HPC/Applications/lammps: Difference between revisions
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=== Sample job file === | === Sample job file gen1 === | ||
<syntaxhighlight lang="bash"> | <syntaxhighlight lang="bash"> | ||
#!/bin/bash | #!/bin/bash | ||
#PBS -l nodes=20:ppn=8 | #PBS -l nodes=20:ppn=8:gen1 | ||
#PBS -l walltime=3:00:00 | |||
#PBS -N <jobname> | |||
#PBS -A <account> | |||
# | |||
#PBS -o job.out | |||
#PBS -e job.err | |||
#PBS -m ea | |||
# change into the directory where qsub will be executed | |||
cd $PBS_O_WORKDIR | |||
mpirun -machinefile $PBS_NODEFILE \ | |||
-np $(wc -l < $PBS_NODEFILE) \ | |||
-mca btl self,tcp \ | |||
lmp_openmpi < lammps.in > lammps.out 2> lammps.err | |||
</syntaxhighlight> | |||
=== Sample job file gen2 === | |||
<syntaxhighlight lang="bash"> | |||
#!/bin/bash | |||
#PBS -l nodes=20:ppn=8:gen2 | |||
#PBS -l walltime=3:00:00 | #PBS -l walltime=3:00:00 | ||
#PBS -N <jobname> | #PBS -N <jobname> | ||
| Line 42: | Line 63: | ||
mpirun -machinefile $PBS_NODEFILE \ | mpirun -machinefile $PBS_NODEFILE \ | ||
-np $(wc -l < $PBS_NODEFILE) \ | -np $(wc -l < $PBS_NODEFILE) \ | ||
lmp_openmpi < lammps.in > lammps.out 2> lammps.err | lmp_openmpi < lammps.in > lammps.out 2> lammps.err | ||
</syntaxhighlight> | </syntaxhighlight> | ||
Revision as of 21:38, January 23, 2012
Benchmark
Using a sample workload from Sanket ("run9"), I tested various OpenMPI options on both node types.
LAMMPS performs best on gen2 nodes without extra opiotns, and pretty well on gen1 nodes over ethernet(!).
| Job | Type | Interconnect | Additional OpenMPI options | Relative speed (1000 steps/3 hours) |
Notes |
|---|---|---|---|---|---|
| gen1 | gen1 | IB | (none) | 36 | |
| gen1srq | gen1 | IB | (none) | 39 (to be confirmed) | not useful (IB and eth. options) |
| gen1srqpin | gen1 | IB | -mca btl_openib_use_srq 1 -mca mpi_paffinity_alone 1 |
39 | |
| gen1srqeth | gen1 | Ethernet | -mca btl_openib_use_srq 1 -mca btl self,tcp |
42 | not useful (IB and eth. options) |
| gen1eth | gen1 | Ethernet | -mca btl self,tcp | 44 | fastest for gen1 |
| gen2eth | gen2 | Ethernet | -mca btl self,tcp | 49 | |
| gen2srq | gen2 | IB | -mca btl_openib_use_srq 1 | 59 | |
| gen2 | gen2 | IB | (none) | 59 | fastest for gen2 |
Sample job file gen1
#!/bin/bash
#PBS -l nodes=20:ppn=8:gen1
#PBS -l walltime=3:00:00
#PBS -N <jobname>
#PBS -A <account>
#
#PBS -o job.out
#PBS -e job.err
#PBS -m ea
# change into the directory where qsub will be executed
cd $PBS_O_WORKDIR
mpirun -machinefile $PBS_NODEFILE \
-np $(wc -l < $PBS_NODEFILE) \
-mca btl self,tcp \
lmp_openmpi < lammps.in > lammps.out 2> lammps.err
Sample job file gen2
#!/bin/bash
#PBS -l nodes=20:ppn=8:gen2
#PBS -l walltime=3:00:00
#PBS -N <jobname>
#PBS -A <account>
#
#PBS -o job.out
#PBS -e job.err
#PBS -m ea
# change into the directory where qsub will be executed
cd $PBS_O_WORKDIR
mpirun -machinefile $PBS_NODEFILE \
-np $(wc -l < $PBS_NODEFILE) \
lmp_openmpi < lammps.in > lammps.out 2> lammps.err