.2 #dump 6 all custom 5000 dumpidtype.dat id type x y z run 10 -Memory usage per processor = 440.212 Mbytes +Per MPI rank memory allocation (min/avg/max) = 470 | 470 | 470 Mbytes Step Temp E_pair TotEng Press 10 497.02486 -836425.19 -810825.72 59260.714 11 601.65141 -841814.22 -810825.91 59489.422 @@ -98,20 +109,20 @@ Step Temp E_pair TotEng Press 18 1623.072 -894534.04 -810937.04 61739.541 19 1812.1865 -904337.99 -811000.57 62200.561 20 2011.5899 -915379.19 -811771.41 63361.151 -Loop time of 20.3051 on 1 procs for 10 steps with 17280 atoms +Loop time of 21.362 on 1 procs for 10 steps with 17280 atoms -Performance: 0.009 ns/day, 2820.155 hours/ns, 0.492 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.008 ns/day, 2966.945 hours/ns, 0.468 timesteps/s +98.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 18.008 | 18.008 | 18.008 | 0.0 | 88.69 -Neigh | 0.069963 | 0.069963 | 0.069963 | 0.0 | 0.34 -Comm | 0.00077033 | 0.00077033 | 0.00077033 | 0.0 | 0.00 -Output | 0.00077224 | 0.00077224 | 0.00077224 | 0.0 | 0.00 -Modify | 2.225 | 2.225 | 2.225 | 0.0 | 10.96 -Other | | 0.0005276 | | | 0.00 +Pair | 18.793 | 18.793 | 18.793 | 0.0 | 87.97 +Neigh | 0.077047 | 0.077047 | 0.077047 | 0.0 | 0.36 +Comm | 0.00080276 | 0.00080276 | 0.00080276 | 0.0 | 0.00 +Output | 0.0010097 | 0.0010097 | 0.0010097 | 0.0 | 0.00 +Modify | 2.4897 | 2.4897 | 2.4897 | 0.0 | 11.65 +Other | | 0.0004568 | | | 0.00 Nlocal: 17280 ave 17280 max 17280 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -127,4 +138,4 @@ Dangerous builds not checked Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:45 +Total wall time: 0:00:47 diff --git a/examples/reax/FC/log.5Oct16.FC.g++.4 b/examples/reax/FC/log.8Mar18.FC.g++.4 similarity index 67% rename from examples/reax/FC/log.5Oct16.FC.g++.4 rename to examples/reax/FC/log.8Mar18.FC.g++.4 index f231107270786e0398f4e1b88525019072e2a11d..76dcadfb0f1d2d884ba9f1b759d28e94ef36eaf1 100644 --- a/examples/reax/FC/log.5Oct16.FC.g++.4 +++ b/examples/reax/FC/log.8Mar18.FC.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (8 Mar 2018) + using 1 OpenMP thread(s) per MPI task # REAX potential for Nitroamines system # ..... @@ -29,13 +30,23 @@ thermo 1 dump 4 all xyz 5000 dumpnpt.xyz run 10 Neighbor list info ... - 2 neighbor list requests update every 10 steps, delay 0 steps, check no max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 - binsize = 6 -> bins = 28 27 17 -Memory usage per processor = 140.018 Mbytes + binsize = 6, bins = 28 27 17 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reax/c, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: half/ghost/bin/3d/newtoff + bin: standard + (2) fix qeq/reax, perpetual, copy from (1) + attributes: half, newton off, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 149.3 | 149.3 | 149.3 Mbytes Step Temp E_pair TotEng Press 0 0 -808525.04 -808525.04 58194.694 1 4.9935726 -808803.89 -808546.69 58205.825 @@ -48,20 +59,20 @@ Step Temp E_pair TotEng Press 8 320.17692 -826387.27 -809896.43 58886.877 9 404.17073 -831129.48 -810312.5 59064.551 10 497.02486 -836425.19 -810825.72 59260.714 -Loop time of 5.47494 on 4 procs for 10 steps with 17280 atoms +Loop time of 6.02109 on 4 procs for 10 steps with 17280 atoms -Performance: 0.032 ns/day, 760.408 hours/ns, 1.827 timesteps/s -99.9% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.029 ns/day, 836.262 hours/ns, 1.661 timesteps/s +99.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 4.5958 | 4.7748 | 4.8852 | 5.4 | 87.21 -Neigh | 0.021961 | 0.022104 | 0.022431 | 0.1 | 0.40 -Comm | 0.0077388 | 0.11804 | 0.29694 | 34.2 | 2.16 -Output | 0.00047708 | 0.00051123 | 0.0005939 | 0.2 | 0.01 -Modify | 0.55906 | 0.55927 | 0.55946 | 0.0 | 10.22 -Other | | 0.0002034 | | | 0.00 +Pair | 4.9482 | 5.1186 | 5.3113 | 7.4 | 85.01 +Neigh | 0.024811 | 0.025702 | 0.027556 | 0.7 | 0.43 +Comm | 0.0027421 | 0.19541 | 0.36565 | 38.1 | 3.25 +Output | 0.00053239 | 0.00057119 | 0.00067186 | 0.0 | 0.01 +Modify | 0.67876 | 0.68059 | 0.68165 | 0.1 | 11.30 +Other | | 0.0001779 | | | 0.00 Nlocal: 4320 ave 4320 max 4320 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -85,7 +96,7 @@ timestep 0.2 #dump 6 all custom 5000 dumpidtype.dat id type x y z run 10 -Memory usage per processor = 140.018 Mbytes +Per MPI rank memory allocation (min/avg/max) = 149.3 | 149.3 | 149.3 Mbytes Step Temp E_pair TotEng Press 10 497.02486 -836425.19 -810825.72 59260.714 11 601.65141 -841814.22 -810825.91 59489.422 @@ -98,20 +109,20 @@ Step Temp E_pair TotEng Press 18 1623.072 -894534.04 -810937.04 61739.541 19 1812.1865 -904337.99 -811000.57 62200.561 20 2011.5899 -915379.19 -811771.41 63361.151 -Loop time of 5.49026 on 4 procs for 10 steps with 17280 atoms +Loop time of 6.08805 on 4 procs for 10 steps with 17280 atoms -Performance: 0.031 ns/day, 762.536 hours/ns, 1.821 timesteps/s -99.9% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.028 ns/day, 845.563 hours/ns, 1.643 timesteps/s +99.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 4.5657 | 4.7603 | 4.8596 | 5.4 | 86.70 -Neigh | 0.021023 | 0.021468 | 0.022176 | 0.3 | 0.39 -Comm | 0.016467 | 0.1157 | 0.31031 | 34.7 | 2.11 -Output | 0.00047684 | 0.00050694 | 0.00059295 | 0.2 | 0.01 -Modify | 0.59135 | 0.59207 | 0.59251 | 0.1 | 10.78 -Other | | 0.0001938 | | | 0.00 +Pair | 4.9124 | 5.1008 | 5.3405 | 8.3 | 83.78 +Neigh | 0.023652 | 0.024473 | 0.025996 | 0.6 | 0.40 +Comm | 0.0020971 | 0.24171 | 0.43023 | 38.0 | 3.97 +Output | 0.00056076 | 0.00060701 | 0.00072312 | 0.0 | 0.01 +Modify | 0.71869 | 0.72023 | 0.72107 | 0.1 | 11.83 +Other | | 0.0001827 | | | 0.00 Nlocal: 4320 ave 4320 max 4320 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -127,4 +138,4 @@ Dangerous builds not checked Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:12 +Total wall time: 0:00:13 diff --git a/examples/reax/HNS/in.reaxc.hns b/examples/reax/HNS/in.reaxc.hns index 51cec6afd22a57cec9d2671bc6f4cd9afa972d1f..775a389eca849319eb0806db55f8fc59d120bd9e 100644 --- a/examples/reax/HNS/in.reaxc.hns +++ b/examples/reax/HNS/in.reaxc.hns @@ -1,6 +1,12 @@ # Pure HNS crystal, ReaxFF tests for benchmarking LAMMPS # See README for more info +variable x index 2 +variable y index 2 +variable z index 2 +variable t index 100 + + units real atom_style charge atom_modify sort 100 0.0 # optional @@ -24,7 +30,7 @@ timestep 0.1 thermo_style custom step temp pe press evdwl ecoul vol thermo_modify norm yes -thermo 100 +thermo 10 velocity all create 300.0 41279 loop geom diff --git a/examples/reax/HNS/log.8Mar18.reaxc.hns.g++.1 b/examples/reax/HNS/log.8Mar18.reaxc.hns.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..d418d287b1e0ebd6c138fa878750774a7e377cfc --- /dev/null +++ b/examples/reax/HNS/log.8Mar18.reaxc.hns.g++.1 @@ -0,0 +1,115 @@ +LAMMPS (8 Mar 2018) + using 1 OpenMP thread(s) per MPI task +# Pure HNS crystal, ReaxFF tests for benchmarking LAMMPS +# See README for more info + +variable x index 2 +variable y index 2 +variable z index 2 +variable t index 100 + + +units real +atom_style charge +atom_modify sort 100 0.0 # optional +dimension 3 +boundary p p p +box tilt large + +read_data data.hns-equil + triclinic box = (0 0 0) to (22.326 11.1412 13.779) with tilt (0 -5.02603 0) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 304 atoms + reading velocities ... + 304 velocities +replicate $x $y $z bbox +replicate 2 $y $z bbox +replicate 2 2 $z bbox +replicate 2 2 2 bbox + triclinic box = (0 0 0) to (44.652 22.2824 27.5579) with tilt (0 -10.0521 0) + 1 by 1 by 1 MPI processor grid + 2432 atoms + Time spent = 0.000789404 secs + + +pair_style reax/c NULL +pair_coeff * * ffield.reax.hns C H O N + +compute reax all pair reax/c + +neighbor 1.0 bin +neigh_modify every 20 delay 0 check no + +timestep 0.1 + +thermo_style custom step temp pe press evdwl ecoul vol +thermo_modify norm yes +thermo 10 + +velocity all create 300.0 41279 loop geom + +fix 1 all nve +fix 2 all qeq/reax 1 0.0 10.0 1e-6 reax/c + +run 100 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 11 + ghost atom cutoff = 11 + binsize = 5.5, bins = 10 5 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reax/c, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: half/ghost/bin/3d/newtoff + bin: standard + (2) fix qeq/reax, perpetual, copy from (1) + attributes: half, newton off, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 262.4 | 262.4 | 262.4 Mbytes +Step Temp PotEng Press E_vdwl E_coul Volume + 0 300 -113.27833 437.52103 -111.57687 -1.7014647 27418.867 + 10 299.87174 -113.27778 2033.6337 -111.57645 -1.7013325 27418.867 + 20 300.81718 -113.28046 4817.5889 -111.57931 -1.7011463 27418.867 + 30 301.8622 -113.28323 8303.0039 -111.58237 -1.7008608 27418.867 + 40 302.4646 -113.28493 10519.459 -111.58446 -1.700467 27418.867 + 50 300.79064 -113.27989 10402.291 -111.57987 -1.7000218 27418.867 + 60 296.11534 -113.26599 7929.1348 -111.5664 -1.6995929 27418.867 + 70 291.73354 -113.25289 5071.5459 -111.5537 -1.6991916 27418.867 + 80 292.189 -113.25399 5667.0962 -111.55519 -1.6987993 27418.867 + 90 298.40792 -113.27253 7513.3806 -111.57409 -1.6984403 27418.867 + 100 303.58246 -113.28809 10017.879 -111.58991 -1.698177 27418.867 +Loop time of 59.5461 on 1 procs for 100 steps with 2432 atoms + +Performance: 0.015 ns/day, 1654.060 hours/ns, 1.679 timesteps/s +97.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 49.922 | 49.922 | 49.922 | 0.0 | 83.84 +Neigh | 0.53154 | 0.53154 | 0.53154 | 0.0 | 0.89 +Comm | 0.011399 | 0.011399 | 0.011399 | 0.0 | 0.02 +Output | 0.00064397 | 0.00064397 | 0.00064397 | 0.0 | 0.00 +Modify | 9.0782 | 9.0782 | 9.0782 | 0.0 | 15.25 +Other | | 0.002116 | | | 0.00 + +Nlocal: 2432 ave 2432 max 2432 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 10687 ave 10687 max 10687 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 823977 ave 823977 max 823977 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 823977 +Ave neighs/atom = 338.806 +Neighbor list builds = 5 +Dangerous builds not checked + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:01:00 diff --git a/examples/reax/HNS/log.8Mar18.reaxc.hns.g++.4 b/examples/reax/HNS/log.8Mar18.reaxc.hns.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..aef07f80eb11e7e6a96965f2b08500b6e8064b9b --- /dev/null +++ b/examples/reax/HNS/log.8Mar18.reaxc.hns.g++.4 @@ -0,0 +1,115 @@ +LAMMPS (8 Mar 2018) + using 1 OpenMP thread(s) per MPI task +# Pure HNS crystal, ReaxFF tests for benchmarking LAMMPS +# See README for more info + +variable x index 2 +variable y index 2 +variable z index 2 +variable t index 100 + + +units real +atom_style charge +atom_modify sort 100 0.0 # optional +dimension 3 +boundary p p p +box tilt large + +read_data data.hns-equil + triclinic box = (0 0 0) to (22.326 11.1412 13.779) with tilt (0 -5.02603 0) + 2 by 1 by 2 MPI processor grid + reading atoms ... + 304 atoms + reading velocities ... + 304 velocities +replicate $x $y $z bbox +replicate 2 $y $z bbox +replicate 2 2 $z bbox +replicate 2 2 2 bbox + triclinic box = (0 0 0) to (44.652 22.2824 27.5579) with tilt (0 -10.0521 0) + 2 by 1 by 2 MPI processor grid + 2432 atoms + Time spent = 0.000398397 secs + + +pair_style reax/c NULL +pair_coeff * * ffield.reax.hns C H O N + +compute reax all pair reax/c + +neighbor 1.0 bin +neigh_modify every 20 delay 0 check no + +timestep 0.1 + +thermo_style custom step temp pe press evdwl ecoul vol +thermo_modify norm yes +thermo 10 + +velocity all create 300.0 41279 loop geom + +fix 1 all nve +fix 2 all qeq/reax 1 0.0 10.0 1e-6 reax/c + +run 100 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 11 + ghost atom cutoff = 11 + binsize = 5.5, bins = 10 5 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reax/c, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: half/ghost/bin/3d/newtoff + bin: standard + (2) fix qeq/reax, perpetual, copy from (1) + attributes: half, newton off, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 126.6 | 126.6 | 126.6 Mbytes +Step Temp PotEng Press E_vdwl E_coul Volume + 0 300 -113.27833 437.52112 -111.57687 -1.7014647 27418.867 + 10 299.87174 -113.27778 2033.632 -111.57645 -1.7013325 27418.867 + 20 300.81719 -113.28046 4817.5761 -111.57931 -1.7011463 27418.867 + 30 301.8622 -113.28323 8302.9767 -111.58237 -1.7008609 27418.867 + 40 302.4646 -113.28493 10519.481 -111.58446 -1.700467 27418.867 + 50 300.79064 -113.27989 10402.312 -111.57987 -1.7000217 27418.867 + 60 296.11534 -113.26599 7929.1393 -111.5664 -1.6995929 27418.867 + 70 291.73354 -113.25289 5071.5368 -111.5537 -1.6991916 27418.867 + 80 292.18901 -113.25399 5667.1118 -111.55519 -1.6987993 27418.867 + 90 298.40793 -113.27253 7513.4029 -111.57409 -1.6984403 27418.867 + 100 303.58247 -113.28809 10017.892 -111.58991 -1.698177 27418.867 +Loop time of 21.3933 on 4 procs for 100 steps with 2432 atoms + +Performance: 0.040 ns/day, 594.257 hours/ns, 4.674 timesteps/s +97.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 14.863 | 16.367 | 18.027 | 28.6 | 76.51 +Neigh | 0.23943 | 0.2422 | 0.24658 | 0.6 | 1.13 +Comm | 0.024331 | 1.6845 | 3.189 | 89.2 | 7.87 +Output | 0.00051165 | 0.00056899 | 0.00068665 | 0.0 | 0.00 +Modify | 3.0933 | 3.0969 | 3.0999 | 0.1 | 14.48 +Other | | 0.001784 | | | 0.01 + +Nlocal: 608 ave 608 max 608 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 5738.25 ave 5742 max 5734 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +Neighs: 231544 ave 231625 max 231466 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 926176 +Ave neighs/atom = 380.829 +Neighbor list builds = 5 +Dangerous builds not checked + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:21 diff --git a/examples/reax/RDX/log.5Oct16.RDX.g++.1 b/examples/reax/RDX/log.8Mar18.RDX.g++.1 similarity index 51% rename from examples/reax/RDX/log.5Oct16.RDX.g++.1 rename to examples/reax/RDX/log.8Mar18.RDX.g++.1 index 92bb048d435f3e0290add82792bd372c4186af51..d0765a97a5d6222314a94795fb43b36802537f08 100644 --- a/examples/reax/RDX/log.5Oct16.RDX.g++.1 +++ b/examples/reax/RDX/log.8Mar18.RDX.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (8 Mar 2018) + using 1 OpenMP thread(s) per MPI task # REAX potential for high energy CHON systems # ..... @@ -28,43 +29,53 @@ timestep 0.25 run 3000 Neighbor list info ... - 2 neighbor list requests update every 10 steps, delay 0 steps, check no max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 - binsize = 6 -> bins = 5 5 5 -Memory usage per processor = 18.1116 Mbytes + binsize = 6, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reax/c, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: half/ghost/bin/3d/newtoff + bin: standard + (2) fix qeq/reax, perpetual, copy from (1) + attributes: half, newton off, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 19 | 19 | 19 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10197.932 0 -10197.932 38.347492 - 3000 510.85923 -10091.694 0 -9933.3253 1668.5084 -Loop time of 18.9088 on 1 procs for 3000 steps with 105 atoms + 3000 510.63767 -10091.537 0 -9933.2374 1144.545 +Loop time of 21.2931 on 1 procs for 3000 steps with 105 atoms -Performance: 3.427 ns/day, 7.003 hours/ns, 158.657 timesteps/s -99.5% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 3.043 ns/day, 7.886 hours/ns, 140.891 timesteps/s +97.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 17.724 | 17.724 | 17.724 | 0.0 | 93.73 -Neigh | 0.27457 | 0.27457 | 0.27457 | 0.0 | 1.45 -Comm | 0.015814 | 0.015814 | 0.015814 | 0.0 | 0.08 -Output | 1.1921e-05 | 1.1921e-05 | 1.1921e-05 | 0.0 | 0.00 -Modify | 0.89014 | 0.89014 | 0.89014 | 0.0 | 4.71 -Other | | 0.004246 | | | 0.02 +Pair | 19.887 | 19.887 | 19.887 | 0.0 | 93.40 +Neigh | 0.33143 | 0.33143 | 0.33143 | 0.0 | 1.56 +Comm | 0.02079 | 0.02079 | 0.02079 | 0.0 | 0.10 +Output | 2.5272e-05 | 2.5272e-05 | 2.5272e-05 | 0.0 | 0.00 +Modify | 1.0478 | 1.0478 | 1.0478 | 0.0 | 4.92 +Other | | 0.006125 | | | 0.03 Nlocal: 105 ave 105 max 105 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 645 ave 645 max 645 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 3061 ave 3061 max 3061 min +Neighs: 3063 ave 3063 max 3063 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 3061 -Ave neighs/atom = 29.1524 +Total # of neighbors = 3063 +Ave neighs/atom = 29.1714 Neighbor list builds = 300 Dangerous builds not checked Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:19 +Total wall time: 0:00:21 diff --git a/examples/reax/RDX/log.5Oct16.RDX.g++.4 b/examples/reax/RDX/log.8Mar18.RDX.g++.4 similarity index 50% rename from examples/reax/RDX/log.5Oct16.RDX.g++.4 rename to examples/reax/RDX/log.8Mar18.RDX.g++.4 index bcffe8f813d6bfe2150c77bc78e847c5e2582215..7082d306363b5603796cf410085a4db703e3e3ec 100644 --- a/examples/reax/RDX/log.5Oct16.RDX.g++.4 +++ b/examples/reax/RDX/log.8Mar18.RDX.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (8 Mar 2018) + using 1 OpenMP thread(s) per MPI task # REAX potential for high energy CHON systems # ..... @@ -28,43 +29,53 @@ timestep 0.25 run 3000 Neighbor list info ... - 2 neighbor list requests update every 10 steps, delay 0 steps, check no max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 - binsize = 6 -> bins = 5 5 5 -Memory usage per processor = 12.2102 Mbytes + binsize = 6, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reax/c, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: half/ghost/bin/3d/newtoff + bin: standard + (2) fix qeq/reax, perpetual, copy from (1) + attributes: half, newton off, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 12.14 | 13.04 | 13.9 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10197.932 0 -10197.932 38.347492 - 3000 504.05354 -10089.494 0 -9933.2351 868.32505 -Loop time of 9.70759 on 4 procs for 3000 steps with 105 atoms + 3000 509.89257 -10091.36 0 -9933.2916 1406.1215 +Loop time of 10.8858 on 4 procs for 3000 steps with 105 atoms -Performance: 6.675 ns/day, 3.595 hours/ns, 309.037 timesteps/s -99.2% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 5.953 ns/day, 4.032 hours/ns, 275.588 timesteps/s +98.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 8.4621 | 8.5307 | 8.6001 | 1.9 | 87.88 -Neigh | 0.12583 | 0.14931 | 0.17341 | 4.5 | 1.54 -Comm | 0.053017 | 0.12311 | 0.19244 | 16.2 | 1.27 -Output | 1.9073e-05 | 2.0802e-05 | 2.408e-05 | 0.0 | 0.00 -Modify | 0.87638 | 0.9012 | 0.92557 | 1.9 | 9.28 -Other | | 0.003213 | | | 0.03 +Pair | 9.3081 | 9.4054 | 9.4994 | 2.6 | 86.40 +Neigh | 0.15541 | 0.18258 | 0.2099 | 4.7 | 1.68 +Comm | 0.070516 | 0.16621 | 0.26541 | 19.7 | 1.53 +Output | 2.2173e-05 | 2.5153e-05 | 3.3855e-05 | 0.0 | 0.00 +Modify | 1.0979 | 1.1272 | 1.1568 | 2.1 | 10.35 +Other | | 0.004379 | | | 0.04 Nlocal: 26.25 ave 46 max 8 min Histogram: 1 0 0 1 0 1 0 0 0 1 Nghost: 399.5 ave 512 max 288 min Histogram: 1 0 0 1 0 0 1 0 0 1 -Neighs: 1010.75 ave 1818 max 420 min +Neighs: 1011.25 ave 1819 max 420 min Histogram: 1 0 1 1 0 0 0 0 0 1 -Total # of neighbors = 4043 -Ave neighs/atom = 38.5048 +Total # of neighbors = 4045 +Ave neighs/atom = 38.5238 Neighbor list builds = 300 Dangerous builds not checked Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:10 +Total wall time: 0:00:11 diff --git a/examples/reax/VOH/log.5Oct16.VOH.g++.4 b/examples/reax/VOH/log.5Oct16.VOH.g++.4 deleted file mode 100644 index 8afe957732d2bf67fe2dfdbe08df794fd7c439f6..0000000000000000000000000000000000000000 --- a/examples/reax/VOH/log.5Oct16.VOH.g++.4 +++ /dev/null @@ -1,70 +0,0 @@ -LAMMPS (5 Oct 2016) -# REAX potential for VOH system -# ..... - -units real - -atom_style charge -read_data data.VOH - orthogonal box = (0 0 0) to (25 25 25) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 100 atoms - -pair_style reax/c lmp_control -pair_coeff * * ffield.reax.V_O_C_H H C O V -Reading potential file ffield.reax.V_O_C_H with DATE: 2011-02-18 - -neighbor 2 bin -neigh_modify every 10 delay 0 check no - -fix 1 all nve -fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq -fix 3 all temp/berendsen 500.0 500.0 100.0 - -timestep 0.25 - -#dump 1 all atom 30 dump.reax.voh - -run 3000 -Neighbor list info ... - 2 neighbor list requests - update every 10 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12 - ghost atom cutoff = 12 - binsize = 6 -> bins = 5 5 5 -Memory usage per processor = 12.1769 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -10246.825 0 -10246.825 42.256092 - 3000 518.1493 -10196.234 0 -10043.328 -334.5971 -Loop time of 5.59178 on 4 procs for 3000 steps with 100 atoms - -Performance: 11.588 ns/day, 2.071 hours/ns, 536.502 timesteps/s -99.1% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 4.2807 | 4.3532 | 4.398 | 2.1 | 77.85 -Neigh | 0.12328 | 0.14561 | 0.16815 | 4.2 | 2.60 -Comm | 0.051619 | 0.097282 | 0.1697 | 14.1 | 1.74 -Output | 1.7881e-05 | 1.9372e-05 | 2.3842e-05 | 0.1 | 0.00 -Modify | 0.9701 | 0.99258 | 1.0148 | 1.6 | 17.75 -Other | | 0.003097 | | | 0.06 - -Nlocal: 25 ave 38 max 11 min -Histogram: 1 0 0 0 1 0 1 0 0 1 -Nghost: 368.25 ave 449 max 283 min -Histogram: 1 0 0 0 1 0 1 0 0 1 -Neighs: 1084.5 ave 1793 max 418 min -Histogram: 1 0 0 1 0 0 1 0 0 1 - -Total # of neighbors = 4338 -Ave neighs/atom = 43.38 -Neighbor list builds = 300 -Dangerous builds not checked - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:05 diff --git a/examples/reax/VOH/log.5Oct16.VOH.g++.1 b/examples/reax/VOH/log.8Mar18.VOH.g++.1 similarity index 50% rename from examples/reax/VOH/log.5Oct16.VOH.g++.1 rename to examples/reax/VOH/log.8Mar18.VOH.g++.1 index 9a7a6a59c727275e463aa10ba88b6c7e3093380b..924769e5703191863a42b508ca7177493d7e99fa 100644 --- a/examples/reax/VOH/log.5Oct16.VOH.g++.1 +++ b/examples/reax/VOH/log.8Mar18.VOH.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (8 Mar 2018) + using 1 OpenMP thread(s) per MPI task # REAX potential for VOH system # ..... @@ -28,43 +29,53 @@ timestep 0.25 run 3000 Neighbor list info ... - 2 neighbor list requests update every 10 steps, delay 0 steps, check no max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 - binsize = 6 -> bins = 5 5 5 -Memory usage per processor = 16.9211 Mbytes + binsize = 6, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reax/c, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: half/ghost/bin/3d/newtoff + bin: standard + (2) fix qeq/reax, perpetual, copy from (1) + attributes: half, newton off, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 17.79 | 17.79 | 17.79 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10246.825 0 -10246.825 42.256089 - 3000 479.39686 -10186.225 0 -10044.755 -454.82798 -Loop time of 10.4348 on 1 procs for 3000 steps with 100 atoms + 3000 476.73301 -10185.256 0 -10044.572 -694.70737 +Loop time of 11.0577 on 1 procs for 3000 steps with 100 atoms -Performance: 6.210 ns/day, 3.865 hours/ns, 287.499 timesteps/s -99.2% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 5.860 ns/day, 4.095 hours/ns, 271.304 timesteps/s +98.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 9.2216 | 9.2216 | 9.2216 | 0.0 | 88.37 -Neigh | 0.2757 | 0.2757 | 0.2757 | 0.0 | 2.64 -Comm | 0.015626 | 0.015626 | 0.015626 | 0.0 | 0.15 -Output | 1.1921e-05 | 1.1921e-05 | 1.1921e-05 | 0.0 | 0.00 -Modify | 0.91782 | 0.91782 | 0.91782 | 0.0 | 8.80 -Other | | 0.004039 | | | 0.04 +Pair | 9.6785 | 9.6785 | 9.6785 | 0.0 | 87.53 +Neigh | 0.32599 | 0.32599 | 0.32599 | 0.0 | 2.95 +Comm | 0.017231 | 0.017231 | 0.017231 | 0.0 | 0.16 +Output | 2.5511e-05 | 2.5511e-05 | 2.5511e-05 | 0.0 | 0.00 +Modify | 1.0311 | 1.0311 | 1.0311 | 0.0 | 9.32 +Other | | 0.004857 | | | 0.04 Nlocal: 100 ave 100 max 100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 598 ave 598 max 598 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 3384 ave 3384 max 3384 min +Neighs: 3390 ave 3390 max 3390 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 3384 -Ave neighs/atom = 33.84 +Total # of neighbors = 3390 +Ave neighs/atom = 33.9 Neighbor list builds = 300 Dangerous builds not checked Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:10 +Total wall time: 0:00:11 diff --git a/examples/reax/VOH/log.8Mar18.VOH.g++.4 b/examples/reax/VOH/log.8Mar18.VOH.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..0395af6671bb98582d2855fa370798edd68fb3f0 --- /dev/null +++ b/examples/reax/VOH/log.8Mar18.VOH.g++.4 @@ -0,0 +1,81 @@ +LAMMPS (8 Mar 2018) + using 1 OpenMP thread(s) per MPI task +# REAX potential for VOH system +# ..... + +units real + +atom_style charge +read_data data.VOH + orthogonal box = (0 0 0) to (25 25 25) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 100 atoms + +pair_style reax/c lmp_control +pair_coeff * * ffield.reax.V_O_C_H H C O V +Reading potential file ffield.reax.V_O_C_H with DATE: 2011-02-18 + +neighbor 2 bin +neigh_modify every 10 delay 0 check no + +fix 1 all nve +fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq +fix 3 all temp/berendsen 500.0 500.0 100.0 + +timestep 0.25 + +#dump 1 all atom 30 dump.reax.voh + +run 3000 +Neighbor list info ... + update every 10 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reax/c, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: half/ghost/bin/3d/newtoff + bin: standard + (2) fix qeq/reax, perpetual, copy from (1) + attributes: half, newton off, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 11.21 | 12.52 | 13.64 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -10246.825 0 -10246.825 42.256092 + 3000 489.67803 -10188.866 0 -10044.362 -553.7513 +Loop time of 6.49847 on 4 procs for 3000 steps with 100 atoms + +Performance: 9.972 ns/day, 2.407 hours/ns, 461.647 timesteps/s +97.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.7412 | 4.8453 | 4.9104 | 2.9 | 74.56 +Neigh | 0.1468 | 0.17834 | 0.20151 | 4.7 | 2.74 +Comm | 0.071841 | 0.14037 | 0.24502 | 17.2 | 2.16 +Output | 2.1219e-05 | 2.408e-05 | 3.1948e-05 | 0.0 | 0.00 +Modify | 1.3072 | 1.3308 | 1.3627 | 1.7 | 20.48 +Other | | 0.003713 | | | 0.06 + +Nlocal: 25 ave 38 max 11 min +Histogram: 1 0 0 0 1 0 1 0 0 1 +Nghost: 369.75 ave 453 max 283 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Neighs: 1082.25 ave 1788 max 417 min +Histogram: 1 0 1 0 0 0 1 0 0 1 + +Total # of neighbors = 4329 +Ave neighs/atom = 43.29 +Neighbor list builds = 300 +Dangerous builds not checked + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:06 diff --git a/examples/reax/ZnOH2/log.5Oct16.ZnOH2.g++.1 b/examples/reax/ZnOH2/log.8Mar18.ZnOH2.g++.1 similarity index 50% rename from examples/reax/ZnOH2/log.5Oct16.ZnOH2.g++.1 rename to examples/reax/ZnOH2/log.8Mar18.ZnOH2.g++.1 index 8fcc86dd17b0375bb1b0263c0c2495dd7b9ee538..58b1a36719cf9d5a874b05944449c352ba26f2e2 100644 --- a/examples/reax/ZnOH2/log.5Oct16.ZnOH2.g++.1 +++ b/examples/reax/ZnOH2/log.8Mar18.ZnOH2.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (8 Mar 2018) + using 1 OpenMP thread(s) per MPI task # REAX potential for ZnOH2 system # ..... @@ -28,43 +29,53 @@ timestep 0.25 run 3000 Neighbor list info ... - 2 neighbor list requests update every 10 steps, delay 0 steps, check no max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 - binsize = 6 -> bins = 5 5 5 -Memory usage per processor = 17.485 Mbytes + binsize = 6, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reax/c, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: half/ghost/bin/3d/newtoff + bin: standard + (2) fix qeq/reax, perpetual, copy from (1) + attributes: half, newton off, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 18.36 | 18.36 | 18.36 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7900.2668 0 -7900.2668 60.076093 - 3000 522.42599 -7928.9641 0 -7767.0098 -755.28778 -Loop time of 6.38119 on 1 procs for 3000 steps with 105 atoms + 3000 535.58577 -7934.7287 0 -7768.6948 -475.46237 +Loop time of 7.29784 on 1 procs for 3000 steps with 105 atoms -Performance: 10.155 ns/day, 2.363 hours/ns, 470.132 timesteps/s -99.0% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 8.879 ns/day, 2.703 hours/ns, 411.081 timesteps/s +97.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 5.2711 | 5.2711 | 5.2711 | 0.0 | 82.60 -Neigh | 0.30669 | 0.30669 | 0.30669 | 0.0 | 4.81 -Comm | 0.015599 | 0.015599 | 0.015599 | 0.0 | 0.24 -Output | 1.0967e-05 | 1.0967e-05 | 1.0967e-05 | 0.0 | 0.00 -Modify | 0.78376 | 0.78376 | 0.78376 | 0.0 | 12.28 -Other | | 0.004036 | | | 0.06 +Pair | 5.9988 | 5.9988 | 5.9988 | 0.0 | 82.20 +Neigh | 0.37455 | 0.37455 | 0.37455 | 0.0 | 5.13 +Comm | 0.019186 | 0.019186 | 0.019186 | 0.0 | 0.26 +Output | 2.4557e-05 | 2.4557e-05 | 2.4557e-05 | 0.0 | 0.00 +Modify | 0.89915 | 0.89915 | 0.89915 | 0.0 | 12.32 +Other | | 0.006108 | | | 0.08 Nlocal: 105 ave 105 max 105 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 649 ave 649 max 649 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 3956 ave 3956 max 3956 min +Neighs: 3971 ave 3971 max 3971 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 3956 -Ave neighs/atom = 37.6762 +Total # of neighbors = 3971 +Ave neighs/atom = 37.819 Neighbor list builds = 300 Dangerous builds not checked Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:06 +Total wall time: 0:00:07 diff --git a/examples/reax/ZnOH2/log.5Oct16.ZnOH2.g++.4 b/examples/reax/ZnOH2/log.8Mar18.ZnOH2.g++.4 similarity index 51% rename from examples/reax/ZnOH2/log.5Oct16.ZnOH2.g++.4 rename to examples/reax/ZnOH2/log.8Mar18.ZnOH2.g++.4 index 104d806c33bf2deb3dc9e50884fd7b3ffa966a81..77c5cbe1b7651843d15da5caa74b0896e37aa448 100644 --- a/examples/reax/ZnOH2/log.5Oct16.ZnOH2.g++.4 +++ b/examples/reax/ZnOH2/log.8Mar18.ZnOH2.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (8 Mar 2018) + using 1 OpenMP thread(s) per MPI task # REAX potential for ZnOH2 system # ..... @@ -28,40 +29,50 @@ timestep 0.25 run 3000 Neighbor list info ... - 2 neighbor list requests update every 10 steps, delay 0 steps, check no max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 - binsize = 6 -> bins = 5 5 5 -Memory usage per processor = 12.0066 Mbytes + binsize = 6, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reax/c, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: half/ghost/bin/3d/newtoff + bin: standard + (2) fix qeq/reax, perpetual, copy from (1) + attributes: half, newton off, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 11.28 | 12.77 | 14.21 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7900.2668 0 -7900.2668 60.076093 - 3000 536.8256 -7935.1437 0 -7768.7255 -479.27959 -Loop time of 3.77632 on 4 procs for 3000 steps with 105 atoms + 3000 538.25796 -7935.6159 0 -7768.7536 -525.47078 +Loop time of 4.48824 on 4 procs for 3000 steps with 105 atoms -Performance: 17.160 ns/day, 1.399 hours/ns, 794.423 timesteps/s -99.0% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 14.438 ns/day, 1.662 hours/ns, 668.414 timesteps/s +97.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.7337 | 2.7808 | 2.8316 | 2.5 | 73.64 -Neigh | 0.13455 | 0.16558 | 0.19493 | 5.3 | 4.38 -Comm | 0.046741 | 0.099375 | 0.14663 | 13.6 | 2.63 -Output | 1.7881e-05 | 2.0027e-05 | 2.408e-05 | 0.1 | 0.00 -Modify | 0.69792 | 0.7275 | 0.75887 | 2.5 | 19.26 -Other | | 0.003084 | | | 0.08 +Pair | 3.1031 | 3.1698 | 3.2378 | 3.3 | 70.62 +Neigh | 0.16642 | 0.20502 | 0.25003 | 6.6 | 4.57 +Comm | 0.074932 | 0.14224 | 0.21025 | 15.6 | 3.17 +Output | 0.00011349 | 0.00011736 | 0.00012231 | 0.0 | 0.00 +Modify | 0.92089 | 0.96736 | 1.0083 | 3.2 | 21.55 +Other | | 0.003731 | | | 0.08 Nlocal: 26.25 ave 45 max 15 min Histogram: 1 0 2 0 0 0 0 0 0 1 Nghost: 399 ave 509 max 295 min Histogram: 1 0 0 0 2 0 0 0 0 1 -Neighs: 1150 ave 2061 max 701 min +Neighs: 1151.5 ave 2066 max 701 min Histogram: 1 2 0 0 0 0 0 0 0 1 -Total # of neighbors = 4600 -Ave neighs/atom = 43.8095 +Total # of neighbors = 4606 +Ave neighs/atom = 43.8667 Neighbor list builds = 300 Dangerous builds not checked diff --git a/examples/reax/ci-reaxFF/input.in b/examples/reax/ci-reaxFF/in.ci-reax.CH similarity index 100% rename from examples/reax/ci-reaxFF/input.in rename to examples/reax/ci-reaxFF/in.ci-reax.CH diff --git a/examples/reax/ci-reaxFF/log.23Oct17.g++.1 b/examples/reax/ci-reaxFF/log.8Mar18.ci-reax.CH.g++.1 similarity index 77% rename from examples/reax/ci-reaxFF/log.23Oct17.g++.1 rename to examples/reax/ci-reaxFF/log.8Mar18.ci-reax.CH.g++.1 index 1be46a9699b3ee293054b6894cb3e0064cc5e705..e966fd26b6c10036267c4339cb72b318f3781428 100644 --- a/examples/reax/ci-reaxFF/log.23Oct17.g++.1 +++ b/examples/reax/ci-reaxFF/log.8Mar18.ci-reax.CH.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (23 Oct 2017) +LAMMPS (8 Mar 2018) + using 1 OpenMP thread(s) per MPI task #ci-reax potential for CH systems with tabulated ZBL correction atom_style charge units real @@ -31,6 +32,7 @@ fix 2 all temp/berendsen 500.0 500.0 100.0 #dump 1 all atom 30 dump.ci-reax.lammpstrj run 3000 +WARNING: Total cutoff < 2*bond cutoff. May need to use an increased neighbor list skin. (../pair_reaxc.cpp:392) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 @@ -52,20 +54,20 @@ Per MPI rank memory allocation (min/avg/max) = 43.46 | 43.46 | 43.46 Mbytes Step Temp E_pair E_mol TotEng Press 0 508.42043 -28736.654 0 -28260.785 1678.3276 3000 480.41333 -28707.835 0 -28258.181 -3150.0762 -Loop time of 21.5509 on 1 procs for 3000 steps with 315 atoms +Loop time of 45.3959 on 1 procs for 3000 steps with 315 atoms -Performance: 3.007 ns/day, 7.982 hours/ns, 139.205 timesteps/s -100.0% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 1.427 ns/day, 16.813 hours/ns, 66.085 timesteps/s +96.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 21.315 | 21.315 | 21.315 | 0.0 | 98.91 -Neigh | 0.17846 | 0.17846 | 0.17846 | 0.0 | 0.83 -Comm | 0.028676 | 0.028676 | 0.028676 | 0.0 | 0.13 -Output | 2.6941e-05 | 2.6941e-05 | 2.6941e-05 | 0.0 | 0.00 -Modify | 0.018969 | 0.018969 | 0.018969 | 0.0 | 0.09 -Other | | 0.009438 | | | 0.04 +Pair | 44.955 | 44.955 | 44.955 | 0.0 | 99.03 +Neigh | 0.29903 | 0.29903 | 0.29903 | 0.0 | 0.66 +Comm | 0.056547 | 0.056547 | 0.056547 | 0.0 | 0.12 +Output | 4.8399e-05 | 4.8399e-05 | 4.8399e-05 | 0.0 | 0.00 +Modify | 0.058722 | 0.058722 | 0.058722 | 0.0 | 0.13 +Other | | 0.02632 | | | 0.06 Nlocal: 315 ave 315 max 315 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -81,4 +83,4 @@ Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:21 +Total wall time: 0:00:45 diff --git a/examples/reax/ci-reaxFF/log.8Mar18.ci-reax.CH.g++.4 b/examples/reax/ci-reaxFF/log.8Mar18.ci-reax.CH.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..ccc87b3536b264a2ace057a00f702c71c3f4b41c --- /dev/null +++ b/examples/reax/ci-reaxFF/log.8Mar18.ci-reax.CH.g++.4 @@ -0,0 +1,86 @@ +LAMMPS (8 Mar 2018) + using 1 OpenMP thread(s) per MPI task +#ci-reax potential for CH systems with tabulated ZBL correction +atom_style charge +units real + +read_data CH4.dat + orthogonal box = (0 0 0) to (20 20 20) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 315 atoms + reading velocities ... + 315 velocities + +pair_style hybrid/overlay reax/c control checkqeq no table linear 11000 +pair_coeff * * reax/c ffield.ci-reax.CH C H +Reading potential file ffield.ci-reax.CH with DATE: 2017-11-20 +pair_coeff 1 1 table ci-reaxFF_ZBL.dat CC_cireaxFF +WARNING: 2 of 10000 force values in table are inconsistent with -dE/dr. + Should only be flagged at inflection points (../pair_table.cpp:481) +pair_coeff 1 2 table ci-reaxFF_ZBL.dat CH_cireaxFF +WARNING: 2 of 11000 force values in table are inconsistent with -dE/dr. + Should only be flagged at inflection points (../pair_table.cpp:481) +pair_coeff 2 2 table ci-reaxFF_ZBL.dat HH_cireaxFF +WARNING: 2 of 6000 force values in table are inconsistent with -dE/dr. + Should only be flagged at inflection points (../pair_table.cpp:481) + +timestep 0.25 +fix 1 all nve +fix 2 all temp/berendsen 500.0 500.0 100.0 + +#dump 1 all atom 30 dump.ci-reax.lammpstrj + +run 3000 +WARNING: Total cutoff < 2*bond cutoff. May need to use an increased neighbor list skin. (../pair_reaxc.cpp:392) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 9.5 + ghost atom cutoff = 9.5 + binsize = 4.75, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reax/c, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: half/ghost/bin/3d/newtoff + bin: standard + (2) pair table, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 24.48 | 25.61 | 27.27 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 508.42043 -28736.654 0 -28260.785 1678.3276 + 3000 480.41333 -28707.835 0 -28258.181 -3150.0762 +Loop time of 24.7034 on 4 procs for 3000 steps with 315 atoms + +Performance: 2.623 ns/day, 9.149 hours/ns, 121.441 timesteps/s +95.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 18.945 | 21.367 | 24.046 | 39.3 | 86.49 +Neigh | 0.1456 | 0.15254 | 0.16101 | 1.6 | 0.62 +Comm | 0.39168 | 3.0859 | 5.5185 | 103.9 | 12.49 +Output | 3.5763e-05 | 4.065e-05 | 5.2452e-05 | 0.0 | 0.00 +Modify | 0.05831 | 0.068811 | 0.077666 | 2.9 | 0.28 +Other | | 0.0292 | | | 0.12 + +Nlocal: 78.75 ave 96 max 65 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 1233 ave 1348 max 1116 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Neighs: 9467.25 ave 12150 max 7160 min +Histogram: 1 1 0 0 0 0 0 1 0 1 + +Total # of neighbors = 37869 +Ave neighs/atom = 120.219 +Neighbor list builds = 37 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:24 diff --git a/examples/reax/log.5Oct16.reax.rdx.g++.1 b/examples/reax/log.5Oct16.reax.rdx.g++.1 deleted file mode 100644 index 08a24cf635a91f9ef23bdc46241dd100bff8a207..0000000000000000000000000000000000000000 --- a/examples/reax/log.5Oct16.reax.rdx.g++.1 +++ /dev/null @@ -1,101 +0,0 @@ -LAMMPS (5 Oct 2016) -# ReaxFF potential for RDX system - -units real - -atom_style charge -read_data data.rdx - orthogonal box = (35 35 35) to (48 48 48) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 21 atoms - -# reax args: hbcut hbnewflag tripflag precision - -pair_style reax 6.0 1 1 1.0e-6 -WARNING: The pair_style reax command will be deprecated soon - users should switch to pair_style reax/c (../pair_reax.cpp:49) -pair_coeff * * ffield.reax 1 2 3 4 - -compute reax all pair reax - -variable eb equal c_reax[1] -variable ea equal c_reax[2] -variable elp equal c_reax[3] -variable emol equal c_reax[4] -variable ev equal c_reax[5] -variable epen equal c_reax[6] -variable ecoa equal c_reax[7] -variable ehb equal c_reax[8] -variable et equal c_reax[9] -variable eco equal c_reax[10] -variable ew equal c_reax[11] -variable ep equal c_reax[12] -variable efi equal c_reax[13] -variable eqeq equal c_reax[14] - -neighbor 2.5 bin -neigh_modify every 10 delay 0 check no - -fix 1 all nve - -thermo 10 -thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - -timestep 1.0 - -#dump 1 all custom 10 dump.reax.rdx id type q xs ys zs - -#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 - -#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 - -run 100 -Neighbor list info ... - 1 neighbor list requests - update every 10 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12.5 - ghost atom cutoff = 12.5 - binsize = 6.25 -> bins = 3 3 3 -Memory usage per processor = 2.95105 Mbytes -Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - 0 0 -1885.1268 -1885.1268 27233.074 -2958.4712 79.527715 0.31082031 0 97.771125 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79971 0 168.88435 - 10 1281.7558 -1989.1322 -1912.7188 -19609.913 -2733.8828 -15.775275 0.20055725 0 55.020231 3.1070522 -77.710916 0 14.963568 -5.8082204 843.41939 -180.17724 0 107.5115 - 20 516.83079 -1941.677 -1910.8655 -12525.41 -2801.8626 7.4107974 0.073134188 0 81.986982 0.2281551 -57.494871 0 30.656735 -10.102557 877.78696 -158.93385 0 88.574158 - 30 467.2641 -1940.978 -1913.1215 -35957.487 -2755.021 -6.9179959 0.049322439 0 78.853175 0.13604392 -51.653634 0 19.862872 -9.7098575 853.79334 -151.232 0 80.861768 - 40 647.45541 -1951.1994 -1912.6006 -5883.7147 -2798.3556 17.334807 0.15102863 0 63.23512 0.18070931 -54.598962 0 17.325008 -12.052277 883.01667 -164.21335 0 96.777422 - 50 716.38057 -1949.4749 -1906.767 5473.2085 -2800.931 9.2056917 0.15413274 0 85.371449 3.2986106 -78.253597 0 34.861773 -8.5531236 882.01435 -193.85275 0 117.2096 - 60 1175.2707 -1975.9611 -1905.8959 -1939.4971 -2726.5816 -11.651982 0.24296788 0 48.320663 7.1799636 -75.363641 0 16.520132 -4.8869463 844.754 -194.23296 0 119.73837 - 70 1156.7 -1975.3486 -1906.3905 24628.344 -2880.5223 25.652478 0.26894312 0 83.724884 7.1049303 -68.700942 0 24.750744 -8.6338218 911.20067 -183.4058 0 113.21158 - 80 840.23687 -1955.4768 -1905.3851 -17731.383 -2755.7295 -8.0168306 0.13867962 0 86.14748 2.2387306 -76.945841 0 23.595858 -7.2609645 853.6346 -167.88289 0 94.603895 - 90 365.79169 -1926.406 -1904.5989 898.37155 -2842.183 47.368211 0.23109 0 92.288131 0.38031313 -61.361483 0 18.476377 -12.255472 900.24202 -186.48056 0 116.88831 - 100 801.32078 -1953.4177 -1905.646 -2417.5518 -2802.7244 4.6676973 0.18046558 0 76.730114 5.4177372 -77.102556 0 24.997234 -7.7554179 898.67306 -196.8912 0 120.38952 -Loop time of 0.512828 on 1 procs for 100 steps with 21 atoms - -Performance: 16.848 ns/day, 1.425 hours/ns, 194.997 timesteps/s -99.4% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.51126 | 0.51126 | 0.51126 | 0.0 | 99.69 -Neigh | 0.00071597 | 0.00071597 | 0.00071597 | 0.0 | 0.14 -Comm | 0.00040317 | 0.00040317 | 0.00040317 | 0.0 | 0.08 -Output | 0.00027037 | 0.00027037 | 0.00027037 | 0.0 | 0.05 -Modify | 7.2241e-05 | 7.2241e-05 | 7.2241e-05 | 0.0 | 0.01 -Other | | 0.000108 | | | 0.02 - -Nlocal: 21 ave 21 max 21 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 546 ave 546 max 546 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1106 ave 1106 max 1106 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 1106 -Ave neighs/atom = 52.6667 -Neighbor list builds = 10 -Dangerous builds not checked -Total wall time: 0:00:00 diff --git a/examples/reax/log.5Oct16.reax.rdx.g++.4 b/examples/reax/log.5Oct16.reax.rdx.g++.4 deleted file mode 100644 index 2f052fbf74a95681728b83341392dfa0f13a284a..0000000000000000000000000000000000000000 --- a/examples/reax/log.5Oct16.reax.rdx.g++.4 +++ /dev/null @@ -1,101 +0,0 @@ -LAMMPS (5 Oct 2016) -# ReaxFF potential for RDX system - -units real - -atom_style charge -read_data data.rdx - orthogonal box = (35 35 35) to (48 48 48) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 21 atoms - -# reax args: hbcut hbnewflag tripflag precision - -pair_style reax 6.0 1 1 1.0e-6 -WARNING: The pair_style reax command will be deprecated soon - users should switch to pair_style reax/c (../pair_reax.cpp:49) -pair_coeff * * ffield.reax 1 2 3 4 - -compute reax all pair reax - -variable eb equal c_reax[1] -variable ea equal c_reax[2] -variable elp equal c_reax[3] -variable emol equal c_reax[4] -variable ev equal c_reax[5] -variable epen equal c_reax[6] -variable ecoa equal c_reax[7] -variable ehb equal c_reax[8] -variable et equal c_reax[9] -variable eco equal c_reax[10] -variable ew equal c_reax[11] -variable ep equal c_reax[12] -variable efi equal c_reax[13] -variable eqeq equal c_reax[14] - -neighbor 2.5 bin -neigh_modify every 10 delay 0 check no - -fix 1 all nve - -thermo 10 -thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - -timestep 1.0 - -#dump 1 all custom 10 dump.reax.rdx id type q xs ys zs - -#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 - -#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 - -run 100 -Neighbor list info ... - 1 neighbor list requests - update every 10 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12.5 - ghost atom cutoff = 12.5 - binsize = 6.25 -> bins = 3 3 3 -Memory usage per processor = 3.0718 Mbytes -Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - 0 0 -1885.1268 -1885.1268 27233.074 -2958.4712 79.527715 0.31082031 0 97.771125 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79972 0 168.8843 - 10 1281.7558 -1989.1322 -1912.7188 -19609.913 -2733.8828 -15.775275 0.20055725 0 55.020231 3.1070523 -77.710916 0 14.963568 -5.8082204 843.41939 -180.17725 0 107.51148 - 20 516.8308 -1941.677 -1910.8655 -12525.411 -2801.8626 7.4107973 0.07313419 0 81.986982 0.2281551 -57.494871 0 30.656735 -10.102557 877.78696 -158.93385 0 88.574155 - 30 467.26411 -1940.978 -1913.1215 -35957.487 -2755.021 -6.9179966 0.049322437 0 78.853175 0.13604391 -51.653634 0 19.862872 -9.7098574 853.79333 -151.232 0 80.861765 - 40 647.45584 -1951.1994 -1912.6006 -5883.7102 -2798.3557 17.334812 0.15102857 0 63.235124 0.18070914 -54.598951 0 17.325006 -12.052278 883.01674 -164.21335 0 96.777418 - 50 716.38108 -1949.4679 -1906.76 5473.1803 -2800.9311 9.2057064 0.15413272 0 85.371443 3.2986124 -78.253597 0 34.861778 -8.5531235 882.01441 -193.85213 0 117.21596 - 60 1175.2703 -1975.9632 -1905.898 -1939.6676 -2726.5815 -11.652032 0.24296779 0 48.320636 7.1799647 -75.363643 0 16.520124 -4.8869416 844.75396 -194.25563 0 119.75889 - 70 1156.7016 -1975.3469 -1906.3887 24628.125 -2880.5225 25.65252 0.26894309 0 83.724869 7.1048931 -68.700978 0 24.750754 -8.6338341 911.20067 -183.41947 0 113.22722 - 80 840.3323 -1955.4867 -1905.3893 -17732.956 -2755.7336 -8.0168615 0.13869303 0 86.143454 2.2388975 -76.946365 0 23.594977 -7.2608903 853.63682 -167.88599 0 94.604168 - 90 365.75853 -1926.4192 -1904.6141 902.29004 -2842.1715 47.360077 0.23110905 0 92.28805 0.38040356 -61.364192 0 18.473252 -12.253964 900.23128 -186.47889 0 116.88518 - 100 801.64661 -1953.4392 -1905.6481 -2464.5533 -2802.6922 4.6510183 0.18048786 0 76.715675 5.41849 -77.102069 0 24.987058 -7.7531389 898.65974 -196.87724 0 120.37303 -Loop time of 0.405054 on 4 procs for 100 steps with 21 atoms - -Performance: 21.331 ns/day, 1.125 hours/ns, 246.881 timesteps/s -96.9% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.16194 | 0.24674 | 0.40012 | 18.4 | 60.92 -Neigh | 7.3671e-05 | 0.00024015 | 0.00053477 | 1.1 | 0.06 -Comm | 0.0037704 | 0.1575 | 0.24247 | 23.1 | 38.88 -Output | 0.00037122 | 0.00040913 | 0.0004406 | 0.1 | 0.10 -Modify | 4.22e-05 | 6.175e-05 | 8.3685e-05 | 0.2 | 0.02 -Other | | 0.0001087 | | | 0.03 - -Nlocal: 5.25 ave 15 max 0 min -Histogram: 1 0 2 0 0 0 0 0 0 1 -Nghost: 355.5 ave 432 max 282 min -Histogram: 1 0 0 0 1 1 0 0 0 1 -Neighs: 301.25 ave 827 max 0 min -Histogram: 1 0 2 0 0 0 0 0 0 1 - -Total # of neighbors = 1205 -Ave neighs/atom = 57.381 -Neighbor list builds = 10 -Dangerous builds not checked -Total wall time: 0:00:00 diff --git a/examples/reax/log.5Oct16.reaxc.rdx.g++.1 b/examples/reax/log.5Oct16.reaxc.rdx.g++.1 deleted file mode 100644 index 5c8bb737b90bb1d8f15323a6b03eea1762fd4ad8..0000000000000000000000000000000000000000 --- a/examples/reax/log.5Oct16.reaxc.rdx.g++.1 +++ /dev/null @@ -1,104 +0,0 @@ -LAMMPS (5 Oct 2016) -# ReaxFF potential for RDX system -# this run is equivalent to reax/in.reax.rdx - -units real - -atom_style charge -read_data data.rdx - orthogonal box = (35 35 35) to (48 48 48) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 21 atoms - -pair_style reax/c control.reax_c.rdx -pair_coeff * * ffield.reax C H O N -Reading potential file ffield.reax with DATE: 2010-02-19 - -compute reax all pair reax/c - -variable eb equal c_reax[1] -variable ea equal c_reax[2] -variable elp equal c_reax[3] -variable emol equal c_reax[4] -variable ev equal c_reax[5] -variable epen equal c_reax[6] -variable ecoa equal c_reax[7] -variable ehb equal c_reax[8] -variable et equal c_reax[9] -variable eco equal c_reax[10] -variable ew equal c_reax[11] -variable ep equal c_reax[12] -variable efi equal c_reax[13] -variable eqeq equal c_reax[14] - -neighbor 2.5 bin -neigh_modify every 10 delay 0 check no - -fix 1 all nve -fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c - -thermo 10 -thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - -timestep 1.0 - -#dump 1 all atom 10 dump.reaxc.rdx - -#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 - -#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 - -run 100 -Neighbor list info ... - 2 neighbor list requests - update every 10 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12.5 - ghost atom cutoff = 12.5 - binsize = 6.25 -> bins = 3 3 3 -Memory usage per processor = 14.4462 Mbytes -Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - 0 0 -1884.3081 -1884.3081 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79931 0 168.88396 - 10 1288.6116 -1989.6644 -1912.8422 -19456.353 -2734.6769 -15.607221 0.2017796 0 54.629557 3.125229 -77.7067 0 14.933901 -5.8108541 843.92073 -180.43321 0 107.75935 - 20 538.95819 -1942.7037 -1910.5731 -10725.639 -2803.7394 7.9078269 0.07792668 0 81.610053 0.22951941 -57.557107 0 30.331207 -10.178049 878.99009 -159.68914 0 89.313379 - 30 463.09535 -1933.5765 -1905.9686 -33255.546 -2749.859 -8.0154745 0.02762893 0 81.627395 0.11972413 -50.262293 0 20.820303 -9.6327015 851.88715 -149.49499 0 79.205727 - 40 885.49171 -1958.9125 -1906.1229 -4814.6856 -2795.644 9.150669 0.13747498 0 70.947982 0.24360485 -57.862663 0 19.076496 -11.141218 873.73893 -159.99393 0 92.434096 - 50 861.16578 -1954.4599 -1903.1205 -1896.7713 -2784.845 3.8270515 0.15793266 0 79.851823 3.3492142 -78.06613 0 32.629016 -7.956541 872.81838 -190.98567 0 114.75995 - 60 1167.7852 -1971.8429 -1902.224 -3482.7305 -2705.863 -17.12171 0.22749077 0 44.507654 7.8560745 -74.788955 0 16.256483 -4.6046431 835.8304 -188.33691 0 114.19413 - 70 1439.9966 -1989.3024 -1903.4553 23845.651 -2890.7895 31.958845 0.26671721 0 85.758695 3.1803544 -71.002903 0 24.357134 -10.31131 905.86775 -175.38471 0 106.79648 - 80 502.39438 -1930.7544 -1900.8035 -20356.316 -2703.8115 -18.662467 0.11286011 0 99.804201 2.0329024 -76.171317 0 19.237028 -6.2786907 826.47451 -166.03125 0 92.539398 - 90 749.08499 -1946.9838 -1902.3262 17798.51 -2863.7576 42.068717 0.2433807 0 96.181613 0.96184887 -69.955448 0 24.615302 -11.582765 903.68818 -190.13843 0 120.69141 - 100 1109.6968 -1968.5874 -1902.4315 -4490.1018 -2755.8965 -7.1231014 0.21757699 0 61.806018 7.0827673 -75.645345 0 20.114997 -6.2371964 863.5635 -198.56976 0 122.09961 -Loop time of 0.362895 on 1 procs for 100 steps with 21 atoms - -Performance: 23.809 ns/day, 1.008 hours/ns, 275.562 timesteps/s -100.