Unverified Commit c8561ece authored by Axel Kohlmeyer's avatar Axel Kohlmeyer Committed by GitHub
Browse files

Merge pull request #1879 from akohlmey/user-plumed-update 

Update USER-PLUMED to include support for version 2.6.0. Fix bug in API check
parents d01b0ed5 4cacc470

cmake/Modules/Packages/USER-PLUMED.cmake

+2 −2
Original line number Diff line number Diff line
@@ -49,8 +49,8 @@ if(PKG_USER-PLUMED) 
    message(STATUS "PLUMED download requested - we will build our own")

    include(ExternalProject)

    ExternalProject_Add(plumed_build

      URL https://github.com/plumed/plumed2/releases/download/v2.5.3/plumed-src-2.5.3.tgz

      URL_MD5 de30d6e7c2dcc0973298e24a6da24286

      URL https://github.com/plumed/plumed2/releases/download/v2.6.0/plumed-src-2.6.0.tgz

      URL_MD5 204d2edae58d9b10ba3ad460cad64191

      BUILD_IN_SOURCE 1

      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>

                                               ${CONFIGURE_REQUEST_PIC}

doc/src/Build_extras.rst

+3 −0
Original line number Diff line number Diff line
@@ -880,6 +880,9 @@ USER-PLUMED package 
Before building LAMMPS with this package, you must first build PLUMED.

PLUMED can be built as part of the LAMMPS build or installed separately

from LAMMPS using the generic `plumed installation instructions <plumedinstall_>`_.

The USER-PLUMED package has been tested to work with Plumed versions

2.4.x, 2.5.x, and 2.6.x and will error out, when trying to run calculations

with a different version of the Plumed kernel.





PLUMED can be linked into MD codes in three different modes: static,

examples/USER/plumed/log.27Nov18.peptide-plumed.g++.1→examples/USER/plumed/log.4Feb20.peptide-plumed.g++.1

+18 −16
Original line number Diff line number Diff line 
LAMMPS (27 Nov 2018)

  using 1 OpenMP thread(s) per MPI task

LAMMPS (4 Feb 2020)

# Solvated 5-mer peptide



units		real
@@ -39,6 +38,8 @@ read_data data.peptide 
  7 = max # of 1-3 neighbors

  14 = max # of 1-4 neighbors

  18 = max # of special neighbors

  special bonds CPU = 0.000809431 secs

  read_data CPU = 0.0102327 secs



neighbor	2.0 bin

neigh_modify	delay 5
@@ -66,6 +67,7 @@ fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 
  6 = # of size 3 clusters

  3 = # of size 4 clusters

  640 = # of frozen angles

  find clusters CPU = 0.000631809 secs



#dump		1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz

#dump_modify 1 sort id
@@ -77,13 +79,13 @@ variable pe equal pe 


run		101

PPPM initialization ...

  using 12-bit tables for long-range coulomb (src/kspace.cpp:321)

  using 12-bit tables for long-range coulomb (src/kspace.cpp:332)

  G vector (1/distance) = 0.268725

  grid = 15 15 15

  stencil order = 5

  estimated absolute RMS force accuracy = 0.0228209

  estimated relative force accuracy = 6.87243e-05

  using double precision FFTs

  using double precision FFTW3

  3d grid and FFT values/proc = 10648 3375

Neighbor list info ...

  update every 1 steps, delay 5 steps, check yes
@@ -106,7 +108,7 @@ SHAKE stats (type/ave/delta) on step 0 
  14 0.96 0

  18 0.957206 4.37979e-05

  31 104.519 0.00396029

Per MPI rank memory allocation (min/avg/max) = 18.74 | 18.74 | 18.74 Mbytes

Per MPI rank memory allocation (min/avg/max) = 19.07 | 19.07 | 19.07 Mbytes

Step Temp TotEng PotEng KinEng E_pair E_bond f_2 

       0    282.10052    -5237.458   -6372.3766    1134.9186    -6442.768    16.557152            0 

