Benchmark / test report
Container name: Singularity.lammps-30Jul2021-intel-2021a.localimage.sif
test script
#!/bin/bash
#SBATCH -N2
#SBATCH --ntasks-per-node=48
#SBATCH -J plcr-lammps-test
PLCR=${PLCR:-/net/ascratch/groups/plggsoftware/containers}
CONT=${1:-Singularity.lammps-30Jul2021-intel-2021a.localimage.sif}
echo "PLCR test: $SLURM_JOB_NAME"
echo "PLCR jobid: $SLURM_JOBID"
echo "PLCR path: $PLCR"
echo "Test performed on: "`date`
echo "Testing container: $CONT"
SHA=`dd bs=1M if=$PLCR/images/$CONT 2>/dev/null | sha256sum | cut -d' ' -f1`
echo "Container checksum: $SHA"
export I_MPI_PMI_LIBRARY=$PLCR/local/pmi2/libpmi2.so
wget https://www.lammps.org/inputs/in.lj.txt
srun --mpi=pmi2 --cpu-bind=cores singularity -s run -B $I_MPI_PMI_LIBRARY -B $PWD:/host_pwd --pwd /host_pwd $PLCR/images/$CONT lmp_pl -i in.lj.txt
RC=$?
grep 'Performance:' $SLURM_SUBMIT_DIR/slurm-${SLURM_JOB_ID}.out > result
echo "Test completed, rc=$RC, " $(cat result)
test results
PLCR test: plcr-lammps-cpu-test
PLCR jobid: 196607
PLCR path: /net/ascratch/groups/plggsoftware/containers
Test performed on: Tue Jan 11 13:49:38 CET 2022
Testing container: Singularity.lammps-30Jul2021-intel-2021a.localimage.sif
Container checksum: 2d84cae20e9917c91778e7f8526859e5f9742959f46ca70357d60e93d50c4de5
--2022-01-11 13:49:48-- https://www.lammps.org/inputs/in.lj.txt
Resolving www.lammps.org (www.lammps.org)... 129.32.84.230
Connecting to www.lammps.org (www.lammps.org)|129.32.84.230|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 470 [text/plain]
Saving to: ‘in.lj.txt’
0K 100% 2.23M=0s
2022-01-11 13:49:49 (2.23 MB/s) - ‘in.lj.txt’ saved [470/470]
LAMMPS (30 Jul 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (33.591924 33.591924 33.591924)
4 by 4 by 6 MPI processor grid
Created 32000 atoms
using lattice units in orthogonal box = (0.0000000 0.0000000 0.0000000) to (33.591924 33.591924 33.591924)
create_atoms CPU = 0.005 seconds
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 24 24 24
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : lj
Current step : 0
Time step : 0.005
Per MPI rank memory allocation (min/avg/max) = 2.756 | 2.760 | 2.768 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
Loop time of 0.0366193 on 96 procs for 100 steps with 32000 atoms
Performance: 1179704.676 tau/day, 2730.798 timesteps/s
91.8% CPU use with 96 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.013669 | 0.014997 | 0.016266 | 0.5 | 40.95
Neigh | 0.0019618 | 0.0021067 | 0.002314 | 0.2 | 5.75
Comm | 0.017343 | 0.018759 | 0.020203 | 0.5 | 51.23
Output | 5.5275e-05 | 0.00010064 | 0.00040156 | 0.0 | 0.27
Modify | 0.00021146 | 0.00023324 | 0.00025849 | 0.0 | 0.64
Other | | 0.0004228 | | | 1.15
Nlocal: 333.333 ave 364 max 313 min
Histogram: 4 15 18 21 12 5 9 5 6 1
Nghost: 1576.40 ave 1629 max 1512 min
Histogram: 13 7 10 2 0 5 12 24 20 3
Neighs: 12529.5 ave 13905 max 11310 min
Histogram: 1 4 13 23 13 18 9 12 2 1
Total # of neighbors = 1202833
Ave neighs/atom = 37.588531
Neighbor list builds = 5
Dangerous builds not checked
Total wall time: 0:00:00
Test completed, rc=0, Performance: 1179704.676 tau/day, 2730.798 timesteps/s