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.34367 | 0.34367 | 0.34367 | 0.0 | 94.70 -Neigh | 0.0078354 | 0.0078354 | 0.0078354 | 0.0 | 2.16 -Comm | 0.00043559 | 0.00043559 | 0.00043559 | 0.0 | 0.12 -Output | 0.00019908 | 0.00019908 | 0.00019908 | 0.0 | 0.05 -Modify | 0.010645 | 0.010645 | 0.010645 | 0.0 | 2.93 -Other | | 0.0001094 | | | 0.03 - -Nlocal: 21 ave 21 max 21 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 546 ave 546 max 546 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1096 ave 1096 max 1096 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 1096 -Ave neighs/atom = 52.1905 -Neighbor list builds = 10 -Dangerous builds not checked - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:00 diff --git a/examples/reax/log.5Oct16.reaxc.rdx.g++.4 b/examples/reax/log.5Oct16.reaxc.rdx.g++.4 deleted file mode 100644 index 10f11811cfaccb047df1e71ee7ba31b8e5ee26fe..0000000000000000000000000000000000000000 --- a/examples/reax/log.5Oct16.reaxc.rdx.g++.4 +++ /dev/null @@ -1,104 +0,0 @@ -LAMMPS (5 Oct 2016) -# ReaxFF potential for RDX system -# this run is equivalent to reax/in.reax.rdx - -units real - -atom_style charge -read_data data.rdx - orthogonal box = (35 35 35) to (48 48 48) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 21 atoms - -pair_style reax/c control.reax_c.rdx -pair_coeff * * ffield.reax C H O N -Reading potential file ffield.reax with DATE: 2010-02-19 - -compute reax all pair reax/c - -variable eb equal c_reax[1] -variable ea equal c_reax[2] -variable elp equal c_reax[3] -variable emol equal c_reax[4] -variable ev equal c_reax[5] -variable epen equal c_reax[6] -variable ecoa equal c_reax[7] -variable ehb equal c_reax[8] -variable et equal c_reax[9] -variable eco equal c_reax[10] -variable ew equal c_reax[11] -variable ep equal c_reax[12] -variable efi equal c_reax[13] -variable eqeq equal c_reax[14] - -neighbor 2.5 bin -neigh_modify every 10 delay 0 check no - -fix 1 all nve -fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c - -thermo 10 -thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - -timestep 1.0 - -#dump 1 all atom 10 dump.reaxc.rdx - -#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 - -#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 - -run 100 -Neighbor list info ... - 2 neighbor list requests - update every 10 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12.5 - ghost atom cutoff = 12.5 - binsize = 6.25 -> bins = 3 3 3 -Memory usage per processor = 12.531 Mbytes -Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - 0 0 -1884.3081 -1884.3081 27186.18 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79953 0 168.88418 - 10 1288.6115 -1989.6644 -1912.8422 -19456.354 -2734.6769 -15.60722 0.2017796 0 54.629558 3.1252288 -77.7067 0 14.933901 -5.8108542 843.92073 -180.43321 0 107.75934 - 20 538.95831 -1942.7037 -1910.5731 -10725.671 -2803.7395 7.9078306 0.077926651 0 81.610051 0.22951926 -57.557099 0 30.331204 -10.178049 878.99014 -159.69268 0 89.316921 - 30 463.09502 -1933.5765 -1905.9685 -33255.512 -2749.8591 -8.015455 0.027628766 0 81.6274 0.11972393 -50.262275 0 20.820315 -9.6327041 851.88722 -149.49498 0 79.205714 - 40 885.49378 -1958.9125 -1906.1228 -4814.644 -2795.644 9.1506485 0.13747497 0 70.948 0.24360511 -57.862677 0 19.076502 -11.141216 873.73898 -159.99393 0 92.43409 - 50 861.16297 -1954.4602 -1903.1209 -1896.8002 -2784.8451 3.8270162 0.157933 0 79.851673 3.3492148 -78.066132 0 32.628944 -7.9565368 872.81852 -190.98572 0 114.76001 - 60 1167.7835 -1971.8433 -1902.2245 -3482.8296 -2705.8635 -17.121613 0.2274909 0 44.507674 7.85602 -74.788998 0 16.256483 -4.6046575 835.83058 -188.33691 0 114.19414 - 70 1439.9939 -1989.3026 -1903.4556 23846.042 -2890.7893 31.958672 0.26671708 0 85.758381 3.1804035 -71.002944 0 24.357195 -10.311284 905.8679 -175.38487 0 106.79661 - 80 502.39535 -1930.7548 -1900.8039 -20356.194 -2703.8126 -18.662209 0.11286005 0 99.803849 2.0329206 -76.171278 0 19.23716 -6.2787147 826.47505 -166.03123 0 92.539386 - 90 749.07874 -1946.9841 -1902.3269 17798.394 -2863.7576 42.068612 0.24338059 0 96.181423 0.96185061 -69.95542 0 24.615344 -11.582758 903.68812 -190.13826 0 120.69124 - 100 1109.6904 -1968.5879 -1902.4323 -4490.0667 -2755.8991 -7.1224194 0.21757691 0 61.805857 7.0827218 -75.645383 0 20.115437 -6.23727 863.56487 -198.56975 0 122.09963 -Loop time of 0.293673 on 4 procs for 100 steps with 21 atoms - -Performance: 29.420 ns/day, 0.816 hours/ns, 340.514 timesteps/s -99.1% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.24143 | 0.24223 | 0.24409 | 0.2 | 82.48 -Neigh | 0.003767 | 0.0049117 | 0.0061524 | 1.2 | 1.67 -Comm | 0.0030656 | 0.0048578 | 0.0057402 | 1.5 | 1.65 -Output | 0.00033545 | 0.00036347 | 0.00038052 | 0.1 | 0.12 -Modify | 0.039885 | 0.041207 | 0.042435 | 0.4 | 14.03 -Other | | 0.0001001 | | | 0.03 - -Nlocal: 5.25 ave 15 max 0 min -Histogram: 1 0 2 0 0 0 0 0 0 1 -Nghost: 355.5 ave 432 max 282 min -Histogram: 1 0 0 0 1 1 0 0 0 1 -Neighs: 298.75 ave 822 max 0 min -Histogram: 1 0 2 0 0 0 0 0 0 1 - -Total # of neighbors = 1195 -Ave neighs/atom = 56.9048 -Neighbor list builds = 10 -Dangerous builds not checked - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:00 diff --git a/examples/reax/log.8March18.reax.rdx.g++.1 b/examples/reax/log.8March18.reax.rdx.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..c2edc5d51f33667e51e4c38c778cfe19cbc49d94 --- /dev/null +++ b/examples/reax/log.8March18.reax.rdx.g++.1 @@ -0,0 +1,107 @@ +LAMMPS (8 Mar 2018) + using 1 OpenMP thread(s) per MPI task +# ReaxFF potential for RDX system + +units real + +atom_style charge +read_data data.rdx + orthogonal box = (35 35 35) to (48 48 48) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 21 atoms + +# reax args: hbcut hbnewflag tripflag precision + +pair_style reax 6.0 1 1 1.0e-6 +WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49) +pair_coeff * * ffield.reax 1 2 3 4 + +compute reax all pair reax + +variable eb equal c_reax[1] +variable ea equal c_reax[2] +variable elp equal c_reax[3] +variable emol equal c_reax[4] +variable ev equal c_reax[5] +variable epen equal c_reax[6] +variable ecoa equal c_reax[7] +variable ehb equal c_reax[8] +variable et equal c_reax[9] +variable eco equal c_reax[10] +variable ew equal c_reax[11] +variable ep equal c_reax[12] +variable efi equal c_reax[13] +variable eqeq equal c_reax[14] + +neighbor 2.5 bin +neigh_modify every 10 delay 0 check no + +fix 1 all nve + +thermo 10 +thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq + +timestep 1.0 + +#dump 1 all custom 10 dump.reax.rdx id type q xs ys zs + +#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +run 100 +Neighbor list info ... + update every 10 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12.5 + ghost atom cutoff = 12.5 + binsize = 6.25, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair reax, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.278 | 3.278 | 3.278 Mbytes +Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq + 0 0 -1885.1269 -1885.1269 27233.074 -2958.4712 79.527715 0.31082031 0 97.771125 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79973 0 168.8842 + 10 1281.7558 -1989.1322 -1912.7188 -19609.913 -2733.8828 -15.775275 0.20055725 0 55.02023 3.1070523 -77.710916 0 14.963568 -5.8082203 843.41939 -180.17724 0 107.5115 + 20 516.83079 -1941.677 -1910.8655 -12525.412 -2801.8626 7.410797 0.073134186 0 81.986983 0.2281551 -57.494871 0 30.656735 -10.102557 877.78695 -158.93385 0 88.574159 + 30 467.26411 -1940.978 -1913.1215 -35957.489 -2755.021 -6.9179958 0.049322453 0 78.853173 0.13604393 -51.653635 0 19.862871 -9.7098575 853.79334 -151.232 0 80.86177 + 40 647.45528 -1951.1994 -1912.6006 -5883.713 -2798.3556 17.334814 0.15102862 0 63.235117 0.18070924 -54.598957 0 17.325007 -12.052278 883.0167 -164.21335 0 96.777424 + 50 716.38088 -1949.4735 -1906.7656 5473.1969 -2800.9309 9.2056861 0.15413274 0 85.371466 3.2986127 -78.253597 0 34.861774 -8.553123 882.01431 -193.85254 0 117.21068 + 60 1175.2705 -1975.961 -1905.8958 -1939.4966 -2726.5816 -11.651996 0.24296786 0 48.320654 7.1799691 -75.363638 0 16.520127 -4.8869441 844.75401 -194.23297 0 119.73841 + 70 1156.701 -1975.3497 -1906.3916 24628.304 -2880.5225 25.652501 0.26894311 0 83.724852 7.1049152 -68.70096 0 24.750735 -8.6338267 911.20079 -183.40562 0 113.21047 + 80 840.23677 -1955.4769 -1905.3851 -17731.334 -2755.7299 -8.0167723 0.1386797 0 86.147417 2.2387319 -76.945843 0 23.595869 -7.260968 853.63487 -167.88288 0 94.603961 + 90 365.79122 -1926.4061 -1904.599 898.38479 -2842.1832 47.368107 0.23109002 0 92.288071 0.38031213 -61.361485 0 18.476336 -12.25546 900.24233 -186.48046 0 116.88827 + 100 801.32158 -1953.418 -1905.6462 -2417.6887 -2802.7247 4.6676477 0.18046575 0 76.729987 5.4177322 -77.102566 0 24.997175 -7.7554074 898.67337 -196.89114 0 120.38946 +Loop time of 0.463306 on 1 procs for 100 steps with 21 atoms + +Performance: 18.649 ns/day, 1.287 hours/ns, 215.840 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.46143 | 0.46143 | 0.46143 | 0.0 | 99.60 +Neigh | 0.00087953 | 0.00087953 | 0.00087953 | 0.0 | 0.19 +Comm | 0.00042653 | 0.00042653 | 0.00042653 | 0.0 | 0.09 +Output | 0.00034237 | 0.00034237 | 0.00034237 | 0.0 | 0.07 +Modify | 0.00010109 | 0.00010109 | 0.00010109 | 0.0 | 0.02 +Other | | 0.000124 | | | 0.03 + +Nlocal: 21 ave 21 max 21 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 546 ave 546 max 546 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1106 ave 1106 max 1106 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1106 +Ave neighs/atom = 52.6667 +Neighbor list builds = 10 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/reax/log.8March18.reax.rdx.g++.4 b/examples/reax/log.8March18.reax.rdx.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..9526e2566191d08f59bf3fcc6839808e12a8650c --- /dev/null +++ b/examples/reax/log.8March18.reax.rdx.g++.4 @@ -0,0 +1,107 @@ +LAMMPS (8 Mar 2018) + using 1 OpenMP thread(s) per MPI task +# ReaxFF potential for RDX system + +units real + +atom_style charge +read_data data.rdx + orthogonal box = (35 35 35) to (48 48 48) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 21 atoms + +# reax args: hbcut hbnewflag tripflag precision + +pair_style reax 6.0 1 1 1.0e-6 +WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49) +pair_coeff * * ffield.reax 1 2 3 4 + +compute reax all pair reax + +variable eb equal c_reax[1] +variable ea equal c_reax[2] +variable elp equal c_reax[3] +variable emol equal c_reax[4] +variable ev equal c_reax[5] +variable epen equal c_reax[6] +variable ecoa equal c_reax[7] +variable ehb equal c_reax[8] +variable et equal c_reax[9] +variable eco equal c_reax[10] +variable ew equal c_reax[11] +variable ep equal c_reax[12] +variable efi equal c_reax[13] +variable eqeq equal c_reax[14] + +neighbor 2.5 bin +neigh_modify every 10 delay 0 check no + +fix 1 all nve + +thermo 10 +thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq + +timestep 1.0 + +#dump 1 all custom 10 dump.reax.rdx id type q xs ys zs + +#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +run 100 +Neighbor list info ... + update every 10 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12.5 + ghost atom cutoff = 12.5 + binsize = 6.25, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair reax, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.262 | 3.36 | 3.647 Mbytes +Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq + 0 0 -1885.1268 -1885.1268 27233.074 -2958.4712 79.527715 0.31082031 0 97.771125 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79972 0 168.88428 + 10 1281.7558 -1989.1322 -1912.7187 -19609.913 -2733.8828 -15.775275 0.20055725 0 55.020231 3.1070523 -77.710916 0 14.963568 -5.8082203 843.41939 -180.17724 0 107.51152 + 20 516.83079 -1941.677 -1910.8655 -12525.412 -2801.8626 7.410797 0.073134187 0 81.986983 0.2281551 -57.494871 0 30.656735 -10.102557 877.78695 -158.93385 0 88.574168 + 30 467.26411 -1940.978 -1913.1215 -35957.489 -2755.021 -6.9179959 0.049322449 0 78.853173 0.13604392 -51.653635 0 19.862871 -9.7098575 853.79334 -151.232 0 80.861765 + 40 647.45479 -1951.1995 -1912.6007 -5883.7199 -2798.3556 17.334805 0.15102868 0 63.235116 0.18070946 -54.59897 0 17.32501 -12.052277 883.0166 -164.21339 0 96.777473 + 50 716.37927 -1949.466 -1906.7582 5473.2486 -2800.9309 9.2056758 0.15413278 0 85.37143 3.2986099 -78.253596 0 34.861773 -8.5531243 882.01424 -193.85223 0 117.21791 + 60 1175.2698 -1975.9612 -1905.896 -1939.5206 -2726.5818 -11.651942 0.24296793 0 48.320679 7.1799538 -75.36365 0 16.520134 -4.8869515 844.75405 -194.23289 0 119.7383 + 70 1156.6963 -1975.3494 -1906.3915 24628.423 -2880.5221 25.65242 0.26894312 0 83.724787 7.1049615 -68.700925 0 24.750729 -8.6338123 911.2006 -183.40591 0 113.21091 + 80 840.238 -1955.4788 -1905.387 -17731.371 -2755.7301 -8.0167357 0.13868007 0 86.147246 2.2387405 -76.945868 0 23.595868 -7.2609697 853.6349 -167.88312 0 94.602512 + 90 365.78645 -1926.4072 -1904.6004 898.36945 -2842.1831 47.368307 0.23108998 0 92.288039 0.38031101 -61.361464 0 18.476388 -12.255481 900.24216 -186.48066 0 116.88716 + 100 801.31322 -1953.4165 -1905.6452 -2417.2041 -2802.7247 4.6678077 0.18046498 0 76.730367 5.4176812 -77.102592 0 24.9973 -7.7554425 898.6732 -196.89097 0 120.39043 +Loop time of 0.404551 on 4 procs for 100 steps with 21 atoms + +Performance: 21.357 ns/day, 1.124 hours/ns, 247.188 timesteps/s +97.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.2191 | 0.28038 | 0.39839 | 13.2 | 69.31 +Neigh | 5.8651e-05 | 0.00025928 | 0.00062203 | 0.0 | 0.06 +Comm | 0.0046599 | 0.12307 | 0.1845 | 19.9 | 30.42 +Output | 0.00055337 | 0.00062728 | 0.00071192 | 0.0 | 0.16 +Modify | 5.3167e-05 | 7.844e-05 | 0.00010109 | 0.0 | 0.02 +Other | | 0.0001363 | | | 0.03 + +Nlocal: 5.25 ave 15 max 0 min +Histogram: 1 0 2 0 0 0 0 0 0 1 +Nghost: 355.5 ave 432 max 282 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Neighs: 301.25 ave 827 max 0 min +Histogram: 1 0 2 0 0 0 0 0 0 1 + +Total # of neighbors = 1205 +Ave neighs/atom = 57.381 +Neighbor list builds = 10 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/reax/log.5Oct16.reax.tatb.g++.1 b/examples/reax/log.8March18.reax.tatb.g++.1 similarity index 61% rename from examples/reax/log.5Oct16.reax.tatb.g++.1 rename to examples/reax/log.8March18.reax.tatb.g++.1 index cc8d42a583891b216e9631eb3103a73b67bf9db4..53d77cd1da8a10d5c5ecf42a23a819aa8d55a203 100644 --- a/examples/reax/log.5Oct16.reax.tatb.g++.1 +++ b/examples/reax/log.8March18.reax.tatb.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (8 Mar 2018) + using 1 OpenMP thread(s) per MPI task # ReaxFF potential for TATB system units real @@ -12,7 +13,7 @@ read_data data.tatb # reax args: hbcut hbnewflag tripflag precision pair_style reax 6.0 1 1 1.0e-6 -WARNING: The pair_style reax command will be deprecated soon - users should switch to pair_style reax/c (../pair_reax.cpp:49) +WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49) pair_coeff * * ffield.reax 1 2 3 4 compute reax all pair reax @@ -54,34 +55,39 @@ fix 2 all reax/bonds 25 bonds.reax.tatb run 25 Neighbor list info ... - 1 neighbor list requests update every 5 steps, delay 0 steps, check no max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12.5 ghost atom cutoff = 12.5 - binsize = 6.25 -> bins = 5 4 3 -Memory usage per processor = 6.61277 Mbytes + binsize = 6.25, bins = 5 4 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair reax, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.764 | 7.764 | 7.764 Mbytes Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq 0 0 -44767.08 -44767.08 7294.6353 -61120.591 486.4378 4.7236377 0 1568.024 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6378 0 6391.0231 - 5 0.63682807 -44767.737 -44767.01 8391.5966 -61118.763 486.82916 4.723415 0 1567.835 20.768662 -278.20804 -1557.6962 252.64683 -655.74117 18859.328 -8738.2727 0 6388.8127 - 10 2.4306957 -44769.41 -44766.635 11717.369 -61113.142 487.89093 4.7227063 0 1567.2936 20.705084 -274.37509 -1560.8546 252.87219 -655.43578 18850.19 -8731.0713 0 6381.7946 - 15 5.0590478 -44772.63 -44766.854 17125.033 -61103.34 489.28007 4.7214008 0 1566.4744 20.590604 -268.28963 -1566.5961 252.97781 -654.93836 18835.335 -8719.3112 0 6370.4665 - 20 8.0678579 -44775.923 -44766.713 24620.824 -61088.791 490.42346 4.7193467 0 1565.5541 20.415031 -260.38512 -1574.1001 253.39805 -654.26837 18815.312 -8703.3104 0 6355.1097 - 25 10.975539 -44777.231 -44764.701 34381.278 -61068.889 490.53149 4.7164093 0 1566.5715 20.169755 -251.2311 -1582.8552 253.88696 -653.46042 18790.855 -8683.8362 0 6336.3099 -Loop time of 7.48375 on 1 procs for 25 steps with 384 atoms + 5 0.63682806 -44767.737 -44767.01 8391.5964 -61118.763 486.82916 4.723415 0 1567.835 20.768662 -278.20804 -1557.6962 252.64683 -655.74117 18859.328 -8738.2728 0 6388.8127 + 10 2.4306958 -44769.409 -44766.634 11717.376 -61113.142 487.89093 4.7227063 0 1567.2936 20.705084 -274.37509 -1560.8546 252.87219 -655.43578 18850.19 -8731.0693 0 6381.7942 + 15 5.0590493 -44772.631 -44766.855 17125.067 -61103.34 489.28007 4.7214008 0 1566.4744 20.590604 -268.28962 -1566.5961 252.97781 -654.93836 18835.335 -8719.3013 0 6370.4551 + 20 8.067859 -44775.936 -44766.725 24620.627 -61088.791 490.42346 4.7193467 0 1565.5541 20.415031 -260.38512 -1574.1001 253.39805 -654.26837 18815.312 -8703.3748 0 6355.1614 + 25 10.975538 -44777.233 -44764.702 34381.173 -61068.889 490.53149 4.7164093 0 1566.5715 20.169755 -251.23109 -1582.8552 253.88696 -653.46042 18790.855 -8683.8691 0 6336.3409 +Loop time of 7.80129 on 1 procs for 25 steps with 384 atoms -Performance: 0.018 ns/day, 1330.444 hours/ns, 3.341 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.017 ns/day, 1386.896 hours/ns, 3.205 timesteps/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 7.4284 | 7.4284 | 7.4284 | 0.0 | 99.26 -Neigh | 0.051549 | 0.051549 | 0.051549 | 0.0 | 0.69 -Comm | 0.0021887 | 0.0021887 | 0.0021887 | 0.0 | 0.03 -Output | 0.00025821 | 0.00025821 | 0.00025821 | 0.0 | 0.00 -Modify | 0.00099206 | 0.00099206 | 0.00099206 | 0.0 | 0.01 -Other | | 0.0003154 | | | 0.00 +Pair | 7.7384 | 7.7384 | 7.7384 | 0.0 | 99.19 +Neigh | 0.058615 | 0.058615 | 0.058615 | 0.0 | 0.75 +Comm | 0.0022428 | 0.0022428 | 0.0022428 | 0.0 | 0.03 +Output | 0.00033212 | 0.00033212 | 0.00033212 | 0.0 | 0.00 +Modify | 0.0013618 | 0.0013618 | 0.0013618 | 0.0 | 0.02 +Other | | 0.0003309 | | | 0.00 Nlocal: 384 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -94,4 +100,4 @@ Total # of neighbors = 286828 Ave neighs/atom = 746.948 Neighbor list builds = 5 Dangerous builds not checked -Total wall time: 0:00:07 +Total wall time: 0:00:08 diff --git a/examples/reax/log.5Oct16.reax.tatb.g++.4 b/examples/reax/log.8March18.reax.tatb.g++.4 similarity index 61% rename from examples/reax/log.5Oct16.reax.tatb.g++.4 rename to examples/reax/log.8March18.reax.tatb.g++.4 index 8fa9a608cfbd7862a6ff0f2e79f981efcc4f26a4..e3acac9d0efde524cae8ef28cd5f3eedac5c8dba 100644 --- a/examples/reax/log.5Oct16.reax.tatb.g++.4 +++ b/examples/reax/log.8March18.reax.tatb.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (8 Mar 2018) + using 1 OpenMP thread(s) per MPI task # ReaxFF potential for TATB system units real @@ -12,7 +13,7 @@ read_data data.tatb # reax args: hbcut hbnewflag tripflag precision pair_style reax 6.0 1 1 1.0e-6 -WARNING: The pair_style reax command will be deprecated soon - users should switch to pair_style reax/c (../pair_reax.cpp:49) +WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49) pair_coeff * * ffield.reax 1 2 3 4 compute reax all pair reax @@ -54,34 +55,39 @@ fix 2 all reax/bonds 25 bonds.reax.tatb run 25 Neighbor list info ... - 1 neighbor list requests update every 5 steps, delay 0 steps, check no max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12.5 ghost atom cutoff = 12.5 - binsize = 6.25 -> bins = 5 4 3 -Memory usage per processor = 4.03843 Mbytes + binsize = 6.25, bins = 5 4 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair reax, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.402 | 4.402 | 4.402 Mbytes Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq 0 0 -44767.08 -44767.08 7294.6353 -61120.591 486.4378 4.7236377 0 1568.024 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6378 0 6391.0231 - 5 0.63682726 -44767.816 -44767.089 8391.165 -61118.763 486.82916 4.723415 0 1567.835 20.768662 -278.20804 -1557.6962 252.64683 -655.74117 18859.328 -8738.3995 0 6388.86 - 10 2.4306905 -44769.408 -44766.633 11717.247 -61113.142 487.89094 4.7227063 0 1567.2936 20.705084 -274.3751 -1560.8546 252.87219 -655.43578 18850.19 -8731.0965 0 6381.8216 - 15 5.0590422 -44772.626 -44766.85 17124.943 -61103.34 489.2801 4.7214008 0 1566.4744 20.590604 -268.28963 -1566.5961 252.97781 -654.93836 18835.335 -8719.3383 0 6370.4973 - 20 8.0678512 -44775.934 -44766.723 24620.531 -61088.791 490.42349 4.7193467 0 1565.5541 20.415031 -260.38513 -1574.1001 253.39804 -654.26837 18815.312 -8703.4033 0 6355.1921 - 25 10.97553 -44777.231 -44764.701 34381.242 -61068.889 490.53154 4.7164093 0 1566.5715 20.169755 -251.23111 -1582.8552 253.88696 -653.46042 18790.855 -8683.8451 0 6336.3185 -Loop time of 3.27945 on 4 procs for 25 steps with 384 atoms + 5 0.63682727 -44767.816 -44767.089 8391.1708 -61118.763 486.82916 4.723415 0 1567.835 20.768662 -278.20804 -1557.6962 252.64683 -655.74117 18859.328 -8738.3973 0 6388.8581 + 10 2.4306941 -44769.405 -44766.63 11717.306 -61113.142 487.89094 4.7227063 0 1567.2936 20.705084 -274.3751 -1560.8546 252.87219 -655.43578 18850.19 -8731.08 0 6381.8083 + 15 5.0590444 -44772.6 -44766.824 17125.207 -61103.34 489.28008 4.7214008 0 1566.4744 20.590604 -268.28963 -1566.5961 252.97781 -654.93836 18835.335 -8719.2653 0 6370.4505 + 20 8.0678523 -44775.983 -44766.772 24620.114 -61088.791 490.42348 4.7193467 0 1565.5541 20.415031 -260.38513 -1574.1001 253.39804 -654.26837 18815.312 -8703.5228 0 6355.2629 + 25 10.975532 -44777.234 -44764.704 34381.065 -61068.889 490.53151 4.7164093 0 1566.5715 20.169755 -251.23111 -1582.8552 253.88696 -653.46042 18790.855 -8683.898 0 6336.3682 +Loop time of 3.74388 on 4 procs for 25 steps with 384 atoms -Performance: 0.041 ns/day, 583.013 hours/ns, 7.623 timesteps/s -99.8% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.036 ns/day, 665.579 hours/ns, 6.678 timesteps/s +98.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 3.0329 | 3.1456 | 3.2612 | 5.2 | 95.92 -Neigh | 0.011087 | 0.011261 | 0.011608 | 0.2 | 0.34 -Comm | 0.0057111 | 0.12121 | 0.23398 | 26.2 | 3.70 -Output | 0.00039172 | 0.0005855 | 0.00080633 | 0.6 | 0.02 -Modify | 0.00035787 | 0.00059456 | 0.00082469 | 0.7 | 0.02 -Other | | 0.0002265 | | | 0.01 +Pair | 3.478 | 3.6025 | 3.7215 | 4.8 | 96.22 +Neigh | 0.012731 | 0.01299 | 0.013174 | 0.2 | 0.35 +Comm | 0.0073411 | 0.12653 | 0.25119 | 25.4 | 3.38 +Output | 0.00050354 | 0.00081849 | 0.0011628 | 0.0 | 0.02 +Modify | 0.00049281 | 0.00082356 | 0.001157 | 0.0 | 0.02 +Other | | 0.0002663 | | | 0.01 Nlocal: 96 ave 96 max 96 min Histogram: 4 0 0 0 0 0 0 0 0 0 diff --git a/examples/reax/log.8March18.reaxc.rdx.g++.1 b/examples/reax/log.8March18.reaxc.rdx.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..4ae10e3f527aeac458e61a46232ddd355f253376 --- /dev/null +++ b/examples/reax/log.8March18.reaxc.rdx.g++.1 @@ -0,0 +1,115 @@ +LAMMPS (8 Mar 2018) + using 1 OpenMP thread(s) per MPI task +# ReaxFF potential for RDX system +# this run is equivalent to reax/in.reax.rdx + +units real + +atom_style charge +read_data data.rdx + orthogonal box = (35 35 35) to (48 48 48) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 21 atoms + +pair_style reax/c control.reax_c.rdx +pair_coeff * * ffield.reax C H O N +Reading potential file ffield.reax with DATE: 2010-02-19 + +compute reax all pair reax/c + +variable eb equal c_reax[1] +variable ea equal c_reax[2] +variable elp equal c_reax[3] +variable emol equal c_reax[4] +variable ev equal c_reax[5] +variable epen equal c_reax[6] +variable ecoa equal c_reax[7] +variable ehb equal c_reax[8] +variable et equal c_reax[9] +variable eco equal c_reax[10] +variable ew equal c_reax[11] +variable ep equal c_reax[12] +variable efi equal c_reax[13] +variable eqeq equal c_reax[14] + +neighbor 2.5 bin +neigh_modify every 10 delay 0 check no + +fix 1 all nve +fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c + +thermo 10 +thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq + +timestep 1.0 + +#dump 1 all atom 10 dump.reaxc.rdx + +#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +run 100 +Neighbor list info ... + update every 10 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12.5 + ghost atom cutoff = 12.5 + binsize = 6.25, bins = 3 3 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reax/c, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: half/ghost/bin/3d/newtoff + bin: standard + (2) fix qeq/reax, perpetual, copy from (1) + attributes: half, newton off, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 15.28 | 15.28 | 15.28 Mbytes +Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq + 0 0 -1884.3081 -1884.3081 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79937 0 168.88402 + 10 1288.6114 -1989.6644 -1912.8422 -19456.35 -2734.6769 -15.607219 0.20177961 0 54.629556 3.1252294 -77.7067 0 14.933901 -5.8108541 843.92074 -180.43322 0 107.75935 + 20 538.95849 -1942.7037 -1910.5731 -10725.658 -2803.7395 7.9078331 0.077926702 0 81.610043 0.22951937 -57.557104 0 30.331203 -10.178049 878.99015 -159.69092 0 89.315159 + 30 463.09542 -1933.5765 -1905.9685 -33255.507 -2749.8591 -8.0154628 0.027628767 0 81.627403 0.11972403 -50.262284 0 20.82032 -9.6327022 851.88722 -149.495 0 79.205731 + 40 885.49449 -1958.9126 -1906.1228 -4814.7123 -2795.644 9.1506221 0.1374749 0 70.948046 0.24360579 -57.8627 0 19.076515 -11.141211 873.73892 -159.9939 0 92.434059 + 50 861.1646 -1954.4599 -1903.1206 -1896.7387 -2784.8446 3.8269113 0.1579328 0 79.851775 3.3492107 -78.066127 0 32.628975 -7.9565255 872.81826 -190.98565 0 114.75994 + 60 1167.785 -1971.8432 -1902.2243 -3482.6975 -2705.8638 -17.121582 0.22749067 0 44.507705 7.856069 -74.788959 0 16.256519 -4.6046602 835.8308 -188.33691 0 114.19414 + 70 1439.9947 -1989.3024 -1903.4554 23845.067 -2890.7896 31.958874 0.26671735 0 85.758608 3.1803486 -71.002907 0 24.357106 -10.311315 905.86799 -175.38482 0 106.79659 + 80 502.40024 -1930.7547 -1900.8035 -20356.557 -2703.8096 -18.663105 0.11286226 0 99.803799 2.0329394 -76.171387 0 19.236609 -6.2786041 826.47358 -166.03157 0 92.539694 + 90 749.09267 -1946.9834 -1902.3254 17798.812 -2863.7586 42.068927 0.24338042 0 96.18195 0.96181754 -69.955528 0 24.61541 -11.58277 903.68895 -190.13838 0 120.69139 + 100 1109.7046 -1968.5875 -1902.4311 -4490.6736 -2755.8953 -7.1235173 0.21757663 0 61.806405 7.0825933 -75.645487 0 20.114745 -6.2371664 863.56285 -198.56939 0 122.09923 +Loop time of 0.395195 on 1 procs for 100 steps with 21 atoms + +Performance: 21.863 ns/day, 1.098 hours/ns, 253.039 timesteps/s +99.3% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.3722 | 0.3722 | 0.3722 | 0.0 | 94.18 +Neigh | 0.0098455 | 0.0098455 | 0.0098455 | 0.0 | 2.49 +Comm | 0.00047445 | 0.00047445 | 0.00047445 | 0.0 | 0.12 +Output | 0.00034022 | 0.00034022 | 0.00034022 | 0.0 | 0.09 +Modify | 0.012187 | 0.012187 | 0.012187 | 0.0 | 3.08 +Other | | 0.0001521 | | | 0.04 + +Nlocal: 21 ave 21 max 21 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 546 ave 546 max 546 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1096 ave 1096 max 1096 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1096 +Ave neighs/atom = 52.1905 +Neighbor list builds = 10 +Dangerous builds not checked + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 diff --git a/examples/reax/log.8March18.reaxc.rdx.g++.4 b/examples/reax/log.8March18.reaxc.rdx.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..6ea4835402351cb014cc99f689c0217a82be8ea4 --- /dev/null +++ b/examples/reax/log.8March18.reaxc.rdx.g++.4 @@ -0,0 +1,115 @@ +LAMMPS (8 Mar 2018) + using 1 OpenMP thread(s) per MPI task +# ReaxFF potential for RDX system +# this run is equivalent to reax/in.reax.rdx + +units real + +atom_style charge +read_data data.rdx + orthogonal box = (35 35 35) to (48 48 48) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 21 atoms + +pair_style reax/c control.reax_c.rdx +pair_coeff * * ffield.reax C H O N +Reading potential file ffield.reax with DATE: 2010-02-19 + +compute reax all pair reax/c + +variable eb equal c_reax[1] +variable ea equal c_reax[2] +variable elp equal c_reax[3] +variable emol equal c_reax[4] +variable ev equal c_reax[5] +variable epen equal c_reax[6] +variable ecoa equal c_reax[7] +variable ehb equal c_reax[8] +variable et equal c_reax[9] +variable eco equal c_reax[10] +variable ew equal c_reax[11] +variable ep equal c_reax[12] +variable efi equal c_reax[13] +variable eqeq equal c_reax[14] + +neighbor 2.5 bin +neigh_modify every 10 delay 0 check no + +fix 1 all nve +fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c + +thermo 10 +thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq + +timestep 1.0 + +#dump 1 all atom 10 dump.reaxc.rdx + +#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +run 100 +Neighbor list info ... + update every 10 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12.5 + ghost atom cutoff = 12.5 + binsize = 6.25, bins = 3 3 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reax/c, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: half/ghost/bin/3d/newtoff + bin: standard + (2) fix qeq/reax, perpetual, copy from (1) + attributes: half, newton off, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 10.37 | 11.76 | 13.34 Mbytes +Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq + 0 0 -1884.3081 -1884.3081 27186.178 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79988 0 168.88453 + 10 1288.6115 -1989.6644 -1912.8422 -19456.354 -2734.6769 -15.60722 0.2017796 0 54.629558 3.1252286 -77.7067 0 14.933902 -5.8108544 843.92073 -180.43321 0 107.75934 + 20 538.95818 -1942.7037 -1910.5731 -10725.623 -2803.7394 7.9078307 0.077926702 0 81.61005 0.22951942 -57.557107 0 30.331206 -10.178049 878.9901 -159.68951 0 89.313749 + 30 463.09514 -1933.5765 -1905.9685 -33255.525 -2749.859 -8.0154737 0.027628797 0 81.627408 0.11972402 -50.262283 0 20.82031 -9.6327021 851.88715 -149.49499 0 79.205724 + 40 885.49412 -1958.9125 -1906.1227 -4814.6606 -2795.6439 9.150622 0.13747487 0 70.948029 0.24360517 -57.862679 0 19.076509 -11.141214 873.7389 -159.99392 0 92.434078 + 50 861.16393 -1954.46 -1903.1207 -1896.7323 -2784.8449 3.8270197 0.1579328 0 79.851743 3.3492115 -78.066132 0 32.628992 -7.9565379 872.81841 -190.98568 0 114.75996 + 60 1167.7846 -1971.8432 -1902.2243 -3482.8111 -2705.8633 -17.121657 0.2274907 0 44.507681 7.8560366 -74.788989 0 16.256493 -4.6046537 835.8305 -188.33687 0 114.1941 + 70 1439.9942 -1989.3023 -1903.4554 23845.444 -2890.7894 31.958784 0.26671721 0 85.758586 3.1803655 -71.002918 0 24.357158 -10.311304 905.86792 -175.38481 0 106.79657 + 80 502.3975 -1930.7546 -1900.8036 -20356.439 -2703.8105 -18.662812 0.11286123 0 99.80391 2.0329293 -76.171334 0 19.236803 -6.2786439 826.47397 -166.03141 0 92.539551 + 90 749.09048 -1946.9837 -1902.3258 17798.718 -2863.7582 42.068719 0.24338057 0 96.181773 0.96183581 -69.955529 0 24.615414 -11.582758 903.68862 -190.1384 0 120.69139 + 100 1109.6999 -1968.5875 -1902.4314 -4490.3728 -2755.8964 -7.1231468 0.21757685 0 61.806149 7.0826648 -75.645428 0 20.115002 -6.2371958 863.56343 -198.56957 0 122.09942 +Loop time of 0.329552 on 4 procs for 100 steps with 21 atoms + +Performance: 26.217 ns/day, 0.915 hours/ns, 303.443 timesteps/s +96.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.26372 | 0.26499 | 0.26754 | 0.3 | 80.41 +Neigh | 0.0045478 | 0.0062494 | 0.0076699 | 1.5 | 1.90 +Comm | 0.0041637 | 0.0064691 | 0.0080271 | 1.8 | 1.96 +Output | 0.00054169 | 0.00056636 | 0.00060368 | 0.0 | 0.17 +Modify | 0.049433 | 0.051134 | 0.05311 | 0.6 | 15.52 +Other | | 0.000141 | | | 0.04 + +Nlocal: 5.25 ave 15 max 0 min +Histogram: 1 0 2 0 0 0 0 0 0 1 +Nghost: 355.5 ave 432 max 282 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Neighs: 298.75 ave 822 max 0 min +Histogram: 1 0 2 0 0 0 0 0 0 1 + +Total # of neighbors = 1195 +Ave neighs/atom = 56.9048 +Neighbor list builds = 10 +Dangerous builds not checked + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 diff --git a/examples/reax/log.5Oct16.reaxc.tatb.g++.1 b/examples/reax/log.8March18.reaxc.tatb.g++.1 similarity index 57% rename from examples/reax/log.5Oct16.reaxc.tatb.g++.1 rename to examples/reax/log.8March18.reaxc.tatb.g++.1 index deb1c5f1d79855de007b4041cd9bdff1293495af..ac5537bba406c015de04f83c1dcee125fbbac972 100644 --- a/examples/reax/log.5Oct16.reaxc.tatb.g++.1 +++ b/examples/reax/log.8March18.reaxc.tatb.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (8 Mar 2018) + using 1 OpenMP thread(s) per MPI task # ReaxFF potential for TATB system # this run is equivalent to reax/in.reax.tatb, @@ -56,34 +57,44 @@ fix 3 all reax/c/species 1 5 5 species.tatb run 25 Neighbor list info ... - 2 neighbor list requests update every 5 steps, delay 0 steps, check no max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12.5 ghost atom cutoff = 12.5 - binsize = 6.25 -> bins = 5 4 3 -Memory usage per processor = 155.82 Mbytes + binsize = 6.25, bins = 5 4 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reax/c, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: half/ghost/bin/3d/newtoff + bin: standard + (2) fix qeq/reax, perpetual, copy from (1) + attributes: half, newton off, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 176.7 | 176.7 | 176.7 Mbytes Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - 0 0 -44760.998 -44760.998 7827.7879 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6394 0 6391.0274 - 5 0.61603942 -44761.698 -44760.994 8934.6281 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.193 0 6388.6691 - 10 2.3525551 -44763.227 -44760.541 12288.607 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50358 -1560.7569 252.85309 -655.44063 18850.391 -8730.9688 0 6381.7066 - 15 4.9013326 -44766.36 -44760.764 17717.015 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.237 0 6370.4033 - 20 7.829471 -44769.686 -44760.747 25205.558 -61089.006 490.21313 4.719302 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.5091 0 6355.2604 - 25 10.697926 -44772.904 -44760.691 34232.793 -61069.308 490.25886 4.7163736 0 1570.7397 20.181346 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.3608 0 6336.8416 -Loop time of 4.34725 on 1 procs for 25 steps with 384 atoms + 0 0 -44760.998 -44760.998 7827.7874 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6395 0 6391.0275 + 5 0.61603968 -44761.698 -44760.994 8934.6347 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1911 0 6388.6671 + 10 2.3525551 -44763.227 -44760.541 12288.583 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9768 0 6381.7146 + 15 4.9013279 -44766.36 -44760.764 17717.01 -61103.434 489.14722 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2375 0 6370.4038 + 20 7.8294645 -44769.686 -44760.747 25205.624 -61089.006 490.21314 4.719302 0 1571.7022 20.420943 -260.85564 -1573.7378 253.3539 -654.31623 18816.07 -8703.4889 0 6355.2402 + 25 10.697904 -44772.904 -44760.691 34232.965 -61069.308 490.25888 4.7163736 0 1570.7397 20.181346 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.3125 0 6336.7934 +Loop time of 4.72562 on 1 procs for 25 steps with 384 atoms -Performance: 0.031 ns/day, 772.845 hours/ns, 5.751 timesteps/s -99.8% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.029 ns/day, 840.110 hours/ns, 5.290 timesteps/s +99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 3.5264 | 3.5264 | 3.5264 | 0.0 | 81.12 -Neigh | 0.40335 | 0.40335 | 0.40335 | 0.0 | 9.28 -Comm | 0.0021031 | 0.0021031 | 0.0021031 | 0.0 | 0.05 -Output | 0.00019765 | 0.00019765 | 0.00019765 | 0.0 | 0.00 -Modify | 0.41479 | 0.41479 | 0.41479 | 0.0 | 9.54 -Other | | 0.0004084 | | | 0.01 +Pair | 3.775 | 3.775 | 3.775 | 0.0 | 79.88 +Neigh | 0.47047 | 0.47047 | 0.47047 | 0.0 | 9.96 +Comm | 0.0025151 | 0.0025151 | 0.0025151 | 0.0 | 0.05 +Output | 0.0003159 | 0.0003159 | 0.0003159 | 0.0 | 0.01 +Modify | 0.47676 | 0.47676 | 0.47676 | 0.0 | 10.09 +Other | | 0.0005293 | | | 0.01 Nlocal: 384 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -99,4 +110,4 @@ Dangerous builds not checked Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:04 +Total wall time: 0:00:05 diff --git a/examples/reax/log.5Oct16.reaxc.tatb.g++.4 b/examples/reax/log.8March18.reaxc.tatb.g++.4 similarity index 57% rename from examples/reax/log.5Oct16.reaxc.tatb.g++.4 rename to examples/reax/log.8March18.reaxc.tatb.g++.4 index 064a4da54c0e9742b65715443a0fd63d37061498..12558be68a7b74f21812b82bed945a5d83696303 100644 --- a/examples/reax/log.5Oct16.reaxc.tatb.g++.4 +++ b/examples/reax/log.8March18.reaxc.tatb.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (8 Mar 2018) + using 1 OpenMP thread(s) per MPI task # ReaxFF potential for TATB system # this run is equivalent to reax/in.reax.tatb, @@ -56,34 +57,44 @@ fix 3 all reax/c/species 1 5 5 species.tatb run 25 Neighbor list info ... - 2 neighbor list requests update every 5 steps, delay 0 steps, check no max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12.5 ghost atom cutoff = 12.5 - binsize = 6.25 -> bins = 5 4 3 -Memory usage per processor = 105.386 Mbytes + binsize = 6.25, bins = 5 4 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reax/c, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: half/ghost/bin/3d/newtoff + bin: standard + (2) fix qeq/reax, perpetual, copy from (1) + attributes: half, newton off, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 118 | 118 | 118 Mbytes Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - 0 0 -44760.998 -44760.998 7827.7867 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6397 0 6391.0277 - 5 0.61603967 -44761.698 -44760.994 8934.6339 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1905 0 6388.6665 - 10 2.3525545 -44763.227 -44760.541 12288.586 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9762 0 6381.714 - 15 4.9013281 -44766.36 -44760.764 17716.982 -61103.434 489.14722 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2476 0 6370.4138 - 20 7.8294637 -44769.686 -44760.747 25205.512 -61089.006 490.21314 4.719302 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.518 0 6355.2692 - 25 10.697905 -44772.904 -44760.691 34232.815 -61069.308 490.25887 4.7163736 0 1570.7397 20.181346 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.3481 0 6336.829 -Loop time of 2.60733 on 4 procs for 25 steps with 384 atoms + 0 0 -44760.998 -44760.998 7827.7866 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6398 0 6391.0277 + 5 0.61603968 -44761.698 -44760.994 8934.6335 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1906 0 6388.6666 + 10 2.3525544 -44763.227 -44760.541 12288.587 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9764 0 6381.7141 + 15 4.9013311 -44766.36 -44760.764 17716.955 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2558 0 6370.4221 + 20 7.8294715 -44769.686 -44760.747 25205.613 -61089.006 490.21314 4.7193021 0 1571.7022 20.420943 -260.85564 -1573.7378 253.3539 -654.31623 18816.07 -8703.4906 0 6355.2419 + 25 10.697924 -44772.904 -44760.691 34232.794 -61069.308 490.25886 4.7163736 0 1570.7397 20.181347 -251.91376 -1582.3261 253.82253 -653.53183 18791.975 -8684.3641 0 6336.8449 +Loop time of 2.84068 on 4 procs for 25 steps with 384 atoms -Performance: 0.052 ns/day, 463.526 hours/ns, 9.588 timesteps/s -99.9% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.048 ns/day, 505.009 hours/ns, 8.801 timesteps/s +98.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.1835 | 2.1843 | 2.1854 | 0.0 | 83.77 -Neigh | 0.22091 | 0.22364 | 0.22821 | 0.6 | 8.58 -Comm | 0.005677 | 0.0069622 | 0.0078082 | 1.0 | 0.27 -Output | 0.00036621 | 0.0028675 | 0.0037034 | 2.7 | 0.11 -Modify | 0.18736 | 0.18921 | 0.19102 | 0.4 | 7.26 -Other | | 0.0003636 | | | 0.01 +Pair | 2.3253 | 2.328 | 2.3305 | 0.2 | 81.95 +Neigh | 0.2589 | 0.26458 | 0.26897 | 0.7 | 9.31 +Comm | 0.0094428 | 0.012062 | 0.014872 | 2.3 | 0.42 +Output | 0.00043392 | 0.0042209 | 0.0054941 | 3.4 | 0.15 +Modify | 0.22563 | 0.23134 | 0.23579 | 0.8 | 8.14 +Other | | 0.0005122 | | | 0.02 Nlocal: 96 ave 96 max 96 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -99,4 +110,4 @@ Dangerous builds not checked Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:02 +Total wall time: 0:00:03 diff --git a/lib/colvars/Makefile.deps b/lib/colvars/Makefile.deps index e0c768dbc9b042b3ae14731b6319929af9a20705..9a7de0647db57eeb3d62ee866e71f6e363b6c802 100644 --- a/lib/colvars/Makefile.deps +++ b/lib/colvars/Makefile.deps @@ -1,9 +1,9 @@ $(COLVARS_OBJ_DIR)colvaratoms.o: colvaratoms.cpp colvarmodule.h \ - colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h \ + colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h \ colvarparse.h colvaratoms.h colvardeps.h $(COLVARS_OBJ_DIR)colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h \ - colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h colvar.h \ + colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h colvar.h \ colvarparse.h colvardeps.h lepton/include/Lepton.h \ lepton/include/lepton/CompiledExpression.h \ lepton/include/lepton/ExpressionTreeNode.h \ @@ -16,9 +16,9 @@ $(COLVARS_OBJ_DIR)colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h \ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \ colvarbias_abf.h colvarbias.h colvargrid.h colvar_UIestimator.h $(COLVARS_OBJ_DIR)colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h \ - colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h \ - colvarbias_alb.h colvar.h colvarparse.h colvardeps.h \ - lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \ + colvars_version.h colvarbias.h colvar.h colvarvalue.h colvartypes.h \ + colvarparse.h colvardeps.h lepton/include/Lepton.h \ + lepton/include/lepton/CompiledExpression.h \ lepton/include/lepton/ExpressionTreeNode.h \ lepton/include/lepton/windowsIncludes.h \ lepton/include/lepton/CustomFunction.h \ @@ -27,9 +27,9 @@ $(COLVARS_OBJ_DIR)colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h \ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \ lepton/include/lepton/Exception.h \ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \ - colvarbias.h + colvarbias_alb.h $(COLVARS_OBJ_DIR)colvarbias.o: colvarbias.cpp colvarmodule.h \ - colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h colvarbias.h \ + colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h colvarbias.h \ colvar.h colvarparse.h colvardeps.h lepton/include/Lepton.h \ lepton/include/lepton/CompiledExpression.h \ lepton/include/lepton/ExpressionTreeNode.h \ @@ -42,8 +42,8 @@ $(COLVARS_OBJ_DIR)colvarbias.o: colvarbias.cpp colvarmodule.h \ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \ colvargrid.h $(COLVARS_OBJ_DIR)colvarbias_histogram.o: colvarbias_histogram.cpp \ - colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \ - colvarvalue.h colvar.h colvarparse.h colvardeps.h \ + colvarmodule.h colvars_version.h colvarproxy.h colvarvalue.h \ + colvartypes.h colvar.h colvarparse.h colvardeps.h \ lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \ lepton/include/lepton/ExpressionTreeNode.h \ lepton/include/lepton/windowsIncludes.h \ @@ -54,9 +54,9 @@ $(COLVARS_OBJ_DIR)colvarbias_histogram.o: colvarbias_histogram.cpp \ lepton/include/lepton/Exception.h \ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \ colvarbias_histogram.h colvarbias.h colvargrid.h -$(COLVARS_OBJ_DIR)colvarbias_meta.o: colvarbias_meta.cpp colvar.h \ - colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \ - colvarvalue.h colvarparse.h colvardeps.h lepton/include/Lepton.h \ +$(COLVARS_OBJ_DIR)colvarbias_meta.o: colvarbias_meta.cpp colvarmodule.h \ + colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h colvar.h \ + colvarparse.h colvardeps.h lepton/include/Lepton.h \ lepton/include/lepton/CompiledExpression.h \ lepton/include/lepton/ExpressionTreeNode.h \ lepton/include/lepton/windowsIncludes.h \ @@ -68,8 +68,8 @@ $(COLVARS_OBJ_DIR)colvarbias_meta.o: colvarbias_meta.cpp colvar.h \ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \ colvarbias_meta.h colvarbias.h colvargrid.h $(COLVARS_OBJ_DIR)colvarbias_restraint.o: colvarbias_restraint.cpp \ - colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \ - colvarvalue.h colvarbias_restraint.h colvarbias.h colvar.h colvarparse.h \ + colvarmodule.h colvars_version.h colvarproxy.h colvarvalue.h \ + colvartypes.h colvarbias_restraint.h colvarbias.h colvar.h colvarparse.h \ colvardeps.h lepton/include/Lepton.h \ lepton/include/lepton/CompiledExpression.h \ lepton/include/lepton/ExpressionTreeNode.h \ @@ -81,9 +81,9 @@ $(COLVARS_OBJ_DIR)colvarbias_restraint.o: colvarbias_restraint.cpp \ lepton/include/lepton/Exception.h \ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h $(COLVARS_OBJ_DIR)colvarcomp_angles.o: colvarcomp_angles.cpp \ - colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \ - colvarvalue.h colvar.h colvarparse.h colvardeps.h \ - lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \ + colvarmodule.h colvars_version.h colvar.h colvarvalue.h colvartypes.h \ + colvarparse.h colvardeps.h lepton/include/Lepton.h \ + lepton/include/lepton/CompiledExpression.h \ lepton/include/lepton/ExpressionTreeNode.h \ lepton/include/lepton/windowsIncludes.h \ lepton/include/lepton/CustomFunction.h \ @@ -92,10 +92,10 @@ $(COLVARS_OBJ_DIR)colvarcomp_angles.o: colvarcomp_angles.cpp \ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \ lepton/include/lepton/Exception.h \ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \ - colvarcomp.h colvaratoms.h + colvarcomp.h colvaratoms.h colvarproxy.h $(COLVARS_OBJ_DIR)colvarcomp_coordnums.o: colvarcomp_coordnums.cpp \ - colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \ - colvarvalue.h colvarparse.h colvaratoms.h colvardeps.h colvar.h \ + colvarmodule.h colvars_version.h colvarparse.h colvarvalue.h \ + colvartypes.h colvaratoms.h colvarproxy.h colvardeps.h colvar.h \ lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \ lepton/include/lepton/ExpressionTreeNode.h \ lepton/include/lepton/windowsIncludes.h \ @@ -107,8 +107,8 @@ $(COLVARS_OBJ_DIR)colvarcomp_coordnums.o: colvarcomp_coordnums.cpp \ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \ colvarcomp.h $(COLVARS_OBJ_DIR)colvarcomp.o: colvarcomp.cpp colvarmodule.h \ - colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h colvar.h \ - colvarparse.h colvardeps.h lepton/include/Lepton.h \ + colvars_version.h colvarvalue.h colvartypes.h colvar.h colvarparse.h \ + colvardeps.h lepton/include/Lepton.h \ lepton/include/lepton/CompiledExpression.h \ lepton/include/lepton/ExpressionTreeNode.h \ lepton/include/lepton/windowsIncludes.h \ @@ -118,11 +118,11 @@ $(COLVARS_OBJ_DIR)colvarcomp.o: colvarcomp.cpp colvarmodule.h \ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \ lepton/include/lepton/Exception.h \ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \ - colvarcomp.h colvaratoms.h + colvarcomp.h colvaratoms.h colvarproxy.h $(COLVARS_OBJ_DIR)colvarcomp_distances.o: colvarcomp_distances.cpp \ - colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \ - colvarvalue.h colvarparse.h colvar.h colvardeps.h \ - lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \ + colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \ + colvarparse.h colvar.h colvardeps.h lepton/include/Lepton.h \ + lepton/include/lepton/CompiledExpression.h \ lepton/include/lepton/ExpressionTreeNode.h \ lepton/include/lepton/windowsIncludes.h \ lepton/include/lepton/CustomFunction.h \ @@ -131,11 +131,11 @@ $(COLVARS_OBJ_DIR)colvarcomp_distances.o: colvarcomp_distances.cpp \ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \ lepton/include/lepton/Exception.h \ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \ - colvarcomp.h colvaratoms.h + colvarcomp.h colvaratoms.h colvarproxy.h $(COLVARS_OBJ_DIR)colvarcomp_protein.o: colvarcomp_protein.cpp \ - colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \ - colvarvalue.h colvarparse.h colvar.h colvardeps.h \ - lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \ + colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \ + colvarparse.h colvar.h colvardeps.h lepton/include/Lepton.h \ + lepton/include/lepton/CompiledExpression.h \ lepton/include/lepton/ExpressionTreeNode.h \ lepton/include/lepton/windowsIncludes.h \ lepton/include/lepton/CustomFunction.h \ @@ -144,11 +144,11 @@ $(COLVARS_OBJ_DIR)colvarcomp_protein.o: colvarcomp_protein.cpp \ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \ lepton/include/lepton/Exception.h \ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \ - colvarcomp.h colvaratoms.h + colvarcomp.h colvaratoms.h colvarproxy.h $(COLVARS_OBJ_DIR)colvarcomp_rotations.o: colvarcomp_rotations.cpp \ - colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \ - colvarvalue.h colvarparse.h colvar.h colvardeps.h \ - lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \ + colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \ + colvarparse.h colvar.h colvardeps.h lepton/include/Lepton.h \ + lepton/include/lepton/CompiledExpression.h \ lepton/include/lepton/ExpressionTreeNode.h \ lepton/include/lepton/windowsIncludes.h \ lepton/include/lepton/CustomFunction.h \ @@ -157,11 +157,10 @@ $(COLVARS_OBJ_DIR)colvarcomp_rotations.o: colvarcomp_rotations.cpp \ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \ lepton/include/lepton/Exception.h \ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \ - colvarcomp.h colvaratoms.h + colvarcomp.h colvaratoms.h colvarproxy.h $(COLVARS_OBJ_DIR)colvar.o: colvar.cpp colvarmodule.h colvars_version.h \ - colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvar.h \ - colvardeps.h lepton/include/Lepton.h \ - lepton/include/lepton/CompiledExpression.h \ + colvarvalue.h colvartypes.h colvarparse.h colvar.h colvardeps.h \ + lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \ lepton/include/lepton/ExpressionTreeNode.h \ lepton/include/lepton/windowsIncludes.h \ lepton/include/lepton/CustomFunction.h \ @@ -170,13 +169,13 @@ $(COLVARS_OBJ_DIR)colvar.o: colvar.cpp colvarmodule.h colvars_version.h \ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \ lepton/include/lepton/Exception.h \ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \ - colvarcomp.h colvaratoms.h colvarscript.h colvarbias.h -$(COLVARS_OBJ_DIR)colvardeps.o: colvardeps.cpp colvardeps.h \ - colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \ - colvarvalue.h colvarparse.h + colvarcomp.h colvaratoms.h colvarproxy.h colvarscript.h colvarbias.h +$(COLVARS_OBJ_DIR)colvardeps.o: colvardeps.cpp colvarmodule.h \ + colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h colvardeps.h \ + colvarparse.h $(COLVARS_OBJ_DIR)colvargrid.o: colvargrid.cpp colvarmodule.h \ - colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h \ - colvarparse.h colvar.h colvardeps.h lepton/include/Lepton.h \ + colvars_version.h colvarvalue.h colvartypes.h colvarparse.h colvar.h \ + colvardeps.h lepton/include/Lepton.h \ lepton/include/lepton/CompiledExpression.h \ lepton/include/lepton/ExpressionTreeNode.h \ lepton/include/lepton/windowsIncludes.h \ @@ -186,10 +185,10 @@ $(COLVARS_OBJ_DIR)colvargrid.o: colvargrid.cpp colvarmodule.h \ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \ lepton/include/lepton/Exception.h \ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \ - colvarcomp.h colvaratoms.h colvargrid.h + colvarcomp.h colvaratoms.h colvarproxy.h colvargrid.h $(COLVARS_OBJ_DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h \ - colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h \ - colvarparse.h colvar.h colvardeps.h lepton/include/Lepton.h \ + colvars_version.h colvarparse.h colvarvalue.h colvartypes.h \ + colvarproxy.h colvar.h colvardeps.h lepton/include/Lepton.h \ lepton/include/lepton/CompiledExpression.h \ lepton/include/lepton/ExpressionTreeNode.h \ lepton/include/lepton/windowsIncludes.h \ @@ -203,10 +202,9 @@ $(COLVARS_OBJ_DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h \ colvarbias_alb.h colvarbias_histogram.h colvarbias_meta.h \ colvarbias_restraint.h colvarscript.h colvaratoms.h colvarcomp.h $(COLVARS_OBJ_DIR)colvarparse.o: colvarparse.cpp colvarmodule.h \ - colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h \ - colvarparse.h + colvars_version.h colvarvalue.h colvartypes.h colvarparse.h $(COLVARS_OBJ_DIR)colvarproxy.o: colvarproxy.cpp colvarmodule.h \ - colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h \ + colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h \ colvarscript.h colvarbias.h colvar.h colvarparse.h colvardeps.h \ lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \ lepton/include/lepton/ExpressionTreeNode.h \ @@ -219,9 +217,9 @@ $(COLVARS_OBJ_DIR)colvarproxy.o: colvarproxy.cpp colvarmodule.h \ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \ colvaratoms.h $(COLVARS_OBJ_DIR)colvarscript.o: colvarscript.cpp colvarscript.h \ - colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \ - colvarvalue.h colvarbias.h colvar.h colvarparse.h colvardeps.h \ - lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \ + colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \ + colvarbias.h colvar.h colvarparse.h colvardeps.h lepton/include/Lepton.h \ + lepton/include/lepton/CompiledExpression.h \ lepton/include/lepton/ExpressionTreeNode.h \ lepton/include/lepton/windowsIncludes.h \ lepton/include/lepton/CustomFunction.h \ @@ -229,9 +227,9 @@ $(COLVARS_OBJ_DIR)colvarscript.o: colvarscript.cpp colvarscript.h \ lepton/include/lepton/ExpressionTreeNode.h \ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \ lepton/include/lepton/Exception.h \ - lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h + lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \ + colvarproxy.h $(COLVARS_OBJ_DIR)colvartypes.o: colvartypes.cpp colvarmodule.h \ - colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h \ - colvarparse.h + colvars_version.h colvartypes.h colvarparse.h colvarvalue.h $(COLVARS_OBJ_DIR)colvarvalue.o: colvarvalue.cpp colvarmodule.h \ - colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h + colvars_version.h colvarvalue.h colvartypes.h diff --git a/lib/colvars/colvar.cpp b/lib/colvars/colvar.cpp index ce76b3b9eb2c8bd5f37b85af332611fa7ca963b3..5a4e8b617a9007fff02e87233b8f8dfebb1e7a25 100644 --- a/lib/colvars/colvar.cpp +++ b/lib/colvars/colvar.cpp @@ -195,7 +195,7 @@ int colvar::init(std::string const &conf) // - it is homogeneous // - all cvcs are periodic // - all cvcs have the same period - if (cvcs[0]->b_periodic) { // TODO make this a CVC feature + if (is_enabled(f_cv_homogeneous) && cvcs[0]->b_periodic) { // TODO make this a CVC feature bool b_periodic = true; period = cvcs[0]->period; for (i = 1; i < cvcs.size(); i++) { diff --git a/lib/colvars/colvar.h b/lib/colvars/colvar.h index 20dad2771b6c25afef9c4667ca23f24cfe61d46d..32c329460d06cfa5ceba43e245aa08a0d0810100 100644 --- a/lib/colvars/colvar.h +++ b/lib/colvars/colvar.h @@ -11,8 +11,6 @@ #define COLVAR_H #include -#include -#include #include "colvarmodule.h" #include "colvarvalue.h" @@ -60,10 +58,13 @@ public: /// \brief Current actual value (not extended DOF) colvarvalue const & actual_value() const; - + + /// \brief Current running average (if calculated as set by analysis flag) + colvarvalue const & run_ave() const; + /// \brief Force constant of the spring cvm::real const & force_constant() const; - + /// \brief Current velocity (previously set by calc() or by read_traj()) colvarvalue const & velocity() const; @@ -516,7 +517,7 @@ public: // collective variable component base class class cvc; - // currently available collective variable components + // list of available collective variable components // scalar colvar components class distance; @@ -611,12 +612,15 @@ inline colvarvalue const & colvar::value() const return x_reported; } - inline colvarvalue const & colvar::actual_value() const { return x; } +inline colvarvalue const & colvar::run_ave() const +{ + return runave; +} inline colvarvalue const & colvar::velocity() const { diff --git a/lib/colvars/colvar_UIestimator.h b/lib/colvars/colvar_UIestimator.h index 7fc7f870a10932d176525bb3c6c42d574a572fb1..36ed938119d41232dfdbdc42589cd35f8f67a735 100644 --- a/lib/colvars/colvar_UIestimator.h +++ b/lib/colvars/colvar_UIestimator.h @@ -45,7 +45,7 @@ namespace UIestimator { this->width = width; this->dimension = lowerboundary.size(); this->y_size = y_size; // keep in mind the internal (spare) matrix is stored in diagonal form - this->y_total_size = int(pow(double(y_size), dimension) + EPSILON); + this->y_total_size = int(std::pow(double(y_size), double(dimension)) + EPSILON); // the range of the matrix is [lowerboundary, upperboundary] x_total_size = 1; @@ -121,7 +121,7 @@ namespace UIestimator { int index = 0; for (i = 0; i < dimension; i++) { if (i + 1 < dimension) - index += temp[i] * int(pow(double(y_size), dimension - i - 1) + EPSILON); + index += temp[i] * int(std::pow(double(y_size), double(dimension - i - 1)) + EPSILON); else index += temp[i]; } diff --git a/lib/colvars/colvaratoms.cpp b/lib/colvars/colvaratoms.cpp index d2a0f0a807d2727500d96e6a19a56eaa0af23f39..1be6f42e594f86adf16a5b4702a631a6bef9c1e7 100644 --- a/lib/colvars/colvaratoms.cpp +++ b/lib/colvars/colvaratoms.cpp @@ -8,9 +8,11 @@ // Colvars repository at GitHub. #include "colvarmodule.h" +#include "colvarproxy.h" #include "colvarparse.h" #include "colvaratoms.h" + cvm::atom::atom() { index = -1; diff --git a/lib/colvars/colvaratoms.h b/lib/colvars/colvaratoms.h index 71c587e23084e516c6b66358e97327c8d404822f..0dda6ab792d8ae20afcf6a9aeaa615675f332d1b 100644 --- a/lib/colvars/colvaratoms.h +++ b/lib/colvars/colvaratoms.h @@ -11,6 +11,7 @@ #define COLVARATOMS_H #include "colvarmodule.h" +#include "colvarproxy.h" #include "colvarparse.h" #include "colvardeps.h" diff --git a/lib/colvars/colvarbias.cpp b/lib/colvars/colvarbias.cpp index 301e83e73015a91f14ff75a82c045954083d4074..29620fbee8f103a032b5698c52ca841b2f122cbc 100644 --- a/lib/colvars/colvarbias.cpp +++ b/lib/colvars/colvarbias.cpp @@ -8,6 +8,7 @@ // Colvars repository at GitHub. #include "colvarmodule.h" +#include "colvarproxy.h" #include "colvarvalue.h" #include "colvarbias.h" #include "colvargrid.h" diff --git a/lib/colvars/colvarbias_abf.cpp b/lib/colvars/colvarbias_abf.cpp index e4aea8eb86e7dcb6712fc6dc2c771adeeb6909f6..b3b5b3eb1654df12992b2fafb206d82851d3788b 100644 --- a/lib/colvars/colvarbias_abf.cpp +++ b/lib/colvars/colvarbias_abf.cpp @@ -8,6 +8,7 @@ // Colvars repository at GitHub. #include "colvarmodule.h" +#include "colvarproxy.h" #include "colvar.h" #include "colvarbias_abf.h" @@ -18,16 +19,18 @@ colvarbias_abf::colvarbias_abf(char const *key) b_CZAR_estimator(false), system_force(NULL), gradients(NULL), + pmf(NULL), samples(NULL), z_gradients(NULL), z_samples(NULL), czar_gradients(NULL), + czar_pmf(NULL), last_gradients(NULL), - last_samples(NULL) + last_samples(NULL), + pabf_freq(0) { } - int colvarbias_abf::init(std::string const &conf) { colvarbias::init(conf); @@ -91,7 +94,7 @@ int colvarbias_abf::init(std::string const &conf) // ************* checking the associated colvars ******************* - if (colvars.size() == 0) { + if (num_variables() == 0) { cvm::error("Error: no collective variables specified for the ABF bias.