HPC/Applications/lammps/Package OMP: Difference between revisions
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== Package OMP == | == Package OMP == | ||
LAMMPS modules since 2012 are compiled with [http://lammps.sandia.gov/doc/Section_accelerate.html#acc_2 <code>yes-user-omp</code>], permitting multi-threaded runs of selected pair styles, and in particular MPI/OpenMP hybrid parallel runs. To set up such runs, see [[HPC/Submitting and Managing Jobs/Advanced node selection]]. | LAMMPS modules since 2012 are compiled with [http://lammps.sandia.gov/doc/Section_accelerate.html#acc_2 <code>yes-user-omp</code>], permitting multi-threaded runs of selected pair styles, and in particular MPI/OpenMP hybrid parallel runs. To set up such runs, see [[HPC/Submitting and Managing Jobs/Advanced node selection]]. | ||
* The number of MPI tasks running on a node is determined by options to mpirun. | * The number of MPI tasks running on a node is determined by options to mpirun. | ||
* The number of threads that each MPI task runs with is usually determined by the environment variable <code>OMP_NUM_THREADS</code>, which is 1 by default on Carbon. | * The number of threads that each MPI task runs with is usually determined by the environment variable <code>OMP_NUM_THREADS</code>, which is 1 by default on Carbon. | ||
* The LAMMPS <code>package omp</code> command has a mandatory argument <code>''Nthreads''</code> to either ''override'' <code>OMP_NUM_THREADS</code>, or ''use'' it when set to <code>*</code>. | * The LAMMPS <code>package omp</code> command has a mandatory argument <code>''Nthreads''</code> to either ''override'' <code>OMP_NUM_THREADS</code>, or ''use'' it when set to <code>*</code> - the recommended practice. It appears to be sensible to specify a concrete thread number only once, which means in the job file, and let LAMMPS inherit this value with <code>''Nthreads''</code> set to <code>*</code>. | ||
=== Usage === | === Usage === | ||
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#:* Use the [http://lammps.sandia.gov/doc/suffix.html '''suffix omp''' command]. | #:* Use the [http://lammps.sandia.gov/doc/suffix.html '''suffix omp''' command]. | ||
#:* On the command line, use the [http://lammps.sandia.gov/doc/Section_start.html#start_7 '''-suffix omp''' switch]. | #:* On the command line, use the [http://lammps.sandia.gov/doc/Section_start.html#start_7 '''-suffix omp''' switch]. | ||
# In the job file or qsub command line, [[HPC/Submitting and Managing Jobs/Advanced node selection|reserve | # In the job file or qsub command line, [[HPC/Submitting and Managing Jobs/Advanced node selection#Multithreading (OpenMP) |reserve nodes and ppn]] suitable for OpenMP runs. | ||
# Call the <code>lmp_openmpi</code> (regular) binary. | # Call the <code>lmp_openmpi</code> (regular) binary. | ||
=== Input file example === | === Input file example === | ||
Examples: | Examples: | ||
# recommended - inherit OMP_NUM_THREADS | |||
package omp * force/neigh | package omp * force/neigh | ||
# '''not''' recommended | |||
package omp 4 force | package omp 4 force | ||
=== Job file example === | === Job file example === | ||
* Single node: | * Single node - choose from: | ||
** [[HPC/Submitting and Managing Jobs/Advanced node selection#Pure OpenMP, single entire node | pure OpenMP, single entire node]], or | |||
** [[HPC/Submitting and Managing Jobs/Advanced node selection#Pure OpenMP, single node, possibly shared | pure OpenMP, single node, possibly shared]]. | |||
lmp_openmpi -suffix omp -in ''infile'' | : And for the main command: | ||
* Multiple nodes: | lmp_openmpi '''-suffix omp''' -in ''infile'' | ||
* Multiple nodes - use: | |||
** [[HPC/Submitting and Managing Jobs/Advanced node selection#OpenMP/MPI hybrid]]. | |||
mpirun | : And for the main command: | ||
mpirun … lmp_openmpi '''-suffix omp''' -in ''infile'' | |||
Latest revision as of 15:21, June 25, 2013
Package OMP
LAMMPS modules since 2012 are compiled with yes-user-omp, permitting multi-threaded runs of selected pair styles, and in particular MPI/OpenMP hybrid parallel runs. To set up such runs, see HPC/Submitting and Managing Jobs/Advanced node selection.
- The number of MPI tasks running on a node is determined by options to mpirun.
- The number of threads that each MPI task runs with is usually determined by the environment variable
OMP_NUM_THREADS, which is 1 by default on Carbon. - The LAMMPS
package ompcommand has a mandatory argumentNthreadsto either overrideOMP_NUM_THREADS, or use it when set to*- the recommended practice. It appears to be sensible to specify a concrete thread number only once, which means in the job file, and let LAMMPS inherit this value withNthreadsset to*.
Usage
- Use the command
package omp Nthreads modenear the beginning of your LAMMPS control script. - Do one of the following:
- Append /omp to the style name (e.g. pair_style lj/cut/omp)
- Use the suffix omp command.
- On the command line, use the -suffix omp switch.
- In the job file or qsub command line, reserve nodes and ppn suitable for OpenMP runs.
- Call the
lmp_openmpi(regular) binary.
Input file example
Examples:
# recommended - inherit OMP_NUM_THREADS package omp * force/neigh
# not recommended package omp 4 force
Job file example
- Single node - choose from:
- And for the main command:
lmp_openmpi -suffix omp -in infile
- Multiple nodes - use:
- And for the main command:
mpirun … lmp_openmpi -suffix omp -in infile