update manual links that got broken when removing and renumbering a section

:link(start_6,Section_start.html#start_6)

:link(start_7,Section_start.html#start_7)

:link(start_8,Section_start.html#start_8)

:link(start_9,Section_start.html#start_9)

:link(cmd_1,Section_commands.html#cmd_1)

:link(cmd_2,Section_commands.html#cmd_2)

For the set of runs, look at the timing data printed to the screen and

log file at the end of each LAMMPS run.  "This

section"_Section_start.html#start_8 of the manual has an overview.

section"_Section_start.html#start_7 of the manual has an overview.

Running on one (or a few processors) should give a good estimate of

the serial performance and what portions of the timestep are taking

  make machine |

prepare and test a regular LAMMPS simulation |

  lmp_machine -in in.script; mpirun -np 32 lmp_machine -in in.script |

enable specific accelerator support via '-k on' "command-line switch"_Section_start.html#start_7, |

enable specific accelerator support via '-k on' "command-line switch"_Section_start.html#start_6, |

  only needed for KOKKOS package |

set any needed options for the package via "-pk" "command-line switch"_Section_start.html#start_7 or "package"_package.html command, |

set any needed options for the package via "-pk" "command-line switch"_Section_start.html#start_6 or "package"_package.html command, |

  only if defaults need to be changed |

use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_7 or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu

use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_6 or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu

:tb(c=2,s=|)

Note that the first 4 steps can be done as a single command, using the

src/Make.py tool.  This tool is discussed in "Section

2.4"_Section_start.html#start_4 of the manual, and its use is

4"_Section_packages.html of the manual, and its use is

illustrated in the individual accelerator sections.  Typically these

steps only need to be done once, to create an executable that uses one

or more accelerator packages.

mistyped the style name or that the command is part of an optional

package which was not compiled into your executable.  The list of

available styles in your executable can be listed by using "the -h

command-line argument"_Section_start.html#start_7.  The installation

command-line argument"_Section_start.html#start_6.  The installation

and compilation of optional packages is explained in the "installation

instructions"_Section_start.html#start_3.

command.  At a later time, these binary files can be read via a

"read_restart"_read_restart.html command in a new script.  Or they can

be converted to text data files using the "-r command-line

switch"_Section_start.html#start_7 and read by a

switch"_Section_start.html#start_6 and read by a

"read_data"_read_data.html command in a new script.

Here we give examples of 2 scripts that read either a binary restart

multiple processors, but assumed you are running LAMMPS on a single

partition of processors.  LAMMPS can be run on multiple partitions via

the "-partition" command-line switch as described in "this

section"_Section_start.html#start_7 of the manual.

section"_Section_start.html#start_6 of the manual.

In the last 2 examples, if LAMMPS were run on 3 partitions, the same

scripts could be used if the "index" and "loop" variables were

In all these cases, you must run with one or more processors per

replica.  The processors assigned to each replica are determined at

run-time by using the "-partition command-line

switch"_Section_start.html#start_7 to launch LAMMPS on multiple

switch"_Section_start.html#start_6 to launch LAMMPS on multiple

partitions, which in this context are the same as replicas.  E.g.

these commands:

mpirun -np 8 lmp_linux -partition 8x1 -in in.neb :pre

would each run 8 replicas, on either 16 or 8 processors.  Note the use

of the "-in command-line switch"_Section_start.html#start_7 to specify

of the "-in command-line switch"_Section_start.html#start_6 to specify

the input script which is required when running in multi-replica mode.

Also note that with MPI installed on a machine (e.g. your desktop),

The lammps_open() function is used to initialize LAMMPS, passing in a

list of strings as if they were "command-line

arguments"_Section_start.html#start_7 when LAMMPS is run in

arguments"_Section_start.html#start_6 when LAMMPS is run in

stand-alone mode from the command line, and a MPI communicator for

LAMMPS to run under.  It returns a ptr to the LAMMPS object that is

created, and which is used in subsequent library calls.  The

details of what hardware and Cuda software is required on your system,

and details on how to build and use this package.  Its styles can be

invoked at run time via the "-sf gpu" or "-suffix gpu" "command-line

switches"_Section_start.html#start_7.  See also the "KOKKOS"_#KOKKOS

switches"_Section_start.html#start_6.  See also the "KOKKOS"_#KOKKOS

package, which has GPU-enabled styles.