\n"); return COLVARS_ERROR; } @@ -102,7 +105,8 @@ int colvarbias_abf::init(std::string const &conf) } bool b_extended = false; - for (size_t i = 0; i < colvars.size(); i++) { + size_t i; + for (i = 0; i < num_variables(); i++) { if (colvars[i]->value().type() != colvarvalue::type_scalar) { cvm::error("Error: ABF bias can only use scalar-type variables.\n"); @@ -132,10 +136,10 @@ int colvarbias_abf::init(std::string const &conf) } if (get_keyval(conf, "maxForce", max_force)) { - if (max_force.size() != colvars.size()) { + if (max_force.size() != num_variables()) { cvm::error("Error: Number of parameters to maxForce does not match number of colvars."); } - for (size_t i = 0; i < colvars.size(); i++) { + for (i = 0; i < num_variables(); i++) { if (max_force[i] < 0.0) { cvm::error("Error: maxForce should be non-negative."); } @@ -145,9 +149,9 @@ int colvarbias_abf::init(std::string const &conf) cap_force = false; } - bin.assign(colvars.size(), 0); - force_bin.assign(colvars.size(), 0); - system_force = new cvm::real [colvars.size()]; + bin.assign(num_variables(), 0); + force_bin.assign(num_variables(), 0); + system_force = new cvm::real [num_variables()]; // Construct empty grids based on the colvars if (cvm::debug()) { @@ -159,14 +163,14 @@ int colvarbias_abf::init(std::string const &conf) gradients->samples = samples; samples->has_parent_data = true; - // Data for eABF z-based estimator - if (b_extended) { + // Data for eAB F z-based estimator + if ( b_extended ) { get_keyval(conf, "CZARestimator", b_CZAR_estimator, true); // CZAR output files for stratified eABF get_keyval(conf, "writeCZARwindowFile", b_czar_window_file, false, colvarparse::parse_silent); - z_bin.assign(colvars.size(), 0); + z_bin.assign(num_variables(), 0); z_samples = new colvar_grid_count(colvars); z_samples->request_actual_value(); z_gradients = new colvar_grid_gradient(colvars); @@ -176,6 +180,27 @@ int colvarbias_abf::init(std::string const &conf) czar_gradients = new colvar_grid_gradient(colvars); } + // For now, we integrate on-the-fly iff the grid is < 3D + if ( num_variables() <= 3 ) { + pmf = new integrate_potential(colvars, gradients); + if ( b_CZAR_estimator ) { + czar_pmf = new integrate_potential(colvars, czar_gradients); + } + get_keyval(conf, "integrate", b_integrate, true); // Integrate for output + if ( num_variables() > 1 ) { + // Projected ABF + get_keyval(conf, "pABFintegrateFreq", pabf_freq, 0); + // Parameters for integrating initial (and final) gradient data + get_keyval(conf, "integrateInitSteps", integrate_initial_steps, 1e4); + get_keyval(conf, "integrateInitTol", integrate_initial_tol, 1e-6); + // for updating the integrated PMF on the fly + get_keyval(conf, "integrateSteps", integrate_steps, 100); + get_keyval(conf, "integrateTol", integrate_tol, 1e-4); + } + } else { + b_integrate = false; + } + // For shared ABF, we store a second set of grids. // This used to be only if "shared" was defined, // but now we allow calling share externally (e.g. from Tcl). @@ -188,6 +213,8 @@ int colvarbias_abf::init(std::string const &conf) // If custom grids are provided, read them if ( input_prefix.size() > 0 ) { read_gradients_samples(); + // Update divergence to account for input data + pmf->set_div(); } // if extendedLangrangian is on, then call UI estimator @@ -202,7 +229,7 @@ int colvarbias_abf::init(std::string const &conf) bool UI_restart = (input_prefix.size() > 0); - for (size_t i = 0; i < colvars.size(); i++) + for (i = 0; i < num_variables(); i++) { UI_lowerboundary.push_back(colvars[i]->lower_boundary); UI_upperboundary.push_back(colvars[i]->upper_boundary); @@ -238,6 +265,11 @@ colvarbias_abf::~colvarbias_abf() gradients = NULL; } + if (pmf) { + delete pmf; + pmf = NULL; + } + if (z_samples) { delete z_samples; z_samples = NULL; @@ -253,6 +285,11 @@ colvarbias_abf::~colvarbias_abf() czar_gradients = NULL; } + if (czar_pmf) { + delete czar_pmf; + czar_pmf = NULL; + } + // shared ABF // We used to only do this if "shared" was defined, // but now we can call shared externally @@ -278,44 +315,48 @@ colvarbias_abf::~colvarbias_abf() int colvarbias_abf::update() { - if (cvm::debug()) cvm::log("Updating ABF bias " + this->name); + int iter; - if (cvm::step_relative() == 0) { - - // At first timestep, do only: - // initialization stuff (file operations relying on n_abf_biases - // compute current value of colvars - - for (size_t i = 0; i < colvars.size(); i++) { - bin[i] = samples->current_bin_scalar(i); - } + if (cvm::debug()) cvm::log("Updating ABF bias " + this->name); - } else { + size_t i; + for (i = 0; i < num_variables(); i++) { + bin[i] = samples->current_bin_scalar(i); + } + if (cvm::proxy->total_forces_same_step()) { + // e.g. in LAMMPS, total forces are current + force_bin = bin; + } - for (size_t i = 0; i < colvars.size(); i++) { - bin[i] = samples->current_bin_scalar(i); - } + if (cvm::step_relative() > 0 || cvm::proxy->total_forces_same_step()) { - if ( update_bias && samples->index_ok(force_bin) ) { - // Only if requested and within bounds of the grid... + if (update_bias) { +// if (b_adiabatic_reweighting) { +// // Update gradients non-locally based on conditional distribution of +// // fictitious variable TODO +// +// } else + if (samples->index_ok(force_bin)) { + // Only if requested and within bounds of the grid... - for (size_t i = 0; i < colvars.size(); i++) { - // get total forces (lagging by 1 timestep) from colvars - // and subtract previous ABF force if necessary - update_system_force(i); - } - if (cvm::proxy->total_forces_same_step()) { - // e.g. in LAMMPS, total forces are current - force_bin = bin; + for (i = 0; i < num_variables(); i++) { + // get total forces (lagging by 1 timestep) from colvars + // and subtract previous ABF force if necessary + update_system_force(i); + } + gradients->acc_force(force_bin, system_force); + if ( b_integrate ) { + pmf->update_div_neighbors(force_bin); + } } - gradients->acc_force(force_bin, system_force); } + if ( z_gradients && update_bias ) { - for (size_t i = 0; i < colvars.size(); i++) { + for (i = 0; i < num_variables(); i++) { z_bin[i] = z_samples->current_bin_scalar(i); } if ( z_samples->index_ok(z_bin) ) { - for (size_t i = 0; i < colvars.size(); i++) { + for (i = 0; i < num_variables(); i++) { // If we are outside the range of xi, the force has not been obtained above // the function is just an accessor, so cheap to call again anyway update_system_force(i); @@ -323,6 +364,14 @@ int colvarbias_abf::update() z_gradients->acc_force(z_bin, system_force); } } + + if ( b_integrate ) { + if ( pabf_freq && cvm::step_relative() % pabf_freq == 0 ) { + cvm::real err; + iter = pmf->integrate(integrate_steps, integrate_tol, err); + pmf->set_zero_minimum(); // TODO: do this only when necessary + } + } } if (!cvm::proxy->total_forces_same_step()) { @@ -332,14 +381,14 @@ int colvarbias_abf::update() } // Reset biasing forces from previous timestep - for (size_t i = 0; i < colvars.size(); i++) { + for (i = 0; i < num_variables(); i++) { colvar_forces[i].reset(); } // Compute and apply the new bias, if applicable if (is_enabled(f_cvb_apply_force) && samples->index_ok(bin)) { - size_t count = samples->value(bin); + cvm::real count = samples->value(bin); cvm::real fact = 1.0; // Factor that ensures smooth introduction of the force @@ -348,21 +397,34 @@ int colvarbias_abf::update() (cvm::real(count - min_samples)) / (cvm::real(full_samples - min_samples)); } - const cvm::real * grad = &(gradients->value(bin)); + std::vector grad(num_variables()); + if ( pabf_freq ) { + // In projected ABF, the force is the PMF gradient estimate + pmf->vector_gradient_finite_diff(bin, grad); + } else { + // Normal ABF + gradients->vector_value(bin, grad); + } + +// if ( b_adiabatic_reweighting) { +// // Average of force according to conditional distribution of fictitious variable +// // need freshly integrated PMF, gradient TODO +// } else if ( fact != 0.0 ) { - if ( (colvars.size() == 1) && colvars[0]->periodic_boundaries() ) { + if ( (num_variables() == 1) && colvars[0]->periodic_boundaries() ) { // Enforce a zero-mean bias on periodic, 1D coordinates // in other words: boundary condition is that the biasing potential is periodic - colvar_forces[0].real_value = fact * (grad[0] / cvm::real(count) - gradients->average()); + // This is enforced naturally if using integrated PMF + colvar_forces[0].real_value = fact * (grad[0] - gradients->average ()); } else { - for (size_t i = 0; i < colvars.size(); i++) { + for (size_t i = 0; i < num_variables(); i++) { // subtracting the mean force (opposite of the FE gradient) means adding the gradient - colvar_forces[i].real_value = fact * grad[i] / cvm::real(count); + colvar_forces[i].real_value = fact * grad[i]; } } if (cap_force) { - for (size_t i = 0; i < colvars.size(); i++) { + for (size_t i = 0; i < num_variables(); i++) { if ( colvar_forces[i].real_value * colvar_forces[i].real_value > max_force[i] * max_force[i] ) { colvar_forces[i].real_value = (colvar_forces[i].real_value > 0 ? max_force[i] : -1.0 * max_force[i]); } @@ -407,9 +469,9 @@ int colvarbias_abf::update() // update UI estimator every step if (b_UI_estimator) { - std::vector x(colvars.size(),0); - std::vector y(colvars.size(),0); - for (size_t i = 0; i < colvars.size(); i++) + std::vector x(num_variables(),0); + std::vector y(num_variables(),0); + for (size_t i = 0; i < num_variables(); i++) { x[i] = colvars[i]->actual_value(); y[i] = colvars[i]->value(); @@ -509,26 +571,60 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app cvm::proxy->output_stream(samples_out_name, mode); if (!samples_os) { cvm::error("Error opening ABF samples file " + samples_out_name + " for writing"); + return; } samples->write_multicol(*samples_os); cvm::proxy->close_output_stream(samples_out_name); + // In dimension higher than 2, dx is easier to handle and visualize + if (num_variables() > 2) { + std::string samples_dx_out_name = prefix + ".count.dx"; + std::ostream *samples_dx_os = cvm::proxy->output_stream(samples_dx_out_name, mode); + if (!samples_os) { + cvm::error("Error opening samples file " + samples_dx_out_name + " for writing"); + return; + } + samples->write_opendx(*samples_dx_os); + *samples_dx_os << std::endl; + cvm::proxy->close_output_stream(samples_dx_out_name); + } + std::ostream *gradients_os = cvm::proxy->output_stream(gradients_out_name, mode); if (!gradients_os) { cvm::error("Error opening ABF gradient file " + gradients_out_name + " for writing"); + return; } gradients->write_multicol(*gradients_os); cvm::proxy->close_output_stream(gradients_out_name); - if (colvars.size() == 1) { - // Do numerical integration and output a PMF + if (b_integrate) { + // Do numerical integration (to high precision) and output a PMF + cvm::real err; + pmf->integrate(integrate_initial_steps, integrate_initial_tol, err); + pmf->set_zero_minimum(); + std::string pmf_out_name = prefix + ".pmf"; std::ostream *pmf_os = cvm::proxy->output_stream(pmf_out_name, mode); if (!pmf_os) { cvm::error("Error opening pmf file " + pmf_out_name + " for writing"); + return; + } + pmf->write_multicol(*pmf_os); + + // In dimension higher than 2, dx is easier to handle and visualize + if (num_variables() > 2) { + std::string pmf_dx_out_name = prefix + ".pmf.dx"; + std::ostream *pmf_dx_os = cvm::proxy->output_stream(pmf_dx_out_name, mode); + if (!pmf_dx_os) { + cvm::error("Error opening pmf file " + pmf_dx_out_name + " for writing"); + return; + } + pmf->write_opendx(*pmf_dx_os); + *pmf_dx_os << std::endl; + cvm::proxy->close_output_stream(pmf_dx_out_name); } - gradients->write_1D_integral(*pmf_os); + *pmf_os << std::endl; cvm::proxy->close_output_stream(pmf_out_name); } @@ -542,6 +638,7 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app cvm::proxy->output_stream(z_samples_out_name, mode); if (!z_samples_os) { cvm::error("Error opening eABF z-histogram file " + z_samples_out_name + " for writing"); + return; } z_samples->write_multicol(*z_samples_os); cvm::proxy->close_output_stream(z_samples_out_name); @@ -553,6 +650,7 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app cvm::proxy->output_stream(z_gradients_out_name, mode); if (!z_gradients_os) { cvm::error("Error opening eABF z-gradient file " + z_gradients_out_name + " for writing"); + return; } z_gradients->write_multicol(*z_gradients_os); cvm::proxy->close_output_stream(z_gradients_out_name); @@ -563,8 +661,7 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app czar_gradients->index_ok(ix); czar_gradients->incr(ix)) { for (size_t n = 0; n < czar_gradients->multiplicity(); n++) { czar_gradients->set_value(ix, z_gradients->value_output(ix, n) - - cvm::temperature() * cvm::boltzmann() * z_samples->log_gradient_finite_diff(ix, n), - n); + - cvm::temperature() * cvm::boltzmann() * z_samples->log_gradient_finite_diff(ix, n), n); } } @@ -574,17 +671,39 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app cvm::proxy->output_stream(czar_gradients_out_name, mode); if (!czar_gradients_os) { cvm::error("Error opening CZAR gradient file " + czar_gradients_out_name + " for writing"); + return; } czar_gradients->write_multicol(*czar_gradients_os); cvm::proxy->close_output_stream(czar_gradients_out_name); - if (colvars.size() == 1) { - // Do numerical integration and output a PMF + if (b_integrate) { + // Do numerical integration (to high precision) and output a PMF + cvm::real err; + czar_pmf->set_div(); + czar_pmf->integrate(integrate_initial_steps, integrate_initial_tol, err); + czar_pmf->set_zero_minimum(); + std::string czar_pmf_out_name = prefix + ".czar.pmf"; - std::ostream *czar_pmf_os = - cvm::proxy->output_stream(czar_pmf_out_name, mode); - if (!czar_pmf_os) cvm::error("Error opening CZAR pmf file " + czar_pmf_out_name + " for writing"); - czar_gradients->write_1D_integral(*czar_pmf_os); + std::ostream *czar_pmf_os = cvm::proxy->output_stream(czar_pmf_out_name, mode); + if (!czar_pmf_os) { + cvm::error("Error opening CZAR pmf file " + czar_pmf_out_name + " for writing"); + return; + } + czar_pmf->write_multicol(*czar_pmf_os); + + // In dimension higher than 2, dx is easier to handle and visualize + if (num_variables() > 2) { + std::string czar_pmf_dx_out_name = prefix + ".czar.pmf.dx"; + std::ostream *czar_pmf_dx_os = cvm::proxy->output_stream(czar_pmf_dx_out_name, mode); + if (!czar_pmf_dx_os) { + cvm::error("Error opening CZAR pmf file " + czar_pmf_dx_out_name + " for writing"); + return; + } + czar_pmf->write_opendx(*czar_pmf_dx_os); + *czar_pmf_dx_os << std::endl; + cvm::proxy->close_output_stream(czar_pmf_dx_out_name); + } + *czar_pmf_os << std::endl; cvm::proxy->close_output_stream(czar_pmf_out_name); } @@ -708,6 +827,10 @@ std::istream & colvarbias_abf::read_state_data(std::istream& is) if (! gradients->read_raw(is)) { return is; } + if (b_integrate) { + // Update divergence to account for restart data + pmf->set_div(); + } if (b_CZAR_estimator) { diff --git a/lib/colvars/colvarbias_abf.h b/lib/colvars/colvarbias_abf.h index 1defe72268c487e82a536d2f5e441e1067897272..0260401292ecc40ee38c5fce3c282f359603591f 100644 --- a/lib/colvars/colvarbias_abf.h +++ b/lib/colvars/colvarbias_abf.h @@ -40,28 +40,44 @@ private: /// Base filename(s) for reading previous gradient data (replaces data from restart file) std::vector input_prefix; - bool update_bias; - bool hide_Jacobian; - size_t full_samples; - size_t min_samples; + bool update_bias; + bool hide_Jacobian; + bool b_integrate; + + size_t full_samples; + size_t min_samples; /// frequency for updating output files - int output_freq; + int output_freq; /// Write combined files with a history of all output data? - bool b_history_files; + bool b_history_files; /// Write CZAR output file for stratified eABF (.zgrad) - bool b_czar_window_file; - size_t history_freq; + bool b_czar_window_file; + size_t history_freq; /// Umbrella Integration estimator of free energy from eABF UIestimator::UIestimator eabf_UI; - // Run UI estimator? - bool b_UI_estimator; - // Run CZAR estimator? - bool b_CZAR_estimator; - - /// Cap applied biasing force? + /// Run UI estimator? + bool b_UI_estimator; + /// Run CZAR estimator? + bool b_CZAR_estimator; + + /// Frequency for updating pABF PMF (if zero, pABF is not used) + int pabf_freq; + /// Max number of CG iterations for integrating PMF at startup and for file output + int integrate_initial_steps; + /// Tolerance for integrating PMF at startup and for file output + cvm::real integrate_initial_tol; + /// Max number of CG iterations for integrating PMF at on-the-fly pABF updates + int integrate_steps; + /// Tolerance for integrating PMF at on-the-fly pABF updates + cvm::real integrate_tol; + + /// Cap the biasing force to be applied? bool cap_force; std::vector max_force; + // Frequency for updating 2D gradients + int integrate_freq; + // Internal data and methods std::vector bin, force_bin, z_bin; @@ -71,12 +87,16 @@ private: colvar_grid_gradient *gradients; /// n-dim grid of number of samples colvar_grid_count *samples; + /// n-dim grid of pmf (dimension 1 to 3) + integrate_potential *pmf; /// n-dim grid: average force on "real" coordinate for eABF z-based estimator colvar_grid_gradient *z_gradients; /// n-dim grid of number of samples on "real" coordinate for eABF z-based estimator colvar_grid_count *z_samples; /// n-dim grid contining CZAR estimator of "real" free energy gradients colvar_grid_gradient *czar_gradients; + /// n-dim grid of CZAR pmf (dimension 1 to 3) + integrate_potential *czar_pmf; inline int update_system_force(size_t i) { @@ -96,9 +116,9 @@ private: } // shared ABF - bool shared_on; - size_t shared_freq; - int shared_last_step; + bool shared_on; + size_t shared_freq; + int shared_last_step; // Share between replicas -- may be called independently of update virtual int replica_share(); @@ -114,12 +134,12 @@ private: //// Give the count at a given bin index. virtual int bin_count(int bin_index); - /// Write human-readable FE gradients and sample count - void write_gradients_samples(const std::string &prefix, bool append = false); - void write_last_gradients_samples(const std::string &prefix, bool append = false); + /// Write human-readable FE gradients and sample count, and DX file in dim > 2 + void write_gradients_samples(const std::string &prefix, bool append = false); + void write_last_gradients_samples(const std::string &prefix, bool append = false); /// Read human-readable FE gradients and sample count (if not using restart) - void read_gradients_samples(); + void read_gradients_samples(); std::istream& read_state_data(std::istream&); std::ostream& write_state_data(std::ostream&); diff --git a/lib/colvars/colvarbias_alb.cpp b/lib/colvars/colvarbias_alb.cpp index 124a15c5da3f7b59e1e1da4ef5d1d65dc0f60c67..187ecc363a9da559555b7eb296703167f1d26389 100644 --- a/lib/colvars/colvarbias_alb.cpp +++ b/lib/colvars/colvarbias_alb.cpp @@ -7,13 +7,11 @@ // If you wish to distribute your changes, please submit them to the // Colvars repository at GitHub. -#include -#include -#include +#include #include "colvarmodule.h" -#include "colvarbias_alb.h" #include "colvarbias.h" +#include "colvarbias_alb.h" #ifdef _MSC_VER #if _MSC_VER <= 1700 @@ -45,22 +43,22 @@ int colvarbias_alb::init(std::string const &conf) size_t i; // get the initial restraint centers - colvar_centers.resize(colvars.size()); + colvar_centers.resize(num_variables()); - means.resize(colvars.size()); - ssd.resize(colvars.size()); //sum of squares of differences from mean + means.resize(num_variables()); + ssd.resize(num_variables()); //sum of squares of differences from mean //setup force vectors - max_coupling_range.resize(colvars.size()); - max_coupling_rate.resize(colvars.size()); - coupling_accum.resize(colvars.size()); - set_coupling.resize(colvars.size()); - current_coupling.resize(colvars.size()); - coupling_rate.resize(colvars.size()); + max_coupling_range.resize(num_variables()); + max_coupling_rate.resize(num_variables()); + coupling_accum.resize(num_variables()); + set_coupling.resize(num_variables()); + current_coupling.resize(num_variables()); + coupling_rate.resize(num_variables()); enable(f_cvb_apply_force); - for (i = 0; i < colvars.size(); i++) { + for (i = 0; i < num_variables(); i++) { colvar_centers[i].type(colvars[i]->value()); //zero moments means[i] = ssd[i] = 0; @@ -70,7 +68,7 @@ int colvarbias_alb::init(std::string const &conf) } if (get_keyval(conf, "centers", colvar_centers, colvar_centers)) { - for (i = 0; i < colvars.size(); i++) { + for (i = 0; i < num_variables(); i++) { colvar_centers[i].apply_constraints(); } } else { @@ -78,7 +76,7 @@ int colvarbias_alb::init(std::string const &conf) cvm::fatal_error("Error: must define the initial centers of adaptive linear bias .\n"); } - if (colvar_centers.size() != colvars.size()) + if (colvar_centers.size() != num_variables()) cvm::fatal_error("Error: number of centers does not match " "that of collective variables.\n"); @@ -100,17 +98,17 @@ int colvarbias_alb::init(std::string const &conf) //initial guess if (!get_keyval(conf, "forceConstant", set_coupling, set_coupling)) - for (i =0 ; i < colvars.size(); i++) + for (i =0 ; i < num_variables(); i++) set_coupling[i] = 0.; //how we're going to increase to that point - for (i = 0; i < colvars.size(); i++) + for (i = 0; i < num_variables(); i++) coupling_rate[i] = (set_coupling[i] - current_coupling[i]) / update_freq; if (!get_keyval(conf, "forceRange", max_coupling_range, max_coupling_range)) { //set to default - for (i = 0; i < colvars.size(); i++) { + for (i = 0; i < num_variables(); i++) { if (cvm::temperature() > 0) max_coupling_range[i] = 3 * cvm::temperature() * cvm::boltzmann(); else @@ -120,7 +118,7 @@ int colvarbias_alb::init(std::string const &conf) if (!get_keyval(conf, "rateMax", max_coupling_rate, max_coupling_rate)) { //set to default - for (i = 0; i < colvars.size(); i++) { + for (i = 0; i < num_variables(); i++) { max_coupling_rate[i] = max_coupling_range[i] / (10 * update_freq); } } @@ -151,7 +149,7 @@ int colvarbias_alb::update() // Force and energy calculation bool finished_equil_flag = 1; cvm::real delta; - for (size_t i = 0; i < colvars.size(); i++) { + for (size_t i = 0; i < num_variables(); i++) { colvar_forces[i] = -1.0 * restraint_force(restraint_convert_k(current_coupling[i], colvars[i]->width), colvars[i], colvar_centers[i]); @@ -168,7 +166,9 @@ int colvarbias_alb::update() } else { //check if we've reached the setpoint - if (coupling_rate[i] == 0 || pow(current_coupling[i] - set_coupling[i],2) < pow(coupling_rate[i],2)) { + cvm::real const coupling_diff = current_coupling[i] - set_coupling[i]; + if ((coupling_rate[i] == 0) || + ((coupling_diff*coupling_diff) < (coupling_rate[i]*coupling_rate[i]))) { finished_equil_flag &= 1; //we continue equilibrating as long as we haven't reached all the set points } else { @@ -209,7 +209,7 @@ int colvarbias_alb::update() cvm::real temp; //reset means and sum of squares of differences - for (size_t i = 0; i < colvars.size(); i++) { + for (size_t i = 0; i < num_variables(); i++) { temp = 2. * (means[i] / (static_cast (colvar_centers[i])) - 1) * ssd[i] / (update_calls - 1); @@ -222,7 +222,7 @@ int colvarbias_alb::update() ssd[i] = 0; //stochastic if we do that update or not - if (colvars.size() == 1 || rand() < RAND_MAX / ((int) colvars.size())) { + if (num_variables() == 1 || rand() < RAND_MAX / ((int) num_variables())) { coupling_accum[i] += step_size * step_size; current_coupling[i] = set_coupling[i]; set_coupling[i] += max_coupling_range[i] / sqrt(coupling_accum[i]) * step_size; @@ -284,37 +284,37 @@ std::string const colvarbias_alb::get_state_params() const std::ostringstream os; os << " setCoupling "; size_t i; - for (i = 0; i < colvars.size(); i++) { + for (i = 0; i < num_variables(); i++) { os << std::setprecision(cvm::en_prec) << std::setw(cvm::en_width) << set_coupling[i] << "\n"; } os << " currentCoupling "; - for (i = 0; i < colvars.size(); i++) { + for (i = 0; i < num_variables(); i++) { os << std::setprecision(cvm::en_prec) << std::setw(cvm::en_width) << current_coupling[i] << "\n"; } os << " maxCouplingRange "; - for (i = 0; i < colvars.size(); i++) { + for (i = 0; i < num_variables(); i++) { os << std::setprecision(cvm::en_prec) << std::setw(cvm::en_width) << max_coupling_range[i] << "\n"; } os << " couplingRate "; - for (i = 0; i < colvars.size(); i++) { + for (i = 0; i < num_variables(); i++) { os << std::setprecision(cvm::en_prec) << std::setw(cvm::en_width) << coupling_rate[i] << "\n"; } os << " couplingAccum "; - for (i = 0; i < colvars.size(); i++) { + for (i = 0; i < num_variables(); i++) { os << std::setprecision(cvm::en_prec) << std::setw(cvm::en_width) << coupling_accum[i] << "\n"; } os << " mean "; - for (i = 0; i < colvars.size(); i++) { + for (i = 0; i < num_variables(); i++) { os << std::setprecision(cvm::en_prec) << std::setw(cvm::en_width) << means[i] << "\n"; } os << " ssd "; - for (i = 0; i < colvars.size(); i++) { + for (i = 0; i < num_variables(); i++) { os << std::setprecision(cvm::en_prec) << std::setw(cvm::en_width) << ssd[i] << "\n"; } @@ -350,7 +350,7 @@ std::ostream & colvarbias_alb::write_traj_label(std::ostream &os) } if (b_output_centers) - for (size_t i = 0; i < colvars.size(); i++) { + for (size_t i = 0; i < num_variables(); i++) { size_t const this_cv_width = (colvars[i]->value()).output_width(cvm::cv_width); os << " x0_" << cvm::wrap_string(colvars[i]->name, this_cv_width-3); @@ -378,7 +378,7 @@ std::ostream & colvarbias_alb::write_traj(std::ostream &os) if (b_output_centers) - for (size_t i = 0; i < colvars.size(); i++) { + for (size_t i = 0; i < num_variables(); i++) { os << " " << std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width) << colvar_centers[i]; diff --git a/lib/colvars/colvarbias_histogram.cpp b/lib/colvars/colvarbias_histogram.cpp index 0722e6384dc7047e5f6eb0bdf0c623537cfaeb53..329b1d9dc08d918295f5ec89a0519a4a292168a0 100644 --- a/lib/colvars/colvarbias_histogram.cpp +++ b/lib/colvars/colvarbias_histogram.cpp @@ -8,10 +8,10 @@ // Colvars repository at GitHub. #include "colvarmodule.h" +#include "colvarproxy.h" #include "colvar.h" #include "colvarbias_histogram.h" -/// Histogram "bias" constructor colvarbias_histogram::colvarbias_histogram(char const *key) : colvarbias(key), @@ -44,7 +44,7 @@ int colvarbias_histogram::init(std::string const &conf) get_keyval(conf, "gatherVectorColvars", colvar_array, colvar_array); if (colvar_array) { - for (i = 0; i < colvars.size(); i++) { // should be all vector + for (i = 0; i < num_variables(); i++) { // should be all vector if (colvars[i]->value().type() != colvarvalue::type_vector) { cvm::error("Error: used gatherVectorColvars with non-vector colvar.\n", INPUT_ERROR); return INPUT_ERROR; @@ -63,7 +63,7 @@ int colvarbias_histogram::init(std::string const &conf) } } } else { - for (i = 0; i < colvars.size(); i++) { // should be all scalar + for (i = 0; i < num_variables(); i++) { // should be all scalar if (colvars[i]->value().type() != colvarvalue::type_scalar) { cvm::error("Error: only scalar colvars are supported when gatherVectorColvars is off.\n", INPUT_ERROR); return INPUT_ERROR; @@ -77,7 +77,7 @@ int colvarbias_histogram::init(std::string const &conf) get_keyval(conf, "weights", weights, weights); } - for (i = 0; i < colvars.size(); i++) { + for (i = 0; i < num_variables(); i++) { colvars[i]->enable(f_cv_grid); } @@ -116,7 +116,7 @@ int colvarbias_histogram::update() } // assign a valid bin size - bin.assign(colvars.size(), 0); + bin.assign(num_variables(), 0); if (out_name.size() == 0) { // At the first timestep, we need to assign out_name since @@ -137,7 +137,7 @@ int colvarbias_histogram::update() if (colvar_array_size == 0) { // update indices for scalar values size_t i; - for (i = 0; i < colvars.size(); i++) { + for (i = 0; i < num_variables(); i++) { bin[i] = grid->current_bin_scalar(i); } @@ -148,7 +148,7 @@ int colvarbias_histogram::update() // update indices for vector/array values size_t iv, i; for (iv = 0; iv < colvar_array_size; iv++) { - for (i = 0; i < colvars.size(); i++) { + for (i = 0; i < num_variables(); i++) { bin[i] = grid->current_bin_scalar(i, iv); } diff --git a/lib/colvars/colvarbias_meta.cpp b/lib/colvars/colvarbias_meta.cpp index b0d154dfc9ebf591f49b15ba517f4bcf7ba10317..f3ae3631a02f2478cb62a7f9a84e7535926501c4 100644 --- a/lib/colvars/colvarbias_meta.cpp +++ b/lib/colvars/colvarbias_meta.cpp @@ -27,7 +27,8 @@ #define PATHSEP "/" #endif - +#include "colvarmodule.h" +#include "colvarproxy.h" #include "colvar.h" #include "colvarbias_meta.h" diff --git a/lib/colvars/colvarbias_restraint.cpp b/lib/colvars/colvarbias_restraint.cpp index 23534f56eb43c1cd0a2e257ed8581449026d0c8f..4ed1a95f942fe664d336b7dfb170f1ea1c3a62a8 100644 --- a/lib/colvars/colvarbias_restraint.cpp +++ b/lib/colvars/colvarbias_restraint.cpp @@ -7,7 +7,10 @@ // If you wish to distribute your changes, please submit them to the // Colvars repository at GitHub. +#include + #include "colvarmodule.h" +#include "colvarproxy.h" #include "colvarvalue.h" #include "colvarbias_restraint.h" @@ -150,13 +153,14 @@ colvarbias_restraint_k::colvarbias_restraint_k(char const *key) : colvarbias(key), colvarbias_ti(key), colvarbias_restraint(key) { force_k = -1.0; + check_positive_k = true; } int colvarbias_restraint_k::init(std::string const &conf) { get_keyval(conf, "forceConstant", force_k, (force_k > 0.0 ? force_k : 1.0)); - if (force_k < 0.0) { + if (check_positive_k && (force_k < 0.0)) { cvm::error("Error: undefined or invalid force constant.\n", INPUT_ERROR); return INPUT_ERROR; } @@ -177,6 +181,7 @@ colvarbias_restraint_moving::colvarbias_restraint_moving(char const *key) target_nstages = 0; target_nsteps = 0; stage = 0; + acc_work = 0.0; b_chg_centers = false; b_chg_force_k = false; } @@ -203,6 +208,14 @@ int colvarbias_restraint_moving::init(std::string const &conf) cvm::error("Error: targetNumStages and lambdaSchedule are incompatible.\n", INPUT_ERROR); return cvm::get_error(); } + + get_keyval_feature(this, conf, "outputAccumulatedWork", + f_cvb_output_acc_work, + is_enabled(f_cvb_output_acc_work)); + if (is_enabled(f_cvb_output_acc_work) && (target_nstages > 0)) { + return cvm::error("Error: outputAccumulatedWork and targetNumStages " + "are incompatible.\n", INPUT_ERROR); + } } return COLVARS_OK; @@ -246,8 +259,6 @@ colvarbias_restraint_centers_moving::colvarbias_restraint_centers_moving(char co { b_chg_centers = false; b_output_centers = false; - b_output_acc_work = false; - acc_work = 0.0; } @@ -288,9 +299,6 @@ int colvarbias_restraint_centers_moving::init(std::string const &conf) 0.5); } - get_keyval(conf, "outputAccumulatedWork", b_output_acc_work, - b_output_acc_work); // TODO this conflicts with stages - } else { target_centers.clear(); } @@ -382,12 +390,14 @@ int colvarbias_restraint_centers_moving::update() int colvarbias_restraint_centers_moving::update_acc_work() { - if (b_output_acc_work) { - if ((cvm::step_relative() > 0) && - (cvm::step_absolute() <= target_nsteps)) { - for (size_t i = 0; i < num_variables(); i++) { - // project forces on the calculated increments at this step - acc_work += colvar_forces[i] * centers_incr[i]; + if (b_chg_centers) { + if (is_enabled(f_cvb_output_acc_work)) { + if ((cvm::step_relative() > 0) && + (cvm::step_absolute() <= target_nsteps)) { + for (size_t i = 0; i < num_variables(); i++) { + // project forces on the calculated increments at this step + acc_work += colvar_forces[i] * centers_incr[i]; + } } } } @@ -410,7 +420,7 @@ std::string const colvarbias_restraint_centers_moving::get_state_params() const } os << "\n"; - if (b_output_acc_work) { + if (is_enabled(f_cvb_output_acc_work)) { os << "accumulatedWork " << std::setprecision(cvm::en_prec) << std::setw(cvm::en_width) << acc_work << "\n"; @@ -429,7 +439,7 @@ int colvarbias_restraint_centers_moving::set_state_params(std::string const &con // cvm::log ("Reading the updated restraint centers from the restart.\n"); if (!get_keyval(conf, "centers", colvar_centers)) cvm::error("Error: restraint centers are missing from the restart.\n"); - if (b_output_acc_work) { + if (is_enabled(f_cvb_output_acc_work)) { if (!get_keyval(conf, "accumulatedWork", acc_work)) cvm::error("Error: accumulatedWork is missing from the restart.\n"); } @@ -449,7 +459,7 @@ std::ostream & colvarbias_restraint_centers_moving::write_traj_label(std::ostrea } } - if (b_output_acc_work) { + if (b_chg_centers && is_enabled(f_cvb_output_acc_work)) { os << " W_" << cvm::wrap_string(this->name, cvm::en_width-2); } @@ -468,7 +478,7 @@ std::ostream & colvarbias_restraint_centers_moving::write_traj(std::ostream &os) } } - if (b_output_acc_work) { + if (b_chg_centers && is_enabled(f_cvb_output_acc_work)) { os << " " << std::setprecision(cvm::en_prec) << std::setw(cvm::en_width) << acc_work; @@ -488,10 +498,11 @@ colvarbias_restraint_k_moving::colvarbias_restraint_k_moving(char const *key) { b_chg_force_k = false; target_equil_steps = 0; - target_force_k = 0.0; - starting_force_k = 0.0; + target_force_k = -1.0; + starting_force_k = -1.0; force_k_exp = 1.0; restraint_FE = 0.0; + force_k_incr = 0.0; } @@ -569,14 +580,13 @@ int colvarbias_restraint_k_moving::update() if (target_equil_steps == 0 || cvm::step_absolute() % target_nsteps >= target_equil_steps) { // Start averaging after equilibration period, if requested - // Square distance normalized by square colvar width - cvm::real dist_sq = 0.0; + // Derivative of energy with respect to force_k + cvm::real dU_dk = 0.0; for (size_t i = 0; i < num_variables(); i++) { - dist_sq += d_restraint_potential_dk(i); + dU_dk += d_restraint_potential_dk(i); } - - restraint_FE += 0.5 * force_k_exp * std::pow(lambda, force_k_exp - 1.0) - * (target_force_k - starting_force_k) * dist_sq; + restraint_FE += force_k_exp * std::pow(lambda, force_k_exp - 1.0) + * (target_force_k - starting_force_k) * dU_dk; } // Finish current stage... @@ -607,10 +617,13 @@ int colvarbias_restraint_k_moving::update() } else if (cvm::step_absolute() <= target_nsteps) { + // update force constant (slow growth) lambda = cvm::real(cvm::step_absolute()) / cvm::real(target_nsteps); + cvm::real const force_k_old = force_k; force_k = starting_force_k + (target_force_k - starting_force_k) * std::pow(lambda, force_k_exp); + force_k_incr = force_k - force_k_old; } } @@ -618,6 +631,23 @@ int colvarbias_restraint_k_moving::update() } +int colvarbias_restraint_k_moving::update_acc_work() +{ + if (b_chg_force_k) { + if (is_enabled(f_cvb_output_acc_work)) { + if (cvm::step_relative() > 0) { + cvm::real dU_dk = 0.0; + for (size_t i = 0; i < num_variables(); i++) { + dU_dk += d_restraint_potential_dk(i); + } + acc_work += dU_dk * force_k_incr; + } + } + } + return COLVARS_OK; +} + + std::string const colvarbias_restraint_k_moving::get_state_params() const { std::ostringstream os; @@ -626,6 +656,12 @@ std::string const colvarbias_restraint_k_moving::get_state_params() const os << "forceConstant " << std::setprecision(cvm::en_prec) << std::setw(cvm::en_width) << force_k << "\n"; + + if (is_enabled(f_cvb_output_acc_work)) { + os << "accumulatedWork " + << std::setprecision(cvm::en_prec) << std::setw(cvm::en_width) + << acc_work << "\n"; + } } return os.str(); } @@ -639,6 +675,10 @@ int colvarbias_restraint_k_moving::set_state_params(std::string const &conf) // cvm::log ("Reading the updated force constant from the restart.\n"); if (!get_keyval(conf, "forceConstant", force_k, force_k)) cvm::error("Error: force constant is missing from the restart.\n"); + if (is_enabled(f_cvb_output_acc_work)) { + if (!get_keyval(conf, "accumulatedWork", acc_work)) + cvm::error("Error: accumulatedWork is missing from the restart.\n"); + } } return COLVARS_OK; @@ -647,12 +687,21 @@ int colvarbias_restraint_k_moving::set_state_params(std::string const &conf) std::ostream & colvarbias_restraint_k_moving::write_traj_label(std::ostream &os) { + if (b_chg_force_k && is_enabled(f_cvb_output_acc_work)) { + os << " W_" + << cvm::wrap_string(this->name, cvm::en_width-2); + } return os; } std::ostream & colvarbias_restraint_k_moving::write_traj(std::ostream &os) { + if (b_chg_force_k && is_enabled(f_cvb_output_acc_work)) { + os << " " + << std::setprecision(cvm::en_prec) << std::setw(cvm::en_width) + << acc_work; + } return os; } @@ -765,6 +814,7 @@ int colvarbias_restraint_harmonic::update() // update accumulated work using the current forces error_code |= colvarbias_restraint_centers_moving::update_acc_work(); + error_code |= colvarbias_restraint_k_moving::update_acc_work(); return error_code; } @@ -876,8 +926,8 @@ colvarbias_restraint_harmonic_walls::colvarbias_restraint_harmonic_walls(char co colvarbias_restraint_moving(key), colvarbias_restraint_k_moving(key) { - lower_wall_k = 0.0; - upper_wall_k = 0.0; + lower_wall_k = -1.0; + upper_wall_k = -1.0; } @@ -887,26 +937,6 @@ int colvarbias_restraint_harmonic_walls::init(std::string const &conf) colvarbias_restraint_moving::init(conf); colvarbias_restraint_k_moving::init(conf); - get_keyval(conf, "lowerWallConstant", lower_wall_k, - (lower_wall_k > 0.0) ? lower_wall_k : force_k); - get_keyval(conf, "upperWallConstant", upper_wall_k, - (upper_wall_k > 0.0) ? upper_wall_k : force_k); - - if (lower_wall_k * upper_wall_k > 0.0) { - for (size_t i = 0; i < num_variables(); i++) { - if (variables(i)->width != 1.0) - cvm::log("The lower and upper wall force constants for colvar \""+ - variables(i)->name+ - "\" will be rescaled to "+ - cvm::to_str(lower_wall_k / - (variables(i)->width * variables(i)->width))+ - " and "+ - cvm::to_str(upper_wall_k / - (variables(i)->width * variables(i)->width))+ - " according to the specified width.\n"); - } - } - enable(f_cvb_scalar_variables); size_t i; @@ -942,16 +972,23 @@ int colvarbias_restraint_harmonic_walls::init(std::string const &conf) } if ((lower_walls.size() == 0) && (upper_walls.size() == 0)) { - cvm::error("Error: no walls provided.\n", INPUT_ERROR); - return INPUT_ERROR; + return cvm::error("Error: no walls provided.\n", INPUT_ERROR); + } + + if (lower_walls.size() > 0) { + get_keyval(conf, "lowerWallConstant", lower_wall_k, + (lower_wall_k > 0.0) ? lower_wall_k : force_k); + } + if (upper_walls.size() > 0) { + get_keyval(conf, "upperWallConstant", upper_wall_k, + (upper_wall_k > 0.0) ? upper_wall_k : force_k); } if ((lower_walls.size() == 0) || (upper_walls.size() == 0)) { for (i = 0; i < num_variables(); i++) { if (variables(i)->is_enabled(f_cv_periodic)) { - cvm::error("Error: at least one variable is periodic, " - "both walls must be provided.\n", INPUT_ERROR); - return INPUT_ERROR; + return cvm::error("Error: at least one variable is periodic, " + "both walls must be provided.\n", INPUT_ERROR); } } } @@ -972,19 +1009,49 @@ int colvarbias_restraint_harmonic_walls::init(std::string const &conf) INPUT_ERROR); return INPUT_ERROR; } - force_k = lower_wall_k * upper_wall_k; - // transform the two constants to relative values + force_k = std::sqrt(lower_wall_k * upper_wall_k); + // transform the two constants to relative values using gemetric mean as ref + // to preserve force_k if provided as single parameter // (allow changing both via force_k) lower_wall_k /= force_k; upper_wall_k /= force_k; + } else { + // If only one wall is defined, need to rescale as well + if (lower_walls.size() > 0) { + force_k = lower_wall_k; + lower_wall_k = 1.0; + } + if (upper_walls.size() > 0) { + force_k = upper_wall_k; + upper_wall_k = 1.0; + } } - for (i = 0; i < num_variables(); i++) { - if (variables(i)->width != 1.0) - cvm::log("The force constant for colvar \""+variables(i)->name+ - "\" will be rescaled to "+ - cvm::to_str(force_k / (variables(i)->width * variables(i)->width))+ - " according to the specified width.\n"); + // Initialize starting value of the force constant (in case it's changing) + starting_force_k = force_k; + + if (lower_walls.size() > 0) { + for (i = 0; i < num_variables(); i++) { + if (variables(i)->width != 1.0) + cvm::log("The lower wall force constant for colvar \""+ + variables(i)->name+ + "\" will be rescaled to "+ + cvm::to_str(lower_wall_k * force_k / + (variables(i)->width * variables(i)->width))+ + " according to the specified width.\n"); + } + } + + if (upper_walls.size() > 0) { + for (i = 0; i < num_variables(); i++) { + if (variables(i)->width != 1.0) + cvm::log("The upper wall force constant for colvar \""+ + variables(i)->name+ + "\" will be rescaled to "+ + cvm::to_str(upper_wall_k * force_k / + (variables(i)->width * variables(i)->width))+ + " according to the specified width.\n"); + } } return COLVARS_OK; @@ -1001,6 +1068,8 @@ int colvarbias_restraint_harmonic_walls::update() error_code |= colvarbias_restraint::update(); + error_code |= colvarbias_restraint_k_moving::update_acc_work(); + return error_code; } @@ -1134,6 +1203,7 @@ colvarbias_restraint_linear::colvarbias_restraint_linear(char const *key) colvarbias_restraint_centers_moving(key), colvarbias_restraint_k_moving(key) { + check_positive_k = false; } @@ -1177,6 +1247,7 @@ int colvarbias_restraint_linear::update() // update accumulated work using the current forces error_code |= colvarbias_restraint_centers_moving::update_acc_work(); + error_code |= colvarbias_restraint_k_moving::update_acc_work(); return error_code; } diff --git a/lib/colvars/colvarbias_restraint.h b/lib/colvars/colvarbias_restraint.h index b10649cab112f8a10bfedaff0c10823cc7a43f04..3ee999c2624cfe0cfd9997a2ae096106631444ec 100644 --- a/lib/colvars/colvarbias_restraint.h +++ b/lib/colvars/colvarbias_restraint.h @@ -89,8 +89,12 @@ public: virtual int change_configuration(std::string const &conf); protected: + /// \brief Restraint force constant cvm::real force_k; + + /// \brief Whether the force constant should be positive + bool check_positive_k; }; @@ -129,6 +133,9 @@ protected: /// \brief Number of steps required to reach the target force constant /// or restraint centers long target_nsteps; + + /// \brief Accumulated work (computed when outputAccumulatedWork == true) + cvm::real acc_work; }; @@ -157,8 +164,7 @@ protected: /// \brief Initial value of the restraint centers std::vector initial_centers; - /// \brief Amplitude of the restraint centers' increment at each step - /// towards the new values (calculated from target_nsteps) + /// \brief Increment of the restraint centers at each step std::vector centers_incr; /// \brief Update the centers by interpolating between initial and target @@ -167,12 +173,6 @@ protected: /// Whether to write the current restraint centers to the trajectory file bool b_output_centers; - /// Whether to write the current accumulated work to the trajectory file - bool b_output_acc_work; - - /// \brief Accumulated work - cvm::real acc_work; - /// Update the accumulated work int update_acc_work(); }; @@ -212,6 +212,12 @@ protected: /// \brief Equilibration steps for restraint FE calculation through TI cvm::real target_equil_steps; + + /// \brief Increment of the force constant at each step + cvm::real force_k_incr; + + /// Update the accumulated work + int update_acc_work(); }; diff --git a/lib/colvars/colvarcomp.h b/lib/colvars/colvarcomp.h index b94d798be9f0a3cd49abc27bb8cdaf41f88e8c87..52078a3a3059cb91315ac9f52e62b2f06e1e55f3 100644 --- a/lib/colvars/colvarcomp.h +++ b/lib/colvars/colvarcomp.h @@ -20,52 +20,48 @@ // simple_scalar_dist_functions (derived_class) -#include -#include - - #include "colvarmodule.h" #include "colvar.h" #include "colvaratoms.h" -/// \brief Colvar component (base class); most implementations of -/// \link cvc \endlink utilize one or more \link -/// colvarmodule::atom \endlink or \link colvarmodule::atom_group -/// \endlink objects to access atoms. +/// \brief Colvar component (base class for collective variables) /// /// A \link cvc \endlink object (or an object of a -/// cvc-derived class) specifies how to calculate a collective -/// variable, its gradients and other related physical quantities -/// which do not depend only on the numeric value (the \link colvar -/// \endlink class already serves this purpose). +/// cvc-derived class) implements the calculation of a collective +/// variable, its gradients and any other related physical quantities +/// that depend on microscopic degrees of freedom. +/// +/// No restriction is set to what kind of calculation a \link cvc \endlink +/// object performs (usually an analytical function of atomic coordinates). +/// The only constraints are that: \par /// -/// No restriction is set to what kind of calculation a \link -/// cvc \endlink object performs (usually calculate an -/// analytical function of atomic coordinates). The only constraint -/// is that the value calculated is implemented as a \link colvarvalue -/// \endlink object. This serves to provide a unique way to calculate -/// scalar and non-scalar collective variables, and specify if and how -/// they can be combined together by the parent \link colvar \endlink -/// object. +/// - The value is calculated by the \link calc_value() \endlink +/// method, and is an object of \link colvarvalue \endlink class. This +/// provides a transparent way to treat scalar and non-scalar variables +/// alike, and allows an automatic selection of the applicable algorithms. +/// +/// - The object provides an implementation \link apply_force() \endlink to +/// apply forces to atoms. Typically, one or more \link cvm::atom_group +/// \endlink objects are used, but this is not a requirement for as long as +/// the \link cvc \endlink object communicates with the simulation program. /// /// If you wish to implement a new collective variable component, you /// should write your own class by inheriting directly from \link -/// cvc \endlink, or one of its derived classes (for instance, -/// \link distance \endlink is frequently used, because it provides +/// colvar::cvc \endlink, or one of its derived classes (for instance, +/// \link colvar::distance \endlink is frequently used, because it provides /// useful data and function members for any colvar based on two -/// atom groups). The steps are: \par -/// 1. add the name of this class under colvar.h \par -/// 2. add a call to the parser in colvar.C, within the function colvar::colvar() \par -/// 3. declare the class in colvarcomp.h \par -/// 4. implement the class in one of the files colvarcomp_*.C +/// atom groups). +/// +/// The steps are: \par +/// 1. Declare the new class as a derivative of \link colvar::cvc \endlink +/// in the file \link colvarcomp.h \endlink +/// 2. Implement the new class in a file named colvarcomp_.cpp +/// 3. Declare the name of the new class inside the \link colvar \endlink class +/// in \link colvar.h \endlink (see "list of available components") +/// 4. Add a call for the new class in colvar::init_components() +//// (file: colvar.cpp) /// -/// -/// The cvm::atom and cvm::atom_group classes are available to -/// transparently communicate with the simulation program. However, -/// they are not strictly needed, as long as all the degrees of -/// freedom associated to the cvc are properly evolved by a simple -/// call to e.g. apply_force(). class colvar::cvc : public colvarparse, public colvardeps @@ -155,7 +151,7 @@ public: /// \brief Calculate the atomic gradients, to be reused later in /// order to apply forces - virtual void calc_gradients() = 0; + virtual void calc_gradients() {} /// \brief Calculate the atomic fit gradients void calc_fit_gradients(); diff --git a/lib/colvars/colvarcomp_distances.cpp b/lib/colvars/colvarcomp_distances.cpp index ce8055843f93d389117f38926e81d97c66bc7954..9911f4c87edef9c17605403f21a0ffc1a45826e9 100644 --- a/lib/colvars/colvarcomp_distances.cpp +++ b/lib/colvars/colvarcomp_distances.cpp @@ -581,6 +581,12 @@ colvar::distance_inv::distance_inv(std::string const &conf) } } + if (is_enabled(f_cvc_debug_gradient)) { + cvm::log("Warning: debugGradients will not give correct results " + "for distanceInv, because its value and gradients are computed " + "simultaneously.\n"); + } + x.type(colvarvalue::type_scalar); } @@ -601,11 +607,9 @@ void colvar::distance_inv::calc_value() for (cvm::atom_iter ai2 = group2->begin(); ai2 != group2->end(); ai2++) { cvm::rvector const dv = ai2->pos - ai1->pos; cvm::real const d2 = dv.norm2(); - cvm::real dinv = 1.0; - for (int ne = 0; ne < exponent/2; ne++) - dinv *= 1.0/d2; + cvm::real const dinv = cvm::integer_power(d2, -1*(exponent/2)); x.real_value += dinv; - cvm::rvector const dsumddv = -(cvm::real(exponent)) * dinv/d2 * dv; + cvm::rvector const dsumddv = -1.0*(exponent/2) * dinv/d2 * 2.0 * dv; ai1->grad += -1.0 * dsumddv; ai2->grad += dsumddv; } @@ -615,11 +619,9 @@ void colvar::distance_inv::calc_value() for (cvm::atom_iter ai2 = group2->begin(); ai2 != group2->end(); ai2++) { cvm::rvector const dv = cvm::position_distance(ai1->pos, ai2->pos); cvm::real const d2 = dv.norm2(); - cvm::real dinv = 1.0; - for (int ne = 0; ne < exponent/2; ne++) - dinv *= 1.0/d2; + cvm::real const dinv = cvm::integer_power(d2, -1*(exponent/2)); x.real_value += dinv; - cvm::rvector const dsumddv = -(cvm::real(exponent)) * dinv/d2 * dv; + cvm::rvector const dsumddv = -1.0*(exponent/2) * dinv/d2 * 2.0 * dv; ai1->grad += -1.0 * dsumddv; ai2->grad += dsumddv; } @@ -627,13 +629,11 @@ void colvar::distance_inv::calc_value() } x.real_value *= 1.0 / cvm::real(group1->size() * group2->size()); - x.real_value = std::pow(x.real_value, -1.0/(cvm::real(exponent))); -} + x.real_value = std::pow(x.real_value, -1.0/cvm::real(exponent)); - -void colvar::distance_inv::calc_gradients() -{ - cvm::real const dxdsum = (-1.0/(cvm::real(exponent))) * std::pow(x.real_value, exponent+1) / cvm::real(group1->size() * group2->size()); + cvm::real const dxdsum = (-1.0/(cvm::real(exponent))) * + cvm::integer_power(x.real_value, exponent+1) / + cvm::real(group1->size() * group2->size()); for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++) { ai1->grad *= dxdsum; } @@ -643,6 +643,11 @@ void colvar::distance_inv::calc_gradients() } +void colvar::distance_inv::calc_gradients() +{ +} + + void colvar::distance_inv::apply_force(colvarvalue const &force) { if (!group1->noforce) diff --git a/lib/colvars/colvardeps.cpp b/lib/colvars/colvardeps.cpp index ac906e7be755fc382d1cb383730522da38860092..a058ad55c2a4911324c9cd07b4ea7bb1e1afb147 100644 --- a/lib/colvars/colvardeps.cpp +++ b/lib/colvars/colvardeps.cpp @@ -8,10 +8,16 @@ // Colvars repository at GitHub. +#include "colvarmodule.h" +#include "colvarproxy.h" #include "colvardeps.h" + colvardeps::colvardeps() - : time_step_factor (1) {} +{ + time_step_factor = 1; +} + colvardeps::~colvardeps() { size_t i; @@ -416,6 +422,9 @@ void colvardeps::init_cvb_requires() { init_feature(f_cvb_get_total_force, "obtain total force", f_type_dynamic); f_req_children(f_cvb_get_total_force, f_cv_total_force); + init_feature(f_cvb_output_acc_work, "output accumulated work", f_type_user); + f_req_self(f_cvb_output_acc_work, f_cvb_apply_force); + init_feature(f_cvb_history_dependent, "history-dependent", f_type_static); init_feature(f_cvb_time_dependent, "time-dependent", f_type_static); diff --git a/lib/colvars/colvardeps.h b/lib/colvars/colvardeps.h index bd892fbca8cef746bb4dfad818b1e4577507a735..940eefb01b1a83c5793f9f7f5de68229b7bfe0ad 100644 --- a/lib/colvars/colvardeps.h +++ b/lib/colvars/colvardeps.h @@ -225,6 +225,8 @@ public: f_cvb_apply_force, /// \brief requires total forces f_cvb_get_total_force, + /// \brief whether this bias should record the accumulated work + f_cvb_output_acc_work, /// \brief depends on simulation history f_cvb_history_dependent, /// \brief depends on time diff --git a/lib/colvars/colvargrid.cpp b/lib/colvars/colvargrid.cpp index 9016e2c23a0ce573f8711075ee6ecd93b694aa5c..1ac4aae133c3a225aa8d4a8bb2dbdd1c3ac381cb 100644 --- a/lib/colvars/colvargrid.cpp +++ b/lib/colvars/colvargrid.cpp @@ -14,6 +14,7 @@ #include "colvarcomp.h" #include "colvargrid.h" +#include colvar_grid_count::colvar_grid_count() : colvar_grid() @@ -22,43 +23,37 @@ colvar_grid_count::colvar_grid_count() } colvar_grid_count::colvar_grid_count(std::vector const &nx_i, - size_t const &def_count) + size_t const &def_count) : colvar_grid(nx_i, def_count, 1) {} colvar_grid_count::colvar_grid_count(std::vector &colvars, - size_t const &def_count) - : colvar_grid(colvars, def_count, 1) + size_t const &def_count, + bool margin) + : colvar_grid(colvars, def_count, 1, margin) {} colvar_grid_scalar::colvar_grid_scalar() - : colvar_grid(), samples(NULL), grad(NULL) + : colvar_grid(), samples(NULL) {} colvar_grid_scalar::colvar_grid_scalar(colvar_grid_scalar const &g) - : colvar_grid(g), samples(NULL), grad(NULL) + : colvar_grid(g), samples(NULL) { - grad = new cvm::real[nd]; } colvar_grid_scalar::colvar_grid_scalar(std::vector const &nx_i) - : colvar_grid(nx_i, 0.0, 1), samples(NULL), grad(NULL) + : colvar_grid(nx_i, 0.0, 1), samples(NULL) { - grad = new cvm::real[nd]; } colvar_grid_scalar::colvar_grid_scalar(std::vector &colvars, bool margin) - : colvar_grid(colvars, 0.0, 1, margin), samples(NULL), grad(NULL) + : colvar_grid(colvars, 0.0, 1, margin), samples(NULL) { - grad = new cvm::real[nd]; } colvar_grid_scalar::~colvar_grid_scalar() { - if (grad) { - delete [] grad; - grad = NULL; - } } cvm::real colvar_grid_scalar::maximum_value() const @@ -143,18 +138,18 @@ void colvar_grid_gradient::write_1D_integral(std::ostream &os) os << "# xi A(xi)\n"; - if ( cv.size() != 1 ) { + if (cv.size() != 1) { cvm::error("Cannot write integral for multi-dimensional gradient grids."); return; } integral = 0.0; - int_vals.push_back( 0.0 ); + int_vals.push_back(0.0); min = 0.0; // correction for periodic colvars, so that the PMF is periodic cvm::real corr; - if ( periodic[0] ) { + if (periodic[0]) { corr = average(); } else { corr = 0.0; @@ -171,7 +166,7 @@ void colvar_grid_gradient::write_1D_integral(std::ostream &os) } if ( integral < min ) min = integral; - int_vals.push_back( integral ); + int_vals.push_back(integral); } bin = 0.0; @@ -192,3 +187,670 @@ void colvar_grid_gradient::write_1D_integral(std::ostream &os) +integrate_potential::integrate_potential(std::vector &colvars, colvar_grid_gradient * gradients) + : colvar_grid_scalar(colvars, true), + gradients(gradients) +{ + // parent class colvar_grid_scalar is constructed with margin option set to true + // hence PMF grid is wider than gradient grid if non-PBC + + if (nd > 1) { + divergence.resize(nt); + + // Compute inverse of Laplacian diagonal for Jacobi preconditioning + // For now all code related to preconditioning is commented out + // until a method better than Jacobi is implemented +// cvm::log("Preparing inverse diagonal for preconditioning..."); +// inv_lap_diag.resize(nt); +// std::vector id(nt), lap_col(nt); +// for (int i = 0; i < nt; i++) { +// if (i % (nt / 100) == 0) +// cvm::log(cvm::to_str(i)); +// id[i] = 1.; +// atimes(id, lap_col); +// id[i] = 0.; +// inv_lap_diag[i] = 1. / lap_col[i]; +// } +// cvm::log("Done."); + } +} + + +int integrate_potential::integrate(const int itmax, const cvm::real &tol, cvm::real & err) +{ + int iter = 0; + + if (nd == 1) { + + cvm::real sum = 0.0; + cvm::real corr; + if ( periodic[0] ) { + corr = gradients->average(); // Enforce PBC by subtracting average gradient + } else { + corr = 0.0; + } + + std::vector ix; + // Iterate over valid indices in gradient grid + for (ix = new_index(); gradients->index_ok(ix); incr(ix)) { + set_value(ix, sum); + sum += (gradients->value_output(ix) - corr) * widths[0]; + } + if (index_ok(ix)) { + // This will happen if non-periodic: then PMF grid has one extra bin wrt gradient grid + set_value(ix, sum); + } + + } else if (nd <= 3) { + + nr_linbcg_sym(divergence, data, tol, itmax, iter, err); + cvm::log("Integrated in " + cvm::to_str(iter) + " steps, error: " + cvm::to_str(err)); + + } else { + cvm::error("Cannot integrate PMF in dimension > 3\n"); + } + + return iter; +} + + +void integrate_potential::set_div() +{ + if (nd == 1) return; + for (std::vector ix = new_index(); index_ok(ix); incr(ix)) { + update_div_local(ix); + } +} + + +void integrate_potential::update_div_neighbors(const std::vector &ix0) +{ + std::vector ix(ix0); + int i, j, k; + + // If not periodic, expanded grid ensures that neighbors of ix0 are valid grid points + if (nd == 1) { + return; + + } else if (nd == 2) { + + update_div_local(ix); + ix[0]++; wrap(ix); + update_div_local(ix); + ix[1]++; wrap(ix); + update_div_local(ix); + ix[0]--; wrap(ix); + update_div_local(ix); + + } else if (nd == 3) { + + for (i = 0; i<2; i++) { + ix[1] = ix0[1]; + for (j = 0; j<2; j++) { + ix[2] = ix0[2]; + for (k = 0; k<2; k++) { + wrap(ix); + update_div_local(ix); + ix[2]++; + } + ix[1]++; + } + ix[0]++; + } + } +} + +void integrate_potential::get_grad(cvm::real * g, std::vector &ix) +{ + size_t count, i; + bool edge = gradients->wrap_edge(ix); // Detect edge if non-PBC + + if (gradients->samples) { + count = gradients->samples->value(ix); + } else { + count = 1; + } + + if (!edge && count) { + cvm::real const *grad = &(gradients->value(ix)); + cvm::real const fact = 1.0 / count; + for ( i = 0; i &ix0) +{ + const int linear_index = address(ix0); + int i, j, k; + std::vector ix = ix0; + const cvm::real * g; + + if (nd == 2) { + // gradients at grid points surrounding the current scalar grid point + cvm::real g00[2], g01[2], g10[2], g11[2]; + + get_grad(g11, ix); + ix[0] = ix0[0] - 1; + get_grad(g01, ix); + ix[1] = ix0[1] - 1; + get_grad(g00, ix); + ix[0] = ix0[0]; + get_grad(g10, ix); + + divergence[linear_index] = ((g10[0]-g00[0] + g11[0]-g01[0]) / widths[0] + + (g01[1]-g00[1] + g11[1]-g10[1]) / widths[1]) * 0.5; + } else if (nd == 3) { + cvm::real gc[24]; // stores 3d gradients in 8 contiguous bins + int index = 0; + + ix[0] = ix0[0] - 1; + for (i = 0; i<2; i++) { + ix[1] = ix0[1] - 1; + for (j = 0; j<2; j++) { + ix[2] = ix0[2] - 1; + for (k = 0; k<2; k++) { + get_grad(gc + index, ix); + index += 3; + ix[2]++; + } + ix[1]++; + } + ix[0]++; + } + + divergence[linear_index] = + ((gc[3*4]-gc[0] + gc[3*5]-gc[3*1] + gc[3*6]-gc[3*2] + gc[3*7]-gc[3*3]) + / widths[0] + + (gc[3*2+1]-gc[0+1] + gc[3*3+1]-gc[3*1+1] + gc[3*6+1]-gc[3*4+1] + gc[3*7+1]-gc[3*5+1]) + / widths[1] + + (gc[3*1+2]-gc[0+2] + gc[3*3+2]-gc[3*2+2] + gc[3*5+2]-gc[3*4+2] + gc[3*7+2]-gc[3*6+2]) + / widths[2]) * 0.25; + } +} + + +/// Multiplication by sparse matrix representing Laplacian +/// NOTE: Laplacian must be symmetric for solving with CG +void integrate_potential::atimes(const std::vector &A, std::vector &LA) +{ + if (nd == 2) { + // DIMENSION 2 + + size_t index, index2; + int i, j; + cvm::real fact; + const cvm::real ffx = 1.0 / (widths[0] * widths[0]); + const cvm::real ffy = 1.0 / (widths[1] * widths[1]); + const int h = nx[1]; + const int w = nx[0]; + // offsets for 4 reference points of the Laplacian stencil + int xm = -h; + int xp = h; + int ym = -1; + int yp = 1; + + // NOTE on performance: this version is slightly sub-optimal because + // it contains two double loops on the core of the array (for x and y terms) + // The slightly faster version is in commit 0254cb5a2958cb2e135f268371c4b45fad34866b + // yet it is much uglier, and probably horrible to extend to dimension 3 + // All terms in the matrix are assigned (=) during the x loops, then updated (+=) + // with the y (and z) contributions + + + // All x components except on x edges + index = h; // Skip first column + + // Halve the term on y edges (if any) to preserve symmetry of the Laplacian matrix + // (Long Chen, Finite Difference Methods, UCI, 2017) + fact = periodic[1] ? 1.0 : 0.5; + + for (i=1; i &b, std::vector &x) +{ + for (size_t i=0; i &b, std::vector &x, const cvm::real &tol, + const int itmax, int &iter, cvm::real &err) +{ + cvm::real ak,akden,bk,bkden,bknum,bnrm; + const cvm::real EPS=1.0e-14; + int j; + std::vector p(nt), r(nt), z(nt); + + iter=0; + atimes(x,r); + for (j=0;j &colvars, - size_t const &def_count = 0); + size_t const &def_count = 0, + bool margin = false); /// Increment the counter at given position inline void incr_count(std::vector const &ix) @@ -1210,12 +1236,13 @@ public: int A0, A1, A2; std::vector ix = ix0; + // TODO this can be rewritten more concisely with wrap_edge() if (periodic[n]) { ix[n]--; wrap(ix); - A0 = data[address(ix)]; + A0 = value(ix); ix = ix0; ix[n]++; wrap(ix); - A1 = data[address(ix)]; + A1 = value(ix); if (A0 * A1 == 0) { return 0.; // can't handle empty bins } else { @@ -1224,10 +1251,10 @@ public: } } else if (ix[n] > 0 && ix[n] < nx[n]-1) { // not an edge ix[n]--; - A0 = data[address(ix)]; + A0 = value(ix); ix = ix0; ix[n]++; - A1 = data[address(ix)]; + A1 = value(ix); if (A0 * A1 == 0) { return 0.; // can't handle empty bins } else { @@ -1238,9 +1265,9 @@ public: // edge: use 2nd order derivative int increment = (ix[n] == 0 ? 1 : -1); // move right from left edge, or the other way around - A0 = data[address(ix)]; - ix[n] += increment; A1 = data[address(ix)]; - ix[n] += increment; A2 = data[address(ix)]; + A0 = value(ix); + ix[n] += increment; A1 = value(ix); + ix[n] += increment; A2 = value(ix); if (A0 * A1 * A2 == 0) { return 0.; // can't handle empty bins } else { @@ -1249,6 +1276,49 @@ public: } } } + + /// \brief Return the gradient of discrete count from finite differences + /// on the *same* grid for dimension n + inline cvm::real gradient_finite_diff(const std::vector &ix0, + int n = 0) + { + int A0, A1, A2; + std::vector ix = ix0; + + // FIXME this can be rewritten more concisely with wrap_edge() + if (periodic[n]) { + ix[n]--; wrap(ix); + A0 = value(ix); + ix = ix0; + ix[n]++; wrap(ix); + A1 = value(ix); + if (A0 * A1 == 0) { + return 0.; // can't handle empty bins + } else { + return cvm::real(A1 - A0) / (widths[n] * 2.); + } + } else if (ix[n] > 0 && ix[n] < nx[n]-1) { // not an edge + ix[n]--; + A0 = value(ix); + ix = ix0; + ix[n]++; + A1 = value(ix); + if (A0 * A1 == 0) { + return 0.; // can't handle empty bins + } else { + return cvm::real(A1 - A0) / (widths[n] * 2.); + } + } else { + // edge: use 2nd order derivative + int increment = (ix[n] == 0 ? 1 : -1); + // move right from left edge, or the other way around + A0 = value(ix); + ix[n] += increment; A1 = value(ix); + ix[n] += increment; A2 = value(ix); + return (-1.5 * cvm::real(A0) + 2. * cvm::real(A1) + - 0.5 * cvm::real(A2)) * increment / widths[n]; + } + } }; @@ -1289,27 +1359,57 @@ public: has_data = true; } - /// Return the gradient of the scalar field from finite differences - inline const cvm::real * gradient_finite_diff( const std::vector &ix0 ) + /// \brief Return the gradient of the scalar field from finite differences + /// Input coordinates are those of gradient grid, shifted wrt scalar grid + /// Should not be called on edges of scalar grid, provided the latter has margins + /// wrt gradient grid + inline void vector_gradient_finite_diff( const std::vector &ix0, std::vector &grad) { cvm::real A0, A1; std::vector ix; - if (nd != 2) { - cvm::error("Finite differences available in dimension 2 only."); - return grad; - } - for (unsigned int n = 0; n < nd; n++) { + size_t i, j, k, n; + + if (nd == 2) { + for (n = 0; n < 2; n++) { + ix = ix0; + A0 = value(ix); + ix[n]++; wrap(ix); + A1 = value(ix); + ix[1-n]++; wrap(ix); + A1 += value(ix); + ix[n]--; wrap(ix); + A0 += value(ix); + grad[n] = 0.5 * (A1 - A0) / widths[n]; + } + } else if (nd == 3) { + + cvm::real p[8]; // potential values within cube, indexed in binary (4 i + 2 j + k) ix = ix0; - A0 = data[address(ix)]; - ix[n]++; wrap(ix); - A1 = data[address(ix)]; - ix[1-n]++; wrap(ix); - A1 += data[address(ix)]; - ix[n]--; wrap(ix); - A0 += data[address(ix)]; - grad[n] = 0.5 * (A1 - A0) / widths[n]; + int index = 0; + for (i = 0; i<2; i++) { + ix[1] = ix0[1]; + for (j = 0; j<2; j++) { + ix[2] = ix0[2]; + for (k = 0; k<2; k++) { + wrap(ix); + p[index++] = value(ix); + ix[2]++; + } + ix[1]++; + } + ix[0]++; + } + + // The following would be easier to read using binary literals + // 100 101 110 111 000 001 010 011 + grad[0] = 0.25 * ((p[4] + p[5] + p[6] + p[7]) - (p[0] + p[1] + p[2] + p[3])) / widths[0]; + // 010 011 110 111 000 001 100 101 + grad[1] = 0.25 * ((p[2] + p[3] + p[6] + p[7]) - (p[0] + p[1] + p[4] + p[5])) / widths[0]; + // 001 011 101 111 000 010 100 110 + grad[2] = 0.25 * ((p[1] + p[3] + p[5] + p[7]) - (p[0] + p[2] + p[4] + p[6])) / widths[0]; + } else { + cvm::error("Finite differences available in dimension 2 and 3 only."); } - return grad; } /// \brief Return the value of the function at ix divided by its @@ -1373,10 +1473,6 @@ public: /// \brief Assuming that the map is a normalized probability density, /// calculates the entropy (uses widths if they are defined) cvm::real entropy() const; - -private: - // gradient - cvm::real * grad; }; @@ -1390,6 +1486,10 @@ public: /// should be divided colvar_grid_count *samples; + /// \brief Provide the floating point weights by which each binned value + /// should be divided (alternate to samples, only one should be non-null) + colvar_grid_scalar *weights; + /// Default constructor colvar_grid_gradient(); @@ -1403,6 +1503,29 @@ public: /// Constructor from a vector of colvars colvar_grid_gradient(std::vector &colvars); + /// \brief Get a vector with the binned value(s) indexed by ix, normalized if applicable + inline void vector_value(std::vector const &ix, std::vector &v) const + { + cvm::real const * p = &value(ix); + if (samples) { + int count = samples->value(ix); + if (count) { + cvm::real invcount = 1.0 / count; + for (size_t i = 0; i < mult; i++) { + v[i] = invcount * p[i]; + } + } else { + for (size_t i = 0; i < mult; i++) { + v[i] = 0.0; + } + } + } else { + for (size_t i = 0; i < mult; i++) { + v[i] = p[i]; + } + } + } + /// \brief Accumulate the value inline void acc_value(std::vector const &ix, std::vector const &values) { for (size_t imult = 0; imult < mult; imult++) { @@ -1412,23 +1535,25 @@ public: samples->incr_count(ix); } - /// \brief Accumulate the gradient - inline void acc_grad(std::vector const &ix, cvm::real const *grads) { + /// \brief Accumulate the gradient based on the force (i.e. sums the + /// opposite of the force) + inline void acc_force(std::vector const &ix, cvm::real const *forces) { for (size_t imult = 0; imult < mult; imult++) { - data[address(ix) + imult] += grads[imult]; + data[address(ix) + imult] -= forces[imult]; } if (samples) samples->incr_count(ix); } /// \brief Accumulate the gradient based on the force (i.e. sums the - /// opposite of the force) - inline void acc_force(std::vector const &ix, cvm::real const *forces) { + /// opposite of the force) with a non-integer weight + inline void acc_force_weighted(std::vector const &ix, + cvm::real const *forces, + cvm::real weight) { for (size_t imult = 0; imult < mult; imult++) { - data[address(ix) + imult] -= forces[imult]; + data[address(ix) + imult] -= forces[imult] * weight; } - if (samples) - samples->incr_count(ix); + weights->acc_value(ix, weight); } /// \brief Return the value of the function at ix divided by its @@ -1498,5 +1623,70 @@ public: }; + +/// Integrate (1D, 2D or 3D) gradients + +class integrate_potential : public colvar_grid_scalar +{ + public: + + integrate_potential(); + + virtual ~integrate_potential() + {} + + /// Constructor from a vector of colvars + gradient grid + integrate_potential (std::vector &colvars, colvar_grid_gradient * gradients); + + /// \brief Calculate potential from divergence (in 2D); return number of steps + int integrate (const int itmax, const cvm::real & tol, cvm::real & err); + + /// \brief Update matrix containing divergence and boundary conditions + /// based on new gradient point value, in neighboring bins + void update_div_neighbors(const std::vector &ix); + + /// \brief Set matrix containing divergence and boundary conditions + /// based on complete gradient grid + void set_div(); + + /// \brief Add constant to potential so that its minimum value is zero + /// Useful e.g. for output + inline void set_zero_minimum() { + add_constant(-1.0 * minimum_value()); + } + + protected: + + // Reference to gradient grid + colvar_grid_gradient *gradients; + + /// Array holding divergence + boundary terms (modified Neumann) if not periodic + std::vector divergence; + +// std::vector inv_lap_diag; // Inverse of the diagonal of the Laplacian; for conditioning + + /// \brief Update matrix containing divergence and boundary conditions + /// called by update_div_neighbors + void update_div_local(const std::vector &ix); + + /// Obtain the gradient vector at given location ix, if available + /// or zero if it is on the edge of the gradient grid + /// ix gets wrapped in PBC + void get_grad(cvm::real * g, std::vector &ix); + + /// \brief Solve linear system based on CG, valid for symmetric matrices only + void nr_linbcg_sym(const std::vector &b, std::vector &x, + const cvm::real &tol, const int itmax, int &iter, cvm::real &err); + + /// l2 norm of a vector + cvm::real l2norm(const std::vector &x); + + /// Multiplication by sparse matrix representing Lagrangian (or its transpose) + void atimes(const std::vector &x, std::vector &r); + +// /// Inversion of preconditioner matrix +// void asolve(const std::vector &b, std::vector &x); +}; + #endif diff --git a/lib/colvars/colvarmodule.cpp b/lib/colvars/colvarmodule.cpp index 200c2d6848f10cf6a52ab70745c6049c9387dff7..9898e2d5e8264d96ba79d12aac5e70bf9dbfd67d 100644 --- a/lib/colvars/colvarmodule.cpp +++ b/lib/colvars/colvarmodule.cpp @@ -24,6 +24,7 @@ #include "colvaratoms.h" #include "colvarcomp.h" + colvarmodule::colvarmodule(colvarproxy *proxy_in) { depth_s = 0; @@ -417,10 +418,10 @@ int colvarmodule::parse_biases(std::string const &conf) "Please ensure that their forces do not counteract each other.\n"); } - if (biases.size() || use_scripted_forces) { + if (num_biases() || use_scripted_forces) { cvm::log(cvm::line_marker); cvm::log("Collective variables biases initialized, "+ - cvm::to_str(biases.size())+" in total.\n"); + cvm::to_str(num_biases())+" in total.\n"); } else { if (!use_scripted_forces) { cvm::log("No collective variables biases were defined.\n"); @@ -431,12 +432,37 @@ int colvarmodule::parse_biases(std::string const &conf) } +int colvarmodule::num_variables() const +{ + return colvars.size(); +} + + +int colvarmodule::num_variables_feature(int feature_id) const +{ + size_t n = 0; + for (std::vector::const_iterator cvi = colvars.begin(); + cvi != colvars.end(); + cvi++) { + if ((*cvi)->is_enabled(feature_id)) { + n++; + } + } + return n; +} + + +int colvarmodule::num_biases() const +{ + return biases.size(); +} + + int colvarmodule::num_biases_feature(int feature_id) const { - colvarmodule *cv = cvm::main(); size_t n = 0; - for (std::vector::iterator bi = cv->biases.begin(); - bi != cv->biases.end(); + for (std::vector::const_iterator bi = biases.begin(); + bi != biases.end(); bi++) { if ((*bi)->is_enabled(feature_id)) { n++; @@ -448,10 +474,9 @@ int colvarmodule::num_biases_feature(int feature_id) const int colvarmodule::num_biases_type(std::string const &type) const { - colvarmodule *cv = cvm::main(); size_t n = 0; - for (std::vector::iterator bi = cv->biases.begin(); - bi != cv->biases.end(); + for (std::vector::const_iterator bi = biases.begin(); + bi != biases.end(); bi++) { if ((*bi)->bias_type == type) { n++; @@ -465,7 +490,7 @@ std::vector const colvarmodule::time_dependent_biases() const { size_t i; std::vector biases_names; - for (i = 0; i < biases.size(); i++) { + for (i = 0; i < num_biases(); i++) { if (biases[i]->is_enabled(colvardeps::f_cvb_apply_force) && biases[i]->is_enabled(colvardeps::f_cvb_active) && (biases[i]->is_enabled(colvardeps::f_cvb_history_dependent) || @@ -790,7 +815,7 @@ int colvarmodule::calc_biases() { // update the biases and communicate their forces to the collective // variables - if (cvm::debug() && biases.size()) + if (cvm::debug() && num_biases()) cvm::log("Updating collective variable biases.\n"); std::vector::iterator bi; @@ -852,7 +877,7 @@ int colvarmodule::update_colvar_forces() std::vector::iterator bi; // sum the forces from all biases for each collective variable - if (cvm::debug() && biases.size()) + if (cvm::debug() && num_biases()) cvm::log("Collecting forces from all biases.\n"); cvm::increase_depth(); for (bi = biases_active()->begin(); bi != biases_active()->end(); bi++) { @@ -1073,8 +1098,6 @@ int colvarmodule::reset() int colvarmodule::setup_input() { - if (this->size() == 0) return cvm::get_error(); - std::string restart_in_name(""); // read the restart configuration, if available @@ -1107,14 +1130,12 @@ int colvarmodule::setup_input() } } - return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK); + return cvm::get_error(); } int colvarmodule::setup_output() { - if (this->size() == 0) return cvm::get_error(); - int error_code = COLVARS_OK; // output state file (restart) @@ -1123,7 +1144,8 @@ int colvarmodule::setup_output() std::string(""); if (restart_out_name.size()) { - cvm::log("The restart output state file will be \""+restart_out_name+"\".\n"); + cvm::log("The restart output state file will be \""+ + restart_out_name+"\".\n"); } output_prefix() = proxy->output_prefix(); @@ -1154,7 +1176,7 @@ int colvarmodule::setup_output() set_error_bits(FILE_ERROR); } - return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK); + return cvm::get_error(); } @@ -1738,6 +1760,89 @@ int cvm::load_coords_xyz(char const *filename, } + +// Wrappers to proxy functions: these may go in the future + +cvm::real cvm::unit_angstrom() +{ + return proxy->unit_angstrom(); +} + + +cvm::real cvm::boltzmann() +{ + return proxy->boltzmann(); +} + + +cvm::real cvm::temperature() +{ + return proxy->temperature(); +} + + +cvm::real cvm::dt() +{ + return proxy->dt(); +} + + +void cvm::request_total_force() +{ + proxy->request_total_force(true); +} + +cvm::rvector cvm::position_distance(atom_pos const &pos1, + atom_pos const &pos2) +{ + return proxy->position_distance(pos1, pos2); +} + +cvm::real cvm::position_dist2(cvm::atom_pos const &pos1, + cvm::atom_pos const &pos2) +{ + return proxy->position_dist2(pos1, pos2); +} + +cvm::real cvm::rand_gaussian(void) +{ + return proxy->rand_gaussian(); +} + + + +bool cvm::replica_enabled() +{ + return proxy->replica_enabled(); +} + +int cvm::replica_index() +{ + return proxy->replica_index(); +} + +int cvm::replica_num() +{ + return proxy->replica_num(); +} + +void cvm::replica_comm_barrier() +{ + return proxy->replica_comm_barrier(); +} + +int cvm::replica_comm_recv(char* msg_data, int buf_len, int src_rep) +{ + return proxy->replica_comm_recv(msg_data,buf_len,src_rep); +} + +int cvm::replica_comm_send(char* msg_data, int msg_len, int dest_rep) +{ + return proxy->replica_comm_send(msg_data,msg_len,dest_rep); +} + + + // shared pointer to the proxy object colvarproxy *colvarmodule::proxy = NULL; diff --git a/lib/colvars/colvarmodule.h b/lib/colvars/colvarmodule.h index 14e5d56701f75730c7bb1ce07764c89edd0b665b..64a98b77a02d59eae598a3f223214fc103018263 100644 --- a/lib/colvars/colvarmodule.h +++ b/lib/colvars/colvarmodule.h @@ -39,16 +39,14 @@ You can browse the class hierarchy or the list of source files. #define FILE_ERROR (1<<4) #define MEMORY_ERROR (1<<5) #define FATAL_ERROR (1<<6) // Should be set, or not, together with other bits -#define DELETE_COLVARS (1<<7) // Instruct the caller to delete cvm +//#define DELETE_COLVARS (1<<7) // Instruct the caller to delete cvm #define COLVARS_NO_SUCH_FRAME (1<<8) // Cannot load the requested frame #include #include -#include -#include -#include #include -#include +#include +#include #include #include @@ -84,12 +82,18 @@ public: /// Defining an abstract real number allows to switch precision typedef double real; - /// Override std::pow with a product for n positive integer - static inline real integer_power(real x, int n) + /// Override std::pow with a product for n integer + static inline real integer_power(real const &x, int const n) { - real result = 1.0; - for (int i = 0; i < n; i++) result *= x; - return result; + // Original code: math_special.h in LAMMPS + double yy, ww; + if (x == 0.0) return 0.0; + int nn = (n > 0) ? n : -n; + ww = x; + for (yy = 1.0; nn != 0; nn >>= 1, ww *=ww) { + if (nn & 1) yy *= ww; + } + return (n > 0) ? yy : 1.0/yy; } /// Residue identifier @@ -301,13 +305,23 @@ private: public: + /// Return how many variables are defined + int num_variables() const; + + /// Return how many variables have this feature enabled + int num_variables_feature(int feature_id) const; + + /// Return how many biases are defined + int num_biases() const; + /// Return how many biases have this feature enabled int num_biases_feature(int feature_id) const; - /// Return how many biases are defined with this type + /// Return how many biases of this type are defined int num_biases_type(std::string const &type) const; - /// Return the names of time-dependent biases with forces enabled + /// Return the names of time-dependent biases with forces enabled (ABF, + /// metadynamics, etc) std::vector const time_dependent_biases() const; private: @@ -602,16 +616,14 @@ public: typedef colvarmodule cvm; -#include "colvartypes.h" - std::ostream & operator << (std::ostream &os, cvm::rvector const &v); std::istream & operator >> (std::istream &is, cvm::rvector &v); template std::string cvm::to_str(T const &x, - size_t const &width, - size_t const &prec) { + size_t const &width, + size_t const &prec) { std::ostringstream os; if (width) os.width(width); if (prec) { @@ -622,9 +634,10 @@ template std::string cvm::to_str(T const &x, return os.str(); } + template std::string cvm::to_str(std::vector const &x, - size_t const &width, - size_t const &prec) { + size_t const &width, + size_t const &prec) { if (!x.size()) return std::string(""); std::ostringstream os; if (prec) { @@ -645,70 +658,4 @@ template std::string cvm::to_str(std::vector const &x, } -#include "colvarproxy.h" - - -inline cvm::real cvm::unit_angstrom() -{ - return proxy->unit_angstrom(); -} - -inline cvm::real cvm::boltzmann() -{ - return proxy->boltzmann(); -} - -inline cvm::real cvm::temperature() -{ - return proxy->temperature(); -} - -inline cvm::real cvm::dt() -{ - return proxy->dt(); -} - -// Replica exchange commands -inline bool cvm::replica_enabled() { - return proxy->replica_enabled(); -} -inline int cvm::replica_index() { - return proxy->replica_index(); -} -inline int cvm::replica_num() { - return proxy->replica_num(); -} -inline void cvm::replica_comm_barrier() { - return proxy->replica_comm_barrier(); -} -inline int cvm::replica_comm_recv(char* msg_data, int buf_len, int src_rep) { - return proxy->replica_comm_recv(msg_data,buf_len,src_rep); -} -inline int cvm::replica_comm_send(char* msg_data, int msg_len, int dest_rep) { - return proxy->replica_comm_send(msg_data,msg_len,dest_rep); -} - - -inline void cvm::request_total_force() -{ - proxy->request_total_force(true); -} - -inline cvm::rvector cvm::position_distance(atom_pos const &pos1, - atom_pos const &pos2) -{ - return proxy->position_distance(pos1, pos2); -} - -inline cvm::real cvm::position_dist2(cvm::atom_pos const &pos1, - cvm::atom_pos const &pos2) -{ - return proxy->position_dist2(pos1, pos2); -} - -inline cvm::real cvm::rand_gaussian(void) -{ - return proxy->rand_gaussian(); -} - #endif diff --git a/lib/colvars/colvarparse.cpp b/lib/colvars/colvarparse.cpp index 9f333b7b76bc029f142fa5443d16c3d73249b77a..43c8c69c040e6b6fdb14a31249f39a293b997d8a 100644 --- a/lib/colvars/colvarparse.cpp +++ b/lib/colvars/colvarparse.cpp @@ -553,7 +553,8 @@ bool colvarparse::key_lookup(std::string const &conf, size_t *save_pos) { if (cvm::debug()) { - cvm::log("Looking for the keyword \""+std::string(key_in)+"\" and its value.\n"); + cvm::log("Looking for the keyword \""+std::string(key_in)+ + "\" and its value.\n"); } // add this keyword to the register (in its camelCase version) diff --git a/lib/colvars/colvarproxy.cpp b/lib/colvars/colvarproxy.cpp index 8160144c6bab1e11d36f4d1b7712e75bce90e6c8..8767d5f459090854cf19ad011f579e752c6d2230 100644 --- a/lib/colvars/colvarproxy.cpp +++ b/lib/colvars/colvarproxy.cpp @@ -14,6 +14,11 @@ #include #endif +#if defined(NAMD_TCL) || defined(VMDTCL) +#define COLVARS_TCL +#include +#endif + #include "colvarmodule.h" #include "colvarproxy.h" #include "colvarscript.h" @@ -420,8 +425,10 @@ colvarproxy_script::colvarproxy_script() colvarproxy_script::~colvarproxy_script() {} -char *colvarproxy_script::script_obj_to_str(unsigned char *obj) +char const *colvarproxy_script::script_obj_to_str(unsigned char *obj) { + cvm::error("Error: trying to print a script object without a scripting " + "language interface.\n", BUG_ERROR); return reinterpret_cast(obj); } @@ -451,6 +458,140 @@ int colvarproxy_script::run_colvar_gradient_callback( +colvarproxy_tcl::colvarproxy_tcl() +{ + _tcl_interp = NULL; +} + + +colvarproxy_tcl::~colvarproxy_tcl() +{ +} + + +void colvarproxy_tcl::init_tcl_pointers() +{ + cvm::error("Error: Tcl support is currently unavailable " + "outside NAMD or VMD.\n", COLVARS_NOT_IMPLEMENTED); +} + + +char const *colvarproxy_tcl::tcl_obj_to_str(unsigned char *obj) +{ +#if defined(COLVARS_TCL) + return Tcl_GetString(reinterpret_cast(obj)); +#else + return NULL; +#endif +} + + +int colvarproxy_tcl::tcl_run_force_callback() +{ +#if defined(COLVARS_TCL) + Tcl_Interp *const tcl_interp = reinterpret_cast(_tcl_interp); + std::string cmd = std::string("calc_colvar_forces ") + + cvm::to_str(cvm::step_absolute()); + int err = Tcl_Eval(tcl_interp, cmd.c_str()); + if (err != TCL_OK) { + cvm::log(std::string("Error while executing calc_colvar_forces:\n")); + cvm::error(Tcl_GetStringResult(tcl_interp)); + return COLVARS_ERROR; + } + return cvm::get_error(); +#else + return COLVARS_NOT_IMPLEMENTED; +#endif +} + + +int colvarproxy_tcl::tcl_run_colvar_callback( + std::string const &name, + std::vector const &cvc_values, + colvarvalue &value) +{ +#if defined(COLVARS_TCL) + + Tcl_Interp *const tcl_interp = reinterpret_cast(_tcl_interp); + size_t i; + std::string cmd = std::string("calc_") + name; + for (i = 0; i < cvc_values.size(); i++) { + cmd += std::string(" {") + (*(cvc_values[i])).to_simple_string() + + std::string("}"); + } + int err = Tcl_Eval(tcl_interp, cmd.c_str()); + const char *result = Tcl_GetStringResult(tcl_interp); + if (err != TCL_OK) { + return cvm::error(std::string("Error while executing ") + + cmd + std::string(":\n") + + std::string(Tcl_GetStringResult(tcl_interp)), COLVARS_ERROR); + } + std::istringstream is(result); + if (value.from_simple_string(is.str()) != COLVARS_OK) { + cvm::log("Error parsing colvar value from script:"); + cvm::error(result); + return COLVARS_ERROR; + } + return cvm::get_error(); + +#else + + return COLVARS_NOT_IMPLEMENTED; + +#endif +} + + +int colvarproxy_tcl::tcl_run_colvar_gradient_callback( + std::string const &name, + std::vector const &cvc_values, + std::vector > &gradient) +{ +#if defined(COLVARS_TCL) + + Tcl_Interp *const tcl_interp = reinterpret_cast(_tcl_interp); + size_t i; + std::string cmd = std::string("calc_") + name + "_gradient"; + for (i = 0; i < cvc_values.size(); i++) { + cmd += std::string(" {") + (*(cvc_values[i])).to_simple_string() + + std::string("}"); + } + int err = Tcl_Eval(tcl_interp, cmd.c_str()); + if (err != TCL_OK) { + return cvm::error(std::string("Error while executing ") + + cmd + std::string(":\n") + + std::string(Tcl_GetStringResult(tcl_interp)), COLVARS_ERROR); + } + Tcl_Obj **list; + int n; + Tcl_ListObjGetElements(tcl_interp, Tcl_GetObjResult(tcl_interp), + &n, &list); + if (n != int(gradient.size())) { + cvm::error("Error parsing list of gradient values from script: found " + + cvm::to_str(n) + " values instead of " + + cvm::to_str(gradient.size())); + return COLVARS_ERROR; + } + for (i = 0; i < gradient.size(); i++) { + std::istringstream is(Tcl_GetString(list[i])); + if (gradient[i].from_simple_string(is.str()) != COLVARS_OK) { + cvm::log("Gradient matrix size: " + cvm::to_str(gradient[i].size())); + cvm::log("Gradient string: " + cvm::to_str(Tcl_GetString(list[i]))); + cvm::error("Error parsing gradient value from script", COLVARS_ERROR); + return COLVARS_ERROR; + } + } + + return cvm::get_error(); + +#else + + return COLVARS_NOT_IMPLEMENTED; + +#endif +} + + colvarproxy_io::colvarproxy_io() {} @@ -541,6 +682,7 @@ colvarproxy::colvarproxy() { colvars = NULL; b_simulation_running = true; + b_delete_requested = false; } @@ -556,6 +698,14 @@ int colvarproxy::reset() } +int colvarproxy::request_deletion() +{ + return cvm::error("Error: \"delete\" command is only available in VMD; " + "please use \"reset\" instead.\n", + COLVARS_NOT_IMPLEMENTED); +} + + int colvarproxy::setup() { return COLVARS_OK; @@ -579,13 +729,3 @@ size_t colvarproxy::restart_frequency() return 0; } - - - - - - - - - - diff --git a/lib/colvars/colvarproxy.h b/lib/colvars/colvarproxy.h index e51ddfbe3bfc16a9d9a77264b86912a2cd8aa34f..bf290482704af3204518c0ffae7daf5ad5d88c0b 100644 --- a/lib/colvars/colvarproxy.h +++ b/lib/colvars/colvarproxy.h @@ -415,7 +415,7 @@ public: }; -/// Method for scripting language interface (Tcl or Python) +/// Methods for scripting language interface (Tcl or Python) class colvarproxy_script { public: @@ -427,7 +427,7 @@ public: virtual ~colvarproxy_script(); /// Convert a script object (Tcl or Python call argument) to a C string - virtual char *script_obj_to_str(unsigned char *obj); + virtual char const *script_obj_to_str(unsigned char *obj); /// Pointer to the scripting interface object /// (does not need to be allocated in a new interface) @@ -454,6 +454,46 @@ public: }; +/// Methods for using Tcl within Colvars +class colvarproxy_tcl { + +public: + + /// Constructor + colvarproxy_tcl(); + + /// Destructor + virtual ~colvarproxy_tcl(); + + /// Is Tcl available? (trigger initialization if needed) + int tcl_available(); + + /// Tcl implementation of script_obj_to_str() + char const *tcl_obj_to_str(unsigned char *obj); + + /// Run a user-defined colvar forces script + int tcl_run_force_callback(); + + int tcl_run_colvar_callback( + std::string const &name, + std::vector const &cvcs, + colvarvalue &value); + + int tcl_run_colvar_gradient_callback( + std::string const &name, + std::vector const &cvcs, + std::vector > &gradient); + +protected: + + /// Pointer to Tcl interpreter object + void *_tcl_interp; + + /// Set Tcl pointers + virtual void init_tcl_pointers(); +}; + + /// Methods for data input/output class colvarproxy_io { @@ -540,6 +580,7 @@ class colvarproxy public colvarproxy_smp, public colvarproxy_replicas, public colvarproxy_script, + public colvarproxy_tcl, public colvarproxy_io { @@ -554,6 +595,15 @@ public: /// Destructor virtual ~colvarproxy(); + /// Request deallocation of the module (currently only implemented by VMD) + virtual int request_deletion(); + + /// Whether deallocation was requested + inline bool delete_requested() + { + return b_delete_requested; + } + /// \brief Reset proxy state, e.g. requested atoms virtual int reset(); @@ -591,6 +641,9 @@ protected: /// Whether a simulation is running (warn against irrecovarable errors) bool b_simulation_running; + /// Whether the entire module should be deallocated by the host engine + bool b_delete_requested; + }; diff --git a/lib/colvars/colvars_version.h b/lib/colvars/colvars_version.h index a92a776f8a3abc88700794228bcf4a1e0ad8da51..dc4b8bd07e420d83289b99f458ed2bf935ab210e 100644 --- a/lib/colvars/colvars_version.h +++ b/lib/colvars/colvars_version.h @@ -1,5 +1,5 @@ #ifndef COLVARS_VERSION -#define COLVARS_VERSION "2017-10-20" +#define COLVARS_VERSION "2018-01-17" // This file is part of the Collective Variables module (Colvars). // The original version of Colvars and its updates are located at: // https://github.com/colvars/colvars diff --git a/lib/colvars/colvarscript.cpp b/lib/colvars/colvarscript.cpp index 9570acd8327252a99e6394f9bd29d6f6a0bd2f4e..0977496b9e1c252e52c5670f44321796cfafd889 100644 --- a/lib/colvars/colvarscript.cpp +++ b/lib/colvars/colvarscript.cpp @@ -74,7 +74,9 @@ int colvarscript::run(int objc, unsigned char *const objv[]) } if (objc < 2) { - return exec_command(cv_help, NULL, objc, objv); + set_str_result("No commands given: use \"cv help\" " + "for a list of commands."); + return COLVARSCRIPT_ERROR; } std::string const cmd(obj_to_str(objv[1])); @@ -123,8 +125,7 @@ int colvarscript::run(int objc, unsigned char *const objv[]) if (cmd == "delete") { // Note: the delete bit may be ignored by some backends // it is mostly useful in VMD - colvars->set_error_bits(DELETE_COLVARS); - return COLVARS_OK; + return proxy->request_deletion(); } if (cmd == "update") { @@ -272,6 +273,11 @@ int colvarscript::proc_colvar(colvar *cv, int objc, unsigned char *const objv[]) return COLVARS_OK; } + if (subcmd == "run_ave") { + result = (cv->run_ave()).to_simple_string(); + return COLVARS_OK; + } + if (subcmd == "width") { result = cvm::to_str(cv->width, 0, cvm::cv_prec); return COLVARS_OK; diff --git a/lib/kokkos/CHANGELOG.md b/lib/kokkos/CHANGELOG.md index e3de6b048d7fdbcbda354497fa86cba7f03acf69..feb2bd547f034a5ef233667a3a9b5c3d0e02d3f8 100644 --- a/lib/kokkos/CHANGELOG.md +++ b/lib/kokkos/CHANGELOG.md @@ -1,5 +1,49 @@ # Change Log +## [2.6.00](https://github.com/kokkos/kokkos/tree/2.6.00) (2018-03-07) +[Full Changelog](https://github.com/kokkos/kokkos/compare/2.5.00...2.6.00) + +**Part of the Kokkos C++ Performance Portability Programming EcoSystem 2.6** + +**Implemented enhancements:** + +- Support NVIDIA Volta microarchitecture [\#1466](https://github.com/kokkos/kokkos/issues/1466) +- Kokkos - Define empty functions when profiling disabled [\#1424](https://github.com/kokkos/kokkos/issues/1424) +- Don't use \_\_constant\_\_ cache for lock arrays, enable once per run update instead of once per call [\#1385](https://github.com/kokkos/kokkos/issues/1385) +- task dag enhancement. [\#1354](https://github.com/kokkos/kokkos/issues/1354) +- Cuda task team collectives and stack size [\#1353](https://github.com/kokkos/kokkos/issues/1353) +- Replace View operator acceptance of more than rank integers with 'access' function [\#1333](https://github.com/kokkos/kokkos/issues/1333) +- Interoperability: Do not shut down backend execution space runtimes upon calling finalize. [\#1305](https://github.com/kokkos/kokkos/issues/1305) +- shmem\_size for LayoutStride [\#1291](https://github.com/kokkos/kokkos/issues/1291) +- Kokkos::resize performs poorly on 1D Views [\#1270](https://github.com/kokkos/kokkos/issues/1270) +- stride\(\) is inconsistent with dimension\(\), extent\(\), etc. [\#1214](https://github.com/kokkos/kokkos/issues/1214) +- Kokkos::sort defaults to std::sort on host [\#1208](https://github.com/kokkos/kokkos/issues/1208) +- DynamicView with host size grow [\#1206](https://github.com/kokkos/kokkos/issues/1206) +- Unmanaged View with Anonymous Memory Space [\#1175](https://github.com/kokkos/kokkos/issues/1175) +- Sort subset of Kokkos::DynamicView [\#1160](https://github.com/kokkos/kokkos/issues/1160) +- MDRange policy doesn't support lambda reductions [\#1054](https://github.com/kokkos/kokkos/issues/1054) +- Add ability to set hook on Kokkos::finalize [\#714](https://github.com/kokkos/kokkos/issues/714) +- Atomics with Serial Backend - Default should be Disable? [\#549](https://github.com/kokkos/kokkos/issues/549) +- KOKKOS\_ENABLE\_DEPRECATED\_CODE [\#1359](https://github.com/kokkos/kokkos/issues/1359) + +**Fixed bugs:** + +- cuda\_internal\_maximum\_warp\_count returns 8, but I believe it should return 16 for P100 [\#1269](https://github.com/kokkos/kokkos/issues/1269) +- Cuda: level 1 scratch memory bug \(reported by Stan Moore\) [\#1434](https://github.com/kokkos/kokkos/issues/1434) +- MDRangePolicy Reduction requires value\_type typedef in Functor [\#1379](https://github.com/kokkos/kokkos/issues/1379) +- Kokkos DeepCopy between empty views fails [\#1369](https://github.com/kokkos/kokkos/issues/1369) +- Several issues with new CMake build infrastructure \(reported by Eric Phipps\) [\#1365](https://github.com/kokkos/kokkos/issues/1365) +- deep\_copy between rank-1 host/device views of differing layouts without UVM no longer works \(reported by Eric Phipps\) [\#1363](https://github.com/kokkos/kokkos/issues/1363) +- Profiling can't be disabled in CMake, and a parallel\_for is missing for tasks \(reported by Kyungjoo Kim\) [\#1349](https://github.com/kokkos/kokkos/issues/1349) +- get\_work\_partition int overflow \(reported by berryj5\) [\#1327](https://github.com/kokkos/kokkos/issues/1327) +- Kokkos::deep\_copy must fence even if the two views are the same [\#1303](https://github.com/kokkos/kokkos/issues/1303) +- CudaUVMSpace::allocate/deallocate must fence [\#1302](https://github.com/kokkos/kokkos/issues/1302) +- ViewResize on CUDA fails in Debug because of too many resources requested [\#1299](https://github.com/kokkos/kokkos/issues/1299) +- Cuda 9 and intrepid2 calls from Panzer. [\#1183](https://github.com/kokkos/kokkos/issues/1183) +- Slowdown due to tracking\_enabled\(\) in 2.04.00 \(found by Albany app\) [\#1016](https://github.com/kokkos/kokkos/issues/1016) +- Bounds checking fails with zero-span Views \(reported by Stan Moore\) [\#1411](https://github.com/kokkos/kokkos/issues/1411) + + ## [2.5.00](https://github.com/kokkos/kokkos/tree/2.5.00) (2017-12-15) [Full Changelog](https://github.com/kokkos/kokkos/compare/2.04.11...2.5.00) diff --git a/lib/kokkos/CMakeLists.txt b/lib/kokkos/CMakeLists.txt index 9c708ded4a460a3b67224a8aeec9e80c6010157b..cd1f4ea981339a5ff01095be9bca144cdb5d9064 100644 --- a/lib/kokkos/CMakeLists.txt +++ b/lib/kokkos/CMakeLists.txt @@ -7,7 +7,7 @@ ELSE() ENDIF() IF(NOT KOKKOS_HAS_TRILINOS) - cmake_minimum_required(VERSION 3.1 FATAL_ERROR) + cmake_minimum_required(VERSION 3.3 FATAL_ERROR) # Define Project Name if this is a standalone build IF(NOT DEFINED ${PROJECT_NAME}) @@ -37,9 +37,19 @@ IF(NOT KOKKOS_HAS_TRILINOS) COMMAND ${KOKKOS_SETTINGS} make -f ${KOKKOS_SRC_PATH}/cmake/Makefile.generate_cmake_settings CXX=${CMAKE_CXX_COMPILER} generate_build_settings WORKING_DIRECTORY "${Kokkos_BINARY_DIR}" OUTPUT_FILE ${Kokkos_BINARY_DIR}/core_src_make.out - RESULT_VARIABLE res + RESULT_VARIABLE GEN_SETTINGS_RESULT ) + if (GEN_SETTINGS_RESULT) + message(FATAL_ERROR "Kokkos settings generation failed:\n" + "${KOKKOS_SETTINGS} make -f ${KOKKOS_SRC_PATH}/cmake/Makefile.generate_cmake_settings CXX=${CMAKE_CXX_COMPILER} generate_build_settings") + endif() include(${Kokkos_BINARY_DIR}/kokkos_generated_settings.cmake) + string(REPLACE " " ";" KOKKOS_TPL_INCLUDE_DIRS "${KOKKOS_GMAKE_TPL_INCLUDE_DIRS}") + string(REPLACE " " ";" KOKKOS_TPL_LIBRARY_DIRS "${KOKKOS_GMAKE_TPL_LIBRARY_DIRS}") + string(REPLACE " " ";" KOKKOS_TPL_LIBRARY_NAMES "${KOKKOS_GMAKE_TPL_LIBRARY_NAMES}") + list(REMOVE_ITEM KOKKOS_TPL_INCLUDE_DIRS "") + list(REMOVE_ITEM KOKKOS_TPL_LIBRARY_DIRS "") + list(REMOVE_ITEM KOKKOS_TPL_LIBRARY_NAMES "") set_kokkos_srcs(KOKKOS_SRC ${KOKKOS_SRC}) #------------ NOW BUILD ------------------------------------------------------ diff --git a/lib/kokkos/Copyright.txt b/lib/kokkos/Copyright.txt index 05980758fa8fe6317bb08fcc6eb70668b5fd1580..50b76995af47381395ba4b9d0ad72ac7f57e4655 100644 --- a/lib/kokkos/Copyright.txt +++ b/lib/kokkos/Copyright.txt @@ -34,7 +34,7 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER diff --git a/lib/kokkos/HOW_TO_SNAPSHOT b/lib/kokkos/HOW_TO_SNAPSHOT index 46bfb4167f9023a8273ebc872ac450c626603bf0..ad3f78efb4f8dd8399e3fb2889def7e841b531f9 100644 --- a/lib/kokkos/HOW_TO_SNAPSHOT +++ b/lib/kokkos/HOW_TO_SNAPSHOT @@ -19,7 +19,7 @@ snapshot Kokkos from github.com/kokkos to Trilinos. 3) Snapshot the current commit in the Kokkos clone into the Trilinos clone. This overwrites ${TRILINOS}/packages/kokkos with the content of ${KOKKOS}: - ${KOKKOS}/config/snapshot.py --verbose ${KOKKOS} ${TRILINOS}/packages + ${KOKKOS}/scripts/snapshot.py --verbose ${KOKKOS} ${TRILINOS}/packages 4) Verify the snapshot commit happened as expected cd ${TRILINOS}/packages/kokkos diff --git a/lib/kokkos/LICENSE b/lib/kokkos/LICENSE index 7341a699d6fc52c7863e7a4dbaab7ad892da4fd5..c68a8a2a9f98983e6bb7e02aaae0ce705a241ffc 100644 --- a/lib/kokkos/LICENSE +++ b/lib/kokkos/LICENSE @@ -36,7 +36,7 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER diff --git a/lib/kokkos/Makefile.kokkos b/lib/kokkos/Makefile.kokkos index 4315b009d5d2eb636079002dbcaed66afbf029ca..a7bb63f190348405267c3ea50e0f55dcf20645a3 100644 --- a/lib/kokkos/Makefile.kokkos +++ b/lib/kokkos/Makefile.kokkos @@ -9,8 +9,8 @@ KOKKOS_DEVICES ?= "OpenMP" #KOKKOS_DEVICES ?= "Pthreads" # Options: # Intel: KNC,KNL,SNB,HSW,BDW,SKX -# NVIDIA: Kepler,Kepler30,Kepler32,Kepler35,Kepler37,Maxwell,Maxwell50,Maxwell52,Maxwell53,Pascal60,Pascal61 -# ARM: ARMv80,ARMv81,ARMv8-ThunderX +# NVIDIA: Kepler,Kepler30,Kepler32,Kepler35,Kepler37,Maxwell,Maxwell50,Maxwell52,Maxwell53,Pascal60,Pascal61,Volta70,Volta72 +# ARM: ARMv80,ARMv81,ARMv8-ThunderX,ARMv8-TX2 # IBM: BGQ,Power7,Power8,Power9 # AMD-GPUS: Kaveri,Carrizo,Fiji,Vega # AMD-CPUS: AMDAVX,Ryzen,Epyc @@ -21,7 +21,7 @@ KOKKOS_DEBUG ?= "no" KOKKOS_USE_TPLS ?= "" # Options: c++11,c++1z KOKKOS_CXX_STANDARD ?= "c++11" -# Options: aggressive_vectorization,disable_profiling +# Options: aggressive_vectorization,disable_profiling,disable_deprecated_code KOKKOS_OPTIONS ?