      10     276.9783   -5234.3057   -6348.6171    1114.3114   -6421.6171    17.024361   0.47785504
@@ -129,22 +131,22 @@ SHAKE stats (type/ave/delta) on step 100 
  31 104.52 0.000760401

     100    270.40648   -5234.9604   -6322.8327    1087.8723     -6417.73    19.666404 0.0094784372 

     101    270.99811   -5235.8295    -6326.082    1090.2525   -6418.8974    17.285816  0.086681332 

Loop time of 2.73445 on 1 procs for 101 steps with 2004 atoms

Loop time of 2.69839 on 1 procs for 101 steps with 2004 atoms



Performance: 6.383 ns/day, 3.760 hours/ns, 36.936 timesteps/s

99.7% CPU use with 1 MPI tasks x 1 OpenMP threads

Performance: 6.468 ns/day, 3.711 hours/ns, 37.430 timesteps/s

99.7% CPU use with 1 MPI tasks x no OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 2.2617     | 2.2617     | 2.2617     |   0.0 | 82.71

Bond    | 0.0044148  | 0.0044148  | 0.0044148  |   0.0 |  0.16

Kspace  | 0.17883    | 0.17883    | 0.17883    |   0.0 |  6.54

Neigh   | 0.23945    | 0.23945    | 0.23945    |   0.0 |  8.76

Comm    | 0.011672   | 0.011672   | 0.011672   |   0.0 |  0.43

Output  | 0.00028348 | 0.00028348 | 0.00028348 |   0.0 |  0.01

Modify  | 0.0365     | 0.0365     | 0.0365     |   0.0 |  1.33

Other   |            | 0.001611   |            |       |  0.06

Pair    | 2.2853     | 2.2853     | 2.2853     |   0.0 | 84.69

Bond    | 0.0065637  | 0.0065637  | 0.0065637  |   0.0 |  0.24

Kspace  | 0.14949    | 0.14949    | 0.14949    |   0.0 |  5.54

Neigh   | 0.1938     | 0.1938     | 0.1938     |   0.0 |  7.18

Comm    | 0.0096588  | 0.0096588  | 0.0096588  |   0.0 |  0.36

Output  | 0.00039172 | 0.00039172 | 0.00039172 |   0.0 |  0.01

Modify  | 0.050643   | 0.050643   | 0.050643   |   0.0 |  1.88

Other   |            | 0.00258    |            |       |  0.10



Nlocal:    2004 ave 2004 max 2004 min

Histogram: 1 0 0 0 0 0 0 0 0 0

examples/USER/plumed/log.27Nov18.peptide-plumed.g++.4→examples/USER/plumed/log.4Feb20.peptide-plumed.g++.4

+18 −16
Original line number Diff line number Diff line 
LAMMPS (27 Nov 2018)

  using 1 OpenMP thread(s) per MPI task

LAMMPS (4 Feb 2020)

# Solvated 5-mer peptide



units		real
@@ -39,6 +38,8 @@ read_data data.peptide 
  7 = max # of 1-3 neighbors

  14 = max # of 1-4 neighbors

  18 = max # of special neighbors

  special bonds CPU = 0.00095129 secs

  read_data CPU = 0.0199838 secs



neighbor	2.0 bin

neigh_modify	delay 5
@@ -66,6 +67,7 @@ fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 
  6 = # of size 3 clusters

  3 = # of size 4 clusters

  640 = # of frozen angles

  find clusters CPU = 0.000829935 secs



#dump		1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz

#dump_modify 1 sort id
@@ -77,13 +79,13 @@ variable pe equal pe 


run		101

PPPM initialization ...

  using 12-bit tables for long-range coulomb (src/kspace.cpp:321)

  using 12-bit tables for long-range coulomb (src/kspace.cpp:332)

