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--- tcr_sri001 [2020/04/18 23:43] – created tmatejuk
+++ tcr_sri001 [2023/08/01 01:08] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
+FIX ME
+FIX ME
+FIX ME
+====== GROMACS 2020.1 ======
 ==== description ====
-GROMACS 2020.1 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/]] .
+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 ====
+FIXME

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