= "" # Default settings specific options. @@ -48,6 +48,7 @@ KOKKOS_INTERNAL_USE_MEMKIND := $(call kokkos_has_string,$(KOKKOS_USE_TPLS),exper KOKKOS_INTERNAL_ENABLE_COMPILER_WARNINGS := $(call kokkos_has_string,$(KOKKOS_OPTIONS),compiler_warnings) KOKKOS_INTERNAL_OPT_RANGE_AGGRESSIVE_VECTORIZATION := $(call kokkos_has_string,$(KOKKOS_OPTIONS),aggressive_vectorization) KOKKOS_INTERNAL_DISABLE_PROFILING := $(call kokkos_has_string,$(KOKKOS_OPTIONS),disable_profiling) +KOKKOS_INTERNAL_DISABLE_DEPRECATED_CODE := $(call kokkos_has_string,$(KOKKOS_OPTIONS),disable_deprecated_code) KOKKOS_INTERNAL_DISABLE_DUALVIEW_MODIFY_CHECK := $(call kokkos_has_string,$(KOKKOS_OPTIONS),disable_dualview_modify_check) KOKKOS_INTERNAL_ENABLE_PROFILING_LOAD_PRINT := $(call kokkos_has_string,$(KOKKOS_OPTIONS),enable_profile_load_print) KOKKOS_INTERNAL_CUDA_USE_LDG := $(call kokkos_has_string,$(KOKKOS_CUDA_OPTIONS),use_ldg) @@ -93,7 +94,7 @@ KOKKOS_INTERNAL_COMPILER_INTEL := $(call kokkos_has_string,$(KOKKOS_CXX_VE KOKKOS_INTERNAL_COMPILER_PGI := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),PGI) KOKKOS_INTERNAL_COMPILER_XL := $(strip $(shell $(CXX) -qversion 2>&1 | grep XL | wc -l)) KOKKOS_INTERNAL_COMPILER_CRAY := $(strip $(shell $(CXX) -craype-verbose 2>&1 | grep "CC-" | wc -l)) -KOKKOS_INTERNAL_COMPILER_NVCC := $(strip $(shell export OMPI_CXX=$(OMPI_CXX); export MPICH_CXX=$(MPICH_CXX); $(CXX) --version 2>&1 | grep nvcc | wc -l)) +KOKKOS_INTERNAL_COMPILER_NVCC := $(strip $(shell export OMPI_CXX=$(OMPI_CXX); export MPICH_CXX=$(MPICH_CXX); $(CXX) --version 2>&1 | grep nvcc | wc -l)) KOKKOS_INTERNAL_COMPILER_CLANG := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),clang) KOKKOS_INTERNAL_COMPILER_APPLE_CLANG := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),apple-darwin) KOKKOS_INTERNAL_COMPILER_HCC := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),HCC) @@ -229,12 +230,16 @@ KOKKOS_INTERNAL_USE_ARCH_MAXWELL52 := $(call kokkos_has_string,$(KOKKOS_ARCH),Ma KOKKOS_INTERNAL_USE_ARCH_MAXWELL53 := $(call kokkos_has_string,$(KOKKOS_ARCH),Maxwell53) KOKKOS_INTERNAL_USE_ARCH_PASCAL61 := $(call kokkos_has_string,$(KOKKOS_ARCH),Pascal61) KOKKOS_INTERNAL_USE_ARCH_PASCAL60 := $(call kokkos_has_string,$(KOKKOS_ARCH),Pascal60) +KOKKOS_INTERNAL_USE_ARCH_VOLTA70 := $(call kokkos_has_string,$(KOKKOS_ARCH),Volta70) +KOKKOS_INTERNAL_USE_ARCH_VOLTA72 := $(call kokkos_has_string,$(KOKKOS_ARCH),Volta72) KOKKOS_INTERNAL_USE_ARCH_NVIDIA := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_KEPLER30) \ + $(KOKKOS_INTERNAL_USE_ARCH_KEPLER32) \ + $(KOKKOS_INTERNAL_USE_ARCH_KEPLER35) \ + $(KOKKOS_INTERNAL_USE_ARCH_KEPLER37) \ + $(KOKKOS_INTERNAL_USE_ARCH_PASCAL61) \ + $(KOKKOS_INTERNAL_USE_ARCH_PASCAL60) \ + + $(KOKKOS_INTERNAL_USE_ARCH_VOLTA70) \ + + $(KOKKOS_INTERNAL_USE_ARCH_VOLTA72) \ + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL50) \ + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL52) \ + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL53)) @@ -249,6 +254,8 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_NVIDIA), 0) + $(KOKKOS_INTERNAL_USE_ARCH_KEPLER37) \ + $(KOKKOS_INTERNAL_USE_ARCH_PASCAL61) \ + $(KOKKOS_INTERNAL_USE_ARCH_PASCAL60) \ + + $(KOKKOS_INTERNAL_USE_ARCH_VOLTA70) \ + + $(KOKKOS_INTERNAL_USE_ARCH_VOLTA72) \ + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL50) \ + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL52) \ + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL53)) @@ -267,7 +274,8 @@ endif KOKKOS_INTERNAL_USE_ARCH_ARMV80 := $(call kokkos_has_string,$(KOKKOS_ARCH),ARMv80) KOKKOS_INTERNAL_USE_ARCH_ARMV81 := $(call kokkos_has_string,$(KOKKOS_ARCH),ARMv81) KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX := $(call kokkos_has_string,$(KOKKOS_ARCH),ARMv8-ThunderX) -KOKKOS_INTERNAL_USE_ARCH_ARM := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_ARMV80)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV81)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX) | bc)) +KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX2 := $(call kokkos_has_string,$(KOKKOS_ARCH),ARMv8-TX2) +KOKKOS_INTERNAL_USE_ARCH_ARM := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_ARMV80)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV81)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX2) | bc)) # IBM based. KOKKOS_INTERNAL_USE_ARCH_BGQ := $(call kokkos_has_string,$(KOKKOS_ARCH),BGQ) @@ -316,6 +324,9 @@ endif # Generating the list of Flags. KOKKOS_CPPFLAGS = -I./ -I$(KOKKOS_PATH)/core/src -I$(KOKKOS_PATH)/containers/src -I$(KOKKOS_PATH)/algorithms/src +KOKKOS_TPL_INCLUDE_DIRS = +KOKKOS_TPL_LIBRARY_DIRS = +KOKKOS_TPL_LIBRARY_NAMES = KOKKOS_CXXFLAGS = ifeq ($(KOKKOS_INTERNAL_ENABLE_COMPILER_WARNINGS), 1) @@ -323,7 +334,9 @@ ifeq ($(KOKKOS_INTERNAL_ENABLE_COMPILER_WARNINGS), 1) endif KOKKOS_LIBS = -ldl +KOKKOS_TPL_LIBRARY_NAMES += dl KOKKOS_LDFLAGS = -L$(shell pwd) +KOKKOS_LINK_FLAGS = KOKKOS_SRC = KOKKOS_HEADERS = @@ -437,21 +450,32 @@ ifeq ($(KOKKOS_INTERNAL_ENABLE_PROFILING_LOAD_PRINT), 1) endif ifeq ($(KOKKOS_INTERNAL_USE_HWLOC), 1) - KOKKOS_CPPFLAGS += -I$(HWLOC_PATH)/include - KOKKOS_LDFLAGS += -L$(HWLOC_PATH)/lib + ifneq ($(HWLOC_PATH),) + KOKKOS_CPPFLAGS += -I$(HWLOC_PATH)/include + KOKKOS_LDFLAGS += -L$(HWLOC_PATH)/lib + KOKKOS_TPL_INCLUDE_DIRS += $(HWLOC_PATH)/include + KOKKOS_TPL_LIBRARY_DIRS += $(HWLOC_PATH)/lib + endif KOKKOS_LIBS += -lhwloc + KOKKOS_TPL_LIBRARY_NAMES += hwloc tmp := $(call kokkos_append_header,"\#define KOKKOS_HAVE_HWLOC") endif ifeq ($(KOKKOS_INTERNAL_USE_LIBRT), 1) tmp := $(call kokkos_append_header,"\#define KOKKOS_USE_LIBRT") KOKKOS_LIBS += -lrt + KOKKOS_TPL_LIBRARY_NAMES += rt endif ifeq ($(KOKKOS_INTERNAL_USE_MEMKIND), 1) - KOKKOS_CPPFLAGS += -I$(MEMKIND_PATH)/include - KOKKOS_LDFLAGS += -L$(MEMKIND_PATH)/lib + ifneq ($(MEMKIND_PATH),) + KOKKOS_CPPFLAGS += -I$(MEMKIND_PATH)/include + KOKKOS_LDFLAGS += -L$(MEMKIND_PATH)/lib + KOKKOS_TPL_INCLUDE_DIRS += $(MEMKIND_PATH)/include + KOKKOS_TPL_LIBRARY_DIRS += $(MEMKIND_PATH)/lib + endif KOKKOS_LIBS += -lmemkind -lnuma + KOKKOS_TPL_LIBRARY_NAMES += memkind numa tmp := $(call kokkos_append_header,"\#define KOKKOS_HAVE_HBWSPACE") endif @@ -459,6 +483,10 @@ ifeq ($(KOKKOS_INTERNAL_DISABLE_PROFILING), 0) tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_PROFILING") endif +ifeq ($(KOKKOS_INTERNAL_DISABLE_DEPRECATED_CODE), 0) + tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_DEPRECATED_CODE") +endif + tmp := $(call kokkos_append_header,"/* Optimization Settings */") ifeq ($(KOKKOS_INTERNAL_OPT_RANGE_AGGRESSIVE_VECTORIZATION), 1) @@ -560,6 +588,24 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX), 1) endif endif +ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX2), 1) + tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_ARMV81") + tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_ARMV8_THUNDERX2") + + ifeq ($(KOKKOS_INTERNAL_COMPILER_CRAY), 1) + KOKKOS_CXXFLAGS += + KOKKOS_LDFLAGS += + else + ifeq ($(KOKKOS_INTERNAL_COMPILER_PGI), 1) + KOKKOS_CXXFLAGS += + KOKKOS_LDFLAGS += + else + KOKKOS_CXXFLAGS += -mtune=thunderx2t99 -mcpu=thunderx2t99 + KOKKOS_LDFLAGS += -mtune=thunderx2t99 -mcpu=thunderx2t99 + endif + endif +endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_SSE42), 1) tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_SSE42") @@ -754,10 +800,11 @@ endif ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC), 1) KOKKOS_INTERNAL_CUDA_ARCH_FLAG=-arch - endif - ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) - KOKKOS_INTERNAL_CUDA_ARCH_FLAG=--cuda-gpu-arch - KOKKOS_CXXFLAGS += -x cuda + else ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) + KOKKOS_INTERNAL_CUDA_ARCH_FLAG=--cuda-gpu-arch + KOKKOS_CXXFLAGS += -x cuda + else + $(error Makefile.kokkos: CUDA is enabled but the compiler is neither NVCC nor Clang) endif ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KEPLER30), 1) @@ -805,6 +852,16 @@ ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_PASCAL61") KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_61 endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_VOLTA70), 1) + tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_VOLTA") + tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_VOLTA70") + KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_70 + endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_VOLTA72), 1) + tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_VOLTA") + tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_VOLTA72") + KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_72 + endif ifneq ($(KOKKOS_INTERNAL_USE_ARCH_NVIDIA), 0) KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG) @@ -850,6 +907,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_ROCM), 1) KOKKOS_CXXFLAGS += $(shell $(ROCM_HCC_PATH)/bin/hcc-config --cxxflags) KOKKOS_LDFLAGS += $(shell $(ROCM_HCC_PATH)/bin/hcc-config --ldflags) -lhc_am -lm + KOKKOS_TPL_LIBRARY_NAMES += hc_am m KOKKOS_LDFLAGS += $(KOKKOS_INTERNAL_ROCM_ARCH_FLAG) KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/core/src/ROCm/*.cpp) @@ -880,13 +938,17 @@ KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/containers/src/impl/*.cpp) ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/core/src/Cuda/*.cpp) KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/Cuda/*.hpp) - KOKKOS_CPPFLAGS += -I$(CUDA_PATH)/include - KOKKOS_LDFLAGS += -L$(CUDA_PATH)/lib64 - KOKKOS_LIBS += -lcudart -lcuda - - ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) - KOKKOS_CXXFLAGS += --cuda-path=$(CUDA_PATH) + ifneq ($(CUDA_PATH),) + KOKKOS_CPPFLAGS += -I$(CUDA_PATH)/include + KOKKOS_LDFLAGS += -L$(CUDA_PATH)/lib64 + KOKKOS_TPL_INCLUDE_DIRS += $(CUDA_PATH)/include + KOKKOS_TPL_LIBRARY_DIRS += $(CUDA_PATH)/lib64 + ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) + KOKKOS_CXXFLAGS += --cuda-path=$(CUDA_PATH) + endif endif + KOKKOS_LIBS += -lcudart -lcuda + KOKKOS_TPL_LIBRARY_NAMES += cudart cuda endif ifeq ($(KOKKOS_INTERNAL_USE_OPENMPTARGET), 1) @@ -911,20 +973,27 @@ ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1) endif KOKKOS_LDFLAGS += $(KOKKOS_INTERNAL_OPENMP_FLAG) + KOKKOS_LINK_FLAGS += $(KOKKOS_INTERNAL_OPENMP_FLAG) endif ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 1) KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/core/src/Threads/*.cpp) KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/Threads/*.hpp) KOKKOS_LIBS += -lpthread + KOKKOS_TPL_LIBRARY_NAMES += pthread endif ifeq ($(KOKKOS_INTERNAL_USE_QTHREADS), 1) KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/core/src/Qthreads/*.cpp) KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/Qthreads/*.hpp) - KOKKOS_CPPFLAGS += -I$(QTHREADS_PATH)/include - KOKKOS_LDFLAGS += -L$(QTHREADS_PATH)/lib + ifneq ($(QTHREADS_PATH),) + KOKKOS_CPPFLAGS += -I$(QTHREADS_PATH)/include + KOKKOS_LDFLAGS += -L$(QTHREADS_PATH)/lib + KOKKOS_TPL_INCLUDE_DIRS += $(QTHREADS_PATH)/include + KOKKOS_TPL_LIBRARY_DIRS += $(QTHREADS_PATH)/lib64 + endif KOKKOS_LIBS += -lqthread + KOKKOS_TPL_LIBRARY_NAMES += qthread endif # Explicitly set the GCC Toolchain for Clang. @@ -940,11 +1009,6 @@ ifneq ($(KOKKOS_INTERNAL_USE_MEMKIND), 1) KOKKOS_SRC := $(filter-out $(KOKKOS_PATH)/core/src/impl/Kokkos_HBWSpace.cpp,$(KOKKOS_SRC)) endif -# Don't include Kokkos_Profiling_Interface.cpp if not using profiling to avoid a link warning. -ifeq ($(KOKKOS_INTERNAL_DISABLE_PROFILING), 1) - KOKKOS_SRC := $(filter-out $(KOKKOS_PATH)/core/src/impl/Kokkos_Profiling_Interface.cpp,$(KOKKOS_SRC)) -endif - # Don't include Kokkos_Serial.cpp or Kokkos_Serial_Task.cpp if not using Serial # device to avoid a link warning. ifneq ($(KOKKOS_INTERNAL_USE_SERIAL), 1) diff --git a/lib/kokkos/README b/lib/kokkos/README index d6c66634dd3914fe0d5aeed52b3737588c2ae66d..31d134bf0add74cf9b36571a3649cf5724f48087 100644 --- a/lib/kokkos/README +++ b/lib/kokkos/README @@ -1,87 +1,101 @@ -Kokkos implements a programming model in C++ for writing performance portable +Kokkos Core implements a programming model in C++ for writing performance portable applications targeting all major HPC platforms. For that purpose it provides abstractions for both parallel execution of code and data management. Kokkos is designed to target complex node architectures with N-level memory hierarchies and multiple types of execution resources. It currently can use OpenMP, Pthreads and CUDA as backend programming models. -Kokkos is licensed under standard 3-clause BSD terms of use. For specifics -see the LICENSE file contained in the repository or distribution. +Kokkos Core is part of the Kokkos C++ Performance Portability Programming EcoSystem, +which also provides math kernels (https://github.com/kokkos/kokkos-kernels), as well as +profiling and debugging tools (https://github.com/kokkos/kokkos-tools). -The core developers of Kokkos are Carter Edwards and Christian Trott -at the Computer Science Research Institute of the Sandia National -Laboratories. +# Learning about Kokkos -The KokkosP interface and associated tools are developed by the Application -Performance Team and Kokkos core developers at Sandia National Laboratories. +A programming guide can be found on the Wiki, the API reference is under development. -To learn more about Kokkos consider watching one of our presentations: -GTC 2015: - http://on-demand.gputechconf.com/gtc/2015/video/S5166.html - http://on-demand.gputechconf.com/gtc/2015/presentation/S5166-H-Carter-Edwards.pdf +For questions find us on Slack: https://kokkosteam.slack.com or open a github issue. -A programming guide can be found under doc/Kokkos_PG.pdf. This is an initial version -and feedback is greatly appreciated. +For non-public questions send an email to +crtrott(at)sandia.gov A separate repository with extensive tutorial material can be found under https://github.com/kokkos/kokkos-tutorials. -If you have a patch to contribute please feel free to issue a pull request against -the develop branch. For major contributions it is better to contact us first -for guidance. - -For questions please send an email to -kokkos-users@software.sandia.gov +Furthermore, the 'example/tutorial' directory provides step by step tutorial +examples which explain many of the features of Kokkos. They work with +simple Makefiles. To build with g++ and OpenMP simply type 'make' +in the 'example/tutorial' directory. This will build all examples in the +subfolders. To change the build options refer to the Programming Guide +in the compilation section. -For non-public questions send an email to -hcedwar(at)sandia.gov and crtrott(at)sandia.gov - -============================================================================ -====Requirements============================================================ -============================================================================ - -Primary tested compilers on X86 are: - GCC 4.8.4 - GCC 4.9.3 - GCC 5.1.0 - GCC 5.3.0 - GCC 6.1.0 - Intel 15.0.2 - Intel 16.0.1 - Intel 17.1.043 - Intel 17.4.196 - Intel 18.0.128 - Clang 3.5.2 - Clang 3.6.1 - Clang 3.7.1 - Clang 3.8.1 - Clang 3.9.0 - Clang 4.0.0 - Clang 4.0.0 for CUDA (CUDA Toolkit 8.0.44) - PGI 17.10 - NVCC 7.0 for CUDA (with gcc 4.8.4) - NVCC 7.5 for CUDA (with gcc 4.8.4) - NVCC 8.0.44 for CUDA (with gcc 5.3.0) - -Primary tested compilers on Power 8 are: - GCC 5.4.0 (OpenMP,Serial) - IBM XL 13.1.5 (OpenMP, Serial) (There is a workaround in place to avoid a compiler bug) - NVCC 8.0.44 for CUDA (with gcc 5.4.0) - NVCC 9.0.103 for CUDA (with gcc 6.3.0) - -Primary tested compilers on Intel KNL are: - GCC 6.2.0 - Intel 16.4.258 (with gcc 4.7.2) - Intel 17.2.174 (with gcc 4.9.3) - Intel 18.0.128 (with gcc 4.9.3) - -Other compilers working: - X86: - Cygwin 2.1.0 64bit with gcc 4.9.3 - -Known non-working combinations: - Power8: - Pthreads backend +To learn more about Kokkos consider watching one of our presentations: +* GTC 2015: + - http://on-demand.gputechconf.com/gtc/2015/video/S5166.html + - http://on-demand.gputechconf.com/gtc/2015/presentation/S5166-H-Carter-Edwards.pdf + + +# Contributing to Kokkos + +We are open and try to encourage contributions from external developers. +To do so please first open an issue describing the contribution and then issue +a pull request against the develop branch. For larger features it may be good +to get guidance from the core development team first through the github issue. + +Note that Kokkos Core is licensed under standard 3-clause BSD terms of use. +Which means contributing to Kokkos allows anyone else to use your contributions +not just for public purposes but also for closed source commercial projects. +For specifics see the LICENSE file contained in the repository or distribution. + +# Requirements + +### Primary tested compilers on X86 are: + * GCC 4.8.4 + * GCC 4.9.3 + * GCC 5.1.0 + * GCC 5.3.0 + * GCC 6.1.0 + * Intel 15.0.2 + * Intel 16.0.1 + * Intel 17.1.043 + * Intel 17.4.196 + * Intel 18.0.128 + * Clang 3.6.1 + * Clang 3.7.1 + * Clang 3.8.1 + * Clang 3.9.0 + * Clang 4.0.0 + * Clang 4.0.0 for CUDA (CUDA Toolkit 8.0.44) + * Clang 6.0.0 for CUDA (CUDA Toolkit 9.1) + * PGI 17.10 + * NVCC 7.0 for CUDA (with gcc 4.8.4) + * NVCC 7.5 for CUDA (with gcc 4.8.4) + * NVCC 8.0.44 for CUDA (with gcc 5.3.0) + * NVCC 9.1 for CUDA (with gcc 6.1.0) + +### Primary tested compilers on Power 8 are: + * GCC 5.4.0 (OpenMP,Serial) + * IBM XL 13.1.6 (OpenMP, Serial) + * NVCC 8.0.44 for CUDA (with gcc 5.4.0) + * NVCC 9.0.103 for CUDA (with gcc 6.3.0 and XL 13.1.6) + +### Primary tested compilers on Intel KNL are: + * GCC 6.2.0 + * Intel 16.4.258 (with gcc 4.7.2) + * Intel 17.2.174 (with gcc 4.9.3) + * Intel 18.0.128 (with gcc 4.9.3) + +### Primary tested compilers on ARM + * GCC 6.1.0 + +### Other compilers working: + * X86: + - Cygwin 2.1.0 64bit with gcc 4.9.3 + +### Known non-working combinations: + * Power8: + - Pthreads backend + * ARM + - Pthreads backend Primary tested compiler are passing in release mode @@ -97,20 +111,7 @@ NVCC: -Wall -Wshadow -pedantic -Werror -Wsign-compare -Wtype-limits -Wuninitiali Other compilers are tested occasionally, in particular when pushing from develop to master branch, without -Werror and only for a select set of backends. -============================================================================ -====Getting started========================================================= -============================================================================ - -In the 'example/tutorial' directory you will find step by step tutorial -examples which explain many of the features of Kokkos. They work with -simple Makefiles. To build with g++ and OpenMP simply type 'make' -in the 'example/tutorial' directory. This will build all examples in the -subfolders. To change the build options refer to the Programming Guide -in the compilation section. - -============================================================================ -====Running Unit Tests====================================================== -============================================================================ +# Running Unit Tests To run the unit tests create a build directory and run the following commands @@ -121,30 +122,35 @@ make test Run KOKKOS_PATH/generate_makefile.bash --help for more detailed options such as changing the device type for which to build. -============================================================================ -====Install the library===================================================== -============================================================================ +# Installing the library To install Kokkos as a library create a build directory and run the following KOKKOS_PATH/generate_makefile.bash --prefix=INSTALL_PATH -make lib +make kokkoslib make install KOKKOS_PATH/generate_makefile.bash --help for more detailed options such as changing the device type for which to build. -============================================================================ -====CMakeFiles============================================================== -============================================================================ +Note that in many cases it is preferable to build Kokkos inline with an +application. The main reason is that you may otherwise need many different +configurations of Kokkos installed depending on the required compile time +features an application needs. For example there is only one default +execution space, which means you need different installations to have OpenMP +or Pthreads as the default space. Also for the CUDA backend there are certain +choices, such as allowing relocatable device code, which must be made at +installation time. Building Kokkos inline uses largely the same process +as compiling an application against an installed Kokkos library. See for +example benchmarks/bytes_and_flops/Makefile which can be used with an installed +library and for an inline build. -The CMake files contained in this repository require Tribits and are used -for integration with Trilinos. They do not currently support a standalone -CMake build. +### CMake -=========================================================================== -====Kokkos and CUDA UVM==================================================== -=========================================================================== +Kokkos supports being build as part of a CMake applications. An example can +be found in example/cmake_build. + +# Kokkos and CUDA UVM Kokkos does support UVM as a specific memory space called CudaUVMSpace. Allocations made with that space are accessible from host and device. @@ -154,25 +160,16 @@ In either case UVM comes with a number of restrictions: running. This will lead to segfaults. To avoid that you either need to call Kokkos::Cuda::fence() (or just Kokkos::fence()), after kernels, or you can set the environment variable CUDA_LAUNCH_BLOCKING=1. -Furthermore in multi socket multi GPU machines, UVM defaults to using -zero copy allocations for technical reasons related to using multiple +Furthermore in multi socket multi GPU machines without NVLINK, UVM defaults +to using zero copy allocations for technical reasons related to using multiple GPUs from the same process. If an executable doesn't do that (e.g. each MPI rank of an application uses a single GPU [can be the same GPU for multiple MPI ranks]) you can set CUDA_MANAGED_FORCE_DEVICE_ALLOC=1. This will enforce proper UVM allocations, but can lead to errors if more than a single GPU is used by a single process. -=========================================================================== -====Contributing=========================================================== -=========================================================================== - -Contributions to Kokkos are welcome. In order to do so, please open an issue -where a feature request or bug can be discussed. Then issue a pull request -with your contribution. Pull requests must be issued against the develop branch. -=========================================================================== -====Citing Kokkos========================================================== -=========================================================================== +# Citing Kokkos If you publish work which mentions Kokkos, please cite the following paper: diff --git a/lib/kokkos/algorithms/src/Kokkos_Random.hpp b/lib/kokkos/algorithms/src/Kokkos_Random.hpp index 3db9a145d7c9dc7ab1da3a1e6f034a2a0e7d929b..1c659e44a45e5cd1d972f441f956ce4e47de2d2e 100644 --- a/lib/kokkos/algorithms/src/Kokkos_Random.hpp +++ b/lib/kokkos/algorithms/src/Kokkos_Random.hpp @@ -35,7 +35,7 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER @@ -1530,7 +1530,7 @@ struct fill_random_functor_range{ typename RandomPool::generator_type gen = rand_pool.get_state(); for(IndexType j=0;j(a.dimension_0())) + if(idx(a.extent(0))) a(idx) = Rand::draw(gen,range); } rand_pool.free_state(gen); @@ -1555,8 +1555,8 @@ struct fill_random_functor_range{ typename RandomPool::generator_type gen = rand_pool.get_state(); for(IndexType j=0;j(a.dimension_0())) { - for(IndexType k=0;k(a.dimension_1());k++) + if(idx(a.extent(0))) { + for(IndexType k=0;k(a.extent(1));k++) a(idx,k) = Rand::draw(gen,range); } } @@ -1583,9 +1583,9 @@ struct fill_random_functor_range{ typename RandomPool::generator_type gen = rand_pool.get_state(); for(IndexType j=0;j(a.dimension_0())) { - for(IndexType k=0;k(a.dimension_1());k++) - for(IndexType l=0;l(a.dimension_2());l++) + if(idx(a.extent(0))) { + for(IndexType k=0;k(a.extent(1));k++) + for(IndexType l=0;l(a.extent(2));l++) a(idx,k,l) = Rand::draw(gen,range); } } @@ -1611,10 +1611,10 @@ struct fill_random_functor_range{ typename RandomPool::generator_type gen = rand_pool.get_state(); for(IndexType j=0;j(a.dimension_0())) { - for(IndexType k=0;k(a.dimension_1());k++) - for(IndexType l=0;l(a.dimension_2());l++) - for(IndexType m=0;m(a.dimension_3());m++) + if(idx(a.extent(0))) { + for(IndexType k=0;k(a.extent(1));k++) + for(IndexType l=0;l(a.extent(2));l++) + for(IndexType m=0;m(a.extent(3));m++) a(idx,k,l,m) = Rand::draw(gen,range); } } @@ -1640,11 +1640,11 @@ struct fill_random_functor_range{ typename RandomPool::generator_type gen = rand_pool.get_state(); for(IndexType j=0;j(a.dimension_0())) { - for(IndexType k=0;k(a.dimension_1());k++) - for(IndexType l=0;l(a.dimension_2());l++) - for(IndexType m=0;m(a.dimension_3());m++) - for(IndexType n=0;n(a.dimension_4());n++) + if(idx(a.extent(0))) { + for(IndexType k=0;k(a.extent(1));k++) + for(IndexType l=0;l(a.extent(2));l++) + for(IndexType m=0;m(a.extent(3));m++) + for(IndexType n=0;n(a.extent(4));n++) a(idx,k,l,m,n) = Rand::draw(gen,range); } } @@ -1670,12 +1670,12 @@ struct fill_random_functor_range{ typename RandomPool::generator_type gen = rand_pool.get_state(); for(IndexType j=0;j(a.dimension_0())) { - for(IndexType k=0;k(a.dimension_1());k++) - for(IndexType l=0;l(a.dimension_2());l++) - for(IndexType m=0;m(a.dimension_3());m++) - for(IndexType n=0;n(a.dimension_4());n++) - for(IndexType o=0;o(a.dimension_5());o++) + if(idx(a.extent(0))) { + for(IndexType k=0;k(a.extent(1));k++) + for(IndexType l=0;l(a.extent(2));l++) + for(IndexType m=0;m(a.extent(3));m++) + for(IndexType n=0;n(a.extent(4));n++) + for(IndexType o=0;o(a.extent(5));o++) a(idx,k,l,m,n,o) = Rand::draw(gen,range); } } @@ -1701,13 +1701,13 @@ struct fill_random_functor_range{ typename RandomPool::generator_type gen = rand_pool.get_state(); for(IndexType j=0;j(a.dimension_0())) { - for(IndexType k=0;k(a.dimension_1());k++) - for(IndexType l=0;l(a.dimension_2());l++) - for(IndexType m=0;m(a.dimension_3());m++) - for(IndexType n=0;n(a.dimension_4());n++) - for(IndexType o=0;o(a.dimension_5());o++) - for(IndexType p=0;p(a.dimension_6());p++) + if(idx(a.extent(0))) { + for(IndexType k=0;k(a.extent(1));k++) + for(IndexType l=0;l(a.extent(2));l++) + for(IndexType m=0;m(a.extent(3));m++) + for(IndexType n=0;n(a.extent(4));n++) + for(IndexType o=0;o(a.extent(5));o++) + for(IndexType p=0;p(a.extent(6));p++) a(idx,k,l,m,n,o,p) = Rand::draw(gen,range); } } @@ -1733,14 +1733,14 @@ struct fill_random_functor_range{ typename RandomPool::generator_type gen = rand_pool.get_state(); for(IndexType j=0;j(a.dimension_0())) { - for(IndexType k=0;k(a.dimension_1());k++) - for(IndexType l=0;l(a.dimension_2());l++) - for(IndexType m=0;m(a.dimension_3());m++) - for(IndexType n=0;n(a.dimension_4());n++) - for(IndexType o=0;o(a.dimension_5());o++) - for(IndexType p=0;p(a.dimension_6());p++) - for(IndexType q=0;q(a.dimension_7());q++) + if(idx(a.extent(0))) { + for(IndexType k=0;k(a.extent(1));k++) + for(IndexType l=0;l(a.extent(2));l++) + for(IndexType m=0;m(a.extent(3));m++) + for(IndexType n=0;n(a.extent(4));n++) + for(IndexType o=0;o(a.extent(5));o++) + for(IndexType p=0;p(a.extent(6));p++) + for(IndexType q=0;q(a.extent(7));q++) a(idx,k,l,m,n,o,p,q) = Rand::draw(gen,range); } } @@ -1765,7 +1765,7 @@ struct fill_random_functor_begin_end{ typename RandomPool::generator_type gen = rand_pool.get_state(); for(IndexType j=0;j(a.dimension_0())) + if(idx(a.extent(0))) a(idx) = Rand::draw(gen,begin,end); } rand_pool.free_state(gen); @@ -1790,8 +1790,8 @@ struct fill_random_functor_begin_end{ typename RandomPool::generator_type gen = rand_pool.get_state(); for(IndexType j=0;j(a.dimension_0())) { - for(IndexType k=0;k(a.dimension_1());k++) + if(idx(a.extent(0))) { + for(IndexType k=0;k(a.extent(1));k++) a(idx,k) = Rand::draw(gen,begin,end); } } @@ -1818,9 +1818,9 @@ struct fill_random_functor_begin_end{ typename RandomPool::generator_type gen = rand_pool.get_state(); for(IndexType j=0;j(a.dimension_0())) { - for(IndexType k=0;k(a.dimension_1());k++) - for(IndexType l=0;l(a.dimension_2());l++) + if(idx(a.extent(0))) { + for(IndexType k=0;k(a.extent(1));k++) + for(IndexType l=0;l(a.extent(2));l++) a(idx,k,l) = Rand::draw(gen,begin,end); } } @@ -1846,10 +1846,10 @@ struct fill_random_functor_begin_end{ typename RandomPool::generator_type gen = rand_pool.get_state(); for(IndexType j=0;j(a.dimension_0())) { - for(IndexType k=0;k(a.dimension_1());k++) - for(IndexType l=0;l(a.dimension_2());l++) - for(IndexType m=0;m(a.dimension_3());m++) + if(idx(a.extent(0))) { + for(IndexType k=0;k(a.extent(1));k++) + for(IndexType l=0;l(a.extent(2));l++) + for(IndexType m=0;m(a.extent(3));m++) a(idx,k,l,m) = Rand::draw(gen,begin,end); } } @@ -1875,11 +1875,11 @@ struct fill_random_functor_begin_end{ typename RandomPool::generator_type gen = rand_pool.get_state(); for(IndexType j=0;j(a.dimension_0())){ - for(IndexType l=0;l(a.dimension_1());l++) - for(IndexType m=0;m(a.dimension_2());m++) - for(IndexType n=0;n(a.dimension_3());n++) - for(IndexType o=0;o(a.dimension_4());o++) + if(idx(a.extent(0))){ + for(IndexType l=0;l(a.extent(1));l++) + for(IndexType m=0;m(a.extent(2));m++) + for(IndexType n=0;n(a.extent(3));n++) + for(IndexType o=0;o(a.extent(4));o++) a(idx,l,m,n,o) = Rand::draw(gen,begin,end); } } @@ -1905,12 +1905,12 @@ struct fill_random_functor_begin_end{ typename RandomPool::generator_type gen = rand_pool.get_state(); for(IndexType j=0;j(a.dimension_0())) { - for(IndexType k=0;k(a.dimension_1());k++) - for(IndexType l=0;l(a.dimension_2());l++) - for(IndexType m=0;m(a.dimension_3());m++) - for(IndexType n=0;n(a.dimension_4());n++) - for(IndexType o=0;o(a.dimension_5());o++) + if(idx(a.extent(0))) { + for(IndexType k=0;k(a.extent(1));k++) + for(IndexType l=0;l(a.extent(2));l++) + for(IndexType m=0;m(a.extent(3));m++) + for(IndexType n=0;n(a.extent(4));n++) + for(IndexType o=0;o(a.extent(5));o++) a(idx,k,l,m,n,o) = Rand::draw(gen,begin,end); } } @@ -1937,13 +1937,13 @@ struct fill_random_functor_begin_end{ typename RandomPool::generator_type gen = rand_pool.get_state(); for(IndexType j=0;j(a.dimension_0())) { - for(IndexType k=0;k(a.dimension_1());k++) - for(IndexType l=0;l(a.dimension_2());l++) - for(IndexType m=0;m(a.dimension_3());m++) - for(IndexType n=0;n(a.dimension_4());n++) - for(IndexType o=0;o(a.dimension_5());o++) - for(IndexType p=0;p(a.dimension_6());p++) + if(idx(a.extent(0))) { + for(IndexType k=0;k(a.extent(1));k++) + for(IndexType l=0;l(a.extent(2));l++) + for(IndexType m=0;m(a.extent(3));m++) + for(IndexType n=0;n(a.extent(4));n++) + for(IndexType o=0;o(a.extent(5));o++) + for(IndexType p=0;p(a.extent(6));p++) a(idx,k,l,m,n,o,p) = Rand::draw(gen,begin,end); } } @@ -1969,14 +1969,14 @@ struct fill_random_functor_begin_end{ typename RandomPool::generator_type gen = rand_pool.get_state(); for(IndexType j=0;j(a.dimension_0())) { - for(IndexType k=0;k(a.dimension_1());k++) - for(IndexType l=0;l(a.dimension_2());l++) - for(IndexType m=0;m(a.dimension_3());m++) - for(IndexType n=0;n(a.dimension_4());n++) - for(IndexType o=0;o(a.dimension_5());o++) - for(IndexType p=0;p(a.dimension_6());p++) - for(IndexType q=0;q(a.dimension_7());q++) + if(idx(a.extent(0))) { + for(IndexType k=0;k(a.extent(1));k++) + for(IndexType l=0;l(a.extent(2));l++) + for(IndexType m=0;m(a.extent(3));m++) + for(IndexType n=0;n(a.extent(4));n++) + for(IndexType o=0;o(a.extent(5));o++) + for(IndexType p=0;p(a.extent(6));p++) + for(IndexType q=0;q(a.extent(7));q++) a(idx,k,l,m,n,o,p,q) = Rand::draw(gen,begin,end); } } @@ -1988,14 +1988,14 @@ struct fill_random_functor_begin_end{ template void fill_random(ViewType a, RandomPool g, typename ViewType::const_value_type range) { - int64_t LDA = a.dimension_0(); + int64_t LDA = a.extent(0); if(LDA>0) parallel_for((LDA+127)/128,Impl::fill_random_functor_range(a,g,range)); } template void fill_random(ViewType a, RandomPool g, typename ViewType::const_value_type begin,typename ViewType::const_value_type end ) { - int64_t LDA = a.dimension_0(); + int64_t LDA = a.extent(0); if(LDA>0) parallel_for((LDA+127)/128,Impl::fill_random_functor_begin_end(a,g,begin,end)); } diff --git a/lib/kokkos/algorithms/src/Kokkos_Sort.hpp b/lib/kokkos/algorithms/src/Kokkos_Sort.hpp index 237de751fe4b30afa1abcf475ca8af8c52cea7ab..888476045b8ee4a424e668a5da71567c408af934 100644 --- a/lib/kokkos/algorithms/src/Kokkos_Sort.hpp +++ b/lib/kokkos/algorithms/src/Kokkos_Sort.hpp @@ -35,7 +35,7 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER @@ -120,7 +120,6 @@ public: KOKKOS_INLINE_FUNCTION void operator() (const int& i) const { - // printf("copy: dst(%i) src(%i)\n",i+dst_offset,i); copy_op::copy(dst_values,i+dst_offset,src_values,i); } }; @@ -151,20 +150,22 @@ public: DstViewType dst_values ; perm_view_type sort_order ; src_view_type src_values ; + int src_offset ; copy_permute_functor( DstViewType const & dst_values_ , PermuteViewType const & sort_order_ , SrcViewType const & src_values_ + , int const & src_offset_ ) : dst_values( dst_values_ ) , sort_order( sort_order_ ) , src_values( src_values_ ) + , src_offset( src_offset_ ) {} KOKKOS_INLINE_FUNCTION void operator() (const int& i) const { - // printf("copy_permute: dst(%i) src(%i)\n",i,sort_order(i)); - copy_op::copy(dst_values,i,src_values,sort_order(i)); + copy_op::copy(dst_values,i,src_values,src_offset+sort_order(i)); } }; @@ -259,19 +260,21 @@ public: // Create the permutation vector, the bin_offset array and the bin_count array. Can be called again if keys changed void create_permute_vector() { const size_t len = range_end - range_begin ; - Kokkos::parallel_for (Kokkos::RangePolicy (0,len),*this); - Kokkos::parallel_scan(Kokkos::RangePolicy (0,bin_op.max_bins()) ,*this); + Kokkos::parallel_for ("Kokkos::Sort::BinCount",Kokkos::RangePolicy (0,len),*this); + Kokkos::parallel_scan("Kokkos::Sort::BinOffset",Kokkos::RangePolicy (0,bin_op.max_bins()) ,*this); Kokkos::deep_copy(bin_count_atomic,0); - Kokkos::parallel_for (Kokkos::RangePolicy (0,len),*this); + Kokkos::parallel_for ("Kokkos::Sort::BinBinning",Kokkos::RangePolicy (0,len),*this); if(sort_within_bins) - Kokkos::parallel_for (Kokkos::RangePolicy(0,bin_op.max_bins()) ,*this); + Kokkos::parallel_for ("Kokkos::Sort::BinSort",Kokkos::RangePolicy(0,bin_op.max_bins()) ,*this); } - // Sort a view with respect ot the first dimension using the permutation array + // Sort a subset of a view with respect to the first dimension using the permutation array template - void sort( ValuesViewType const & values) + void sort( ValuesViewType const & values + , int values_range_begin + , int values_range_end) const { typedef Kokkos::View< typename ValuesViewType::data_type, @@ -280,6 +283,10 @@ public: scratch_view_type ; const size_t len = range_end - range_begin ; + const size_t values_len = values_range_end - values_range_begin ; + if (len != values_len) { + Kokkos::abort("BinSort::sort: values range length != permutation vector length"); + } scratch_view_type sorted_values("Scratch", @@ -297,19 +304,25 @@ public: , offset_type /* PermuteViewType */ , ValuesViewType /* SrcViewType */ > - functor( sorted_values , sort_order , values ); + functor( sorted_values , sort_order , values, values_range_begin - range_begin ); - parallel_for( Kokkos::RangePolicy(0,len),functor); + parallel_for("Kokkos::Sort::CopyPermute", Kokkos::RangePolicy(0,len),functor); } { copy_functor< ValuesViewType , scratch_view_type > functor( values , range_begin , sorted_values ); - parallel_for( Kokkos::RangePolicy(0,len),functor); + parallel_for("Kokkos::Sort::Copy", Kokkos::RangePolicy(0,len),functor); } } + template + void sort( ValuesViewType const & values ) const + { + this->sort( values, 0, /*values.extent(0)*/ range_end - range_begin ); + } + // Get the permutation vector KOKKOS_INLINE_FUNCTION offset_type get_permute_vector() const { return sort_order;} @@ -327,7 +340,7 @@ public: KOKKOS_INLINE_FUNCTION void operator() (const bin_count_tag& tag, const int& i) const { const int j = range_begin + i ; - bin_count_atomic(bin_op.bin(keys,j))++; + bin_count_atomic(bin_op.bin(keys, j))++; } KOKKOS_INLINE_FUNCTION @@ -512,7 +525,7 @@ void sort( ViewType const & view , bool const always_use_kokkos_sort = false) Kokkos::Experimental::MinMaxScalar result; Kokkos::Experimental::MinMax reducer(result); - parallel_reduce(Kokkos::RangePolicy(0,view.extent(0)), + parallel_reduce("Kokkos::Sort::FindExtent",Kokkos::RangePolicy(0,view.extent(0)), Impl::min_max_functor(view),reducer); if(result.min_val == result.max_val) return; BinSort bin_sort(view,CompType(view.extent(0)/2,result.min_val,result.max_val),true); @@ -532,7 +545,7 @@ void sort( ViewType view Kokkos::Experimental::MinMaxScalar result; Kokkos::Experimental::MinMax reducer(result); - parallel_reduce( range_policy( begin , end ) + parallel_reduce("Kokkos::Sort::FindExtent", range_policy( begin , end ) , Impl::min_max_functor(view),reducer ); if(result.min_val == result.max_val) return; @@ -541,8 +554,9 @@ void sort( ViewType view bin_sort(view,begin,end,CompType((end-begin)/2,result.min_val,result.max_val),true); bin_sort.create_permute_vector(); - bin_sort.sort(view); + bin_sort.sort(view,begin,end); } + } #endif diff --git a/lib/kokkos/algorithms/unit_tests/TestCuda.cpp b/lib/kokkos/algorithms/unit_tests/TestCuda.cpp index 710eeb8ada08065dc4f1af33c3f1ee616ceda241..86fdccd0e784e8bc56472782a87a31a050f468fe 100644 --- a/lib/kokkos/algorithms/unit_tests/TestCuda.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestCuda.cpp @@ -35,7 +35,7 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER @@ -61,14 +61,9 @@ class cuda : public ::testing::Test { protected: static void SetUpTestCase() { - std::cout << std::setprecision(5) << std::scientific; - Kokkos::HostSpace::execution_space::initialize(); - Kokkos::Cuda::initialize( Kokkos::Cuda::SelectDevice(0) ); } static void TearDownTestCase() { - Kokkos::Cuda::finalize(); - Kokkos::HostSpace::execution_space::finalize(); } }; diff --git a/lib/kokkos/algorithms/unit_tests/TestOpenMP.cpp b/lib/kokkos/algorithms/unit_tests/TestOpenMP.cpp index c2c118ce1a140e69f0c87ddd7c0fc46870b5f58c..c4ddde7b7f71995bb25655cbbb5270b671db7f3e 100644 --- a/lib/kokkos/algorithms/unit_tests/TestOpenMP.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestOpenMP.cpp @@ -35,7 +35,7 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER @@ -60,25 +60,10 @@ protected: static void SetUpTestCase() { std::cout << std::setprecision(5) << std::scientific; - - int threads_count = 0; - #pragma omp parallel - { - #pragma omp atomic - ++threads_count; - } - - if (threads_count > 3) { - threads_count /= 2; - } - - Kokkos::OpenMP::initialize( threads_count ); - Kokkos::OpenMP::print_configuration( std::cout ); } static void TearDownTestCase() { - Kokkos::OpenMP::finalize(); } }; diff --git a/lib/kokkos/algorithms/unit_tests/TestROCm.cpp b/lib/kokkos/algorithms/unit_tests/TestROCm.cpp index 720b377ed2fb29a74d241ea6c42b46e3b15b5541..15179509bbfc1fe1e193081c8387e237dfa2525c 100644 --- a/lib/kokkos/algorithms/unit_tests/TestROCm.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestROCm.cpp @@ -35,7 +35,7 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER @@ -62,13 +62,9 @@ protected: static void SetUpTestCase() { std::cout << std::setprecision(5) << std::scientific; - Kokkos::HostSpace::execution_space::initialize(); - Kokkos::Experimental::ROCm::initialize( Kokkos::Experimental::ROCm::SelectDevice(0) ); } static void TearDownTestCase() { - Kokkos::Experimental::ROCm::finalize(); - Kokkos::HostSpace::execution_space::finalize(); } }; diff --git a/lib/kokkos/algorithms/unit_tests/TestRandom.hpp b/lib/kokkos/algorithms/unit_tests/TestRandom.hpp index 2771f1793d76371afbab136b9d71641e93131a2b..73bd416f2aba49e311884096c31db295b41f1066 100644 --- a/lib/kokkos/algorithms/unit_tests/TestRandom.hpp +++ b/lib/kokkos/algorithms/unit_tests/TestRandom.hpp @@ -34,7 +34,7 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER diff --git a/lib/kokkos/algorithms/unit_tests/TestSerial.cpp b/lib/kokkos/algorithms/unit_tests/TestSerial.cpp index a1df93e07b51482408c861919968953674de4c2e..9cf998f7732628bf71e8bc8ea90fcf6e41a27f3d 100644 --- a/lib/kokkos/algorithms/unit_tests/TestSerial.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestSerial.cpp @@ -35,7 +35,7 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER @@ -62,13 +62,10 @@ class serial : public ::testing::Test { protected: static void SetUpTestCase() { - std::cout << std::setprecision (5) << std::scientific; - Kokkos::Serial::initialize (); } static void TearDownTestCase () { - Kokkos::Serial::finalize (); } }; diff --git a/lib/kokkos/algorithms/unit_tests/TestSort.hpp b/lib/kokkos/algorithms/unit_tests/TestSort.hpp index 2cb0b897127b1c5401504b27adc24e4abf395f3d..e0c646c199be04841fbf0354905231ec00abf322 100644 --- a/lib/kokkos/algorithms/unit_tests/TestSort.hpp +++ b/lib/kokkos/algorithms/unit_tests/TestSort.hpp @@ -34,7 +34,7 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER @@ -171,10 +171,10 @@ void test_3D_sort(unsigned int n) { double sum_after = 0.0; unsigned int sort_fails = 0; - Kokkos::parallel_reduce(keys.dimension_0(),sum3D(keys),sum_before); + Kokkos::parallel_reduce(keys.extent(0),sum3D(keys),sum_before); int bin_1d = 1; - while( bin_1d*bin_1d*bin_1d*4< (int) keys.dimension_0() ) bin_1d*=2; + while( bin_1d*bin_1d*bin_1d*4< (int) keys.extent(0) ) bin_1d*=2; int bin_max[3] = {bin_1d,bin_1d,bin_1d}; typename KeyViewType::value_type min[3] = {0,0,0}; typename KeyViewType::value_type max[3] = {100,100,100}; @@ -186,8 +186,8 @@ void test_3D_sort(unsigned int n) { Sorter.create_permute_vector(); Sorter.template sort< KeyViewType >(keys); - Kokkos::parallel_reduce(keys.dimension_0(),sum3D(keys),sum_after); - Kokkos::parallel_reduce(keys.dimension_0()-1,bin3d_is_sorted_struct(keys,bin_1d,min[0],max[0]),sort_fails); + Kokkos::parallel_reduce(keys.extent(0),sum3D(keys),sum_after); + Kokkos::parallel_reduce(keys.extent(0)-1,bin3d_is_sorted_struct(keys,bin_1d,min[0],max[0]),sort_fails); double ratio = sum_before/sum_after; double epsilon = 1e-10; @@ -205,24 +205,13 @@ void test_3D_sort(unsigned int n) { template void test_dynamic_view_sort(unsigned int n ) { - typedef typename ExecutionSpace::memory_space memory_space ; typedef Kokkos::Experimental::DynamicView KeyDynamicViewType; typedef Kokkos::View KeyViewType; const size_t upper_bound = 2 * n ; + const size_t min_chunk_size = 1024; - const size_t total_alloc_size = n * sizeof(KeyType) * 1.2 ; - const size_t superblock_size = std::min(total_alloc_size, size_t(1000000)); - - typename KeyDynamicViewType::memory_pool - pool( memory_space() - , n * sizeof(KeyType) * 1.2 - , 500 /* min block size in bytes */ - , 30000 /* max block size in bytes */ - , superblock_size - ); - - KeyDynamicViewType keys("Keys",pool,upper_bound); + KeyDynamicViewType keys("Keys", min_chunk_size, upper_bound); keys.resize_serial(n); @@ -230,13 +219,15 @@ void test_dynamic_view_sort(unsigned int n ) // Test sorting array with all numbers equal Kokkos::deep_copy(keys_view,KeyType(1)); - Kokkos::Experimental::deep_copy(keys,keys_view); + Kokkos::deep_copy(keys,keys_view); Kokkos::sort(keys, 0 /* begin */ , n /* end */ ); Kokkos::Random_XorShift64_Pool g(1931); Kokkos::fill_random(keys_view,g,Kokkos::Random_XorShift64_Pool::generator_type::MAX_URAND); - Kokkos::Experimental::deep_copy(keys,keys_view); + ExecutionSpace::fence(); + Kokkos::deep_copy(keys,keys_view); + //ExecutionSpace::fence(); double sum_before = 0.0; double sum_after = 0.0; @@ -246,7 +237,9 @@ void test_dynamic_view_sort(unsigned int n ) Kokkos::sort(keys, 0 /* begin */ , n /* end */ ); - Kokkos::Experimental::deep_copy( keys_view , keys ); + ExecutionSpace::fence(); // Need this fence to prevent BusError with Cuda + Kokkos::deep_copy( keys_view , keys ); + //ExecutionSpace::fence(); Kokkos::parallel_reduce(n,sum(keys_view),sum_after); Kokkos::parallel_reduce(n-1,is_sorted_struct(keys_view),sort_fails); @@ -269,6 +262,74 @@ void test_dynamic_view_sort(unsigned int n ) //---------------------------------------------------------------------------- +template +void test_issue_1160() +{ + Kokkos::View element_("element", 10); + Kokkos::View x_("x", 10); + Kokkos::View v_("y", 10); + + auto h_element = Kokkos::create_mirror_view(element_); + auto h_x = Kokkos::create_mirror_view(x_); + auto h_v = Kokkos::create_mirror_view(v_); + + h_element(0) = 9; + h_element(1) = 8; + h_element(2) = 7; + h_element(3) = 6; + h_element(4) = 5; + h_element(5) = 4; + h_element(6) = 3; + h_element(7) = 2; + h_element(8) = 1; + h_element(9) = 0; + + for (int i = 0; i < 10; ++i) { + h_v.access(i, 0) = h_x.access(i, 0) = double(h_element(i)); + } + Kokkos::deep_copy(element_, h_element); + Kokkos::deep_copy(x_, h_x); + Kokkos::deep_copy(v_, h_v); + + typedef decltype(element_) KeyViewType; + typedef Kokkos::BinOp1D< KeyViewType > BinOp; + + int begin = 3; + int end = 8; + auto max = h_element(begin); + auto min = h_element(end - 1); + BinOp binner(end - begin, min, max); + + Kokkos::BinSort Sorter(element_,begin,end,binner,false); + Sorter.create_permute_vector(); + Sorter.sort(element_,begin,end); + + Sorter.sort(x_,begin,end); + Sorter.sort(v_,begin,end); + + Kokkos::deep_copy(h_element, element_); + Kokkos::deep_copy(h_x, x_); + Kokkos::deep_copy(h_v, v_); + + ASSERT_EQ(h_element(0), 9); + ASSERT_EQ(h_element(1), 8); + ASSERT_EQ(h_element(2), 7); + ASSERT_EQ(h_element(3), 2); + ASSERT_EQ(h_element(4), 3); + ASSERT_EQ(h_element(5), 4); + ASSERT_EQ(h_element(6), 5); + ASSERT_EQ(h_element(7), 6); + ASSERT_EQ(h_element(8), 1); + ASSERT_EQ(h_element(9), 0); + + for (int i = 0; i < 10; ++i) { + ASSERT_EQ(h_element(i), int(h_x.access(i, 0))); + ASSERT_EQ(h_element(i), int(h_v.access(i, 0))); + } +} + +//---------------------------------------------------------------------------- + template void test_sort(unsigned int N) { @@ -278,6 +339,7 @@ void test_sort(unsigned int N) test_3D_sort(N); test_dynamic_view_sort(N*N); #endif + test_issue_1160(); } } diff --git a/lib/kokkos/algorithms/unit_tests/TestThreads.cpp b/lib/kokkos/algorithms/unit_tests/TestThreads.cpp index 08749779ff56a692cebad20fcf94815c5ff7b732..99cdb7da92a253d9469b956c27ee06f212421c0d 100644 --- a/lib/kokkos/algorithms/unit_tests/TestThreads.