  G vector (1/distance) = 0.268725

  grid = 15 15 15

  stencil order = 5

  estimated absolute RMS force accuracy = 0.0228209

  estimated relative force accuracy = 6.87243e-05

  using double precision FFTs

  using double precision FFTW3

  3d grid and FFT values/proc = 4312 960

Neighbor list info ...

  update every 1 steps, delay 5 steps, check yes
@@ -106,7 +108,7 @@ SHAKE stats (type/ave/delta) on step 0 
  14 0.96 0

  18 0.957206 4.37979e-05

  31 104.519 0.00396029

Per MPI rank memory allocation (min/avg/max) = 15.66 | 15.87 | 16.06 Mbytes

Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.23 | 16.42 Mbytes

Step Temp TotEng PotEng KinEng E_pair E_bond f_2 

       0    282.10052    -5237.458   -6372.3766    1134.9186    -6442.768    16.557152            0 

      10     276.9783   -5234.3057   -6348.6171    1114.3114   -6421.6171    17.024361   0.47785504
@@ -129,22 +131,22 @@ SHAKE stats (type/ave/delta) on step 100 
  31 104.52 0.000760401

     100    270.40648   -5234.9604   -6322.8327    1087.8723     -6417.73    19.666404 0.0094784372 

     101    270.99811   -5235.8295    -6326.082    1090.2525   -6418.8974    17.285816  0.086681332 

Loop time of 0.812799 on 4 procs for 101 steps with 2004 atoms

Loop time of 0.873215 on 4 procs for 101 steps with 2004 atoms



Performance: 21.472 ns/day, 1.118 hours/ns, 124.262 timesteps/s

97.5% CPU use with 4 MPI tasks x 1 OpenMP threads

Performance: 19.987 ns/day, 1.201 hours/ns, 115.664 timesteps/s

92.5% CPU use with 4 MPI tasks x no OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.57957    | 0.59988    | 0.62504    |   2.6 | 73.80

Bond    | 0.00080013 | 0.0017412  | 0.0028315  |   2.1 |  0.21

Kspace  | 0.075724   | 0.10008    | 0.12023    |   6.4 | 12.31

Neigh   | 0.067733   | 0.067947   | 0.068168   |   0.1 |  8.36

Comm    | 0.01375    | 0.014175   | 0.014681   |   0.3 |  1.74

Output  | 0.00025511 | 0.00051183 | 0.001277   |   0.0 |  0.06

Modify  | 0.026406   | 0.026436   | 0.026462   |   0.0 |  3.25

Other   |            | 0.002027   |            |       |  0.25

Pair    | 0.58191    | 0.61681    | 0.66371    |   3.8 | 70.64

Bond    | 0.00099587 | 0.0023546  | 0.0041356  |   2.8 |  0.27

Kspace  | 0.096162   | 0.14486    | 0.18119    |   8.1 | 16.59

Neigh   | 0.059843   | 0.059864   | 0.059876   |   0.0 |  6.86

Comm    | 0.013623   | 0.01368    | 0.013723   |   0.0 |  1.57

Output  | 0.00031137 | 0.0010193  | 0.0024326  |   2.6 |  0.12

Modify  | 0.031552   | 0.031697   | 0.032087   |   0.1 |  3.63

Other   |            | 0.002938   |            |       |  0.34



Nlocal:    501 ave 512 max 492 min

Histogram: 1 0 0 1 0 1 0 0 0 1

examples/USER/plumed/reference/p.log

+17 −16
Original line number Diff line number Diff line 
PLUMED: PLUMED is starting

PLUMED: Version: 2.4.2 (git: Unknown) compiled on Jul 11 2018 at 19:09:03

PLUMED: Please cite this paper when using PLUMED [1]

PLUMED: Version: 2.6.0 (git: Unknown) compiled on Feb 13 2020 at 15:49:44

PLUMED: Please cite these papers when using PLUMED [1][2]

