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.

mpirun -x OMP_NUM_THREADS=2 -np 2 lmp_machine -sf omp -in in.script