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestThreads.cpp @@ -35,7 +35,7 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER @@ -63,25 +63,10 @@ protected: static void SetUpTestCase() { std::cout << std::setprecision(5) << std::scientific; - - unsigned num_threads = 4; - - if (Kokkos::hwloc::available()) { - num_threads = Kokkos::hwloc::get_available_numa_count() - * Kokkos::hwloc::get_available_cores_per_numa() - // * Kokkos::hwloc::get_available_threads_per_core() - ; - - } - - std::cout << "Threads: " << num_threads << std::endl; - - Kokkos::Threads::initialize( num_threads ); } static void TearDownTestCase() { - Kokkos::Threads::finalize(); } }; diff --git a/lib/kokkos/algorithms/unit_tests/UnitTestMain.cpp b/lib/kokkos/algorithms/unit_tests/UnitTestMain.cpp index 9e75b580bc0f64b53c402764197e11d1774203d8..8feb08332fa4d976395edfaf59b8e8653484c0f2 100644 --- a/lib/kokkos/algorithms/unit_tests/UnitTestMain.cpp +++ b/lib/kokkos/algorithms/unit_tests/UnitTestMain.cpp @@ -35,16 +35,20 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER */ #include +#include int main(int argc, char *argv[]) { + Kokkos::initialize(argc,argv); ::testing::InitGoogleTest(&argc,argv); - return RUN_ALL_TESTS(); + int result = RUN_ALL_TESTS(); + Kokkos::finalize(); + return result; } diff --git a/lib/kokkos/benchmarks/atomic/Makefile b/lib/kokkos/benchmarks/atomic/Makefile index 41875ee5e49cc132ffa7879e2812ff80aefa49b4..64b43917de2eadf2f2f96419e83b74cee05265fa 100644 --- a/lib/kokkos/benchmarks/atomic/Makefile +++ b/lib/kokkos/benchmarks/atomic/Makefile @@ -10,7 +10,7 @@ default: build ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES))) -CXX = ${KOKKOS_PATH}/config/nvcc_wrapper +CXX = ${KOKKOS_PATH}/bin/nvcc_wrapper EXE = ${EXE_NAME}.cuda KOKKOS_CUDA_OPTIONS = "enable_lambda" else diff --git a/lib/kokkos/benchmarks/benchmark_suite/scripts/run_tests.bash b/lib/kokkos/benchmarks/benchmark_suite/scripts/run_tests.bash index 63aaca9e402df9de8691b3deaee6c26553043de5..9dded535e8bfe20677d302d8b4f8e2cca1bf02ea 100755 --- a/lib/kokkos/benchmarks/benchmark_suite/scripts/run_tests.bash +++ b/lib/kokkos/benchmarks/benchmark_suite/scripts/run_tests.bash @@ -3,7 +3,7 @@ # BytesAndFlops cd build/bytes_and_flops -USE_CUDA=`grep "_CUDA 1" KokkosCore_config.h | wc -l` +USE_CUDA=`grep "_CUDA" KokkosCore_config.h | wc -l` if [[ ${USE_CUDA} > 0 ]]; then BAF_EXE=bytes_and_flops.cuda @@ -41,4 +41,4 @@ cd ../.. echo "MiniFE: ${FE_PERF_1} ${FE_PERF_2}" PERF_RESULT=`echo "${BAF_PERF_1} ${BAF_PERF_2} ${MD_PERF_1} ${MD_PERF_2} ${FE_PERF_1} ${FE_PERF_2}" | awk '{print ($1+$2+$3+$4+$5+$6)/6}'` -echo "Total Result: " ${PERF_RESULT} \ No newline at end of file +echo "Total Result: " ${PERF_RESULT} diff --git a/lib/kokkos/benchmarks/bytes_and_flops/bench.hpp b/lib/kokkos/benchmarks/bytes_and_flops/bench.hpp index e3fe42a652dfaa963578052664a8df71e03afce1..59b4d50c441eb5d4c58c99c53eee7f9c6b9adbd1 100644 --- a/lib/kokkos/benchmarks/bytes_and_flops/bench.hpp +++ b/lib/kokkos/benchmarks/bytes_and_flops/bench.hpp @@ -35,7 +35,7 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER diff --git a/lib/kokkos/benchmarks/bytes_and_flops/bench_stride.hpp b/lib/kokkos/benchmarks/bytes_and_flops/bench_stride.hpp index b60ec849944b9415d4ad6e1cd3a627cafdc55854..6509c654e71b4fdfd5366e4699972d7d19fe7807 100644 --- a/lib/kokkos/benchmarks/bytes_and_flops/bench_stride.hpp +++ b/lib/kokkos/benchmarks/bytes_and_flops/bench_stride.hpp @@ -35,7 +35,7 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER diff --git a/lib/kokkos/benchmarks/bytes_and_flops/bench_unroll_stride.hpp b/lib/kokkos/benchmarks/bytes_and_flops/bench_unroll_stride.hpp index 0992c5b54b6277f99d728710a37182695d3a6f92..c6651da1e7cf2e6d1a233dc90e9adf1211decf69 100644 --- a/lib/kokkos/benchmarks/bytes_and_flops/bench_unroll_stride.hpp +++ b/lib/kokkos/benchmarks/bytes_and_flops/bench_unroll_stride.hpp @@ -35,7 +35,7 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER diff --git a/lib/kokkos/benchmarks/bytes_and_flops/main.cpp b/lib/kokkos/benchmarks/bytes_and_flops/main.cpp index 8db5ce0eb5e869c565ce8f3872baea5200e4beb4..4f46b38717df237f0d33c0ac101d105f41f3e9d8 100644 --- a/lib/kokkos/benchmarks/bytes_and_flops/main.cpp +++ b/lib/kokkos/benchmarks/bytes_and_flops/main.cpp @@ -35,7 +35,7 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER diff --git a/lib/kokkos/benchmarks/gather/gather.hpp b/lib/kokkos/benchmarks/gather/gather.hpp index 406bd28983bd696e12cb82aeea388f94b6e80047..bbbd65850f75c00a928383d3c6ae2f9af27d7d95 100644 --- a/lib/kokkos/benchmarks/gather/gather.hpp +++ b/lib/kokkos/benchmarks/gather/gather.hpp @@ -35,7 +35,7 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER diff --git a/lib/kokkos/benchmarks/gather/gather_unroll.hpp b/lib/kokkos/benchmarks/gather/gather_unroll.hpp index 1d01b26ca77f2b7e58f5a1cbd5bbe251c3d558d3..1d9c99adf9e9909a21be2899f60000713e0208a4 100644 --- a/lib/kokkos/benchmarks/gather/gather_unroll.hpp +++ b/lib/kokkos/benchmarks/gather/gather_unroll.hpp @@ -35,7 +35,7 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER diff --git a/lib/kokkos/benchmarks/gather/main.cpp b/lib/kokkos/benchmarks/gather/main.cpp index 88eb0493c1861595069ae518a7fab628a37ce150..ca5238e7fdb527e56080f5b76eb6fa7c9487fcd3 100644 --- a/lib/kokkos/benchmarks/gather/main.cpp +++ b/lib/kokkos/benchmarks/gather/main.cpp @@ -35,7 +35,7 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER diff --git a/lib/kokkos/benchmarks/policy_performance/main.cpp b/lib/kokkos/benchmarks/policy_performance/main.cpp index b0ed9bb512f599a60eaa235bb80de1f1df33c755..2f5395734afdcfce41cc43c9b2322de4615a74b1 100644 --- a/lib/kokkos/benchmarks/policy_performance/main.cpp +++ b/lib/kokkos/benchmarks/policy_performance/main.cpp @@ -35,7 +35,7 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER diff --git a/lib/kokkos/benchmarks/policy_performance/policy_perf_test.hpp b/lib/kokkos/benchmarks/policy_performance/policy_perf_test.hpp index 11576413e2dc5e81f719a2dcc8786a156fcaa7b5..1ab437928de761bed614efc8a22d8c4d38fcf38f 100644 --- a/lib/kokkos/benchmarks/policy_performance/policy_perf_test.hpp +++ b/lib/kokkos/benchmarks/policy_performance/policy_perf_test.hpp @@ -35,7 +35,7 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER diff --git a/lib/kokkos/cmake/Modules/FindHWLOC.cmake b/lib/kokkos/cmake/Modules/FindHWLOC.cmake index 273dcb5c8aac9dc7f442844ff48d0827488afe0c..60df8084d80815f79f0215c17b40f80db4c791c0 100644 --- a/lib/kokkos/cmake/Modules/FindHWLOC.cmake +++ b/lib/kokkos/cmake/Modules/FindHWLOC.cmake @@ -2,7 +2,7 @@ # FindHWLOC # ---------- # -# Try to find HWLOC. +# Try to find HWLOC, based on KOKKOS_HWLOC_DIR # # The following variables are defined: # @@ -10,8 +10,8 @@ # HWLOC_INCLUDE_DIR - HWLOC include directory # HWLOC_LIBRARIES - Libraries needed to use HWLOC -find_path(HWLOC_INCLUDE_DIR hwloc.h) -find_library(HWLOC_LIBRARIES hwloc) +find_path(HWLOC_INCLUDE_DIR hwloc.h PATHS "${KOKKOS_HWLOC_DIR}/include") +find_library(HWLOC_LIBRARIES hwloc PATHS "${KOKKOS_HWLOC_DIR}/lib") include(FindPackageHandleStandardArgs) find_package_handle_standard_args(HWLOC DEFAULT_MSG diff --git a/lib/kokkos/cmake/kokkos_build.cmake b/lib/kokkos/cmake/kokkos_build.cmake index f31680d6e28f24a33c941b5d4504d82321efe558..76d0655adb76753d09df3bbfd88ff6d98d7da013 100644 --- a/lib/kokkos/cmake/kokkos_build.cmake +++ b/lib/kokkos/cmake/kokkos_build.cmake @@ -1,7 +1,3 @@ -# kokkos_generated_settings.cmake includes the kokkos library itself in KOKKOS_LIBS -# which we do not want to use for the cmake builds so clean this up -string(REGEX REPLACE "-lkokkos" "" KOKKOS_LIBS ${KOKKOS_LIBS}) - ############################ Detect if submodule ############################### # # With thanks to StackOverflow: @@ -73,6 +69,19 @@ IF(KOKKOS_SEPARATE_LIBS) PUBLIC $<$:${KOKKOS_CXX_FLAGS}> ) + target_include_directories( + kokkoscore + PUBLIC + ${KOKKOS_TPL_INCLUDE_DIRS} + ) + + foreach(lib IN LISTS KOKKOS_TPL_LIBRARY_NAMES) + find_library(LIB_${lib} ${lib} PATHS ${KOKKOS_TPL_LIBRARY_DIRS}) + target_link_libraries(kokkoscore PUBLIC ${LIB_${lib}}) + endforeach() + + target_link_libraries(kokkoscore PUBLIC "${KOKKOS_LINK_FLAGS}") + # Install the kokkoscore library INSTALL (TARGETS kokkoscore EXPORT KokkosTargets @@ -81,12 +90,6 @@ IF(KOKKOS_SEPARATE_LIBS) RUNTIME DESTINATION ${CMAKE_INSTALL_PREFIX}/bin ) - TARGET_LINK_LIBRARIES( - kokkoscore - ${KOKKOS_LD_FLAGS} - ${KOKKOS_EXTRA_LIBS_LIST} - ) - # kokkoscontainers if (DEFINED KOKKOS_CONTAINERS_SRCS) ADD_LIBRARY( @@ -144,12 +147,19 @@ ELSE() PUBLIC $<$:${KOKKOS_CXX_FLAGS}> ) - TARGET_LINK_LIBRARIES( + target_include_directories( kokkos - ${KOKKOS_LD_FLAGS} - ${KOKKOS_EXTRA_LIBS_LIST} + PUBLIC + ${KOKKOS_TPL_INCLUDE_DIRS} ) + foreach(lib IN LISTS KOKKOS_TPL_LIBRARY_NAMES) + find_library(LIB_${lib} ${lib} PATHS ${KOKKOS_TPL_LIBRARY_DIRS}) + target_link_libraries(kokkos PUBLIC ${LIB_${lib}}) + endforeach() + + target_link_libraries(kokkos PUBLIC "${KOKKOS_LINK_FLAGS}") + # Install the kokkos library INSTALL (TARGETS kokkos EXPORT KokkosTargets diff --git a/lib/kokkos/cmake/kokkos_options.cmake b/lib/kokkos/cmake/kokkos_options.cmake index f17710a4ceba2b44b345dbd6a4de00d27a110fe2..25eb8e86ced2e549eefa1d1c0788ffc41654cbd8 100644 --- a/lib/kokkos/cmake/kokkos_options.cmake +++ b/lib/kokkos/cmake/kokkos_options.cmake @@ -25,11 +25,12 @@ list(APPEND KOKKOS_INTERNAL_ENABLE_OPTIONS_LIST Cuda_LDG_Intrinsic Debug Debug_DualView_Modify_Check - Debug_Bounds_Checkt + Debug_Bounds_Check Compiler_Warnings Profiling Profiling_Load_Print Aggressive_Vectorization + Deprecated_Code ) #------------------------------------------------------------------------------- @@ -263,7 +264,8 @@ set(KOKKOS_ENABLE_PROFILING ${KOKKOS_INTERNAL_ENABLE_PROFILING_DEFAULT} CACHE BO set_kokkos_default_default(PROFILING_LOAD_PRINT OFF) set(KOKKOS_ENABLE_PROFILING_LOAD_PRINT ${KOKKOS_INTERNAL_ENABLE_PROFILING_LOAD_PRINT_DEFAULT} CACHE BOOL "Enable profile load print.") - +set_kokkos_default_default(DEPRECATED_CODE ON) +set(KOKKOS_ENABLE_DEPRECATED_CODE ${KOKKOS_INTERNAL_ENABLE_DEPRECATED_CODE_DEFAULT} CACHE BOOL "Enable deprecated code.") #------------------------------------------------------------------------------- diff --git a/lib/kokkos/cmake/kokkos_settings.cmake b/lib/kokkos/cmake/kokkos_settings.cmake index 850a74a670ee8d90bc4095c205da8db4c6e9a665..579fab0c954c230d7690cda72a854d332d598be1 100644 --- a/lib/kokkos/cmake/kokkos_settings.cmake +++ b/lib/kokkos/cmake/kokkos_settings.cmake @@ -14,6 +14,13 @@ #------------------------------------------------------------------------------- # Ensure that KOKKOS_ARCH is in the ARCH_LIST +if (KOKKOS_ARCH MATCHES ",") + message("-- Detected a comma in: KOKKOS_ARCH=${KOKKOS_ARCH}") + message("-- Although we prefer KOKKOS_ARCH to be semicolon-delimited, we do allow") + message("-- comma-delimited values for compatibility with scripts (see github.com/trilinos/Trilinos/issues/2330)") + string(REPLACE "," ";" KOKKOS_ARCH "${KOKKOS_ARCH}") + message("-- Commas were changed to semicolons, now KOKKOS_ARCH=${KOKKOS_ARCH}") +endif() foreach(arch ${KOKKOS_ARCH}) list(FIND KOKKOS_ARCH_LIST ${arch} indx) if (indx EQUAL -1) @@ -23,14 +30,13 @@ foreach(arch ${KOKKOS_ARCH}) endforeach() # KOKKOS_SETTINGS uses KOKKOS_ARCH -string(REPLACE ";" "," KOKKOS_ARCH "${KOKKOS_ARCH}") -set(KOKKOS_ARCH ${KOKKOS_ARCH}) +string(REPLACE ";" "," KOKKOS_GMAKE_ARCH "${KOKKOS_ARCH}") # From Makefile.kokkos: Options: yes,no if(${KOKKOS_ENABLE_DEBUG}) - set(KOKKOS_DEBUG yes) + set(KOKKOS_GMAKE_DEBUG yes) else() - set(KOKKOS_DEBUG no) + set(KOKKOS_GMAKE_DEBUG no) endif() #------------------------------- KOKKOS_DEVICES -------------------------------- @@ -43,10 +49,10 @@ foreach(devopt ${KOKKOS_DEVICES_LIST}) endif () endforeach() # List needs to be comma-delmitted -string(REPLACE ";" "," KOKKOS_DEVICES "${KOKKOS_DEVICESl}") +string(REPLACE ";" "," KOKKOS_GMAKE_DEVICES "${KOKKOS_DEVICESl}") #------------------------------- KOKKOS_OPTIONS -------------------------------- -# From Makefile.kokkos: Options: aggressive_vectorization,disable_profiling +# From Makefile.kokkos: Options: aggressive_vectorization,disable_profiling,disable_deprecated_code #compiler_warnings, aggressive_vectorization, disable_profiling, disable_dualview_modify_check, enable_profile_load_print set(KOKKOS_OPTIONSl) @@ -57,7 +63,10 @@ if(${KOKKOS_ENABLE_AGGRESSIVE_VECTORIZATION}) list(APPEND KOKKOS_OPTIONSl aggressive_vectorization) endif() if(NOT ${KOKKOS_ENABLE_PROFILING}) - list(APPEND KOKKOS_OPTIONSl disable_vectorization) + list(APPEND KOKKOS_OPTIONSl disable_profiling) +endif() +if(NOT ${KOKKOS_ENABLE_DEPRECATED_CODE}) + list(APPEND KOKKOS_OPTIONSl disable_deprecated_code) endif() if(NOT ${KOKKOS_ENABLE_DEBUG_DUALVIEW_MODIFY_CHECK}) list(APPEND KOKKOS_OPTIONSl disable_dualview_modify_check) @@ -66,7 +75,7 @@ if(${KOKKOS_ENABLE_PROFILING_LOAD_PRINT}) list(APPEND KOKKOS_OPTIONSl enable_profile_load_print) endif() # List needs to be comma-delimitted -string(REPLACE ";" "," KOKKOS_OPTIONS "${KOKKOS_OPTIONSl}") +string(REPLACE ";" "," KOKKOS_GMAKE_OPTIONS "${KOKKOS_OPTIONSl}") #------------------------------- KOKKOS_USE_TPLS ------------------------------- @@ -78,19 +87,19 @@ foreach(tplopt ${KOKKOS_USE_TPLS_LIST}) endif () endforeach() # List needs to be comma-delimitted -string(REPLACE ";" "," KOKKOS_USE_TPLS "${KOKKOS_USE_TPLSl}") +string(REPLACE ";" "," KOKKOS_GMAKE_USE_TPLS "${KOKKOS_USE_TPLSl}") #------------------------------- KOKKOS_CUDA_OPTIONS --------------------------- # Construct the Makefile options -set(KOKKOS_CUDA_OPTIONS) +set(KOKKOS_CUDA_OPTIONSl) foreach(cudaopt ${KOKKOS_CUDA_OPTIONS_LIST}) if (${KOKKOS_ENABLE_CUDA_${cudaopt}}) list(APPEND KOKKOS_CUDA_OPTIONSl ${KOKKOS_INTERNAL_${cudaopt}}) endif () endforeach() # List needs to be comma-delmitted -string(REPLACE ";" "," KOKKOS_CUDA_OPTIONS "${KOKKOS_CUDA_OPTIONSl}") +string(REPLACE ";" "," KOKKOS_GMAKE_CUDA_OPTIONS "${KOKKOS_CUDA_OPTIONSl}") #------------------------------- PATH VARIABLES -------------------------------- # Want makefile to use same executables specified which means modifying @@ -100,10 +109,10 @@ string(REPLACE ";" "," KOKKOS_CUDA_OPTIONS "${KOKKOS_CUDA_OPTIONSl}") set(KOKKOS_INTERNAL_PATHS) set(addpathl) -foreach(kvar "CUDA;QTHREADS;${KOKKOS_USE_TPLS_LIST}") +foreach(kvar IN LISTS KOKKOS_USE_TPLS_LIST ITEMS CUDA QTHREADS) if(${KOKKOS_ENABLE_${kvar}}) if(DEFINED KOKKOS_${kvar}_DIR) - set(KOKKOS_INTERNAL_PATHS "${KOKKOS_INTERNAL_PATHS} ${kvar}_PATH=${KOKKOS_${kvar}_DIR}") + set(KOKKOS_INTERNAL_PATHS ${KOKKOS_INTERNAL_PATHS} "${kvar}_PATH=${KOKKOS_${kvar}_DIR}") if(IS_DIRECTORY ${KOKKOS_${kvar}_DIR}/bin) list(APPEND addpathl ${KOKKOS_${kvar}_DIR}/bin) endif() @@ -124,10 +133,9 @@ set(KOKKOS_SETTINGS ${KOKKOS_SETTINGS} KOKKOS_INSTALL_PATH=${CMAKE_INSTALL_PREFI # Form of KOKKOS_foo=$KOKKOS_foo foreach(kvar ARCH;DEVICES;DEBUG;OPTIONS;CUDA_OPTIONS;USE_TPLS) - set(KOKKOS_VAR KOKKOS_${kvar}) - if(DEFINED KOKKOS_${kvar}) - if (NOT "${${KOKKOS_VAR}}" STREQUAL "") - set(KOKKOS_SETTINGS ${KOKKOS_SETTINGS} ${KOKKOS_VAR}=${${KOKKOS_VAR}}) + if(DEFINED KOKKOS_GMAKE_${kvar}) + if (NOT "${KOKKOS_GMAKE_${kvar}}" STREQUAL "") + set(KOKKOS_SETTINGS ${KOKKOS_SETTINGS} KOKKOS_${kvar}=${KOKKOS_GMAKE_${kvar}}) endif() endif() endforeach() @@ -147,7 +155,7 @@ if (NOT "${KOKKOS_INTERNAL_PATHS}" STREQUAL "") set(KOKKOS_SETTINGS ${KOKKOS_SETTINGS} ${KOKKOS_INTERNAL_PATHS}) endif() if (NOT "${KOKKOS_INTERNAL_ADDTOPATH}" STREQUAL "") - set(KOKKOS_SETTINGS ${KOKKOS_SETTINGS} PATH=${KOKKOS_INTERNAL_ADDTOPATH}:\${PATH}) + set(KOKKOS_SETTINGS ${KOKKOS_SETTINGS} "PATH=\"${KOKKOS_INTERNAL_ADDTOPATH}:$ENV{PATH}\"") endif() # Final form that gets passed to make @@ -185,7 +193,7 @@ if(KOKKOS_CMAKE_VERBOSE) message(STATUS "") message(STATUS "Architectures:") - message(STATUS " ${KOKKOS_ARCH}") + message(STATUS " ${KOKKOS_GMAKE_ARCH}") message(STATUS "") message(STATUS "Enabled options") @@ -194,43 +202,14 @@ if(KOKKOS_CMAKE_VERBOSE) message(STATUS " KOKKOS_SEPARATE_LIBS") endif() - if(KOKKOS_ENABLE_HWLOC) - message(STATUS " KOKKOS_ENABLE_HWLOC") - endif() - - if(KOKKOS_ENABLE_MEMKIND) - message(STATUS " KOKKOS_ENABLE_MEMKIND") - endif() - - if(KOKKOS_ENABLE_DEBUG) - message(STATUS " KOKKOS_ENABLE_DEBUG") - endif() - - if(KOKKOS_ENABLE_PROFILING) - message(STATUS " KOKKOS_ENABLE_PROFILING") - endif() - - if(KOKKOS_ENABLE_AGGRESSIVE_VECTORIZATION) - message(STATUS " KOKKOS_ENABLE_AGGRESSIVE_VECTORIZATION") - endif() - - if(KOKKOS_ENABLE_CUDA) - if(KOKKOS_ENABLE_CUDA_LDG_INTRINSIC) - message(STATUS " KOKKOS_ENABLE_CUDA_LDG_INTRINSIC") - endif() - - if(KOKKOS_ENABLE_CUDA_UVM) - message(STATUS " KOKKOS_ENABLE_CUDA_UVM") - endif() - - if(KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE) - message(STATUS " KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE") - endif() - - if(KOKKOS_ENABLE_CUDA_LAMBDA) - message(STATUS " KOKKOS_ENABLE_CUDA_LAMBDA") + foreach(opt IN LISTS KOKKOS_INTERNAL_ENABLE_OPTIONS_LIST) + string(TOUPPER ${opt} OPT) + if (KOKKOS_ENABLE_${OPT}) + message(STATUS " KOKKOS_ENABLE_${OPT}") endif() + endforeach() + if(KOKKOS_ENABLE_CUDA) if(KOKKOS_CUDA_DIR) message(STATUS " KOKKOS_CUDA_DIR: ${KOKKOS_CUDA_DIR}") endif() diff --git a/lib/kokkos/cmake/tribits.cmake b/lib/kokkos/cmake/tribits.cmake index 321704a1c8db89631ddc33a641b8f3dbc2240ce6..1b5a7b2adb4572cf3b454af49ce7db13332fc7ce 100644 --- a/lib/kokkos/cmake/tribits.cmake +++ b/lib/kokkos/cmake/tribits.cmake @@ -3,7 +3,7 @@ INCLUDE(CTest) cmake_policy(SET CMP0054 NEW) -MESSAGE(WARNING "The project name is: ${PROJECT_NAME}") +MESSAGE(STATUS "The project name is: ${PROJECT_NAME}") IF(NOT DEFINED ${PROJECT_NAME}_ENABLE_OpenMP) SET(${PROJECT_NAME}_ENABLE_OpenMP OFF) @@ -84,9 +84,6 @@ ENDFUNCTION() MACRO(TRIBITS_ADD_TEST_DIRECTORIES) - message(STATUS "ProjectName: " ${PROJECT_NAME}) - message(STATUS "Tests: " ${${PROJECT_NAME}_ENABLE_TESTS}) - IF(${${PROJECT_NAME}_ENABLE_TESTS}) FOREACH(TEST_DIR ${ARGN}) ADD_SUBDIRECTORY(${TEST_DIR}) @@ -95,13 +92,11 @@ MACRO(TRIBITS_ADD_TEST_DIRECTORIES) ENDMACRO() MACRO(TRIBITS_ADD_EXAMPLE_DIRECTORIES) - IF(${PACKAGE_NAME}_ENABLE_EXAMPLES OR ${PARENT_PACKAGE_NAME}_ENABLE_EXAMPLES) FOREACH(EXAMPLE_DIR ${ARGN}) ADD_SUBDIRECTORY(${EXAMPLE_DIR}) ENDFOREACH() ENDIF() - ENDMACRO() diff --git a/lib/kokkos/config/configure_compton_cpu.sh b/lib/kokkos/config/configure_compton_cpu.sh deleted file mode 100644 index 17287fb8486977927e4ba29718c79a438378d0a4..0000000000000000000000000000000000000000 --- a/lib/kokkos/config/configure_compton_cpu.sh +++ /dev/null @@ -1,190 +0,0 @@ -#!/bin/sh -# -# Copy this script, put it outside the Trilinos source directory, and -# build there. -# -# Additional command-line arguments given to this script will be -# passed directly to CMake. -# - -# -# Force CMake to re-evaluate build options. -# -rm -rf CMake* Trilinos* packages Dart* Testing cmake_install.cmake MakeFile* - -#----------------------------------------------------------------------------- -# Incrementally construct cmake configure options: - -CMAKE_CONFIGURE="" - -#----------------------------------------------------------------------------- -# Location of Trilinos source tree: - -CMAKE_PROJECT_DIR="${HOME}/Trilinos" - -# Location for installation: - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_INSTALL_PREFIX=/home/projects/kokkos/host/`date +%F`" - -#----------------------------------------------------------------------------- -# General build options. -# Use a variable so options can be propagated to CUDA compiler. - -CMAKE_VERBOSE_MAKEFILE=OFF -CMAKE_BUILD_TYPE=RELEASE -# CMAKE_BUILD_TYPE=DEBUG - -#----------------------------------------------------------------------------- -# Build for CUDA architecture: - -CUDA_ARCH="" -# CUDA_ARCH="20" -# CUDA_ARCH="30" -# CUDA_ARCH="35" - -# Build with Intel compiler - -INTEL=ON - -# Build for MIC architecture: - -# INTEL_XEON_PHI=ON - -# Build with HWLOC at location: - -HWLOC_BASE_DIR="/home/projects/libraries/host/hwloc/1.6.2" - -# Location for MPI to use in examples: - -MPI_BASE_DIR="" - -#----------------------------------------------------------------------------- -# MPI configuation only used for examples: -# -# Must have the MPI_BASE_DIR so that the -# include path can be passed to the Cuda compiler - -if [ -n "${MPI_BASE_DIR}" ] ; -then - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_MPI:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D MPI_BASE_DIR:PATH=${MPI_BASE_DIR}" -else - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_MPI:BOOL=OFF" -fi - -#----------------------------------------------------------------------------- -# Pthread configuation: - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_Pthread:BOOL=ON" -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_Pthread:BOOL=OFF" - -#----------------------------------------------------------------------------- -# OpenMP configuation: - -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_OpenMP:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_OpenMP:BOOL=OFF" - -#----------------------------------------------------------------------------- -#----------------------------------------------------------------------------- -# Configure packages for kokkos-only: - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_ALL_PACKAGES:BOOL=OFF" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_EXAMPLES:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_TESTS:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosCore:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosContainers:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosExample:BOOL=ON" - -#----------------------------------------------------------------------------- -#----------------------------------------------------------------------------- -# Hardware locality cmake configuration: - -if [ -n "${HWLOC_BASE_DIR}" ] ; -then - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_HWLOC:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D HWLOC_INCLUDE_DIRS:FILEPATH=${HWLOC_BASE_DIR}/include" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D HWLOC_LIBRARY_DIRS:FILEPATH=${HWLOC_BASE_DIR}/lib" -fi - -#----------------------------------------------------------------------------- -# Cuda cmake configuration: - -if [ -n "${CUDA_ARCH}" ] ; -then - - # Options to CUDA_NVCC_FLAGS must be semi-colon delimited, - # this is different than the standard CMAKE_CXX_FLAGS syntax. - - CUDA_NVCC_FLAGS="-gencode;arch=compute_${CUDA_ARCH},code=sm_${CUDA_ARCH}" - CUDA_NVCC_FLAGS="${CUDA_NVCC_FLAGS};-Xcompiler;-Wall,-ansi" - - if [ "${CMAKE_BUILD_TYPE}" = "DEBUG" ] ; - then - CUDA_NVCC_FLAGS="${CUDA_NVCC_FLAGS};-g" - else - CUDA_NVCC_FLAGS="${CUDA_NVCC_FLAGS};-O3" - fi - - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_CUDA:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_CUSPARSE:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CUDA_VERBOSE_BUILD:BOOL=OFF" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CUDA_NVCC_FLAGS:STRING=${CUDA_NVCC_FLAGS}" - -fi - -#----------------------------------------------------------------------------- - -if [ "${INTEL}" = "ON" -o "${INTEL_XEON_PHI}" = "ON" ] ; -then - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_C_COMPILER=icc" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_COMPILER=icpc" -fi - -#----------------------------------------------------------------------------- - -# Cross-compile for Intel Xeon Phi: - -if [ "${INTEL_XEON_PHI}" = "ON" ] ; -then - - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_SYSTEM_NAME=Linux" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_FLAGS:STRING=-mmic" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_C_FLAGS:STRING=-mmic" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_Fortran_COMPILER:FILEPATH=ifort" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D BLAS_LIBRARY_DIRS:FILEPATH=${MKLROOT}/lib/mic" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D BLAS_LIBRARY_NAMES='mkl_intel_lp64;mkl_sequential;mkl_core;pthread;m'" - - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_CHECKED_STL:BOOL=OFF" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_WARNINGS_AS_ERRORS_FLAGS:STRING=''" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D BUILD_SHARED_LIBS:BOOL=OFF" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D DART_TESTING_TIMEOUT:STRING=600" - - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D LAPACK_LIBRARY_NAMES=''" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_LAPACK_LIBRARIES=''" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_BinUtils=OFF" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_Pthread_LIBRARIES=pthread" - - # Cannot cross-compile fortran compatibility checks on the MIC: - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_Fortran:BOOL=OFF" - - # Tell cmake the answers to compile-and-execute tests - # to prevent cmake from executing a cross-compiled program. - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D HAVE_GCC_ABI_DEMANGLE_EXITCODE=0" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D HAVE_TEUCHOS_BLASFLOAT_EXITCODE=0" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D LAPACK_SLAPY2_WORKS_EXITCODE=0" - -fi - -#----------------------------------------------------------------------------- - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_VERBOSE_MAKEFILE:BOOL=${CMAKE_VERBOSE_MAKEFILE}" - -#----------------------------------------------------------------------------- - -echo "cmake ${CMAKE_CONFIGURE} ${CMAKE_PROJECT_DIR}" - -cmake ${CMAKE_CONFIGURE} ${CMAKE_PROJECT_DIR} - -#----------------------------------------------------------------------------- - diff --git a/lib/kokkos/config/configure_compton_mic.sh b/lib/kokkos/config/configure_compton_mic.sh deleted file mode 100644 index 7f9aee13f957d503d7fa5a5b1c8ecf924a80e0d8..0000000000000000000000000000000000000000 --- a/lib/kokkos/config/configure_compton_mic.sh +++ /dev/null @@ -1,186 +0,0 @@ -#!/bin/sh -# -# Copy this script, put it outside the Trilinos source directory, and -# build there. -# -# Additional command-line arguments given to this script will be -# passed directly to CMake. -# - -# -# Force CMake to re-evaluate build options. -# -rm -rf CMake* Trilinos* packages Dart* Testing cmake_install.cmake MakeFile* - -#----------------------------------------------------------------------------- -# Incrementally construct cmake configure options: - -CMAKE_CONFIGURE="" - -#----------------------------------------------------------------------------- -# Location of Trilinos source tree: - -CMAKE_PROJECT_DIR="${HOME}/Trilinos" - -# Location for installation: - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_INSTALL_PREFIX=/home/projects/kokkos/mic/`date +%F`" - -#----------------------------------------------------------------------------- -# General build options. -# Use a variable so options can be propagated to CUDA compiler. - -CMAKE_VERBOSE_MAKEFILE=OFF -CMAKE_BUILD_TYPE=RELEASE -# CMAKE_BUILD_TYPE=DEBUG - -#----------------------------------------------------------------------------- -# Build for CUDA architecture: - -CUDA_ARCH="" -# CUDA_ARCH="20" -# CUDA_ARCH="30" -# CUDA_ARCH="35" - -# Build for MIC architecture: - -INTEL_XEON_PHI=ON - -# Build with HWLOC at location: - -HWLOC_BASE_DIR="/home/projects/libraries/mic/hwloc/1.6.2" - -# Location for MPI to use in examples: - -MPI_BASE_DIR="" - -#----------------------------------------------------------------------------- -# MPI configuation only used for examples: -# -# Must have the MPI_BASE_DIR so that the -# include path can be passed to the Cuda compiler - -if [ -n "${MPI_BASE_DIR}" ] ; -then - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_MPI:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D MPI_BASE_DIR:PATH=${MPI_BASE_DIR}" -else - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_MPI:BOOL=OFF" -fi - -#----------------------------------------------------------------------------- -# Pthread configuation: - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_Pthread:BOOL=ON" -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_Pthread:BOOL=OFF" - -#----------------------------------------------------------------------------- -# OpenMP configuation: - -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_OpenMP:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_OpenMP:BOOL=OFF" - -#----------------------------------------------------------------------------- -#----------------------------------------------------------------------------- -# Configure packages for kokkos-only: - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_ALL_PACKAGES:BOOL=OFF" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_EXAMPLES:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_TESTS:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosCore:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosContainers:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosExample:BOOL=ON" - -#----------------------------------------------------------------------------- -#----------------------------------------------------------------------------- -# Hardware locality cmake configuration: - -if [ -n "${HWLOC_BASE_DIR}" ] ; -then - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_HWLOC:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D HWLOC_INCLUDE_DIRS:FILEPATH=${HWLOC_BASE_DIR}/include" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D HWLOC_LIBRARY_DIRS:FILEPATH=${HWLOC_BASE_DIR}/lib" -fi - -#----------------------------------------------------------------------------- -# Cuda cmake configuration: - -if [ -n "${CUDA_ARCH}" ] ; -then - - # Options to CUDA_NVCC_FLAGS must be semi-colon delimited, - # this is different than the standard CMAKE_CXX_FLAGS syntax. - - CUDA_NVCC_FLAGS="-gencode;arch=compute_${CUDA_ARCH},code=sm_${CUDA_ARCH}" - CUDA_NVCC_FLAGS="${CUDA_NVCC_FLAGS};-Xcompiler;-Wall,-ansi" - - if [ "${CMAKE_BUILD_TYPE}" = "DEBUG" ] ; - then - CUDA_NVCC_FLAGS="${CUDA_NVCC_FLAGS};-g" - else - CUDA_NVCC_FLAGS="${CUDA_NVCC_FLAGS};-O3" - fi - - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_CUDA:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_CUSPARSE:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CUDA_VERBOSE_BUILD:BOOL=OFF" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CUDA_NVCC_FLAGS:STRING=${CUDA_NVCC_FLAGS}" - -fi - -#----------------------------------------------------------------------------- - -if [ "${INTEL}" = "ON" -o "${INTEL_XEON_PHI}" = "ON" ] ; -then - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_C_COMPILER=icc" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_COMPILER=icpc" -fi - -#----------------------------------------------------------------------------- - -# Cross-compile for Intel Xeon Phi: - -if [ "${INTEL_XEON_PHI}" = "ON" ] ; -then - - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_SYSTEM_NAME=Linux" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_FLAGS:STRING=-mmic" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_C_FLAGS:STRING=-mmic" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_Fortran_COMPILER:FILEPATH=ifort" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D BLAS_LIBRARY_DIRS:FILEPATH=${MKLROOT}/lib/mic" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D BLAS_LIBRARY_NAMES='mkl_intel_lp64;mkl_sequential;mkl_core;pthread;m'" - - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_CHECKED_STL:BOOL=OFF" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_WARNINGS_AS_ERRORS_FLAGS:STRING=''" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D BUILD_SHARED_LIBS:BOOL=OFF" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D DART_TESTING_TIMEOUT:STRING=600" - - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D LAPACK_LIBRARY_NAMES=''" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_LAPACK_LIBRARIES=''" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_BinUtils=OFF" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_Pthread_LIBRARIES=pthread" - - # Cannot cross-compile fortran compatibility checks on the MIC: - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_Fortran:BOOL=OFF" - - # Tell cmake the answers to compile-and-execute tests - # to prevent cmake from executing a cross-compiled program. - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D HAVE_GCC_ABI_DEMANGLE_EXITCODE=0" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D HAVE_TEUCHOS_BLASFLOAT_EXITCODE=0" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D LAPACK_SLAPY2_WORKS_EXITCODE=0" - -fi - -#----------------------------------------------------------------------------- - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_VERBOSE_MAKEFILE:BOOL=${CMAKE_VERBOSE_MAKEFILE}" - -#----------------------------------------------------------------------------- - -echo "cmake ${CMAKE_CONFIGURE} ${CMAKE_PROJECT_DIR}" - -cmake ${CMAKE_CONFIGURE} ${CMAKE_PROJECT_DIR} - -#----------------------------------------------------------------------------- - diff --git a/lib/kokkos/config/configure_kokkos.sh b/lib/kokkos/config/configure_kokkos.sh deleted file mode 100644 index 592e7f593639c617385b487183f8ea6111cbd732..0000000000000000000000000000000000000000 --- a/lib/kokkos/config/configure_kokkos.sh +++ /dev/null @@ -1,293 +0,0 @@ -#!/bin/sh -# -# Copy this script, put it outside the Trilinos source directory, and -# build there. -# -#----------------------------------------------------------------------------- -# General build options. -# Use a variable so options can be propagated to CUDA compiler. - -CMAKE_BUILD_TYPE=RELEASE -# CMAKE_BUILD_TYPE=DEBUG - -# Source and installation directories: - -TRILINOS_SOURCE_DIR=${HOME}/Trilinos -TRILINOS_INSTALL_DIR=${HOME}/TrilinosInstall/`date +%F` - -#----------------------------------------------------------------------------- - -USE_CUDA_ARCH= -USE_THREAD= -USE_OPENMP= -USE_INTEL= -USE_XEON_PHI= -HWLOC_BASE_DIR= -MPI_BASE_DIR= -BLAS_LIB_DIR= -LAPACK_LIB_DIR= - -if [ 1 ] ; then - # Platform 'kokkos-dev' with Cuda, OpenMP, hwloc, mpi, gnu - USE_CUDA_ARCH="35" - USE_OPENMP=ON - HWLOC_BASE_DIR="/home/projects/hwloc/1.7.1/host/gnu/4.4.7" - MPI_BASE_DIR="/home/projects/mvapich/2.0.0b/gnu/4.4.7" - BLAS_LIB_DIR="/home/projects/blas/host/gnu/lib" - LAPACK_LIB_DIR="/home/projects/lapack/host/gnu/lib" - -elif [ ] ; then - # Platform 'kokkos-dev' with Cuda, Threads, hwloc, mpi, gnu - USE_CUDA_ARCH="35" - USE_THREAD=ON - HWLOC_BASE_DIR="/home/projects/hwloc/1.7.1/host/gnu/4.4.7" - MPI_BASE_DIR="/home/projects/mvapich/2.0.0b/gnu/4.4.7" - BLAS_LIB_DIR="/home/projects/blas/host/gnu/lib" - LAPACK_LIB_DIR="/home/projects/lapack/host/gnu/lib" - -elif [ ] ; then - # Platform 'kokkos-dev' with Xeon Phi and hwloc - USE_OPENMP=ON - USE_INTEL=ON - USE_XEON_PHI=ON - HWLOC_BASE_DIR="/home/projects/hwloc/1.7.1/mic/intel/13.SP1.1.106" - -elif [ ] ; then - # Platform 'kokkos-nvidia' with Cuda, OpenMP, hwloc, mpi, gnu - USE_CUDA_ARCH="20" - USE_OPENMP=ON - HWLOC_BASE_DIR="/home/sems/common/hwloc/current" - MPI_BASE_DIR="/home/sems/common/openmpi/current" - -elif [ ] ; then - # Platform 'kokkos-nvidia' with Cuda, Threads, hwloc, mpi, gnu - USE_CUDA_ARCH="20" - USE_THREAD=ON - HWLOC_BASE_DIR="/home/sems/common/hwloc/current" - MPI_BASE_DIR="/home/sems/common/openmpi/current" - -fi - -#----------------------------------------------------------------------------- -# Incrementally construct cmake configure command line options: - -CMAKE_CONFIGURE="" -CMAKE_CXX_FLAGS="" - -#----------------------------------------------------------------------------- -# Configure for Kokkos subpackages and tests: - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_ALL_PACKAGES:BOOL=OFF" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_EXAMPLES:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_TESTS:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosCore:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosContainers:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_TpetraKernels:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosExample:BOOL=ON" - -#----------------------------------------------------------------------------- - -if [ 1 ] ; then - - # Configure for Tpetra/Kokkos: - - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D BLAS_LIBRARY_DIRS:FILEPATH=${BLAS_LIB_DIR}" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D LAPACK_LIBRARY_DIRS:FILEPATH=${LAPACK_LIB_DIR}" - - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_Tpetra:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_Kokkos:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_TpetraClassic:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_TeuchosKokkosCompat:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_TeuchosKokkosComm:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Tpetra_ENABLE_Kokkos_Refactor:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D KokkosClassic_DefaultNode:STRING=Kokkos::Compat::KokkosOpenMPWrapperNode" - - CMAKE_CXX_FLAGS="${CMAKE_CXX_FLAGS}-DKOKKOS_FAST_COMPILE" - - if [ -n "${USE_CUDA_ARCH}" ] ; then - - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_Cuda:BOOL=ON" - - fi - -fi - -if [ 1 ] ; then - - # Configure for Stokhos: - - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_Sacado:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_Stokhos:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Stokhos_ENABLE_Belos:BOOL=ON" - -fi - -if [ 1 ] ; then - - # Configure for TrilinosCouplings: - - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_TrilinosCouplings:BOOL=ON" - -fi - -#----------------------------------------------------------------------------- -#----------------------------------------------------------------------------- - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}" - -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_VERBOSE_MAKEFILE:BOOL=ON" - -if [ "${CMAKE_BUILD_TYPE}" == "DEBUG" ] ; -then - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_BOUNDS_CHECK:BOOL=ON" -fi - -#----------------------------------------------------------------------------- -# Location for installation: - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_INSTALL_PREFIX=${TRILINOS_INSTALL_DIR}" - -#----------------------------------------------------------------------------- -# MPI configuation only used for examples: -# -# Must have the MPI_BASE_DIR so that the -# include path can be passed to the Cuda compiler - -if [ -n "${MPI_BASE_DIR}" ] ; -then - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_MPI:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D MPI_BASE_DIR:PATH=${MPI_BASE_DIR}" -else - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_MPI:BOOL=OFF" -fi - -#----------------------------------------------------------------------------- -# Kokkos use pthread configuation: - -if [ "${USE_THREAD}" = "ON" ] ; -then - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_Pthread:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_Pthread:BOOL=ON" -else - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_Pthread:BOOL=OFF" -fi - -#----------------------------------------------------------------------------- -# Kokkos use OpenMP configuation: - -if [ "${USE_OPENMP}" = "ON" ] ; -then - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_OpenMP:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_OpenMP:BOOL=ON" -else - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_OpenMP:BOOL=OFF" -fi - -#----------------------------------------------------------------------------- -# Hardware locality configuration: - -if [ -n "${HWLOC_BASE_DIR}" ] ; -then - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_HWLOC:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D HWLOC_INCLUDE_DIRS:FILEPATH=${HWLOC_BASE_DIR}/include" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D HWLOC_LIBRARY_DIRS:FILEPATH=${HWLOC_BASE_DIR}/lib" -fi - -#----------------------------------------------------------------------------- -# Cuda cmake configuration: - -if [ -n "${USE_CUDA_ARCH}" ] ; -then - - # Options to CUDA_NVCC_FLAGS must be semi-colon delimited, - # this is different than the standard CMAKE_CXX_FLAGS syntax. - - CUDA_NVCC_FLAGS="-DKOKKOS_HAVE_CUDA_ARCH=${USE_CUDA_ARCH}0;-gencode;arch=compute_${USE_CUDA_ARCH},code=sm_${USE_CUDA_ARCH}" - - if [ "${USE_OPENMP}" = "ON" ] ; - then - CUDA_NVCC_FLAGS="${CUDA_NVCC_FLAGS};-Xcompiler;-Wall,-ansi,-fopenmp" - else - CUDA_NVCC_FLAGS="${CUDA_NVCC_FLAGS};-Xcompiler;-Wall,-ansi" - fi - - if [ "${CMAKE_BUILD_TYPE}" = "DEBUG" ] ; - then - CUDA_NVCC_FLAGS="${CUDA_NVCC_FLAGS};-g" - else - CUDA_NVCC_FLAGS="${CUDA_NVCC_FLAGS};-O3" - fi - - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_CUDA:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_CUSPARSE:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CUDA_VERBOSE_BUILD:BOOL=OFF" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CUDA_NVCC_FLAGS:STRING=${CUDA_NVCC_FLAGS}" - -fi - -#----------------------------------------------------------------------------- - -if [ "${USE_INTEL}" = "ON" -o "${USE_XEON_PHI}" = "ON" ] ; -then - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_C_COMPILER=icc" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_COMPILER=icpc" -fi - -# Cross-compile for Intel Xeon Phi: - -if [ "${USE_XEON_PHI}" = "ON" ] ; -then - - CMAKE_CXX_FLAGS="${CMAKE_CXX_FLAGS} -mmic" - - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_SYSTEM_NAME=Linux" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_C_FLAGS:STRING=-mmic" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_Fortran_COMPILER:FILEPATH=ifort" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D BLAS_LIBRARY_DIRS:FILEPATH=${MKLROOT}/lib/mic" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D BLAS_LIBRARY_NAMES='mkl_intel_lp64;mkl_sequential;mkl_core;pthread;m'" - - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_CHECKED_STL:BOOL=OFF" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_WARNINGS_AS_ERRORS_FLAGS:STRING=''" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D BUILD_SHARED_LIBS:BOOL=OFF" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D DART_TESTING_TIMEOUT:STRING=600" - - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D LAPACK_LIBRARY_NAMES=''" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_LAPACK_LIBRARIES=''" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_BinUtils=OFF" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_Pthread_LIBRARIES=pthread" - - # Cannot cross-compile fortran compatibility checks on the MIC: - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_Fortran:BOOL=OFF" - - # Tell cmake the answers to compile-and-execute tests - # to prevent cmake from executing a cross-compiled program. - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D HAVE_GCC_ABI_DEMANGLE_EXITCODE=0" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D HAVE_TEUCHOS_BLASFLOAT_EXITCODE=0" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D LAPACK_SLAPY2_WORKS_EXITCODE=0" - -fi - -#----------------------------------------------------------------------------- -#----------------------------------------------------------------------------- - -if [ -n "${CMAKE_CXX_FLAGS}" ] ; then - - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_FLAGS:STRING='${CMAKE_CXX_FLAGS}'" - -fi - -#----------------------------------------------------------------------------- -# -# Remove CMake output files to force reconfigure from scratch. -# - -rm -rf CMake* Trilinos* packages Dart* Testing cmake_install.cmake MakeFile* - -# - -echo "cmake ${CMAKE_CONFIGURE} ${TRILINOS_SOURCE_DIR}" - -cmake ${CMAKE_CONFIGURE} ${TRILINOS_SOURCE_DIR} - -#----------------------------------------------------------------------------- - diff --git a/lib/kokkos/config/configure_kokkos_bgq.sh b/lib/kokkos/config/configure_kokkos_bgq.sh deleted file mode 100755 index 73236937eaa9b311d06027a23aa070a8f62c9153..0000000000000000000000000000000000000000 --- a/lib/kokkos/config/configure_kokkos_bgq.sh +++ /dev/null @@ -1,88 +0,0 @@ -#!/bin/sh -# -# Copy this script, put it outside the Trilinos source directory, and -# build there. -# -# Additional command-line arguments given to this script will be -# passed directly to CMake. -# - -# to build: -# build on bgq-b[1-12] -# module load sierra-devel -# run this configure file -# make - -# to run: -# ssh bgq-login -# cd /scratch/username/... -# export OMP_PROC_BIND and XLSMPOPTS environment variables -# run with srun - -# Note: hwloc does not work to get or set cpubindings on bgq. -# Use the openmp backend and the openmp environment variables. -# -# Only the mpi wrappers seem to be setup for cross-compile, -# so it is important that this configure enables MPI and uses mpigcc wrappers. - - - -# -# Force CMake to re-evaluate build options. -# -rm -rf CMake* Trilinos* packages Dart* Testing cmake_install.cmake MakeFile* - -#----------------------------------------------------------------------------- -# Incrementally construct cmake configure options: - -CMAKE_CONFIGURE="" - -#----------------------------------------------------------------------------- -# Location of Trilinos source tree: - -CMAKE_PROJECT_DIR="../Trilinos" - -# Location for installation: - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_INSTALL_PREFIX=../TrilinosInstall/`date +%F`" - -#----------------------------------------------------------------------------- -# General build options. -# Use a variable so options can be propagated to CUDA compiler. - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_C_COMPILER=mpigcc-4.7.2" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_COMPILER=mpig++-4.7.2" - -CMAKE_VERBOSE_MAKEFILE=OFF -CMAKE_BUILD_TYPE=RELEASE -# CMAKE_BUILD_TYPE=DEBUG - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_MPI:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_OpenMP:BOOL=ON" - -#----------------------------------------------------------------------------- -#----------------------------------------------------------------------------- -# Configure packages for kokkos-only: - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_ALL_PACKAGES:BOOL=OFF" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_EXAMPLES:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_TESTS:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosCore:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosContainers:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_TpetraKernels:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosExample:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_Pthread:BOOL=OFF" - -#----------------------------------------------------------------------------- - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_VERBOSE_MAKEFILE:BOOL=${CMAKE_VERBOSE_MAKEFILE}" - -#----------------------------------------------------------------------------- - -echo "cmake ${CMAKE_CONFIGURE} ${CMAKE_PROJECT_DIR}" - -cmake ${CMAKE_CONFIGURE} ${CMAKE_PROJECT_DIR} - -#----------------------------------------------------------------------------- - diff --git a/lib/kokkos/config/configure_kokkos_dev.sh b/lib/kokkos/config/configure_kokkos_dev.sh deleted file mode 100755 index ac61dec602381b52d96f91a59c0eddbc2d6b5801..0000000000000000000000000000000000000000 --- a/lib/kokkos/config/configure_kokkos_dev.sh +++ /dev/null @@ -1,216 +0,0 @@ -#!/bin/sh -# -# Copy this script, put it outside the Trilinos source directory, and -# build there. -# -# Additional command-line arguments given to this script will be -# passed directly to CMake. -# - -# -# Force CMake to re-evaluate build options. -# -rm -rf CMake* Trilinos* packages Dart* Testing cmake_install.cmake MakeFile* - -#----------------------------------------------------------------------------- -# Incrementally construct cmake configure options: - -CMAKE_CONFIGURE="" - -#----------------------------------------------------------------------------- -# Location of Trilinos source tree: - -CMAKE_PROJECT_DIR="${HOME}/Trilinos" - -# Location for installation: - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_INSTALL_PREFIX=${HOME}/TrilinosInstall/`date +%F`" - -#----------------------------------------------------------------------------- -# General build options. -# Use a variable so options can be propagated to CUDA compiler. - -CMAKE_VERBOSE_MAKEFILE=OFF -CMAKE_BUILD_TYPE=RELEASE -#CMAKE_BUILD_TYPE=DEBUG -#CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_BOUNDS_CHECK:BOOL=ON" - -#----------------------------------------------------------------------------- -# Build for CUDA architecture: - -#CUDA_ARCH="" -#CUDA_ARCH="20" -#CUDA_ARCH="30" -CUDA_ARCH="35" - -# Build with OpenMP - -OPENMP=ON -PTHREADS=ON - -# Build host code with Intel compiler: - -INTEL=OFF - -# Build for MIC architecture: - -INTEL_XEON_PHI=OFF - -# Build with HWLOC at location: - -#HWLOC_BASE_DIR="" -#HWLOC_BASE_DIR="/home/projects/hwloc/1.7.1/host/gnu/4.4.7" -HWLOC_BASE_DIR="/home/projects/hwloc/1.7.1/host/gnu/4.7.3" - -# Location for MPI to use in examples: - -#MPI_BASE_DIR="" -#MPI_BASE_DIR="/home/projects/mvapich/2.0.0b/gnu/4.4.7" -MPI_BASE_DIR="/home/projects/mvapich/2.0.0b/gnu/4.7.3" -#MPI_BASE_DIR="/home/projects/openmpi/1.7.3/llvm/2013-12-02/" - -#----------------------------------------------------------------------------- -# MPI configuation only used for examples: -# -# Must have the MPI_BASE_DIR so that the -# include path can be passed to the Cuda compiler - -if [ -n "${MPI_BASE_DIR}" ] ; -then - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_MPI:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D MPI_BASE_DIR:PATH=${MPI_BASE_DIR}" -else - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_MPI:BOOL=OFF" -fi - -#----------------------------------------------------------------------------- -# Pthread configuation: - -if [ "${PTHREADS}" = "ON" ] ; -then - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_Pthread:BOOL=ON" -else - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_Pthread:BOOL=OFF" -fi - -#----------------------------------------------------------------------------- -# OpenMP configuation: - -if [ "${OPENMP}" = "ON" ] ; -then - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_OpenMP:BOOL=ON" -else - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_OpenMP:BOOL=OFF" -fi - -#----------------------------------------------------------------------------- -#----------------------------------------------------------------------------- -# Configure packages for kokkos-only: - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_ALL_PACKAGES:BOOL=OFF" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_EXAMPLES:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_TESTS:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosCore:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosContainers:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_TpetraKernels:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosExample:BOOL=ON" - -#----------------------------------------------------------------------------- -#----------------------------------------------------------------------------- -# Hardware locality cmake configuration: - -if [ -n "${HWLOC_BASE_DIR}" ] ; -then - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_HWLOC:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D HWLOC_INCLUDE_DIRS:FILEPATH=${HWLOC_BASE_DIR}/include" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D HWLOC_LIBRARY_DIRS:FILEPATH=${HWLOC_BASE_DIR}/lib" -fi - -#----------------------------------------------------------------------------- -# Cuda cmake configuration: - -if [ -n "${CUDA_ARCH}" ] ; -then - - # Options to CUDA_NVCC_FLAGS must be semi-colon delimited, - # this is different than the standard CMAKE_CXX_FLAGS syntax. - - CUDA_NVCC_FLAGS="-gencode;arch=compute_${CUDA_ARCH},code=sm_${CUDA_ARCH}" - - if [ "${OPENMP}" = "ON" ] ; - then - CUDA_NVCC_FLAGS="${CUDA_NVCC_FLAGS};-Xcompiler;-Wall,-ansi,-fopenmp" - else - CUDA_NVCC_FLAGS="${CUDA_NVCC_FLAGS};-Xcompiler;-Wall,-ansi" - fi - - if [ "${CMAKE_BUILD_TYPE}" = "DEBUG" ] ; - then - CUDA_NVCC_FLAGS="${CUDA_NVCC_FLAGS};-g" - else - CUDA_NVCC_FLAGS="${CUDA_NVCC_FLAGS};-O3" - fi - - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_CUDA:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_CUSPARSE:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CUDA_VERBOSE_BUILD:BOOL=OFF" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CUDA_NVCC_FLAGS:STRING=${CUDA_NVCC_FLAGS}" - -fi - -#----------------------------------------------------------------------------- - -if [ "${INTEL}" = "ON" -o "${INTEL_XEON_PHI}" = "ON" ] ; -then - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_C_COMPILER=icc" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_COMPILER=icpc" -fi - -#----------------------------------------------------------------------------- - -# Cross-compile for Intel Xeon Phi: - -if [ "${INTEL_XEON_PHI}" = "ON" ] ; -then - - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_SYSTEM_NAME=Linux" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_FLAGS:STRING=-mmic" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_C_FLAGS:STRING=-mmic" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_Fortran_COMPILER:FILEPATH=ifort" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D BLAS_LIBRARY_DIRS:FILEPATH=${MKLROOT}/lib/mic" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D BLAS_LIBRARY_NAMES='mkl_intel_lp64;mkl_sequential;mkl_core;pthread;m'" - - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_CHECKED_STL:BOOL=OFF" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_WARNINGS_AS_ERRORS_FLAGS:STRING=''" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D BUILD_SHARED_LIBS:BOOL=OFF" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D DART_TESTING_TIMEOUT:STRING=600" - - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D LAPACK_LIBRARY_NAMES=''" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_LAPACK_LIBRARIES=''" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_BinUtils=OFF" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_Pthread_LIBRARIES=pthread" - - # Cannot cross-compile fortran compatibility checks on the MIC: - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_Fortran:BOOL=OFF" - - # Tell cmake the answers to compile-and-execute tests - # to prevent cmake from executing a cross-compiled program. - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D HAVE_GCC_ABI_DEMANGLE_EXITCODE=0" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D HAVE_TEUCHOS_BLASFLOAT_EXITCODE=0" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D LAPACK_SLAPY2_WORKS_EXITCODE=0" - -fi - -#----------------------------------------------------------------------------- - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_VERBOSE_MAKEFILE:BOOL=${CMAKE_VERBOSE_MAKEFILE}" - -#----------------------------------------------------------------------------- - -echo "cmake ${CMAKE_CONFIGURE} ${CMAKE_PROJECT_DIR}" - -cmake ${CMAKE_CONFIGURE} ${CMAKE_PROJECT_DIR} - -#----------------------------------------------------------------------------- - diff --git a/lib/kokkos/config/configure_kokkos_nvidia.sh b/lib/kokkos/config/configure_kokkos_nvidia.sh deleted file mode 100644 index f78b7dce7845474402d61793084d59cfff579e4a..0000000000000000000000000000000000000000 --- a/lib/kokkos/config/configure_kokkos_nvidia.sh +++ /dev/null @@ -1,204 +0,0 @@ -#!