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 runs, and in particular MPI/OpenMP hybrid parallel runs.

Be careful not to Use the following for the core of your job script:

#PBS -l naccesspolicy=SINGLEJOB
...
ppn_mpi=$( uniq -c $PBS_NODEFILE | awk '{print $1; exit}' )	# grab first (and usually only) ppn value of the job
ppn_phys=8										# number of cores on first execution node
#ppn_phys=12										# experimental: 3-to-2 oversubscription of cores.

OMP_NUM_THREADS=$(( ppn_phys / ppn_mpi ))			# calculate number of threads available per MPI process

mpirun -x OMP_NUM_THREADS \
    -machinefile  $PBS_NODEFILE \
    -np $(wc -l < $PBS_NODEFILE) \
    lmp_openmpi -sf omp -in in.script

LAMMPS echoes it parallelization scheme first thing in the output:

LAMMPS (10 Feb 2012)
  using 3 OpenMP thread(s) per MPI task
...
  2 by 2 by 2 MPI processor grid
Lattice spacing in x,y,z = 3.52 4.97803 4.97803
...

and near the end:

Loop time of 11.473 on 24 procs (8 MPI x 3 OpenMP) for 100 steps with 32000 atoms


To learn more: