Table of Contents
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GROMACS 2020.1
description
GROningen MAchine for Chemical Simulations (GROMACS) is a molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. Software page : http://www.gromacs.org/ .
software version
GROMACS 2020.1, http://ftp.gromacs.org/pub/gromacs/gromacs-2020.1.tar.gz .
prepare software
To prepare GROMACS (ver. 2020.1) software login to tcr.cent.uw.edu.pl.
Then open interactive session on any computing node with :
srun -n16 -N1 --pty bash -l
When interactive session is started go through GROMACS installation process described with bellow commands. It will take about 30 minutes.
module load compilers/gcc-5.5.0
module load mpi/openmpi-x86_64
#folder for source files
mkdir -p ~/downloads/gromacs2020.1
#folder for compiled binares
mkdir -p ~/soft/gromacs2020.1
cd ~/downloads/gromacs2020.1
wget http://ftp.gromacs.org/pub/gromacs/gromacs-2020.1.tar.gz
tar xzf gromacs-2020.1.tar.gz
cd gromacs-2020.1
mkdir build
cd build
cmake3 .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_MPI=ON -DGMX_USE_RDTSCP=ON -DCMAKE_INSTALL_PREFIX=/home/users/${USER}/soft/gromacs2020.1
time make -j${SLURM_NTASKS} all
make install
remember to end interactive session with exit command.
If no errors occurred, compiled GROMACS binaries are available in /home/users/${USER}/soft/gromacs2020.1/bin/ .
sbatch example
Use GROMACS 2020.1. This description assumes that path to binaries is /home/users/${USER}/soft/gromacs2020.1/bin . Use bellow gromacs-test.sbatch file to run computation.
#!/bin/bash -l
#SBATCH --job-name="gromacs-test_N2_n32"
#SBATCH --nodes=2 # number of computing_nodes
#SBATCH --ntasks=32 # number of CPU's ( 16*computing_nodes )
#SBATCH --mem-per-cpu=2G
#SBATCH --partition=short
#SBATCH --constraint=intel
#SBATCH --exclusive
#SBATCH --time=2:00:00
module load compilers/gcc-5.5.0
module load mpi/openmpi-x86_64
source /home/users/${USER}/soft/gromacs2020.1/bin/GMXRC
WORKDIR="/home/users/${USER}/soft_tests/gromacs_run_`date +%s`_${RANDOM}/"
mkdir -p ${WORKDIR}
#copy input files and pseudo files to ${WORKDIR}
cp /home/users/${USER}/downloads/gromacs2020.1_input_files/GROMACS_TestCaseA.tar.gz ${WORKDIR}
cd ${WORKDIR}
tar xzf GROMACS_TestCaseA.tar.gz
T1=`date +%s`
mpirun gmx_mpi mdrun -s ion_channel.tpr -maxh 0.50 -resethway -noconfout -nsteps 10000 -g logile
T2=`date +%s`
echo -e "stop ${T2}\t start ${T1}\t ${SLURM_NNODES}"
performance tests