PLUMED: For further information see the PLUMED web page at http://www.plumed.org

PLUMED: Root: /Users/gareth/MD_code/lammps-permanent/lammps/lib/plumed/plumed2-2.4.2/

PLUMED: For installed feature, see /Users/gareth/MD_code/lammps-permanent/lammps/lib/plumed/plumed2-2.4.2//src/config/config.txt

PLUMED: Root: /home/akohlmey/compile/lammps/build-gcc/plumed_build-prefix/lib/plumed

PLUMED: For installed feature, see /home/akohlmey/compile/lammps/build-gcc/plumed_build-prefix/lib/plumed/src/config/config.txt

PLUMED: Molecular dynamics engine: LAMMPS

PLUMED: Precision of reals: 8

PLUMED: Running over 1 node

PLUMED: Running over 4 nodes

PLUMED: Number of threads: 1

PLUMED: Cache line size: 512

PLUMED: Number of atoms: 2004
@@ -14,13 +14,13 @@ PLUMED: File suffix: 
PLUMED: FILE: plumed.dat

PLUMED: Action UNITS

PLUMED:   with label @0

PLUMED:   length: A

PLUMED:   energy: kcal/mol

PLUMED:   length: A = 0.1 nm

PLUMED:   energy: kcal/mol = 4.184 kj/mol

PLUMED:   time: ps

PLUMED:   charge: e

PLUMED:   mass: amu

PLUMED:   using physical units

PLUMED:   inside PLUMED, Boltzmann constant is 0.001987

PLUMED:   inside PLUMED, Boltzmann constant is 0.0019872

PLUMED: Action DISTANCE

PLUMED:   with label dd

PLUMED:   between atoms 45 48
@@ -44,14 +44,15 @@ PLUMED: Timestep: 0.002000 
PLUMED: KbT has not been set by the MD engine

PLUMED: It should be set by hand where needed

PLUMED: Relevant bibliography:

PLUMED:   [1] Tribello, Bonomi, Branduardi, Camilloni, and Bussi, Comput. Phys. Commun. 185, 604 (2014)

PLUMED:   [1] The PLUMED consortium, Nat. Methods 16, 670 (2019)

PLUMED:   [2] Tribello, Bonomi, Branduardi, Camilloni, and Bussi, Comput. Phys. Commun. 185, 604 (2014)

PLUMED: Please read and cite where appropriate!

PLUMED: Finished setup

PLUMED:                                               Cycles        Total      Average      Minumum      Maximum

PLUMED:                                                    1     0.020354     0.020354     0.020354     0.020354

PLUMED: 1 Prepare dependencies                           102     0.000256     0.000003     0.000001     0.000006

PLUMED: 2 Sharing data                                   102     0.010002     0.000098     0.000078     0.000546

PLUMED: 3 Waiting for data                               102     0.001398     0.000014     0.000011     0.000072

PLUMED: 4 Calculating (forward loop)                     102     0.001797     0.000018     0.000013     0.000058

PLUMED: 5 Applying (backward loop)                       102     0.002666     0.000026     0.000022     0.000062

PLUMED: 6 Update                                         102     0.001126     0.000011     0.000007     0.000055
 
PLUMED:                                                    1     0.010018     0.010018     0.010018     0.010018

PLUMED: 1 Prepare dependencies                           102     0.000241     0.000002     0.000001     0.000003

PLUMED: 2 Sharing data                                   102     0.002132     0.000021     0.000006     0.000151

PLUMED: 3 Waiting for data                               102     0.001640     0.000016     0.000008     0.000067

PLUMED: 4 Calculating (forward loop)                     102     0.000825     0.000008     0.000005     0.000013

PLUMED: 5 Applying (backward loop)                       102     0.000522     0.000005     0.000002     0.000015

PLUMED: 6 Update                                         102     0.001755     0.000017     0.000011     0.000067

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