ajout gromacs compile.sh, download.sh, testcase_ion_channel_small

Gromacs/compile.sh

+#!/bin/bash
+export software=gromacs
+export version=2019.4
+
+compile_date=`date +"%m-%d-%y-%H-%M-%S"`
+compile_dir=compile_${compile_date}
+mkdir $compile_dir
+cd $compile_dir
+
+env > env_before_start.out 
+
+Untar(){
+	echo "======== untar package in ======"
+	pwd
+	tar -zxf  ../$software-${version%%-*}.tar.gz
+}
+
+Install_bin(){
+	echo "======== install bin ========"
+	install_dir=${software}/${version%%-*}
+	mkdir -p $install_dir
+	cd $software-${version%%-*}
+	mkdir build
+	cd build
+	echo "
+	cmake ../  -DGMX_MPI=${CFL_GROMACS_MPI} -DGMX_OPENMP=${CFL_GROMACS_OPENMP} -DGMX_GPU=${CFL_GROMACS_GPU} -DCMAKE_INSTALL_PREFIX=../../$install_dir -DGMX_X11=OFF -DBUILD_SHARED_LIBS=OFF -DCMAKE_C_FLAGS="${CFL_GROMACS_DCMAKE_C_FLAGS}" -DCMAKE_CXX_FLAGS="$CFL_GROMACS_DCMAKE_CXX_FLAGS" -DGMX_FFT_LIBRARY="${CFL_GROMACS_DGMX_FFT_LIBRARY}" -DMKL_INCLUDE_DIR="${CFL_GROMACS_DMKL_INCLUDE_DIR}" -DCMAKE_CXX_COMPILER=${mympicxxcomp} -DCMAKE_C_COMPILER=${mympiccomp} "  1>compile.out 2>compile.err
+	cmake  ../  -DGMX_MPI=${CFL_GROMACS_MPI} -DGMX_OPENMP=${CFL_GROMACS_OPENMP} -DGMX_GPU=${CFL_GROMACS_GPU} -DCMAKE_INSTALL_PREFIX=../../$install_dir -DGMX_X11=OFF -DBUILD_SHARED_LIBS=OFF -DCMAKE_C_FLAGS="${CFL_GROMACS_DCMAKE_C_FLAGS}" -DCMAKE_CXX_FLAGS="${CFL_GROMACS_DCMAKE_CXX_FLAGS}" -DGMX_FFT_LIBRARY="${CFL_GROMACS_DGMX_FFT_LIBRARY}" -DMKL_INCLUDE_DIR="${CFL_GROMACS_DMKL_INCLUDE_DIR}" -DCMAKE_CXX_COMPILER=${mympicxxcomp} -DCMAKE_C_COMPILER=${mympiccomp} 1>>compile.out 2>>compile.err
+make -j 40 install 1>>compile.out 2>>compile.err
+}
+
+Deploy(){
+    Untar
+    Install_bin
+}
+
+Deploy

Gromacs/download.sh

-wget http://manual.gromacs.org/documentation/2019.4/download.html
+#!/bin/bash
+wget http://ftp.gromacs.org/pub/gromacs/gromacs-2019.4.tar.gz
+echo "md5sum should be b424b9099f8bb00e1cd716a1295d797e"

Gromacs/testcase_ion_channel_small/batch_small_ion_channel_occgen.aps.slurm

+#!/bin/bash
+#SBATCH -J ion_channel
+#SBATCH -C BDW28
+#SBATCH -t 00:30:00
+#SBATCH --nodes=2
+#SBATCH --ntasks=8
+#SBATCH --ntasks-per-node=4
+#SBATCH --cpus-per-task=7
+
+#before launching job, replace xxxCOMPILE_DIRxxxx by the gromacs compile directory to use on occigen-bdw.
+
+module purge
+module load intel/18.1 intelmpi/2018.1.163
+module load vtune/2019.2
+
+export PATH=xxxCOMPILE_DIRxxxx/gromacs/2019.4/bin:$PATH
+export LD_LIBRARY_PATH=xxxCOMPILE_DIRxxxx/gromacs/2019.4/lib64:$LD_LIBRARY_PATH
+export PKG_CONFIG_PATH=xxxCOMPILE_DIRxxxx/gromacs/2019.4/lib64/pkgconfig:$PKG_CONFIG_PATH
+export GMXBIN=xxxCOMPILE_DIRxxxx/gromacs/2019.4/bin
+export GMXLDLIB=xxxCOMPILE_DIRxxxx/gromacs/2019.4/lib64
+export GMXDATA=xxxCOMPILE_DIRxxxx/gromacs/2019.4/share/gromacs
+
+export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
+export KMP_HW_SUBSET=1T
+export KMP_AFFINITY=compact,1,0,granularity=fine
+
+srun -n $SLURM_NTASKS aps  gmx_mpi mdrun -pin off -notunepme -maxh 0.5 -ntomp $SLURM_CPUS_PER_TASK -nsteps 20000 -noconfout -s ion_channel.tpr -resethway

Gromacs/testcase_ion_channel_small/prepare.sh

+#!/bin/bash
+compile_gromacs_dir_name=$1
+
+if [ -z "$compile_gromacs_dir_name" ]
+then
+echo "compile_gromacs_dir_name missing"
+echo "example : ./prepare.sh compile_01-13-20-16-20-05"
+exit 1
+fi
+
+run_date=`date +"%m-%d-%y-%H-%M-%S"`
+run_dir=run_${run_date}_${compile_gromacs_dir_name}
+mkdir $run_dir
+cd $run_dir
+cp ../ion_channel.tpr .
+cp ../../machines/${GROMACS_MACHINE}/batch_small_ion_channel.slurm batch_small_ion_channel.slurm.tmp.tmp
+awk '$1=$1' FS="GROMACS_HOME" OFS="../../${compile_gromacs_dir_name}/gromacs/2019.4" batch_small_ion_channel.slurm.tmp.tmp > batch_small_ion_channel.slurm.tmp
+awk '$1=$1' FS="GROMACS_HOME" OFS="../../${compile_gromacs_dir_name}/gromacs/2019.4"  batch_small_ion_channel.slurm.tmp >  batch_small_ion_channel.slurm
+rm -f  batch_small_ion_channel.slurm.tmp.tmp batch_small_ion_channel.slurm.tmp

Gromacs/testcase_ion_channel_small/run.sh

+#!/bin/bash
+run_gromacs_dir_name=$1
+
+if [ -z "$run_gromacs_dir_name" ]
+then
+echo "run_gromacs_dir_name missing"
+echo "example : ./run.sh run_01-13-20-17-10-24_compile_01-13-20-16-20-05"
+exit 1
+fi
+
+cd $run_gromacs_dir_name
+${GROMACS_LAUNCH_SCRIPT_COMMAND} batch_small_ion_channel.slurm

Gromacs/testcase_ion_channel_small/validate.sh

+#!/bin/bash
+run_gromacs_dir_name=$1
+
+if [ -z "$run_gromacs_dir_name" ]
+then
+echo "run_gromacs_dir_name missing"
+echo "example : ./validate.sh run_01-13-20-17-10-24_compile_01-13-20-16-20-05"
+exit 1
+fi
+
+cd $run_gromacs_dir_name
+perf=`grep Performance results | awk '{ print $2 }'`
+
+if [ -z "$perf" ]
+then
+    echo "bench is not validated"
+else
+    echo bench is validated
+    echo perf = $perf ns/day
+fi