/bin/sh -# -# Copy this script, put it outside the Trilinos source directory, and -# build there. -# -# Additional command-line arguments given to this script will be -# passed directly to CMake. -# - -# -# Force CMake to re-evaluate build options. -# -rm -rf CMake* Trilinos* packages Dart* Testing cmake_install.cmake MakeFile* - -#----------------------------------------------------------------------------- -# Incrementally construct cmake configure options: - -CMAKE_CONFIGURE="" - -#----------------------------------------------------------------------------- -# Location of Trilinos source tree: - -CMAKE_PROJECT_DIR="${HOME}/Trilinos" - -# Location for installation: - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_INSTALL_PREFIX=/home/sems/common/kokkos/`date +%F`" - -#----------------------------------------------------------------------------- -# General build options. -# Use a variable so options can be propagated to CUDA compiler. - -CMAKE_VERBOSE_MAKEFILE=OFF -CMAKE_BUILD_TYPE=RELEASE -# CMAKE_BUILD_TYPE=DEBUG - -#----------------------------------------------------------------------------- -# Build for CUDA architecture: - -# CUDA_ARCH="" -CUDA_ARCH="20" -# CUDA_ARCH="30" -# CUDA_ARCH="35" - -# Build with OpenMP - -OPENMP=ON - -# Build host code with Intel compiler: - -# INTEL=ON - -# Build for MIC architecture: - -# INTEL_XEON_PHI=ON - -# Build with HWLOC at location: - -HWLOC_BASE_DIR="/home/sems/common/hwloc/current" - -# Location for MPI to use in examples: - -MPI_BASE_DIR="/home/sems/common/openmpi/current" - -#----------------------------------------------------------------------------- -# MPI configuation only used for examples: -# -# Must have the MPI_BASE_DIR so that the -# include path can be passed to the Cuda compiler - -if [ -n "${MPI_BASE_DIR}" ] ; -then - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_MPI:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D MPI_BASE_DIR:PATH=${MPI_BASE_DIR}" -else - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_MPI:BOOL=OFF" -fi - -#----------------------------------------------------------------------------- -# Pthread configuation: - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_Pthread:BOOL=ON" -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_Pthread:BOOL=OFF" - -#----------------------------------------------------------------------------- -# OpenMP configuation: - -if [ "${OPENMP}" = "ON" ] ; -then - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_OpenMP:BOOL=ON" -else - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_OpenMP:BOOL=OFF" -fi - -#----------------------------------------------------------------------------- -#----------------------------------------------------------------------------- -# Configure packages for kokkos-only: - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_ALL_PACKAGES:BOOL=OFF" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_EXAMPLES:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_TESTS:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosCore:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosContainers:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosExample:BOOL=ON" - -#----------------------------------------------------------------------------- -#----------------------------------------------------------------------------- -# Hardware locality cmake configuration: - -if [ -n "${HWLOC_BASE_DIR}" ] ; -then - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_HWLOC:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D HWLOC_INCLUDE_DIRS:FILEPATH=${HWLOC_BASE_DIR}/include" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D HWLOC_LIBRARY_DIRS:FILEPATH=${HWLOC_BASE_DIR}/lib" -fi - -#----------------------------------------------------------------------------- -# Cuda cmake configuration: - -if [ -n "${CUDA_ARCH}" ] ; -then - - # Options to CUDA_NVCC_FLAGS must be semi-colon delimited, - # this is different than the standard CMAKE_CXX_FLAGS syntax. - - CUDA_NVCC_FLAGS="-gencode;arch=compute_${CUDA_ARCH},code=sm_${CUDA_ARCH}" - - if [ "${OPENMP}" = "ON" ] ; - then - CUDA_NVCC_FLAGS="${CUDA_NVCC_FLAGS};-Xcompiler;-Wall,-ansi,-fopenmp" - else - CUDA_NVCC_FLAGS="${CUDA_NVCC_FLAGS};-Xcompiler;-Wall,-ansi" - fi - - if [ "${CMAKE_BUILD_TYPE}" = "DEBUG" ] ; - then - CUDA_NVCC_FLAGS="${CUDA_NVCC_FLAGS};-g" - else - CUDA_NVCC_FLAGS="${CUDA_NVCC_FLAGS};-O3" - fi - - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_CUDA:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_CUSPARSE:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CUDA_VERBOSE_BUILD:BOOL=OFF" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CUDA_NVCC_FLAGS:STRING=${CUDA_NVCC_FLAGS}" - -fi - -#----------------------------------------------------------------------------- - -if [ "${INTEL}" = "ON" -o "${INTEL_XEON_PHI}" = "ON" ] ; -then - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_C_COMPILER=icc" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_COMPILER=icpc" -fi - -#----------------------------------------------------------------------------- - -# Cross-compile for Intel Xeon Phi: - -if [ "${INTEL_XEON_PHI}" = "ON" ] ; -then - - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_SYSTEM_NAME=Linux" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_FLAGS:STRING=-mmic" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_C_FLAGS:STRING=-mmic" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_Fortran_COMPILER:FILEPATH=ifort" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D BLAS_LIBRARY_DIRS:FILEPATH=${MKLROOT}/lib/mic" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D BLAS_LIBRARY_NAMES='mkl_intel_lp64;mkl_sequential;mkl_core;pthread;m'" - - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_CHECKED_STL:BOOL=OFF" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_WARNINGS_AS_ERRORS_FLAGS:STRING=''" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D BUILD_SHARED_LIBS:BOOL=OFF" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D DART_TESTING_TIMEOUT:STRING=600" - - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D LAPACK_LIBRARY_NAMES=''" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_LAPACK_LIBRARIES=''" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_BinUtils=OFF" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_Pthread_LIBRARIES=pthread" - - # Cannot cross-compile fortran compatibility checks on the MIC: - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_Fortran:BOOL=OFF" - - # Tell cmake the answers to compile-and-execute tests - # to prevent cmake from executing a cross-compiled program. - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D HAVE_GCC_ABI_DEMANGLE_EXITCODE=0" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D HAVE_TEUCHOS_BLASFLOAT_EXITCODE=0" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D LAPACK_SLAPY2_WORKS_EXITCODE=0" - -fi - -#----------------------------------------------------------------------------- - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_VERBOSE_MAKEFILE:BOOL=${CMAKE_VERBOSE_MAKEFILE}" - -#----------------------------------------------------------------------------- - -echo "cmake ${CMAKE_CONFIGURE} ${CMAKE_PROJECT_DIR}" - -cmake ${CMAKE_CONFIGURE} ${CMAKE_PROJECT_DIR} - -#----------------------------------------------------------------------------- - diff --git a/lib/kokkos/config/configure_shannon.sh b/lib/kokkos/config/configure_shannon.sh deleted file mode 100644 index 8bd175b0314ffc74c9c6ffb02188d599a1b5a573..0000000000000000000000000000000000000000 --- a/lib/kokkos/config/configure_shannon.sh +++ /dev/null @@ -1,190 +0,0 @@ -#!/bin/sh -# -# Copy this script, put it outside the Trilinos source directory, and -# build there. -# -# Additional command-line arguments given to this script will be -# passed directly to CMake. -# - -# -# Force CMake to re-evaluate build options. -# -rm -rf CMake* Trilinos* packages Dart* Testing cmake_install.cmake MakeFile* - -#----------------------------------------------------------------------------- -# Incrementally construct cmake configure options: - -CMAKE_CONFIGURE="" - -#----------------------------------------------------------------------------- -# Location of Trilinos source tree: - -CMAKE_PROJECT_DIR="${HOME}/Trilinos" - -# Location for installation: - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_INSTALL_PREFIX=/home/projects/kokkos/`date +%F`" - -#----------------------------------------------------------------------------- -# General build options. -# Use a variable so options can be propagated to CUDA compiler. - -CMAKE_VERBOSE_MAKEFILE=OFF -CMAKE_BUILD_TYPE=RELEASE -# CMAKE_BUILD_TYPE=DEBUG - -#----------------------------------------------------------------------------- -# Build for CUDA architecture: - -# CUDA_ARCH="" -# CUDA_ARCH="20" -# CUDA_ARCH="30" -CUDA_ARCH="35" - -# Build host code with Intel compiler: - -INTEL=ON - -# Build for MIC architecture: - -# INTEL_XEON_PHI=ON - -# Build with HWLOC at location: - -HWLOC_BASE_DIR="/home/projects/hwloc/1.6.2" - -# Location for MPI to use in examples: - -MPI_BASE_DIR="" - -#----------------------------------------------------------------------------- -# MPI configuation only used for examples: -# -# Must have the MPI_BASE_DIR so that the -# include path can be passed to the Cuda compiler - -if [ -n "${MPI_BASE_DIR}" ] ; -then - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_MPI:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D MPI_BASE_DIR:PATH=${MPI_BASE_DIR}" -else - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_MPI:BOOL=OFF" -fi - -#----------------------------------------------------------------------------- -# Pthread configuation: - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_Pthread:BOOL=ON" -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_Pthread:BOOL=OFF" - -#----------------------------------------------------------------------------- -# OpenMP configuation: - -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_OpenMP:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_OpenMP:BOOL=OFF" - -#----------------------------------------------------------------------------- -#----------------------------------------------------------------------------- -# Configure packages for kokkos-only: - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_ALL_PACKAGES:BOOL=OFF" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_EXAMPLES:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_TESTS:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosCore:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosContainers:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosExample:BOOL=ON" - -#----------------------------------------------------------------------------- -#----------------------------------------------------------------------------- -# Hardware locality cmake configuration: - -if [ -n "${HWLOC_BASE_DIR}" ] ; -then - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_HWLOC:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D HWLOC_INCLUDE_DIRS:FILEPATH=${HWLOC_BASE_DIR}/include" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D HWLOC_LIBRARY_DIRS:FILEPATH=${HWLOC_BASE_DIR}/lib" -fi - -#----------------------------------------------------------------------------- -# Cuda cmake configuration: - -if [ -n "${CUDA_ARCH}" ] ; -then - - # Options to CUDA_NVCC_FLAGS must be semi-colon delimited, - # this is different than the standard CMAKE_CXX_FLAGS syntax. - - CUDA_NVCC_FLAGS="-gencode;arch=compute_${CUDA_ARCH},code=sm_${CUDA_ARCH}" - CUDA_NVCC_FLAGS="${CUDA_NVCC_FLAGS};-Xcompiler;-Wall,-ansi" - - if [ "${CMAKE_BUILD_TYPE}" = "DEBUG" ] ; - then - CUDA_NVCC_FLAGS="${CUDA_NVCC_FLAGS};-g" - else - CUDA_NVCC_FLAGS="${CUDA_NVCC_FLAGS};-O3" - fi - - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_CUDA:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_CUSPARSE:BOOL=ON" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CUDA_VERBOSE_BUILD:BOOL=OFF" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CUDA_NVCC_FLAGS:STRING=${CUDA_NVCC_FLAGS}" - -fi - -#----------------------------------------------------------------------------- - -if [ "${INTEL}" = "ON" -o "${INTEL_XEON_PHI}" = "ON" ] ; -then - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_C_COMPILER=icc" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_COMPILER=icpc" -fi - -#----------------------------------------------------------------------------- - -# Cross-compile for Intel Xeon Phi: - -if [ "${INTEL_XEON_PHI}" = "ON" ] ; -then - - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_SYSTEM_NAME=Linux" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_FLAGS:STRING=-mmic" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_C_FLAGS:STRING=-mmic" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_Fortran_COMPILER:FILEPATH=ifort" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D BLAS_LIBRARY_DIRS:FILEPATH=${MKLROOT}/lib/mic" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D BLAS_LIBRARY_NAMES='mkl_intel_lp64;mkl_sequential;mkl_core;pthread;m'" - - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_CHECKED_STL:BOOL=OFF" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_WARNINGS_AS_ERRORS_FLAGS:STRING=''" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D BUILD_SHARED_LIBS:BOOL=OFF" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D DART_TESTING_TIMEOUT:STRING=600" - - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D LAPACK_LIBRARY_NAMES=''" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_LAPACK_LIBRARIES=''" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_BinUtils=OFF" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_Pthread_LIBRARIES=pthread" - - # Cannot cross-compile fortran compatibility checks on the MIC: - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_Fortran:BOOL=OFF" - - # Tell cmake the answers to compile-and-execute tests - # to prevent cmake from executing a cross-compiled program. - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D HAVE_GCC_ABI_DEMANGLE_EXITCODE=0" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D HAVE_TEUCHOS_BLASFLOAT_EXITCODE=0" - CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D LAPACK_SLAPY2_WORKS_EXITCODE=0" - -fi - -#----------------------------------------------------------------------------- - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_VERBOSE_MAKEFILE:BOOL=${CMAKE_VERBOSE_MAKEFILE}" - -#----------------------------------------------------------------------------- - -echo "cmake ${CMAKE_CONFIGURE} ${CMAKE_PROJECT_DIR}" - -cmake ${CMAKE_CONFIGURE} ${CMAKE_PROJECT_DIR} - -#----------------------------------------------------------------------------- - diff --git a/lib/kokkos/config/configure_tpetra_kokkos_cuda_nvcc_wrapper.sh b/lib/kokkos/config/configure_tpetra_kokkos_cuda_nvcc_wrapper.sh deleted file mode 100755 index 0baa83aefee66f6db0e131c2a0c77ce62d7545b6..0000000000000000000000000000000000000000 --- a/lib/kokkos/config/configure_tpetra_kokkos_cuda_nvcc_wrapper.sh +++ /dev/null @@ -1,140 +0,0 @@ -#!/bin/bash -# -# This script uses CUDA, OpenMP, and MPI. -# -# Before invoking this script, set the OMPI_CXX environment variable -# to point to nvcc_wrapper, wherever it happens to live. (If you use -# an MPI implementation other than OpenMPI, set the corresponding -# environment variable instead.) -# - -rm -f CMakeCache.txt; -rm -rf CMakeFiles -EXTRA_ARGS=$@ -MPI_PATH="/opt/mpi/openmpi/1.8.2/nvcc-gcc/4.8.3-6.5" -CUDA_PATH="/opt/nvidia/cuda/6.5.14" - -# -# As long as there are any .cu files in Trilinos, we'll need to set -# CUDA_NVCC_FLAGS. If Trilinos gets rid of all of its .cu files and -# lets nvcc_wrapper handle them as .cpp files, then we won't need to -# set CUDA_NVCC_FLAGS. As it is, given that we need to set -# CUDA_NVCC_FLAGS, we must make sure that they are the same flags as -# nvcc_wrapper passes to nvcc. -# -CUDA_NVCC_FLAGS="-gencode;arch=compute_35,code=sm_35;-I${MPI_PATH}/include" -CUDA_NVCC_FLAGS="${CUDA_NVCC_FLAGS};-Xcompiler;-Wall,-ansi,-fopenmp" -CUDA_NVCC_FLAGS="${CUDA_NVCC_FLAGS};-O3;-DKOKKOS_USE_CUDA_UVM" - -cmake \ - -D CMAKE_INSTALL_PREFIX:PATH="$PWD/../install/" \ - -D CMAKE_BUILD_TYPE:STRING=DEBUG \ - -D CMAKE_CXX_FLAGS:STRING="-g -Wall" \ - -D CMAKE_C_FLAGS:STRING="-g -Wall" \ - -D CMAKE_FORTRAN_FLAGS:STRING="" \ - -D CMAKE_SHARED_LIBRARY_LINK_CXX_FLAGS="" \ - -D Trilinos_ENABLE_Triutils=OFF \ - -D Trilinos_ENABLE_INSTALL_CMAKE_CONFIG_FILES:BOOL=OFF \ - -D Trilinos_ENABLE_DEBUG:BOOL=OFF \ - -D Trilinos_ENABLE_CHECKED_STL:BOOL=OFF \ - -D Trilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=OFF \ - -D Trilinos_WARNINGS_AS_ERRORS_FLAGS:STRING="" \ - -D Trilinos_ENABLE_ALL_PACKAGES:BOOL=OFF \ - -D Trilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=OFF \ - -D BUILD_SHARED_LIBS:BOOL=OFF \ - -D DART_TESTING_TIMEOUT:STRING=600 \ - -D CMAKE_VERBOSE_MAKEFILE:BOOL=OFF \ - \ - \ - -D CMAKE_CXX_COMPILER:FILEPATH="${MPI_PATH}/bin/mpicxx" \ - -D CMAKE_C_COMPILER:FILEPATH="${MPI_PATH}/bin/mpicc" \ - -D MPI_CXX_COMPILER:FILEPATH="${MPI_PATH}/bin/mpicxx" \ - -D MPI_C_COMPILER:FILEPATH="${MPI_PATH}/bin/mpicc" \ - -D CMAKE_Fortran_COMPILER:FILEPATH="${MPI_PATH}/bin/mpif77" \ - -D MPI_EXEC:FILEPATH="${MPI_PATH}/bin/mpirun" \ - -D MPI_EXEC_POST_NUMPROCS_FLAGS:STRING="-bind-to;socket;--map-by;socket;env;CUDA_MANAGED_FORCE_DEVICE_ALLOC=1;CUDA_LAUNCH_BLOCKING=1;OMP_NUM_THREADS=2" \ - \ - \ - -D Trilinos_ENABLE_CXX11:BOOL=OFF \ - -D TPL_ENABLE_MPI:BOOL=ON \ - -D Trilinos_ENABLE_OpenMP:BOOL=ON \ - -D Trilinos_ENABLE_ThreadPool:BOOL=ON \ - \ - \ - -D TPL_ENABLE_CUDA:BOOL=ON \ - -D CUDA_TOOLKIT_ROOT_DIR:FILEPATH="${CUDA_PATH}" \ - -D CUDA_PROPAGATE_HOST_FLAGS:BOOL=OFF \ - -D TPL_ENABLE_Thrust:BOOL=OFF \ - -D Thrust_INCLUDE_DIRS:FILEPATH="${CUDA_PATH}/include" \ - -D TPL_ENABLE_CUSPARSE:BOOL=OFF \ - -D TPL_ENABLE_Cusp:BOOL=OFF \ - -D Cusp_INCLUDE_DIRS="/home/crtrott/Software/cusp" \ - -D CUDA_VERBOSE_BUILD:BOOL=OFF \ - -D CUDA_NVCC_FLAGS:STRING=${CUDA_NVCC_FLAGS} \ - \ - \ - -D TPL_ENABLE_HWLOC=OFF \ - -D HWLOC_INCLUDE_DIRS="/usr/local/software/hwloc/current/include" \ - -D HWLOC_LIBRARY_DIRS="/usr/local/software/hwloc/current/lib" \ - -D TPL_ENABLE_BinUtils=OFF \ - -D TPL_ENABLE_BLAS:STRING=ON \ - -D TPL_ENABLE_LAPACK:STRING=ON \ - -D TPL_ENABLE_MKL:STRING=OFF \ - -D TPL_ENABLE_HWLOC:STRING=OFF \ - -D TPL_ENABLE_GTEST:STRING=ON \ - -D TPL_ENABLE_SuperLU=ON \ - -D TPL_ENABLE_BLAS=ON \ - -D TPL_ENABLE_LAPACK=ON \ - -D TPL_SuperLU_LIBRARIES="/home/crtrott/Software/SuperLU_4.3/lib/libsuperlu_4.3.a" \ - -D TPL_SuperLU_INCLUDE_DIRS="/home/crtrott/Software/SuperLU_4.3/SRC" \ - \ - \ - -D Trilinos_Enable_Kokkos:BOOL=ON \ - -D Trilinos_ENABLE_KokkosCore:BOOL=ON \ - -D Trilinos_ENABLE_TeuchosKokkosCompat:BOOL=ON \ - -D Trilinos_ENABLE_KokkosContainers:BOOL=ON \ - -D Trilinos_ENABLE_TpetraKernels:BOOL=ON \ - -D Trilinos_ENABLE_KokkosAlgorithms:BOOL=ON \ - -D Trilinos_ENABLE_TeuchosKokkosComm:BOOL=ON \ - -D Trilinos_ENABLE_KokkosExample:BOOL=ON \ - -D Kokkos_ENABLE_EXAMPLES:BOOL=ON \ - -D Kokkos_ENABLE_TESTS:BOOL=OFF \ - -D KokkosClassic_DefaultNode:STRING="Kokkos::Compat::KokkosCudaWrapperNode" \ - -D TpetraClassic_ENABLE_OpenMPNode=OFF \ - -D TpetraClassic_ENABLE_TPINode=OFF \ - -D TpetraClassic_ENABLE_MKL=OFF \ - -D Kokkos_ENABLE_Cuda_UVM=ON \ - \ - \ - -D Trilinos_ENABLE_Teuchos:BOOL=ON \ - -D Teuchos_ENABLE_COMPLEX:BOOL=OFF \ - \ - \ - -D Trilinos_ENABLE_Tpetra:BOOL=ON \ - -D Tpetra_ENABLE_KokkosCore=ON \ - -D Tpetra_ENABLE_Kokkos_DistObject=OFF \ - -D Tpetra_ENABLE_Kokkos_Refactor=ON \ - -D Tpetra_ENABLE_TESTS=ON \ - -D Tpetra_ENABLE_EXAMPLES=ON \ - -D Tpetra_ENABLE_MPI_CUDA_RDMA:BOOL=ON \ - \ - \ - -D Trilinos_ENABLE_Belos=OFF \ - -D Trilinos_ENABLE_Amesos=OFF \ - -D Trilinos_ENABLE_Amesos2=OFF \ - -D Trilinos_ENABLE_Ifpack=OFF \ - -D Trilinos_ENABLE_Ifpack2=OFF \ - -D Trilinos_ENABLE_Epetra=OFF \ - -D Trilinos_ENABLE_EpetraExt=OFF \ - -D Trilinos_ENABLE_Zoltan=OFF \ - -D Trilinos_ENABLE_Zoltan2=OFF \ - -D Trilinos_ENABLE_MueLu=OFF \ - -D Belos_ENABLE_TESTS=ON \ - -D Belos_ENABLE_EXAMPLES=ON \ - -D MueLu_ENABLE_TESTS=ON \ - -D MueLu_ENABLE_EXAMPLES=ON \ - -D Ifpack2_ENABLE_TESTS=ON \ - -D Ifpack2_ENABLE_EXAMPLES=ON \ - $EXTRA_ARGS \ -${HOME}/Trilinos - diff --git a/lib/kokkos/config/kokkos-trilinos-integration-procedure.txt b/lib/kokkos/config/kokkos-trilinos-integration-procedure.txt deleted file mode 100644 index 0f2448781425bdf8b4099ab9c60017811bda840b..0000000000000000000000000000000000000000 --- a/lib/kokkos/config/kokkos-trilinos-integration-procedure.txt +++ /dev/null @@ -1,148 +0,0 @@ -// -------------------------------------------------------------------------------- // - -The following steps are for workstations/servers with the SEMS environment installed. - -// -------------------------------------------------------------------------------- // -Summary: - -- Step 1: Rigorous testing of Kokkos' develop branch for each backend (Serial, OpenMP, Threads, Cuda) with all supported compilers. - -- Step 2: Snapshot Kokkos' develop branch into current Trilinos develop branch. - -- Step 3: Build and test Trilinos with combinations of compilers, types, backends. - -- Step 4: Promote Kokkos develop branch to master if the snapshot does not cause any new tests to fail; else track/fix causes of new failures. - -- Step 5: Snapshot Kokkos tagged master branch into Trilinos and push Trilinos. -// -------------------------------------------------------------------------------- // - - -// -------------------------------------------------------------------------------- // - -Step 1: - 1.1. Update kokkos develop branch (NOT a fork) - - (From kokkos directory): - git fetch --all - git checkout develop - git reset --hard origin/develop - - 1.2. Create a testing directory - here the directory is created within the kokkos directory - - mkdir testing - cd testing - - 1.3. Run the test_all_sandia script; various compiler and build-list options can be specified - - ../config/test_all_sandia - - 1.4 Clean repository of untracked files - - cd ../ - git clean -df - -// -------------------------------------------------------------------------------- // - -Step 2: - 2.1 Update Trilinos develop branch - - (From Trilinos directory): - git checkout develop - git fetch --all - git reset --hard origin/develop - git clean -df - - 2.2 Snapshot Kokkos into Trilinos - this requires python/2.7.9 and that both Trilinos and Kokkos be clean - no untracked or modified files - - module load python/2.7.9 - python KOKKOS_PATH/config/snapshot.py KOKKOS_PATH TRILINOS_PATH/packages - -// -------------------------------------------------------------------------------- // - -Step 3: - 3.1. Build and test Trilinos with 4 different configurations; Run scripts for white and shepard are provided in kokkos/config/trilinos-integration - - Usually its a good idea to run those script via nohup. - You can run all four at the same time, use separate directories for each. - - 3.2. Compare the failed test output between the pristine and the updated runs; investigate and fix problems if new tests fail after the Kokkos snapshot - -// -------------------------------------------------------------------------------- // - -Step 4: Once all Trilinos tests pass promote Kokkos develop branch to master on Github - 4.1. Generate Changelog (You need a github API token) - - Close all Open issues with "InDevelop" tag on github - - (Not from kokkos directory) - gitthub_changelog_generator kokkos/kokkos --token TOKEN --no-pull-requests --include-labels 'InDevelop' --enhancement-labels 'enhancement,Feature Request' --future-release 'NEWTAG' --between-tags 'NEWTAG,OLDTAG' - - (Copy the new section from the generated CHANGELOG.md to the kokkos/CHANGELOG.md) - (Make desired changes to CHANGELOG.md to enhance clarity) - (Commit and push the CHANGELOG to develop) - - 4.2 Merge develop into Master - - - DO NOT fast-forward the merge!!!! - - (From kokkos directory): - git checkout master - git fetch --all - # Ensure we are on the current origin/master - git reset --hard origin/master - git merge --no-ff origin/develop - - 4.3. Update the tag in kokkos/config/master_history.txt - Tag description: MajorNumber.MinorNumber.WeeksSinceMinorNumberUpdate - Tag format: #.#.## - - # Prepend master_history.txt with - - # tag: #.#.## - # date: mm/dd/yyyy - # master: sha1 - # develop: sha1 - # ----------------------- - - git commit --amend -a - - git tag -a #.#.## - tag: #.#.## - date: mm/dd/yyyy - master: sha1 - develop: sha1 - - 4.4. Do NOT push yet - -// -------------------------------------------------------------------------------- // - -Step 5: - 5.1. Make sure Trilinos is up-to-date - chances are other changes have been committed since the integration testing process began. If a substantial change has occurred that may be affected by the snapshot the testing procedure may need to be repeated - - (From Trilinos directory): - git checkout develop - git fetch --all - git reset --hard origin/develop - git clean -df - - 5.2. Snapshot Kokkos master branch into Trilinos - - (From kokkos directory): - git fetch --all - git checkout tags/#.#.## - git clean -df - - python KOKKOS_PATH/config/snapshot.py KOKKOS_PATH TRILINOS_PATH/packages - - 5.3. Run checkin-test to push to trilinos using the CI build modules (gcc/4.9.3) - - The modules are listed in kokkos/config/trilinos-integration/checkin-test - Run checkin-test, forward dependencies and optional dependencies must be enabled - If push failed because someone else clearly broke something, push manually. - If push failed for unclear reasons, investigate, fix, and potentially start over from step 2 after reseting your local kokkos/master branch - -Step 6: Push Kokkos to master - - git push --follow-tags origin master - -// -------------------------------------------------------------------------------- // diff --git a/lib/kokkos/config/kokkos_dev/config-core-all.sh b/lib/kokkos/config/kokkos_dev/config-core-all.sh deleted file mode 100755 index 1867de7204af4e1a0d0a83a881937256a4c51ee7..0000000000000000000000000000000000000000 --- a/lib/kokkos/config/kokkos_dev/config-core-all.sh +++ /dev/null @@ -1,110 +0,0 @@ -#!/bin/sh -# -# Copy this script, put it outside the Trilinos source directory, and -# build there. -# -#----------------------------------------------------------------------------- -# Building on 'kokkos-dev.sandia.gov' with enabled capabilities: -# -# Cuda, OpenMP, Threads, Qthreads, hwloc -# -# module loaded on 'kokkos-dev.sandia.gov' for this build -# -# module load cmake/2.8.11.2 gcc/4.8.3 cuda/6.5.14 nvcc-wrapper/gnu -# -# The 'nvcc-wrapper' module should load a script that matches -# kokkos/bin/nvcc_wrapper -# -#----------------------------------------------------------------------------- -# Source and installation directories: - -TRILINOS_SOURCE_DIR=${HOME}/Trilinos -TRILINOS_INSTALL_DIR=${HOME}/TrilinosInstall/`date +%F` - -CMAKE_CONFIGURE="" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_INSTALL_PREFIX=${TRILINOS_INSTALL_DIR}" - -#----------------------------------------------------------------------------- -# Debug/optimized - -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_BUILD_TYPE:STRING=DEBUG" -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_BOUNDS_CHECK:BOOL=ON" - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_BUILD_TYPE:STRING=RELEASE" - -#----------------------------------------------------------------------------- - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_FLAGS:STRING=-Wall" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_C_COMPILER=gcc" - -#----------------------------------------------------------------------------- -# Cuda using GNU, use the nvcc_wrapper to build CUDA source - -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_COMPILER=g++" - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_COMPILER=nvcc_wrapper" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_CUDA:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_CUSPARSE:BOOL=ON" - -#----------------------------------------------------------------------------- -# Configure for Kokkos subpackages and tests: - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_Fortran:BOOL=OFF" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_ALL_PACKAGES:BOOL=OFF" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_EXAMPLES:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_TESTS:BOOL=ON" - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosCore:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosContainers:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosAlgorithms:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_TpetraKernels:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosExample:BOOL=ON" - -#----------------------------------------------------------------------------- -# Hardware locality configuration: - -HWLOC_BASE_DIR="/home/projects/hwloc/1.7.1/host/gnu/4.7.3" - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_HWLOC:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D HWLOC_INCLUDE_DIRS:FILEPATH=${HWLOC_BASE_DIR}/include" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D HWLOC_LIBRARY_DIRS:FILEPATH=${HWLOC_BASE_DIR}/lib" - -#----------------------------------------------------------------------------- -# Pthread - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_Pthread:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_Pthread:BOOL=ON" - -#----------------------------------------------------------------------------- -# OpenMP - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_OpenMP:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_OpenMP:BOOL=ON" - -#----------------------------------------------------------------------------- -# Qthreads - -QTHREADS_BASE_DIR="/home/projects/qthreads/2014-07-08/host/gnu/4.7.3" - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_QTHREADS:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D QTHREADS_INCLUDE_DIRS:FILEPATH=${QTHREADS_BASE_DIR}/include" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D QTHREADS_LIBRARY_DIRS:FILEPATH=${QTHREADS_BASE_DIR}/lib" - -#----------------------------------------------------------------------------- -# C++11 - -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_CXX11:BOOL=ON" -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_CXX11:BOOL=ON" - -#----------------------------------------------------------------------------- -# -# Remove CMake output files to force reconfigure from scratch. -# - -rm -rf CMake* Trilinos* packages Dart* Testing cmake_install.cmake MakeFile* - -# - -echo cmake ${CMAKE_CONFIGURE} ${TRILINOS_SOURCE_DIR} - -cmake ${CMAKE_CONFIGURE} ${TRILINOS_SOURCE_DIR} diff --git a/lib/kokkos/config/kokkos_dev/config-core-cuda-omp-hwloc.sh b/lib/kokkos/config/kokkos_dev/config-core-cuda-omp-hwloc.sh deleted file mode 100755 index 5a6cc1493eb7cdbca7ac29ff2c2104249116d061..0000000000000000000000000000000000000000 --- a/lib/kokkos/config/kokkos_dev/config-core-cuda-omp-hwloc.sh +++ /dev/null @@ -1,104 +0,0 @@ -#!/bin/sh -# -# Copy this script, put it outside the Trilinos source directory, and -# build there. -# -#----------------------------------------------------------------------------- -# Building on 'kokkos-dev.sandia.gov' with enabled capabilities: -# -# Cuda, OpenMP, hwloc -# -# module loaded on 'kokkos-dev.sandia.gov' for this build -# -# module load cmake/2.8.11.2 gcc/4.8.3 cuda/6.5.14 nvcc-wrapper/gnu -# -# The 'nvcc-wrapper' module should load a script that matches -# kokkos/bin/nvcc_wrapper -# -#----------------------------------------------------------------------------- -# Source and installation directories: - -TRILINOS_SOURCE_DIR=${HOME}/Trilinos -TRILINOS_INSTALL_DIR=${HOME}/TrilinosInstall/`date +%F` - -CMAKE_CONFIGURE="" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_INSTALL_PREFIX=${TRILINOS_INSTALL_DIR}" - -#----------------------------------------------------------------------------- -# Debug/optimized - -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_BUILD_TYPE:STRING=DEBUG" -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_BOUNDS_CHECK:BOOL=ON" - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_BUILD_TYPE:STRING=RELEASE" - -#----------------------------------------------------------------------------- - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_FLAGS:STRING=-Wall" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_C_COMPILER=gcc" - -#----------------------------------------------------------------------------- -# Cuda using GNU, use the nvcc_wrapper to build CUDA source - -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_COMPILER=g++" - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_COMPILER=nvcc_wrapper" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_CUDA:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_CUSPARSE:BOOL=ON" - -#----------------------------------------------------------------------------- -# Configure for Kokkos subpackages and tests: - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_Fortran:BOOL=OFF" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_ALL_PACKAGES:BOOL=OFF" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_EXAMPLES:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_TESTS:BOOL=ON" - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosCore:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosContainers:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosAlgorithms:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_TpetraKernels:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosExample:BOOL=ON" - -#----------------------------------------------------------------------------- -# Hardware locality configuration: - -HWLOC_BASE_DIR="/home/projects/hwloc/1.7.1/host/gnu/4.7.3" - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_HWLOC:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D HWLOC_INCLUDE_DIRS:FILEPATH=${HWLOC_BASE_DIR}/include" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D HWLOC_LIBRARY_DIRS:FILEPATH=${HWLOC_BASE_DIR}/lib" - -#----------------------------------------------------------------------------- -# Pthread explicitly OFF so tribits doesn't automatically turn it on - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_Pthread:BOOL=OFF" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_Pthread:BOOL=OFF" - -#----------------------------------------------------------------------------- -# OpenMP - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_OpenMP:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_OpenMP:BOOL=ON" - -#----------------------------------------------------------------------------- -# C++11 - -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_CXX11:BOOL=ON" -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_CXX11:BOOL=ON" - -#----------------------------------------------------------------------------- -# -# Remove CMake output files to force reconfigure from scratch. -# - -rm -rf CMake* Trilinos* packages Dart* Testing cmake_install.cmake MakeFile* - -# - -echo cmake ${CMAKE_CONFIGURE} ${TRILINOS_SOURCE_DIR} - -cmake ${CMAKE_CONFIGURE} ${TRILINOS_SOURCE_DIR} - -#----------------------------------------------------------------------------- - diff --git a/lib/kokkos/config/kokkos_dev/config-core-cuda.sh b/lib/kokkos/config/kokkos_dev/config-core-cuda.sh deleted file mode 100755 index 606755da81f0cb7afa16c136798e15155c02b7d5..0000000000000000000000000000000000000000 --- a/lib/kokkos/config/kokkos_dev/config-core-cuda.sh +++ /dev/null @@ -1,88 +0,0 @@ -#!/bin/sh -# -# Copy this script, put it outside the Trilinos source directory, and -# build there. -# -#----------------------------------------------------------------------------- -# Building on 'kokkos-dev.sandia.gov' with enabled capabilities: -# -# Cuda -# -# module loaded on 'kokkos-dev.sandia.gov' for this build -# -# module load cmake/2.8.11.2 gcc/4.8.3 cuda/6.5.14 nvcc-wrapper/gnu -# -# The 'nvcc-wrapper' module should load a script that matches -# kokkos/bin/nvcc_wrapper -# -#----------------------------------------------------------------------------- -# Source and installation directories: - -TRILINOS_SOURCE_DIR=${HOME}/Trilinos -TRILINOS_INSTALL_DIR=${HOME}/TrilinosInstall/`date +%F` - -CMAKE_CONFIGURE="" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_INSTALL_PREFIX=${TRILINOS_INSTALL_DIR}" - -#----------------------------------------------------------------------------- -# Debug/optimized - -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_BUILD_TYPE:STRING=DEBUG" -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_BOUNDS_CHECK:BOOL=ON" - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_BUILD_TYPE:STRING=RELEASE" - -#----------------------------------------------------------------------------- - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_FLAGS:STRING=-Wall" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_C_COMPILER=gcc" - -#----------------------------------------------------------------------------- -# Cuda using GNU, use the nvcc_wrapper to build CUDA source - -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_COMPILER=g++" - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_COMPILER=nvcc_wrapper" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_CUDA:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_CUSPARSE:BOOL=ON" - -# Pthread explicitly OFF, otherwise tribits will automatically turn it on - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_Pthread:BOOL=OFF" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_Pthread:BOOL=OFF" - -#----------------------------------------------------------------------------- -# Configure for Kokkos subpackages and tests: - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_Fortran:BOOL=OFF" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_ALL_PACKAGES:BOOL=OFF" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_EXAMPLES:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_TESTS:BOOL=ON" - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosCore:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosContainers:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosAlgorithms:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_TpetraKernels:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosExample:BOOL=ON" - -#----------------------------------------------------------------------------- -# C++11 - -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_CXX11:BOOL=ON" -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_CXX11:BOOL=ON" - -#----------------------------------------------------------------------------- -# -# Remove CMake output files to force reconfigure from scratch. -# - -rm -rf CMake* Trilinos* packages Dart* Testing cmake_install.cmake MakeFile* - -# - -echo cmake ${CMAKE_CONFIGURE} ${TRILINOS_SOURCE_DIR} - -cmake ${CMAKE_CONFIGURE} ${TRILINOS_SOURCE_DIR} - -#----------------------------------------------------------------------------- - diff --git a/lib/kokkos/config/kokkos_dev/config-core-cxx11-omp.sh b/lib/kokkos/config/kokkos_dev/config-core-cxx11-omp.sh deleted file mode 100755 index b83a535416064febc732a4fd0d7dbf34274b1adf..0000000000000000000000000000000000000000 --- a/lib/kokkos/config/kokkos_dev/config-core-cxx11-omp.sh +++ /dev/null @@ -1,84 +0,0 @@ -#!/bin/sh -# -# Copy this script, put it outside the Trilinos source directory, and -# build there. -# -#----------------------------------------------------------------------------- -# Building on 'kokkos-dev.sandia.gov' with enabled capabilities: -# -# C++11, OpenMP -# -# module loaded on 'kokkos-dev.sandia.gov' for this build -# -# module load cmake/2.8.11.2 gcc/4.8.3 -# -#----------------------------------------------------------------------------- -# Source and installation directories: - -TRILINOS_SOURCE_DIR=${HOME}/Trilinos -TRILINOS_INSTALL_DIR=${HOME}/TrilinosInstall/`date +%F` - -CMAKE_CONFIGURE="" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_INSTALL_PREFIX=${TRILINOS_INSTALL_DIR}" - -#----------------------------------------------------------------------------- -# Debug/optimized - -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_BUILD_TYPE:STRING=DEBUG" -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_BOUNDS_CHECK:BOOL=ON" - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_BUILD_TYPE:STRING=RELEASE" - -#----------------------------------------------------------------------------- - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_FLAGS:STRING=-Wall" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_C_COMPILER=gcc" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_COMPILER=g++" - -#----------------------------------------------------------------------------- -# Configure for Kokkos subpackages and tests: - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_Fortran:BOOL=OFF" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_ALL_PACKAGES:BOOL=OFF" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_EXAMPLES:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_TESTS:BOOL=ON" - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosCore:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosContainers:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosAlgorithms:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_TpetraKernels:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosExample:BOOL=ON" - -#----------------------------------------------------------------------------- -# Pthread explicitly OFF so tribits doesn't automatically activate - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_Pthread:BOOL=OFF" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_Pthread:BOOL=OFF" - -#----------------------------------------------------------------------------- -# OpenMP - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_OpenMP:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_OpenMP:BOOL=ON" - -#----------------------------------------------------------------------------- -# C++11 - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_CXX11:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_CXX11:BOOL=ON" - -#----------------------------------------------------------------------------- -# -# Remove CMake output files to force reconfigure from scratch. -# - -rm -rf CMake* Trilinos* packages Dart* Testing cmake_install.cmake MakeFile* - -# - -echo cmake ${CMAKE_CONFIGURE} ${TRILINOS_SOURCE_DIR} - -cmake ${CMAKE_CONFIGURE} ${TRILINOS_SOURCE_DIR} - -#----------------------------------------------------------------------------- - diff --git a/lib/kokkos/config/kokkos_dev/config-core-dbg-none.sh b/lib/kokkos/config/kokkos_dev/config-core-dbg-none.sh deleted file mode 100755 index d2e06a4ebd92080b255754b80b2af6ba93662090..0000000000000000000000000000000000000000 --- a/lib/kokkos/config/kokkos_dev/config-core-dbg-none.sh +++ /dev/null @@ -1,78 +0,0 @@ -#!/bin/sh -# -# Copy this script, put it outside the Trilinos source directory, and -# build there. -# -#----------------------------------------------------------------------------- -# Building on 'kokkos-dev.sandia.gov' with enabled capabilities: -# -# -# -# module loaded on 'kokkos-dev.sandia.gov' for this build -# -# module load cmake/2.8.11.2 gcc/4.8.3 -# -#----------------------------------------------------------------------------- -# Source and installation directories: - -TRILINOS_SOURCE_DIR=${HOME}/Trilinos -TRILINOS_INSTALL_DIR=${HOME}/TrilinosInstall/`date +%F` - -CMAKE_CONFIGURE="" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_INSTALL_PREFIX=${TRILINOS_INSTALL_DIR}" - -#----------------------------------------------------------------------------- -# Debug/optimized - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_BUILD_TYPE:STRING=DEBUG" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_BOUNDS_CHECK:BOOL=ON" - -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_BUILD_TYPE:STRING=RELEASE" - -#----------------------------------------------------------------------------- - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_FLAGS:STRING=-Wall" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_C_COMPILER=gcc" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_COMPILER=g++" - -#----------------------------------------------------------------------------- -# Configure for Kokkos subpackages and tests: - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_Fortran:BOOL=OFF" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_ALL_PACKAGES:BOOL=OFF" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_EXAMPLES:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_TESTS:BOOL=ON" - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosCore:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosContainers:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosAlgorithms:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_TpetraKernels:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosExample:BOOL=ON" - -#----------------------------------------------------------------------------- -# Kokkos Pthread explicitly OFF, TPL Pthread ON for gtest - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_Pthread:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_Pthread:BOOL=OFF" - -#----------------------------------------------------------------------------- -# C++11 - -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_CXX11:BOOL=ON" -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_CXX11:BOOL=ON" - -#----------------------------------------------------------------------------- -# -# Remove CMake output files to force reconfigure from scratch. -# - -rm -rf CMake* Trilinos* packages Dart* Testing cmake_install.cmake MakeFile* - -# - -echo cmake ${CMAKE_CONFIGURE} ${TRILINOS_SOURCE_DIR} - -cmake ${CMAKE_CONFIGURE} ${TRILINOS_SOURCE_DIR} - -#----------------------------------------------------------------------------- - diff --git a/lib/kokkos/config/kokkos_dev/config-core-intel-cuda-omp.sh b/lib/kokkos/config/kokkos_dev/config-core-intel-cuda-omp.sh deleted file mode 100755 index e2ab1f1c00168ed3ea646c9f297dc040e2c5a33f..0000000000000000000000000000000000000000 --- a/lib/kokkos/config/kokkos_dev/config-core-intel-cuda-omp.sh +++ /dev/null @@ -1,89 +0,0 @@ -#!/bin/sh -# -# Copy this script, put it outside the Trilinos source directory, and -# build there. -# -#----------------------------------------------------------------------------- -# Building on 'kokkos-dev.sandia.gov' with enabled capabilities: -# -# Intel, OpenMP, Cuda -# -# module loaded on 'kokkos-dev.sandia.gov' for this build -# -# module load cmake/2.8.11.2 cuda/7.0.4 intel/2015.0.090 nvcc-wrapper/intel -# -#----------------------------------------------------------------------------- -# Source and installation directories: - -TRILINOS_SOURCE_DIR=${HOME}/Trilinos -TRILINOS_INSTALL_DIR=${HOME}/TrilinosInstall/`date +%F` - -CMAKE_CONFIGURE="" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_INSTALL_PREFIX=${TRILINOS_INSTALL_DIR}" - -#----------------------------------------------------------------------------- -# Debug/optimized - -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_BUILD_TYPE:STRING=DEBUG" -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_BOUNDS_CHECK:BOOL=ON" - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_BUILD_TYPE:STRING=RELEASE" - -#----------------------------------------------------------------------------- - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_FLAGS:STRING=-Wall" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_C_COMPILER=icc" - -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_COMPILER=icpc" - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_COMPILER=nvcc_wrapper" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_CUDA:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_CUSPARSE:BOOL=ON" - -#----------------------------------------------------------------------------- -# Configure for Kokkos subpackages and tests: - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_Fortran:BOOL=OFF" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_ALL_PACKAGES:BOOL=OFF" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_EXAMPLES:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_TESTS:BOOL=ON" - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosCore:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosContainers:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosAlgorithms:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_TpetraKernels:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosExample:BOOL=ON" - -#----------------------------------------------------------------------------- -# Pthread explicitly OFF - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_Pthread:BOOL=OFF" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_Pthread:BOOL=OFF" - -#----------------------------------------------------------------------------- -# OpenMP - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_OpenMP:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_OpenMP:BOOL=ON" - -#----------------------------------------------------------------------------- -# C++11 - -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_CXX11:BOOL=ON" -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_CXX11:BOOL=ON" - -#----------------------------------------------------------------------------- -# -# Remove CMake output files to force reconfigure from scratch. -# - -rm -rf CMake* Trilinos* packages Dart* Testing cmake_install.cmake MakeFile* - -# - -echo cmake ${CMAKE_CONFIGURE} ${TRILINOS_SOURCE_DIR} - -cmake ${CMAKE_CONFIGURE} ${TRILINOS_SOURCE_DIR} - -#----------------------------------------------------------------------------- - diff --git a/lib/kokkos/config/kokkos_dev/config-core-intel-omp.sh b/lib/kokkos/config/kokkos_dev/config-core-intel-omp.sh deleted file mode 100755 index fd56d41161a567bca1eb3601600cdc9fbe3b0104..0000000000000000000000000000000000000000 --- a/lib/kokkos/config/kokkos_dev/config-core-intel-omp.sh +++ /dev/null @@ -1,84 +0,0 @@ -#!/bin/sh -# -# Copy this script, put it outside the Trilinos source directory, and -# build there. -# -#----------------------------------------------------------------------------- -# Building on 'kokkos-dev.sandia.gov' with enabled capabilities: -# -# Intel, OpenMP -# -# module loaded on 'kokkos-dev.sandia.gov' for this build -# -# module load cmake/2.8.11.2 intel/13.SP1.1.106 -# -#----------------------------------------------------------------------------- -# Source and installation directories: - -TRILINOS_SOURCE_DIR=${HOME}/Trilinos -TRILINOS_INSTALL_DIR=${HOME}/TrilinosInstall/`date +%F` - -CMAKE_CONFIGURE="" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_INSTALL_PREFIX=${TRILINOS_INSTALL_DIR}" - -#----------------------------------------------------------------------------- -# Debug/optimized - -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_BUILD_TYPE:STRING=DEBUG" -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_BOUNDS_CHECK:BOOL=ON" - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_BUILD_TYPE:STRING=RELEASE" - -#----------------------------------------------------------------------------- - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_FLAGS:STRING=-Wall" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_C_COMPILER=icc" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_COMPILER=icpc" - -#----------------------------------------------------------------------------- -# Configure for Kokkos subpackages and tests: - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_Fortran:BOOL=OFF" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_ALL_PACKAGES:BOOL=OFF" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_EXAMPLES:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_TESTS:BOOL=ON" - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosCore:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosContainers:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosAlgorithms:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_TpetraKernels:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosExample:BOOL=ON" - -#----------------------------------------------------------------------------- -# Pthread explicitly OFF - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_Pthread:BOOL=OFF" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_Pthread:BOOL=OFF" - -#----------------------------------------------------------------------------- -# OpenMP - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_OpenMP:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_OpenMP:BOOL=ON" - -#----------------------------------------------------------------------------- -# C++11 - -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_CXX11:BOOL=ON" -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_CXX11:BOOL=ON" - -#----------------------------------------------------------------------------- -# -# Remove CMake output files to force reconfigure from scratch. -# - -rm -rf CMake* Trilinos* packages Dart* Testing cmake_install.cmake MakeFile* - -# - -echo cmake ${CMAKE_CONFIGURE} ${TRILINOS_SOURCE_DIR} - -cmake ${CMAKE_CONFIGURE} ${TRILINOS_SOURCE_DIR} - -#----------------------------------------------------------------------------- - diff --git a/lib/kokkos/config/kokkos_dev/config-core-omp.sh b/lib/kokkos/config/kokkos_dev/config-core-omp.sh deleted file mode 100755 index f91ecd525488c40a1d92c9143e727a4a287dfefb..0000000000000000000000000000000000000000 --- a/lib/kokkos/config/kokkos_dev/config-core-omp.sh +++ /dev/null @@ -1,77 +0,0 @@ -#!