[Authors:] Mike Brown (Intel) while at Sandia and ORNL and Trung Nguyen

lib/gpu/README

"Section 5.3"_Section_accelerate.html#acc_3

"Section 5.3.1"_accelerate_gpu.html

"Section 2.7 -sf gpu"_Section_start.html#start_7

"Section 2.7 -pk gpu"_Section_start.html#start_7

"Section 2.6 -sf gpu"_Section_start.html#start_6

"Section 2.6 -pk gpu"_Section_start.html#start_6

"package gpu"_package.html

Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 for pair styles followed by (g)

"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul

what hardware and software is required on your system, and how to

build and use this package.  Its styles can be invoked at run time via

the "-sf kk" or "-suffix kk" "command-line

switches"_Section_start.html#start_7.  Also see the "GPU"_#GPU,

switches"_Section_start.html#start_6.  Also see the "GPU"_#GPU,

"OPT"_#OPT, "USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP

packages, which have styles optimized for CPUs, KNLs, and GPUs.

lib/kokkos/README

"Section 5.3"_Section_accelerate.html#acc_3

"Section 5.3.3"_accelerate_kokkos.html

"Section 2.7 -k on ..."_Section_start.html#start_7

"Section 2.7 -sf kk"_Section_start.html#start_7

"Section 2.7 -pk kokkos"_Section_start.html#start_7

"Section 2.6 -k on ..."_Section_start.html#start_6

"Section 2.6 -sf kk"_Section_start.html#start_6

"Section 2.6 -pk kokkos"_Section_start.html#start_6

"package kokkos"_package.html

Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (k)

"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul

their style name.  "Section 5.3.5"_accelerate_opt.html gives details

of how to build and use this package.  Its styles can be invoked at

run time via the "-sf opt" or "-suffix opt" "command-line

switches"_Section_start.html#start_7.  See also the "KOKKOS"_#KOKKOS,

switches"_Section_start.html#start_6.  See also the "KOKKOS"_#KOKKOS,

"USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP packages, which

have styles optimized for CPU performance.

src/OPT: filenames -> commands

"Section 5.3"_Section_accelerate.html#acc_3

"Section 5.3.5"_accelerate_opt.html

"Section 2.7 -sf opt"_Section_start.html#start_7

"Section 2.6 -sf opt"_Section_start.html#start_6

Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 for pair styles followed by (t)

"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul

5.3.2"_accelerate_intel.html gives details of what hardware and

compilers are required on your system, and how to build and use this

package.  Its styles can be invoked at run time via the "-sf intel" or

"-suffix intel" "command-line switches"_Section_start.html#start_7.

"-suffix intel" "command-line switches"_Section_start.html#start_6.

Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and "USER-OMP"_#USER-OMP

packages, which have styles optimized for CPUs and KNLs.

src/USER-INTEL/README

"Section 5.3"_Section_accelerate.html#acc_3

"Section 5.3.2"_accelerate_gpu.html

"Section 2.7 -sf intel"_Section_start.html#start_7

"Section 2.7 -pk intel"_Section_start.html#start_7

"Section 2.6 -sf intel"_Section_start.html#start_6

"Section 2.6 -pk intel"_Section_start.html#start_6

"package intel"_package.html

Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (i)

src/USER-INTEL/TEST

"Section 5.3.4"_accelerate_omp.html gives details of what hardware and

compilers are required on your system, and how to build and use this

package.  Its styles can be invoked at run time via the "-sf omp" or

"-suffix omp" "command-line switches"_Section_start.html#start_7.

"-suffix omp" "command-line switches"_Section_start.html#start_6.

Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and

"USER-INTEL"_#USER-INTEL packages, which have styles optimized for

CPUs.

src/USER-OMP/README

"Section 5.3"_Section_accelerate.html#acc_3

"Section 5.3.4"_accelerate_omp.html

"Section 2.7 -sf omp"_Section_start.html#start_7

"Section 2.7 -pk omp"_Section_start.html#start_7

"Section 2.6 -sf omp"_Section_start.html#start_6

"Section 2.6 -pk omp"_Section_start.html#start_6

"package omp"_package.html

Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (o)

"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul