Benchmark / test report
Container name: Singularity.gromacs-2021.3-intel-2021a.localimage.sif
test script
#!/bin/bash
#SBATCH -N2
#SBATCH --ntasks-per-node=48
#SBATCH -J plcr-gromacs-cpu-test
PLCR=${PLCR:-/net/ascratch/groups/plggsoftware/containers}
CONT=${1:-Singularity.gromacs-2021.3-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
cd $TMPDIR
wget https://ftp.gromacs.org/pub/benchmarks/water_GMX50_bare.tar.gz
tar xzf water_GMX50_bare.tar.gz
cp water-cut1.0_GMX50_bare/3072/* .
export GMX_MAXBACKUP=-1
time srun --mpi=pmi2 --cpu-bind=cores singularity -s run -B $I_MPI_PMI_LIBRARY -B $PWD:/host_pwd --pwd /host_pwd $PLCR/images/$CONT gmx_mpi grompp -f pme.mdp -o bench.tpr
time srun --mpi=pmi2 --cpu-bind=cores singularity -s run -B $I_MPI_PMI_LIBRARY -B $PWD:/host_pwd --pwd /host_pwd $PLCR/images/$CONT gmx_mpi mdrun -resethway -npme 0 -notunepme -noconfout -nsteps 1000 -v -s bench.tpr
RC=$?
grep 'Performance:' $SLURM_SUBMIT_DIR/slurm-${SLURM_JOB_ID}.out | awk '{print $2}' > result
echo "Test completed, rc=$RC, Performance:" $(cat result) "[ns/day]"
rm -rf $TMPDIR
test results
PLCR test: plcr-gromacs-cpu-test
PLCR jobid: 196603
PLCR path: /net/ascratch/groups/plggsoftware/containers
Test performed on: Tue Jan 11 12:56:51 CET 2022
Testing container: Singularity.gromacs-2021.3-intel-2021a.localimage.sif
Container checksum: 203ef1e9ee79b289b3091dad5208d2da7c550dcb0370a5ed2bbbaf4c26d86ae3
--2022-01-11 12:57:01-- https://ftp.gromacs.org/pub/benchmarks/water_GMX50_bare.tar.gz
Resolving ftp.gromacs.org (ftp.gromacs.org)... 130.237.11.165, 2001:6b0:1:1191:216:3eff:fec7:6e30
Connecting to ftp.gromacs.org (ftp.gromacs.org)|130.237.11.165|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 138438061 (132M) [application/x-gzip]
Saving to: ‘water_GMX50_bare.tar.gz’
(...downloading file...)
2022-01-11 12:57:10 (15.9 MB/s) - ‘water_GMX50_bare.tar.gz’ saved [138438061/138438061]
:-) GROMACS - gmx grompp, 2021.3-EasyBuild-4.4.3.dev0 (-:
GROMACS is written by:
Andrey Alekseenko Emile Apol Rossen Apostolov
Paul Bauer Herman J.C. Berendsen Par Bjelkmar
Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra
Gilles Gouaillardet Alan Gray Gerrit Groenhof
Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan
(...grompp output...)
GROMACS reminds you: "The first 90% of the code accounts for the first 90% of the development time. The remaining 10% of the code accounts for the other 90% of the development ti
me." (Tom Cargill)
real 0m18.121s
user 0m0.014s
sys 0m0.119s
:-) GROMACS - gmx mdrun, 2021.3-EasyBuild-4.4.3.dev0 (-:
GROMACS is written by:
Andrey Alekseenko Emile Apol Rossen Apostolov
Paul Bauer Herman J.C. Berendsen Par Bjelkmar
Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra
Gilles Gouaillardet Alan Gray Gerrit Groenhof
Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan
Dimitrios Karkoulis Peter Kasson Jiri Kraus
Carsten Kutzner Per Larsson Justin A. Lemkul
Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola
Szilard Pall Sander Pronk Roland Schulz
Michael Shirts Alexey Shvetsov Alfons Sijbers
Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx mdrun, version 2021.3-EasyBuild-4.4.3.dev0
Executable: /app/software/GROMACS/2021.3-intel-2021a/bin/gmx_mpi
Data prefix: /app/software/GROMACS/2021.3-intel-2021a
Working dir: /host_pwd
Command line:
gmx_mpi mdrun -resethway -npme 0 -notunepme -noconfout -nsteps 1000 -v -s bench.tpr
Reading file bench.tpr, VERSION 2021.3-EasyBuild-4.4.3.dev0 (single precision)
Overriding nsteps with value passed on the command line: 1000 steps, 2 ps
Changing nstlist from 10 to 40, rlist from 1 to 1.099
Using 96 MPI processes
Non-default thread affinity set, disabling internal thread affinity
starting mdrun 'Water'
1000 steps, 2.0 ps.
step 0
step 100, remaining wall clock time: 31 s
vol 0.92 imb F 5% step 200, remaining wall clock time: 27 s
step 300, remaining wall clock time: 23 s
vol 0.89 imb F 1% step 400, remaining wall clock time: 20 s
step 500: resetting all time and cycle counters
step 500, remaining wall clock time: 16 s
vol 0.90 imb F 1% step 600, remaining wall clock time: 13 s
step 700, remaining wall clock time: 9 s
vol 0.90 imb F 9% step 800, remaining wall clock time: 6 s
step 900, remaining wall clock time: 3 s
vol 0.90 imb F 1% step 1000, remaining wall clock time: 0 s
Dynamic load balancing report:
DLB was turned on during the run due to measured imbalance.
Average load imbalance: 2.8%.
The balanceable part of the MD step is 51%, load imbalance is computed from this.
Part of the total run time spent waiting due to load imbalance: 1.4%.
Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 0 %
Core t (s) Wall t (s) (%)
Time: 1622.527 16.903 9599.0
(ns/day) (hour/ns)
Performance: 5.122 4.686
GROMACS reminds you: "I Need a Little Poison" (Throwing Muses)
real 0m40.032s
user 0m0.014s
sys 0m0.016s
Test completed, rc=0, Performance: 5.122 [ns/day]