HPC/Applications/lammps
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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 options, and pretty well on gen1 nodes over ethernet(!).
Job tag | Node type | Interconnect | Additional OpenMPI options | Relative speed (1000 steps/3 hours) |
Notes |
---|---|---|---|---|---|
gen1 | gen1 | IB | (none) | 36 | |
gen1srqpin | gen1 | IB | -mca btl_openib_use_srq 1 -mca mpi_paffinity_alone 1 |
39 | |
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=10:ppn=8:gen1
#PBS -l walltime=1:00:00:00
#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=10:ppn=8:gen2
#PBS -l walltime=1:00:00:00
#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 < $PBS_NODEFILE) \
lmp_openmpi < lammps.in > lammps.out 2> lammps.err
OpenMP usage (experimental)
LAMMPS modules since 2012 are compiled with yes-user-omp
, permitting multi-threaded use.
Reviewing HPC/Submitting_Jobs/Advanced node selection#Multithreading (OpenMP) it appears the correct job script stub would be:
...
ppn_mpi=$( uniq -c $PBS_NODEFILE | awk '{print $1; exit}' ) # grab first (and usually only) ppn from qsub
ppn_phys=$( grep -c ^processor /proc/cpuinfo )
# Calculate number of threads available per MPI process
OMP_NUM_THREADS=$(( ppn_phys / ppn_mpi ))
mpirun -x OMP_NUM_THREADS \
-machinefile $PBS_NODEFILE \
-np $(wc -l < $PBS_NODEFILE) \
lmp_openmpi -sf omp -in in.script