/bin/sh -# -# Copy this script, put it outside the Trilinos source directory, and -# build there. -# -#----------------------------------------------------------------------------- -# Building on 'kokkos-dev.sandia.gov' with enabled capabilities: -# -# OpenMP -# -# module loaded on 'kokkos-dev.sandia.gov' for this build -# -# module load cmake/2.8.11.2 gcc/4.8.3 -# -#----------------------------------------------------------------------------- -# Source and installation directories: - -TRILINOS_SOURCE_DIR=${HOME}/Trilinos -TRILINOS_INSTALL_DIR=${HOME}/TrilinosInstall/`date +%F` - -CMAKE_CONFIGURE="" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_INSTALL_PREFIX=${TRILINOS_INSTALL_DIR}" - -#----------------------------------------------------------------------------- -# Debug/optimized - -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_BUILD_TYPE:STRING=DEBUG" -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_BOUNDS_CHECK:BOOL=ON" - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_BUILD_TYPE:STRING=RELEASE" - -#----------------------------------------------------------------------------- - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_FLAGS:STRING=-Wall" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_C_COMPILER=gcc" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_COMPILER=g++" - -#----------------------------------------------------------------------------- -# Configure for Kokkos subpackages and tests: - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_Fortran:BOOL=OFF" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_ALL_PACKAGES:BOOL=OFF" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_EXAMPLES:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_TESTS:BOOL=ON" - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosCore:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosContainers:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosAlgorithms:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_TpetraKernels:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosExample:BOOL=ON" - -#----------------------------------------------------------------------------- -# OpenMP - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_OpenMP:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_OpenMP:BOOL=ON" - -# Pthread explicitly OFF, otherwise tribits will automatically turn it on - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_Pthread:BOOL=OFF" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_Pthread:BOOL=OFF" - -#----------------------------------------------------------------------------- -# -# Remove CMake output files to force reconfigure from scratch. -# - -rm -rf CMake* Trilinos* packages Dart* Testing cmake_install.cmake MakeFile* - -# - -echo cmake ${CMAKE_CONFIGURE} ${TRILINOS_SOURCE_DIR} - -cmake ${CMAKE_CONFIGURE} ${TRILINOS_SOURCE_DIR} - -#----------------------------------------------------------------------------- - diff --git a/lib/kokkos/config/kokkos_dev/config-core-threads-hwloc.sh b/lib/kokkos/config/kokkos_dev/config-core-threads-hwloc.sh deleted file mode 100755 index 19ab96902340f6ad757fd84546afc2061bdad024..0000000000000000000000000000000000000000 --- a/lib/kokkos/config/kokkos_dev/config-core-threads-hwloc.sh +++ /dev/null @@ -1,87 +0,0 @@ -#!/bin/sh -# -# Copy this script, put it outside the Trilinos source directory, and -# build there. -# -#----------------------------------------------------------------------------- -# Building on 'kokkos-dev.sandia.gov' with enabled capabilities: -# -# Threads, hwloc -# -# module loaded on 'kokkos-dev.sandia.gov' for this build -# -# module load cmake/2.8.11.2 gcc/4.8.3 -# -#----------------------------------------------------------------------------- -# Source and installation directories: - -TRILINOS_SOURCE_DIR=${HOME}/Trilinos -TRILINOS_INSTALL_DIR=${HOME}/TrilinosInstall/`date +%F` - -CMAKE_CONFIGURE="" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_INSTALL_PREFIX=${TRILINOS_INSTALL_DIR}" - -#----------------------------------------------------------------------------- -# Debug/optimized - -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_BUILD_TYPE:STRING=DEBUG" -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_BOUNDS_CHECK:BOOL=ON" - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_BUILD_TYPE:STRING=RELEASE" - -#----------------------------------------------------------------------------- - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_FLAGS:STRING=-Wall" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_C_COMPILER=gcc" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D CMAKE_CXX_COMPILER=g++" - -#----------------------------------------------------------------------------- -# Configure for Kokkos subpackages and tests: - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_Fortran:BOOL=OFF" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_ALL_PACKAGES:BOOL=OFF" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_EXAMPLES:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_TESTS:BOOL=ON" - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosCore:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosContainers:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosAlgorithms:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_TpetraKernels:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_KokkosExample:BOOL=ON" - -#----------------------------------------------------------------------------- -# Hardware locality configuration: - -HWLOC_BASE_DIR="/home/projects/hwloc/1.7.1/host/gnu/4.7.3" - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_HWLOC:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D HWLOC_INCLUDE_DIRS:FILEPATH=${HWLOC_BASE_DIR}/include" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D HWLOC_LIBRARY_DIRS:FILEPATH=${HWLOC_BASE_DIR}/lib" - -#----------------------------------------------------------------------------- -# Pthread - -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D TPL_ENABLE_Pthread:BOOL=ON" -CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_Pthread:BOOL=ON" - -#----------------------------------------------------------------------------- -# C++11 - -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Trilinos_ENABLE_CXX11:BOOL=ON" -# CMAKE_CONFIGURE="${CMAKE_CONFIGURE} -D Kokkos_ENABLE_CXX11:BOOL=ON" - -#----------------------------------------------------------------------------- -# -# Remove CMake output files to force reconfigure from scratch. -# - -rm -rf CMake* Trilinos* packages Dart* Testing cmake_install.cmake MakeFile* - -# - -echo cmake ${CMAKE_CONFIGURE} ${TRILINOS_SOURCE_DIR} - -cmake ${CMAKE_CONFIGURE} ${TRILINOS_SOURCE_DIR} - -#----------------------------------------------------------------------------- - diff --git a/lib/kokkos/config/nvcc_wrapper b/lib/kokkos/config/nvcc_wrapper deleted file mode 100755 index d339da4fcdfa8029af85073adc068a8686253b8c..0000000000000000000000000000000000000000 --- a/lib/kokkos/config/nvcc_wrapper +++ /dev/null @@ -1,340 +0,0 @@ -#!/bin/bash -# -# This shell script (nvcc_wrapper) wraps both the host compiler and -# NVCC, if you are building legacy C or C++ code with CUDA enabled. -# The script remedies some differences between the interface of NVCC -# and that of the host compiler, in particular for linking. -# It also means that a legacy code doesn't need separate .cu files; -# it can just use .cpp files. -# -# Default settings: change those according to your machine. For -# example, you may have have two different wrappers with either icpc -# or g++ as their back-end compiler. The defaults can be overwritten -# by using the usual arguments (e.g., -arch=sm_30 -ccbin icpc). - -default_arch="sm_35" -#default_arch="sm_50" - -# -# The default C++ compiler. -# -host_compiler=${NVCC_WRAPPER_DEFAULT_COMPILER:-"g++"} -#host_compiler="icpc" -#host_compiler="/usr/local/gcc/4.8.3/bin/g++" -#host_compiler="/usr/local/gcc/4.9.1/bin/g++" - -# -# Internal variables -# - -# C++ files -cpp_files="" - -# Host compiler arguments -xcompiler_args="" - -# Cuda (NVCC) only arguments -cuda_args="" - -# Arguments for both NVCC and Host compiler -shared_args="" - -# Argument -c -compile_arg="" - -# Argument -o -output_arg="" - -# Linker arguments -xlinker_args="" - -# Object files passable to NVCC -object_files="" - -# Link objects for the host linker only -object_files_xlinker="" - -# Shared libraries with version numbers are not handled correctly by NVCC -shared_versioned_libraries_host="" -shared_versioned_libraries="" - -# Does the User set the architecture -arch_set=0 - -# Does the user overwrite the host compiler -ccbin_set=0 - -#Error code of compilation -error_code=0 - -# Do a dry run without actually compiling -dry_run=0 - -# Skip NVCC compilation and use host compiler directly -host_only=0 -host_only_args="" - -# Enable workaround for CUDA 6.5 for pragma ident -replace_pragma_ident=0 - -# Mark first host compiler argument -first_xcompiler_arg=1 - -temp_dir=${TMPDIR:-/tmp} - -# Check if we have an optimization argument already -optimization_applied=0 - -# Check if we have -std=c++X or --std=c++X already -stdcxx_applied=0 - -# Run nvcc a second time to generate dependencies if needed -depfile_separate=0 -depfile_output_arg="" -depfile_target_arg="" - -#echo "Arguments: $# $@" - -while [ $# -gt 0 ] -do - case $1 in - #show the executed command - --show|--nvcc-wrapper-show) - dry_run=1 - ;; - #run host compilation only - --host-only) - host_only=1 - ;; - #replace '#pragma ident' with '#ident' this is needed to compile OpenMPI due to a configure script bug and a non standardized behaviour of pragma with macros - --replace-pragma-ident) - replace_pragma_ident=1 - ;; - #handle source files to be compiled as cuda files - *.cpp|*.cxx|*.cc|*.C|*.c++|*.cu) - cpp_files="$cpp_files $1" - ;; - # Ensure we only have one optimization flag because NVCC doesn't allow muliple - -O*) - if [ $optimization_applied -eq 1 ]; then - echo "nvcc_wrapper - *warning* you have set multiple optimization flags (-O*), only the first is used because nvcc can only accept a single optimization setting." - else - shared_args="$shared_args $1" - optimization_applied=1 - fi - ;; - #Handle shared args (valid for both nvcc and the host compiler) - -D*|-I*|-L*|-l*|-g|--help|--version|-E|-M|-shared) - shared_args="$shared_args $1" - ;; - #Handle compilation argument - -c) - compile_arg="$1" - ;; - #Handle output argument - -o) - output_arg="$output_arg $1 $2" - shift - ;; - # Handle depfile arguments. We map them to a separate call to nvcc. - -MD|-MMD) - depfile_separate=1 - host_only_args="$host_only_args $1" - ;; - -MF) - depfile_output_arg="-o $2" - host_only_args="$host_only_args $1 $2" - shift - ;; - -MT) - depfile_target_arg="$1 $2" - host_only_args="$host_only_args $1 $2" - shift - ;; - #Handle known nvcc args - -gencode*|--dryrun|--verbose|--keep|--keep-dir*|-G|--relocatable-device-code*|-lineinfo|-expt-extended-lambda|--resource-usage|-Xptxas*) - cuda_args="$cuda_args $1" - ;; - #Handle more known nvcc args - --expt-extended-lambda|--expt-relaxed-constexpr) - cuda_args="$cuda_args $1" - ;; - #Handle known nvcc args that have an argument - -rdc|-maxrregcount|--default-stream) - cuda_args="$cuda_args $1 $2" - shift - ;; - #Handle c++11 - --std=c++11|-std=c++11|--std=c++14|-std=c++14|--std=c++1z|-std=c++1z) - if [ $stdcxx_applied -eq 1 ]; then - echo "nvcc_wrapper - *warning* you have set multiple optimization flags (-std=c++1* or --std=c++1*), only the first is used because nvcc can only accept a single std setting" - else - shared_args="$shared_args $1" - stdcxx_applied=1 - fi - ;; - - #strip of -std=c++98 due to nvcc warnings and Tribits will place both -std=c++11 and -std=c++98 - -std=c++98|--std=c++98) - ;; - #strip of pedantic because it produces endless warnings about #LINE added by the preprocessor - -pedantic|-Wpedantic|-ansi) - ;; - #strip of -Woverloaded-virtual to avoid "cc1: warning: command line option ‘-Woverloaded-virtual’ is valid for C++/ObjC++ but not for C" - -Woverloaded-virtual) - ;; - #strip -Xcompiler because we add it - -Xcompiler) - if [ $first_xcompiler_arg -eq 1 ]; then - xcompiler_args="$2" - first_xcompiler_arg=0 - else - xcompiler_args="$xcompiler_args,$2" - fi - shift - ;; - #strip of "-x cu" because we add that - -x) - if [[ $2 != "cu" ]]; then - if [ $first_xcompiler_arg -eq 1 ]; then - xcompiler_args="-x,$2" - first_xcompiler_arg=0 - else - xcompiler_args="$xcompiler_args,-x,$2" - fi - fi - shift - ;; - #Handle -ccbin (if its not set we can set it to a default value) - -ccbin) - cuda_args="$cuda_args $1 $2" - ccbin_set=1 - host_compiler=$2 - shift - ;; - #Handle -arch argument (if its not set use a default - -arch*) - cuda_args="$cuda_args $1" - arch_set=1 - ;; - #Handle -Xcudafe argument - -Xcudafe) - cuda_args="$cuda_args -Xcudafe $2" - shift - ;; - #Handle args that should be sent to the linker - -Wl*) - xlinker_args="$xlinker_args -Xlinker ${1:4:${#1}}" - host_linker_args="$host_linker_args ${1:4:${#1}}" - ;; - #Handle object files: -x cu applies to all input files, so give them to linker, except if only linking - *.a|*.so|*.o|*.obj) - object_files="$object_files $1" - object_files_xlinker="$object_files_xlinker -Xlinker $1" - ;; - #Handle object files which always need to use "-Xlinker": -x cu applies to all input files, so give them to linker, except if only linking - @*|*.dylib) - object_files="$object_files -Xlinker $1" - object_files_xlinker="$object_files_xlinker -Xlinker $1" - ;; - #Handle shared libraries with *.so.* names which nvcc can't do. - *.so.*) - shared_versioned_libraries_host="$shared_versioned_libraries_host $1" - shared_versioned_libraries="$shared_versioned_libraries -Xlinker $1" - ;; - #All other args are sent to the host compiler - *) - if [ $first_xcompiler_arg -eq 1 ]; then - xcompiler_args=$1 - first_xcompiler_arg=0 - else - xcompiler_args="$xcompiler_args,$1" - fi - ;; - esac - - shift -done - -#Add default host compiler if necessary -if [ $ccbin_set -ne 1 ]; then - cuda_args="$cuda_args -ccbin $host_compiler" -fi - -#Add architecture command -if [ $arch_set -ne 1 ]; then - cuda_args="$cuda_args -arch=$default_arch" -fi - -#Compose compilation command -nvcc_command="nvcc $cuda_args $shared_args $xlinker_args $shared_versioned_libraries" -if [ $first_xcompiler_arg -eq 0 ]; then - nvcc_command="$nvcc_command -Xcompiler $xcompiler_args" -fi - -#Compose host only command -host_command="$host_compiler $shared_args $host_only_args $compile_arg $output_arg $xcompiler_args $host_linker_args $shared_versioned_libraries_host" - -#nvcc does not accept '#pragma ident SOME_MACRO_STRING' but it does accept '#ident SOME_MACRO_STRING' -if [ $replace_pragma_ident -eq 1 ]; then - cpp_files2="" - for file in $cpp_files - do - var=`grep pragma ${file} | grep ident | grep "#"` - if [ "${#var}" -gt 0 ] - then - sed 's/#[\ \t]*pragma[\ \t]*ident/#ident/g' $file > $temp_dir/nvcc_wrapper_tmp_$file - cpp_files2="$cpp_files2 $temp_dir/nvcc_wrapper_tmp_$file" - else - cpp_files2="$cpp_files2 $file" - fi - done - cpp_files=$cpp_files2 - #echo $cpp_files -fi - -if [ "$cpp_files" ]; then - nvcc_command="$nvcc_command $object_files_xlinker -x cu $cpp_files" -else - nvcc_command="$nvcc_command $object_files" -fi - -if [ "$cpp_files" ]; then - host_command="$host_command $object_files $cpp_files" -else - host_command="$host_command $object_files" -fi - -if [ $depfile_separate -eq 1 ]; then - # run nvcc a second time to generate dependencies (without compiling) - nvcc_depfile_command="$nvcc_command -M $depfile_target_arg $depfile_output_arg" -else - nvcc_depfile_command="" -fi - -nvcc_command="$nvcc_command $compile_arg $output_arg" - -#Print command for dryrun -if [ $dry_run -eq 1 ]; then - if [ $host_only -eq 1 ]; then - echo $host_command - elif [ -n "$nvcc_depfile_command" ]; then - echo $nvcc_command "&&" $nvcc_depfile_command - else - echo $nvcc_command - fi - exit 0 -fi - -#Run compilation command -if [ $host_only -eq 1 ]; then - $host_command -elif [ -n "$nvcc_depfile_command" ]; then - $nvcc_command && $nvcc_depfile_command -else - $nvcc_command -fi -error_code=$? - -#Report error code -exit $error_code diff --git a/lib/kokkos/config/test_all_sandia b/lib/kokkos/config/test_all_sandia index 660ab91ff5ccb1bb17345b52ecc97f6d46cb9dcb..28b4a64b10819538c7f5fc672ada210671343cf4 100755 --- a/lib/kokkos/config/test_all_sandia +++ b/lib/kokkos/config/test_all_sandia @@ -14,25 +14,52 @@ PROCESSOR=`uname -p` if [[ "$HOSTNAME" =~ (white|ride).* ]]; then MACHINE=white -elif [[ "$HOSTNAME" =~ .*bowman.* ]]; then + module load git +fi + +if [[ "$HOSTNAME" =~ .*bowman.* ]]; then MACHINE=bowman -elif [[ "$HOSTNAME" =~ n.* ]]; then # Warning: very generic name + module load git +fi + +if [[ "$HOSTNAME" =~ n.* ]]; then # Warning: very generic name if [[ "$PROCESSOR" = "aarch64" ]]; then MACHINE=sullivan + module load git fi -elif [[ "$HOSTNAME" =~ node.* ]]; then # Warning: very generic name +fi + +if [[ "$HOSTNAME" =~ node.* ]]; then # Warning: very generic name + if [[ "$MACHINE" = "" ]]; then MACHINE=shepard -elif [[ "$HOSTNAME" =~ apollo ]]; then + module load git + fi +fi + +if [[ "$HOSTNAME" =~ apollo ]]; then MACHINE=apollo -elif [[ "$HOSTNAME" =~ sullivan ]]; then + module load git +fi + +if [[ "$HOSTNAME" =~ sullivan ]]; then MACHINE=sullivan -elif [ ! -z "$SEMS_MODULEFILES_ROOT" ]; then - MACHINE=sems -else + module load git +fi + +if [ ! -z "$SEMS_MODULEFILES_ROOT" ]; then + if [[ "$MACHINE" = "" ]]; then + MACHINE=sems + module load sems-git + fi +fi + +if [[ "$MACHINE" = "" ]]; then echo "Unrecognized machine" >&2 exit 1 fi +echo "Running on machine: $MACHINE" + GCC_BUILD_LIST="OpenMP,Pthread,Serial,OpenMP_Serial,Pthread_Serial" IBM_BUILD_LIST="OpenMP,Serial,OpenMP_Serial" ARM_GCC_BUILD_LIST="OpenMP,Serial,OpenMP_Serial" @@ -45,7 +72,8 @@ GCC_WARNING_FLAGS="-Wall,-Wshadow,-pedantic,-Werror,-Wsign-compare,-Wtype-limits IBM_WARNING_FLAGS="-Wall,-Wshadow,-pedantic,-Werror,-Wsign-compare,-Wtype-limits,-Wuninitialized" CLANG_WARNING_FLAGS="-Wall,-Wshadow,-pedantic,-Werror,-Wsign-compare,-Wtype-limits,-Wuninitialized" INTEL_WARNING_FLAGS="-Wall,-Wshadow,-pedantic,-Werror,-Wsign-compare,-Wtype-limits,-Wuninitialized" -CUDA_WARNING_FLAGS="-Wall,-Wshadow,-pedantic,-Werror,-Wsign-compare,-Wtype-limits,-Wuninitialized" +#CUDA_WARNING_FLAGS="-Wall,-Wshadow,-pedantic,-Werror,-Wsign-compare,-Wtype-limits,-Wuninitialized" +CUDA_WARNING_FLAGS="-Wall,-Wshadow,-pedantic,-Wsign-compare,-Wtype-limits,-Wuninitialized" PGI_WARNING_FLAGS="" # Default. Machine specific can override. @@ -142,6 +170,18 @@ else KOKKOS_PATH=$( cd $KOKKOS_PATH && pwd ) fi +UNCOMMITTED=`cd ${KOKKOS_PATH}; git status --porcelain 2>/dev/null` +if ! [ -z "$UNCOMMITTED" ]; then + echo "WARNING!! THE FOLLOWING CHANGES ARE UNCOMMITTED!! :" + echo "$UNCOMMITTED" + echo "" +fi + +GITSTATUS=`cd ${KOKKOS_PATH}; git log -n 1 --format=oneline` +echo "Repository Status: " ${GITSTATUS} +echo "" +echo "" + # # Machine specific config. # @@ -149,7 +189,7 @@ fi if [ "$MACHINE" = "sems" ]; then source /projects/sems/modulefiles/utils/sems-modules-init.sh - BASE_MODULE_LIST="sems-env,kokkos-env,sems-/,kokkos-hwloc/1.10.1/base" + BASE_MODULE_LIST="sems-env,kokkos-env,kokkos-hwloc/1.10.1/base,sems-/" CUDA_MODULE_LIST="sems-env,kokkos-env,kokkos-/,sems-gcc/4.8.4,kokkos-hwloc/1.10.1/base" CUDA8_MODULE_LIST="sems-env,kokkos-env,kokkos-/,sems-gcc/5.3.0,kokkos-hwloc/1.10.1/base" @@ -178,9 +218,9 @@ if [ "$MACHINE" = "sems" ]; then "clang/3.7.1 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS" "clang/3.8.1 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS" "clang/3.9.0 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS" - "cuda/7.0.28 $CUDA_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/config/nvcc_wrapper $CUDA_WARNING_FLAGS" - "cuda/7.5.18 $CUDA_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/config/nvcc_wrapper $CUDA_WARNING_FLAGS" - "cuda/8.0.44 $CUDA8_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/config/nvcc_wrapper $CUDA_WARNING_FLAGS" + "cuda/7.0.28 $CUDA_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" + "cuda/7.5.18 $CUDA_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" + "cuda/8.0.44 $CUDA8_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" ) fi elif [ "$MACHINE" = "white" ]; then @@ -191,14 +231,14 @@ elif [ "$MACHINE" = "white" ]; then BASE_MODULE_LIST="/" IBM_MODULE_LIST="/xl/" CUDA_MODULE_LIST="/,gcc/5.4.0" - CUDA_MODULE_LIST2="/,gcc/6.3.0,ibm/xl/13.1.6-BETA" + CUDA_MODULE_LIST2="/,gcc/6.3.0,ibm/xl/13.1.6" # Don't do pthread on white. GCC_BUILD_LIST="OpenMP,Serial,OpenMP_Serial" # Format: (compiler module-list build-list exe-name warning-flag) COMPILERS=("gcc/5.4.0 $BASE_MODULE_LIST $IBM_BUILD_LIST g++ $GCC_WARNING_FLAGS" - "ibm/13.1.3 $IBM_MODULE_LIST $IBM_BUILD_LIST xlC $IBM_WARNING_FLAGS" + "ibm/13.1.6 $IBM_MODULE_LIST $IBM_BUILD_LIST xlC $IBM_WARNING_FLAGS" "cuda/8.0.44 $CUDA_MODULE_LIST $CUDA_IBM_BUILD_LIST ${KOKKOS_PATH}/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" "cuda/9.0.103 $CUDA_MODULE_LIST2 $CUDA_IBM_BUILD_LIST ${KOKKOS_PATH}/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" ) @@ -281,7 +321,7 @@ elif [ "$MACHINE" = "apollo" ]; then CUDA_MODULE_LIST="sems-env,kokkos-env,kokkos-/,sems-gcc/4.8.4,kokkos-hwloc/1.10.1/base" CUDA8_MODULE_LIST="sems-env,kokkos-env,kokkos-/,sems-gcc/5.3.0,kokkos-hwloc/1.10.1/base" - CLANG_MODULE_LIST="sems-env,kokkos-env,sems-git,sems-cmake/3.5.2,/,cuda/8.0.44" + CLANG_MODULE_LIST="sems-env,kokkos-env,sems-git,sems-cmake/3.5.2,/,cuda/9.0.69" NVCC_MODULE_LIST="sems-env,kokkos-env,sems-git,sems-cmake/3.5.2,/,sems-gcc/5.3.0" BUILD_LIST_CUDA_NVCC="Cuda_Serial,Cuda_OpenMP" @@ -294,13 +334,13 @@ elif [ "$MACHINE" = "apollo" ]; then "gcc/5.1.0 $BASE_MODULE_LIST "Serial" g++ $GCC_WARNING_FLAGS" "intel/16.0.1 $BASE_MODULE_LIST "OpenMP" icpc $INTEL_WARNING_FLAGS" "clang/3.9.0 $BASE_MODULE_LIST "Pthread_Serial" clang++ $CLANG_WARNING_FLAGS" - "clang/4.0.0 $CLANG_MODULE_LIST "Cuda_Pthread" clang++ $CUDA_WARNING_FLAGS" - "cuda/8.0.44 $CUDA_MODULE_LIST "Cuda_OpenMP" $KOKKOS_PATH/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" + "clang/6.0 $CLANG_MODULE_LIST "Cuda_Pthread" clang++ $CUDA_WARNING_FLAGS" + "cuda/9.1 $CUDA_MODULE_LIST "Cuda_OpenMP" $KOKKOS_PATH/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" ) else # Format: (compiler module-list build-list exe-name warning-flag) - COMPILERS=("cuda/8.0.44 $CUDA8_MODULE_LIST $BUILD_LIST_CUDA_NVCC $KOKKOS_PATH/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" - "clang/4.0.0 $CLANG_MODULE_LIST $BUILD_LIST_CUDA_CLANG clang++ $CUDA_WARNING_FLAGS" + COMPILERS=("cuda/9.1 $CUDA8_MODULE_LIST $BUILD_LIST_CUDA_NVCC $KOKKOS_PATH/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" + "clang/6.0 $CLANG_MODULE_LIST $BUILD_LIST_CUDA_CLANG clang++ $CUDA_WARNING_FLAGS" "clang/3.9.0 $CLANG_MODULE_LIST $BUILD_LIST_CLANG clang++ $CLANG_WARNING_FLAGS" "gcc/4.8.4 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS" "gcc/4.9.3 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS" @@ -311,13 +351,11 @@ elif [ "$MACHINE" = "apollo" ]; then "intel/17.0.1 $BASE_MODULE_LIST $INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS" "clang/3.5.2 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS" "clang/3.6.1 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS" - "cuda/7.0.28 $CUDA_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" - "cuda/7.5.18 $CUDA_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" ) fi if [ -z "$ARCH_FLAG" ]; then - ARCH_FLAG="--arch=SNB,Kepler35" + ARCH_FLAG="--arch=SNB,Volta70" fi NUM_JOBS_TO_RUN_IN_PARALLEL=2 @@ -700,17 +738,19 @@ wait_summarize_and_exit() { echo $passed_test $(cat $PASSED_DIR/$passed_test) done - echo "#######################################################" - echo "FAILED TESTS" - echo "#######################################################" - - local failed_test local -i rv=0 - for failed_test in $(\ls -1 $FAILED_DIR | sort) - do - echo $failed_test "("$(cat $FAILED_DIR/$failed_test)" failed)" - rv=$rv+1 - done + if [ "$(ls -A $FAILED_DIR)" ]; then + echo "#######################################################" + echo "FAILED TESTS" + echo "#######################################################" + + local failed_test + for failed_test in $(\ls -1 $FAILED_DIR | sort) + do + echo $failed_test "("$(cat $FAILED_DIR/$failed_test)" failed)" + rv=$rv+1 + done + fi exit $rv } diff --git a/lib/kokkos/containers/performance_tests/TestCuda.cpp b/lib/kokkos/containers/performance_tests/TestCuda.cpp index 208387425f07fe5bef5803715d8b0eda27d25cb4..682f3f52f70a6d7c37ef1006267d3bddffc9cd70 100644 --- a/lib/kokkos/containers/performance_tests/TestCuda.cpp +++ b/lib/kokkos/containers/performance_tests/TestCuda.cpp @@ -35,7 +35,7 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER diff --git a/lib/kokkos/containers/performance_tests/TestDynRankView.hpp b/lib/kokkos/containers/performance_tests/TestDynRankView.hpp index ced74c6f5176040f57c0153e4e39f6d9ec8779a9..0d2fae32a38d7d0ffe11e2790d73d45216da98de 100644 --- a/lib/kokkos/containers/performance_tests/TestDynRankView.hpp +++ b/lib/kokkos/containers/performance_tests/TestDynRankView.hpp @@ -35,7 +35,7 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER @@ -64,8 +64,8 @@ struct InitViewFunctor { KOKKOS_INLINE_FUNCTION void operator()(const int i) const { - for (unsigned j = 0; j < _inview.dimension(1); ++j) { - for (unsigned k = 0; k < _inview.dimension(2); ++k) { + for (unsigned j = 0; j < _inview.extent(1); ++j) { + for (unsigned k = 0; k < _inview.extent(2); ++k) { _inview(i,j,k) = i/2 -j*j + k/3; } } @@ -84,8 +84,8 @@ struct InitViewFunctor { KOKKOS_INLINE_FUNCTION void operator()(const int i) const { - for (unsigned j = 0; j < _inview.dimension(1); ++j) { - for (unsigned k = 0; k < _inview.dimension(2); ++k) { + for (unsigned j = 0; j < _inview.extent(1); ++j) { + for (unsigned k = 0; k < _inview.extent(2); ++k) { _outview(i) += _inview(i,j,k) ; } } @@ -104,8 +104,8 @@ struct InitStrideViewFunctor { KOKKOS_INLINE_FUNCTION void operator()(const int i) const { - for (unsigned j = 0; j < _inview.dimension(1); ++j) { - for (unsigned k = 0; k < _inview.dimension(2); ++k) { + for (unsigned j = 0; j < _inview.extent(1); ++j) { + for (unsigned k = 0; k < _inview.extent(2); ++k) { _inview(i,j,k) = i/2 -j*j + k/3; } } @@ -123,8 +123,8 @@ struct InitViewRank7Functor { KOKKOS_INLINE_FUNCTION void operator()(const int i) const { - for (unsigned j = 0; j < _inview.dimension(1); ++j) { - for (unsigned k = 0; k < _inview.dimension(2); ++k) { + for (unsigned j = 0; j < _inview.extent(1); ++j) { + for (unsigned k = 0; k < _inview.extent(2); ++k) { _inview(i,j,k,0,0,0,0) = i/2 -j*j + k/3; } } @@ -143,8 +143,8 @@ struct InitDynRankViewFunctor { KOKKOS_INLINE_FUNCTION void operator()(const int i) const { - for (unsigned j = 0; j < _inview.dimension(1); ++j) { - for (unsigned k = 0; k < _inview.dimension(2); ++k) { + for (unsigned j = 0; j < _inview.extent(1); ++j) { + for (unsigned k = 0; k < _inview.extent(2); ++k) { _inview(i,j,k) = i/2 -j*j + k/3; } } @@ -163,8 +163,8 @@ struct InitDynRankViewFunctor { KOKKOS_INLINE_FUNCTION void operator()(const int i) const { - for (unsigned j = 0; j < _inview.dimension(1); ++j) { - for (unsigned k = 0; k < _inview.dimension(2); ++k) { + for (unsigned j = 0; j < _inview.extent(1); ++j) { + for (unsigned k = 0; k < _inview.extent(2); ++k) { _outview(i) += _inview(i,j,k) ; } } diff --git a/lib/kokkos/containers/performance_tests/TestGlobal2LocalIds.hpp b/lib/kokkos/containers/performance_tests/TestGlobal2LocalIds.hpp index 66f1fbf092dd4231e359602f4d6850fe757d7333..dcaca776be59b61b56ad82e78d6f715263e6082f 100644 --- a/lib/kokkos/containers/performance_tests/TestGlobal2LocalIds.hpp +++ b/lib/kokkos/containers/performance_tests/TestGlobal2LocalIds.hpp @@ -34,7 +34,7 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER @@ -76,7 +76,7 @@ struct generate_ids generate_ids( local_id_view & ids) : local_2_global(ids) { - Kokkos::parallel_for(local_2_global.dimension_0(), *this); + Kokkos::parallel_for(local_2_global.extent(0), *this); } @@ -116,7 +116,7 @@ struct fill_map fill_map( global_id_view gIds, local_id_view lIds) : global_2_local(gIds) , local_2_global(lIds) { - Kokkos::parallel_for(local_2_global.dimension_0(), *this); + Kokkos::parallel_for(local_2_global.extent(0), *this); } KOKKOS_INLINE_FUNCTION @@ -143,7 +143,7 @@ struct find_test find_test( global_id_view gIds, local_id_view lIds, value_type & num_errors) : global_2_local(gIds) , local_2_global(lIds) { - Kokkos::parallel_reduce(local_2_global.dimension_0(), *this, num_errors); + Kokkos::parallel_reduce(local_2_global.extent(0), *this, num_errors); } KOKKOS_INLINE_FUNCTION diff --git a/lib/kokkos/containers/performance_tests/TestMain.cpp b/lib/kokkos/containers/performance_tests/TestMain.cpp index 1224af7cdb5484101dea69f155810caccf2258cb..217b01a57afccf1bc7658ce41214d77fbffffd67 100644 --- a/lib/kokkos/containers/performance_tests/TestMain.cpp +++ b/lib/kokkos/containers/performance_tests/TestMain.cpp @@ -35,7 +35,7 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER diff --git a/lib/kokkos/containers/performance_tests/TestOpenMP.cpp b/lib/kokkos/containers/performance_tests/TestOpenMP.cpp index 012f45bab78b2ff24f4dd42e9eb5001568d20d14..66d497552e3de2dc09cd409bed204c35bc0ddb68 100644 --- a/lib/kokkos/containers/performance_tests/TestOpenMP.cpp +++ b/lib/kokkos/containers/performance_tests/TestOpenMP.cpp @@ -35,7 +35,7 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER diff --git a/lib/kokkos/containers/performance_tests/TestROCm.cpp b/lib/kokkos/containers/performance_tests/TestROCm.cpp index 6647d23065da7c06815155448bfaae211adc6b5b..3cf9f3bd143c5848af12e7ddb717ab8e4d59ce8e 100644 --- a/lib/kokkos/containers/performance_tests/TestROCm.cpp +++ b/lib/kokkos/containers/performance_tests/TestROCm.cpp @@ -35,7 +35,7 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER diff --git a/lib/kokkos/containers/performance_tests/TestScatterView.hpp b/lib/kokkos/containers/performance_tests/TestScatterView.hpp index 4fd69173c011e23233e9f26f02e2f7bd4eaf8a63..03129d2b09f17b03f34f8cb8a9b4442d9c570709 100644 --- a/lib/kokkos/containers/performance_tests/TestScatterView.hpp +++ b/lib/kokkos/containers/performance_tests/TestScatterView.hpp @@ -35,7 +35,7 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER diff --git a/lib/kokkos/containers/performance_tests/TestThreads.cpp b/lib/kokkos/containers/performance_tests/TestThreads.cpp index a8910a3c72a11eb26c1e7707e160b602d0ef220b..a951a5ca56e4f30fcbe39d0ae797f6bd0d126882 100644 --- a/lib/kokkos/containers/performance_tests/TestThreads.cpp +++ b/lib/kokkos/containers/performance_tests/TestThreads.cpp @@ -35,7 +35,7 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER diff --git a/lib/kokkos/containers/performance_tests/TestUnorderedMapPerformance.hpp b/lib/kokkos/containers/performance_tests/TestUnorderedMapPerformance.hpp index 93a206c9966b05ce026ad16262e4d0248600439c..e8734b259de911489e97ccce7bcfce6e11f3b387 100644 --- a/lib/kokkos/containers/performance_tests/TestUnorderedMapPerformance.hpp +++ b/lib/kokkos/containers/performance_tests/TestUnorderedMapPerformance.hpp @@ -34,7 +34,7 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER diff --git a/lib/kokkos/containers/src/Kokkos_Bitset.hpp b/lib/kokkos/containers/src/Kokkos_Bitset.hpp index 7714506e9217b3dbebc900244398e9c319afa383..c48058d75d774feaf424cf196522dfceadf9e150 100644 --- a/lib/kokkos/containers/src/Kokkos_Bitset.hpp +++ b/lib/kokkos/containers/src/Kokkos_Bitset.hpp @@ -35,7 +35,7 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER @@ -147,7 +147,7 @@ public: if (m_last_block_mask) { //clear the unused bits in the last block typedef Kokkos::Impl::DeepCopy< typename execution_space::memory_space, Kokkos::HostSpace > raw_deep_copy; - raw_deep_copy( m_blocks.ptr_on_device() + (m_blocks.dimension_0() -1u), &m_last_block_mask, sizeof(unsigned)); + raw_deep_copy( m_blocks.data() + (m_blocks.extent(0) -1u), &m_last_block_mask, sizeof(unsigned)); } } @@ -212,7 +212,7 @@ public: KOKKOS_FORCEINLINE_FUNCTION unsigned max_hint() const { - return m_blocks.dimension_0(); + return m_blocks.extent(0); } /// find a bit set to 1 near the hint @@ -221,10 +221,10 @@ public: KOKKOS_INLINE_FUNCTION Kokkos::pair find_any_set_near( unsigned hint , unsigned scan_direction = BIT_SCAN_FORWARD_MOVE_HINT_FORWARD ) const { - const unsigned block_idx = (hint >> block_shift) < m_blocks.dimension_0() ? (hint >> block_shift) : 0; + const unsigned block_idx = (hint >> block_shift) < m_blocks.extent(0) ? (hint >> block_shift) : 0; const unsigned offset = hint & block_mask; unsigned block = volatile_load(&m_blocks[ block_idx ]); - block = !m_last_block_mask || (block_idx < (m_blocks.dimension_0()-1)) ? block : block & m_last_block_mask ; + block = !m_last_block_mask || (block_idx < (m_blocks.extent(0)-1)) ? block : block & m_last_block_mask ; return find_any_helper(block_idx, offset, block, scan_direction); } @@ -238,7 +238,7 @@ public: const unsigned block_idx = hint >> block_shift; const unsigned offset = hint & block_mask; unsigned block = volatile_load(&m_blocks[ block_idx ]); - block = !m_last_block_mask || (block_idx < (m_blocks.dimension_0()-1) ) ? ~block : ~block & m_last_block_mask ; + block = !m_last_block_mask || (block_idx < (m_blocks.extent(0)-1) ) ? ~block : ~block & m_last_block_mask ; return find_any_helper(block_idx, offset, block, scan_direction); } @@ -281,8 +281,8 @@ private: unsigned update_hint( long long block_idx, unsigned offset, unsigned scan_direction ) const { block_idx += scan_direction & MOVE_HINT_BACKWARD ? -1 : 1; - block_idx = block_idx >= 0 ? block_idx : m_blocks.dimension_0() - 1; - block_idx = block_idx < static_cast(m_blocks.dimension_0()) ? block_idx : 0; + block_idx = block_idx >= 0 ? block_idx : m_blocks.extent(0) - 1; + block_idx = block_idx < static_cast(m_blocks.extent(0)) ? block_idx : 0; return static_cast(block_idx)*block_size + offset; } @@ -407,7 +407,7 @@ void deep_copy( Bitset & dst, Bitset const& src) } typedef Kokkos::Impl::DeepCopy< typename DstDevice::memory_space, typename SrcDevice::memory_space > raw_deep_copy; - raw_deep_copy(dst.m_blocks.ptr_on_device(), src.m_blocks.ptr_on_device(), sizeof(unsigned)*src.m_blocks.dimension_0()); + raw_deep_copy(dst.m_blocks.data(), src.m_blocks.data(), sizeof(unsigned)*src.m_blocks.extent(0)); } template @@ -418,7 +418,7 @@ void deep_copy( Bitset & dst, ConstBitset const& src) } typedef Kokkos::Impl::DeepCopy< typename DstDevice::memory_space, typename SrcDevice::memory_space > raw_deep_copy; - raw_deep_copy(dst.m_blocks.ptr_on_device(), src.m_blocks.ptr_on_device(), sizeof(unsigned)*src.m_blocks.dimension_0()); + raw_deep_copy(dst.m_blocks.data(), src.m_blocks.data(), sizeof(unsigned)*src.m_blocks.extent(0)); } template @@ -429,7 +429,7 @@ void deep_copy( ConstBitset & dst, ConstBitset const& src) } typedef Kokkos::Impl::DeepCopy< typename DstDevice::memory_space, typename SrcDevice::memory_space > raw_deep_copy; - raw_deep_copy(dst.m_blocks.ptr_on_device(), src.m_blocks.ptr_on_device(), sizeof(unsigned)*src.m_blocks.dimension_0()); + raw_deep_copy(dst.m_blocks.data(), src.m_blocks.data(), sizeof(unsigned)*src.m_blocks.extent(0)); } } // namespace Kokkos diff --git a/lib/kokkos/containers/src/Kokkos_DualView.hpp b/lib/kokkos/containers/src/Kokkos_DualView.hpp index 35cc8ec7534b8ad1bdc854f338826dabc0e9132a..74fe4418f870854498cd65cfe8e346d7d183e716 100644 --- a/lib/kokkos/containers/src/Kokkos_DualView.hpp +++ b/lib/kokkos/containers/src/Kokkos_DualView.hpp @@ -35,7 +35,7 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER @@ -262,14 +262,14 @@ public: modified_host (View ("DualView::modified_host")) { if ( int(d_view.rank) != int(h_view.rank) || - d_view.dimension_0() != h_view.dimension_0() || - d_view.dimension_1() != h_view.dimension_1() || - d_view.dimension_2() != h_view.dimension_2() || - d_view.dimension_3() != h_view.dimension_3() || - d_view.dimension_4() != h_view.dimension_4() || - d_view.dimension_5() != h_view.dimension_5() || - d_view.dimension_6() != h_view.dimension_6() || - d_view.dimension_7() != h_view.dimension_7() || + d_view.extent(0) != h_view.extent(0) || + d_view.extent(1) != h_view.extent(1) || + d_view.extent(2) != h_view.extent(2) || + d_view.extent(3) != h_view.extent(3) || + d_view.extent(4) != h_view.extent(4) || + d_view.extent(5) != h_view.extent(5) || + d_view.extent(6) != h_view.extent(6) || + d_view.extent(7) != h_view.extent(7) || d_view.stride_0() != h_view.stride_0() || d_view.stride_1() != h_view.stride_1() || d_view.stride_2() != h_view.stride_2() || @@ -503,6 +503,18 @@ public: /* Realloc on Device */ ::Kokkos::realloc(d_view,n0,n1,n2,n3,n4,n5,n6,n7); + + const bool sizeMismatch = ( h_view.extent(0) != n0 ) || + ( h_view.extent(1) != n1 ) || + ( h_view.extent(2) != n2 ) || + ( h_view.extent(3) != n3 ) || + ( h_view.extent(4) != n4 ) || + ( h_view.extent(5) != n5 ) || + ( h_view.extent(6) != n6 ) || + ( h_view.extent(7) != n7 ); + if ( sizeMismatch ) + ::Kokkos::resize(h_view,n0,n1,n2,n3,n4,n5,n6,n7); + t_host temp_view = create_mirror_view( d_view ); /* Remap on Host */ @@ -510,6 +522,8 @@ public: h_view = temp_view; + d_view = create_mirror_view( typename t_dev::execution_space(), h_view ); + /* Mark Host copy as modified */ modified_host() = modified_host()+1; } @@ -530,22 +544,34 @@ public: d_view.stride(stride_); } + template< typename iType > + KOKKOS_INLINE_FUNCTION constexpr + typename std::enable_if< std::is_integral::value , size_t >::type + extent( const iType & r ) const + { return d_view.extent(r); } + + template< typename iType > + KOKKOS_INLINE_FUNCTION constexpr + typename std::enable_if< std::is_integral::value , int >::type + extent_int( const iType & r ) const + { return static_cast(d_view.extent(r)); } + /* \brief return size of dimension 0 */ - size_t dimension_0() const {return d_view.dimension_0();} + size_t dimension_0() const {return d_view.extent(0);} /* \brief return size of dimension 1 */ - size_t dimension_1() const {return d_view.dimension_1();} + size_t dimension_1() const {return d_view.extent(1);} /* \brief return size of dimension 2 */ - size_t dimension_2() const {return d_view.dimension_2();} + size_t dimension_2() const {return d_view.extent(2);} /* \brief return size of dimension 3 */ - size_t dimension_3() const {return d_view.dimension_3();} + size_t dimension_3() const {return d_view.extent(3);} /* \brief return size of dimension 4 */ - size_t dimension_4() const {return d_view.dimension_4();} + size_t dimension_4() const {return d_view.extent(4);} /* \brief return size of dimension 5 */ - size_t dimension_5() const {return d_view.dimension_5();} + size_t dimension_5() const {return d_view.extent(5);} /* \brief return size of dimension 6 */ - size_t dimension_6() const {return d_view.dimension_6();} + size_t dimension_6() const {return d_view.extent(6);} /* \brief return size of dimension 7 */ - size_t dimension_7() const {return d_view.dimension_7();} + size_t dimension_7() const {return d_view.extent(7);} //@} }; diff --git a/lib/kokkos/containers/src/Kokkos_DynRankView.hpp b/lib/kokkos/containers/src/Kokkos_DynRankView.hpp index d22d6b865da99fa11a050e0bedfc5e088001a3ea..ccf53b3d5096574f4446d4cf9d7eee71b6e45c08 100644 --- a/lib/kokkos/containers/src/Kokkos_DynRankView.hpp +++ b/lib/kokkos/containers/src/Kokkos_DynRankView.hpp @@ -35,16 +35,16 @@ // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) // // ************************************************************************ //@HEADER */ /// \file Kokkos_DynRankView.hpp -/// \brief Declaration and definition of Kokkos::Experimental::DynRankView. +/// \brief Declaration and definition of Kokkos::DynRankView. /// -/// This header file declares and defines Kokkos::Experimental::DynRankView and its +/// This header file declares and defines Kokkos::DynRankView and its /// related nonmember functions. #ifndef KOKKOS_DYNRANKVIEW_HPP @@ -55,7 +55,6 @@ #include namespace Kokkos { -namespace Experimental { template< typename DataType , class ... Properties > class DynRankView; //forward declare @@ -156,7 +155,7 @@ struct DynRankDimTraits { // Extra overload to match that for specialize types template KOKKOS_INLINE_FUNCTION - static typename std::enable_if< (std::is_same::value || std::is_same::value || std::is_same::value) , typename Traits::array_layout >::type createLayout( const ViewCtorProp& prop, const typename Traits::array_layout& layout ) + static typename std::enable_if< (std::is_same::value || std::is_same::value || std::is_same::value) , typename Traits::array_layout >::type createLayout( const Kokkos::Impl::ViewCtorProp& prop, const typename Traits::array_layout& layout ) { return createLayout( layout ); } @@ -318,7 +317,6 @@ void dyn_rank_view_verify_operator_bounds struct ViewToDynRankViewTag {}; } // namespace Impl -} // namespace Experimental namespace Impl { @@ -348,7 +346,7 @@ class ViewMapping< DstTraits , SrcTraits , ) ) ) - ) , Kokkos::Experimental::Impl::ViewToDynRankViewTag >::type > + ) , Kokkos::Impl::ViewToDynRankViewTag >::type > { private: @@ -375,7 +373,7 @@ public: template < typename DT , typename ... DP , typename ST , typename ... SP > KOKKOS_INLINE_FUNCTION - static void assign( Kokkos::Experimental::DynRankView< DT , DP...> & dst , const Kokkos::View< ST , SP... > & src ) + static void assign( Kokkos::DynRankView< DT , DP...> & dst , const Kokkos::View< ST , SP... > & src ) { static_assert( is_assignable_value_type , "View assignment must have same value type or const = non-const" ); @@ -395,8 +393,6 @@ public: } //end Impl -namespace Experimental { - /* \class DynRankView * \brief Container that creates a Kokkos view with rank determined at runtime. * Essentially this is a rank 7 view @@ -415,7 +411,7 @@ namespace Experimental { template< class > struct is_dyn_rank_view : public std::false_type {}; template< class D, class ... P > -struct is_dyn_rank_view< Kokkos::Experimental::DynRankView > : public std::true_type {}; +struct is_dyn_rank_view< Kokkos::DynRankView > : public std::true_type {}; template< typename DataType , class ... Properties > @@ -425,7 +421,7 @@ class DynRankView : public ViewTraits< DataType , Properties ... > private: template < class , class ... > friend class DynRankView ; - template < class , class ... > friend class Impl::ViewMapping ; + template < class , class ... > friend class Kokkos::Impl::ViewMapping ; public: typedef ViewTraits< DataType , Properties ... > drvtraits ; @@ -437,7 +433,7 @@ public: private: typedef Kokkos::Impl::ViewMapping< traits , void > map_type ; - typedef Kokkos::Experimental::Impl::SharedAllocationTracker track_type ; + typedef Kokkos::Impl::SharedAllocationTracker track_type ; track_type m_track ; map_type m_map ; @@ -601,7 +597,7 @@ private: // rank of the calling operator - included as first argument in ARG #define KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( ARG ) \ DynRankView::template verify_space< Kokkos::Impl::ActiveExecutionMemorySpace >::check(); \ - Kokkos::Experimental::Impl::dyn_rank_view_verify_operator_bounds< typename traits::memory_space > ARG ; + Kokkos::Impl::dyn_rank_view_verify_operator_bounds< typename traits::memory_space > ARG ; #else @@ -778,6 +774,140 @@ public: return m_map.reference(i0,i1,i2,i3,i4,i5,i6); } + // Rank 0 + KOKKOS_INLINE_FUNCTION + reference_type access() const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (0 , this->rank(), m_track, m_map) ) + return implementation_map().reference(); + //return m_map.reference(0,0,0,0,0,0,0); + } + + // Rank 1 + // Rank 1 parenthesis + template< typename iType > + KOKKOS_INLINE_FUNCTION + typename std::enable_if< (std::is_same::value && std::is_integral::value), reference_type>::type + access(const iType & i0 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (1 , this->rank(), m_track, m_map, i0) ) + return m_map.reference(i0); + } + + template< typename iType > + KOKKOS_INLINE_FUNCTION + typename std::enable_if< !(std::is_same::value && std::is_integral::value), reference_type>::type + access(const iType & i0 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (1 , this->rank(), m_track, m_map, i0) ) + return m_map.reference(i0,0,0,0,0,0,0); + } + + // Rank 2 + template< typename iType0 , typename iType1 > + KOKKOS_INLINE_FUNCTION + typename std::enable_if< (std::is_same::value && std::is_integral::value && std::is_integral::value), reference_type>::type + access(const iType0 & i0 , const iType1 & i1 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (2 , this->rank(), m_track, m_map, i0, i1) ) + return m_map.reference(i0,i1); + } + + template< typename iType0 , typename iType1 > + KOKKOS_INLINE_FUNCTION + typename std::enable_if< !(std::is_same::value && std::is_integral::value), reference_type>::type + access(const iType0 & i0 , const iType1 & i1 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (2 , this->rank(), m_track, m_map, i0, i1) ) + return m_map.reference(i0,i1,0,0,0,0,0); + } + + // Rank 3 + template< typename iType0 , typename iType1 , typename iType2 > + KOKKOS_INLINE_FUNCTION + typename std::enable_if< (std::is_same::value && std::is_integral::value && std::is_integral::value && std::is_integral::value), reference_type>::type + access(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (3 , this->rank(), m_track, m_map, i0, i1, i2) ) + return m_map.reference(i0,i1,i2); + } + + template< typename iType0 , typename iType1 , typename iType2 > + KOKKOS_INLINE_FUNCTION + typename std::enable_if< !(std::is_same::value && std::is_integral::value), reference_type>::type + access(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (3 , this->rank(), m_track, m_map, i0, i1, i2) ) + return m_map.reference(i0,i1,i2,0,0,0,0); + } + + // Rank 4 + template< typename iType0 , typename iType1 , typename iType2 , typename iType3 > + KOKKOS_INLINE_FUNCTION + typename std::enable_if< (std::is_same::value && std::is_integral::value && std::is_integral::value && std::is_integral::value && std::is_integral::value), reference_type>::type + access(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (4 , this->rank(), m_track, m_map, i0, i1, i2, i3) ) + return m_map.reference(i0,i1,i2,i3); + } + + template< typename iType0 , typename iType1 , typename iType2 , typename iType3 > + KOKKOS_INLINE_FUNCTION + typename std::enable_if< !(std::is_same::value && std::is_integral::value), reference_type>::type + access(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (4 , this->rank(), m_track, m_map, i0, i1, i2, i3) ) + return m_map.reference(i0,i1,i2,i3,0,0,0); + } + + // Rank 5 + template< typename iType0 , typename iType1 , typename iType2 , typename iType3, typename iType4 > + KOKKOS_INLINE_FUNCTION + typename std::enable_if< (std::is_same::value && std::is_integral::value && std::is_integral::value && std::is_integral::value && std::is_integral::value && std::is_integral::value), reference_type>::type + access(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (5 , this->rank(), m_track, m_map, i0, i1, i2, i3, i4) ) + return m_map.reference(i0,i1,i2,i3,i4); + } + + template< typename iType0 , typename iType1 , typename iType2 , typename iType3, typename iType4 > + KOKKOS_INLINE_FUNCTION + typename std::enable_if< !(std::is_same::value && std::is_integral::value), reference_type>::type + access(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (5 , this->rank(), m_track, m_map, i0, i1, i2, i3, i4) ) + return m_map.reference(i0,i1,i2,i3,i4,0,0); + } + + // Rank 6 + template< typename iType0 , typename iType1 , typename iType2 , typename iType3, typename iType4 , typename iType5 > + KOKKOS_INLINE_FUNCTION + typename std::enable_if< (std::is_same::value && std::is_integral::value && std::is_integral::value && std::is_integral::value && std::is_integral::value && std::is_integral::value && std::is_integral::value), reference_type>::type + access(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 , const iType5 & i5 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (6 , this->rank(), m_track, m_map, i0, i1, i2, i3, i4, i5) ) + return m_map.reference(i0,i1,i2,i3,i4,i5); + } + + template< typename iType0 , typename iType1 , typename iType2 , typename iType3, typename iType4 , typename iType5 > + KOKKOS_INLINE_FUNCTION + typename std::enable_if< !(std::is_same::value && std::is_integral::value), reference_type>::type + access(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 , const iType5 & i5 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (6 , this->rank(), m_track, m_map, i0, i1, i2, i3, i4, i5) ) + return m_map.reference(i0,i1,i2,i3,i4,i5,0); + } + + // Rank 7 + template< typename iType0 , typename iType1 , typename iType2 , typename iType3, typename iType4 , typename iType5 , typename iType6 > + KOKKOS_INLINE_FUNCTION + typename std::enable_if< (std::is_integral::value && std::is_integral::value && std::is_integral::value && std::is_integral::value && std::is_integral::value && std::is_integral::value && std::is_integral::value), reference_type>::type + access(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 , const iType5 & i5 , const iType6 & i6 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (7 , this->rank(), m_track, m_map, i0, i1, i2, i3, i4, i5, i6) ) + return m_map.reference(i0,i1,i2,i3,i4,i5,i6); + } + #undef KOKKOS_IMPL_VIEW_OPERATOR_VERIFY //---------------------------------------- @@ -830,7 +960,6 @@ public: return *this; } -// Experimental // Copy/Assign View to DynRankView template< class RT , class ... RP > KOKKOS_INLINE_FUNCTION @@ -840,7 +969,7 @@ public: , m_rank( rhs.Rank ) { typedef typename View::traits SrcTraits ; - typedef Kokkos::Impl::ViewMapping< traits , SrcTraits , Kokkos::Experimental::Impl::ViewToDynRankViewTag > Mapping ; + typedef Kokkos::Impl::ViewMapping< traits , SrcTraits , Kokkos::Impl::ViewToDynRankViewTag > Mapping ; static_assert( Mapping::is_assignable , "Incompatible DynRankView copy construction" ); Mapping::assign( *this , rhs ); } @@ -850,7 +979,7 @@ public: DynRankView & operator = ( const View & rhs ) { typedef typename View::traits SrcTraits ; - typedef Kokkos::Impl::ViewMapping< traits , SrcTraits , Kokkos::Experimental::Impl::ViewToDynRankViewTag > Mapping ; + typedef Kokkos::Impl::ViewMapping< traits , SrcTraits , Kokkos::Impl::ViewToDynRankViewTag > Mapping ; static_assert( Mapping::is_assignable , "Incompatible View to DynRankView copy assignment" ); Mapping::assign( *this , rhs ); return *this ; @@ -872,8 +1001,8 @@ public: // unused arg_layout dimensions must be set to ~size_t(0) so that rank deduction can properly take place template< class ... P > explicit inline - DynRankView( const Impl::ViewCtorProp< P ... > & arg_prop - , typename std::enable_if< ! Impl::ViewCtorProp< P... >::has_pointer + DynRankView( const Kokkos::Impl::ViewCtorProp< P ... > & arg_prop + , typename std::enable_if< ! Kokkos::Impl::ViewCtorProp< P... >::has_pointer , typename traits::array_layout >::type const & arg_layout ) @@ -882,11 +1011,11 @@ public: , m_rank( Impl::DynRankDimTraits::template computeRank< typename traits::array_layout, P...>(arg_prop, arg_layout) ) { // Append layout and spaces if not input - typedef Impl::ViewCtorProp< P ... > alloc_prop_input ; + typedef Kokkos::Impl::ViewCtorProp< P ... > alloc_prop_input ; // use 'std::integral_constant' for non-types // to avoid duplicate class error. - typedef Impl::ViewCtorProp + typedef Kokkos::Impl::ViewCtorProp < P ... , typename std::conditional < alloc_prop_input::has_label @@ -931,7 +1060,7 @@ public: #endif //------------------------------------------------------------ - Kokkos::Experimental::Impl::SharedAllocationRecord<> * + Kokkos::Impl::SharedAllocationRecord<> * record = m_map.allocate_shared( prop , Impl::DynRankDimTraits::template createLayout(arg_prop, arg_layout) ); //------------------------------------------------------------ @@ -950,8 +1079,8 @@ public: // Wrappers template< class ... P > explicit KOKKOS_INLINE_FUNCTION - DynRankView( const Impl::ViewCtorProp< P ... > & arg_prop - , typename std::enable_if< Impl::ViewCtorProp< P... >::has_pointer + DynRankView( const Kokkos::Impl::ViewCtorProp< P ... > & arg_prop + , typename std::enable_if< Kokkos::Impl::ViewCtorProp< P... >::has_pointer , typename traits::array_layout >::type const & arg_layout ) @@ -972,8 +1101,8 @@ public: // Simple dimension-only layout template< class ... P > explicit inline - DynRankView( const Impl::ViewCtorProp< P ... > & arg_prop - , typename std::enable_if< ! Impl::ViewCtorProp< P... >::has_pointer + DynRankView( const Kokkos::Impl::ViewCtorProp< P ... > & arg_prop + , typename std::enable_if< ! Kokkos::Impl::ViewCtorProp< P... >::has_pointer , size_t >::type const arg_N0 = ~size_t(0) , const size_t arg_N1 = ~size_t(0) @@ -992,8 +1121,8 @@ public: template< class ... P > explicit KOKKOS_INLINE_FUNCTION - DynRankView( const Impl::ViewCtorProp< P ... > & arg_prop - , typename std::enable_if< Impl::ViewCtorProp< P... >::has_pointer + DynRankView( const Kokkos::Impl::ViewCtorProp< P ... > & arg_prop + , typename std::enable_if< Kokkos::Impl::ViewCtorProp< P... >::has_pointer , size_t >::type const arg_N0 = ~size_t(0) , const size_t arg_N1 = ~size_t(0) @@ -1015,10 +1144,10 @@ public: explicit inline DynRankView( const Label & arg_label , typename std::enable_if< - Kokkos::Experimental::Impl::is_view_label