Merge branch 'develop' of https://dci-gitlab.cines.fr/dci/abs into develop

Gromacs/machines/irene-amd/batch_large_BSG.slurm

+#!/bin/bash
+#MSUB -J benchBSG
+#MSUB -A tgcc0090
+#MSUB -q rome
+#MSUB -m scratch
+#MSUB -T 1800
+#MSUB -N 80
+#MSUB -n 560
+#MSUB -c 16
+#MSUB -o slurm.benchBSG.o.%I
+#MSUB -e slurm.benchBSG.e.%I
+
+module purge
+module load intel/18.0.1.163 mpi/intelmpi/2018.0.1.163 cmake/3.9.1
+
+
+export PATH=GROMACS_HOME/bin:$PATH
+export LD_LIBRARY_PATH=GROMACS_HOME/lib64:$LD_LIBRARY_PATH
+export PKG_CONFIG_PATH=GROMACS_HOME/lib64/pkgconfig:$PKG_CONFIG_PATH
+export GMXBIN=GROMACS_HOME/bin
+export GMXLDLIB=GROMACS_HOME/lib64
+export GMXDATA=GROMACS_HOME/share/gromacs
+
+export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
+export KMP_HW_SUBSET=1T
+export KMP_AFFINITY=compact,1,0,granularity=fine
+
+ccc_mprun gmx_mpi mdrun -g -pin off -notunepme -maxh 0.5 -ntomp $SLURM_CPUS_PER_TASK -nsteps 20000 -noconfout -s systWT250nsGr2018woEne.tpr  -deffnm benchBSG -resethway
+grep Performance slurm* > results
\ No newline at end of file

Gromacs/machines/jean-zay-cpu/batch_large_BSG.slurm

+#!/bin/bash
+#SBATCH -J benchBSG
+#SBATCH -t 00:30:00
+#SBATCH --hint=nomultithread
+# #SBATCH --qos=qos_cpu-dev
+#SBATCH -A qbg@cpu
+#SBATCH --nodes=7
+#SBATCH --ntasks=280
+#SBATCH --ntasks-per-node=40
+#SBATCH --cpus-per-task=1
+
+module purge
+module load intel-compilers/18.0.1 intel-mpi/18.0.1 intel-mkl/18.0.1
+
+export PATH=GROMACS_HOME/bin:$PATH
+export LD_LIBRARY_PATH=GROMACS_HOME/lib64:$LD_LIBRARY_PATH
+export PKG_CONFIG_PATH=GROMACS_HOME/lib64/pkgconfig:$PKG_CONFIG_PATH
+export GMXBIN=GROMACS_HOME/bin
+export GMXLDLIB=GROMACS_HOME /lib64
+export GMXDATA=GROMACS_HOME/share/gromacs
+
+export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
+export KMP_HW_SUBSET=1T
+export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
+export KMP_AFFINITY=compact,1,0,granularity=fine
+
+srun -n $SLURM_NTASKS  gmx_mpi mdrun -g -pin off -notunepme -maxh 0.5 -ntomp $SLURM_CPUS_PER_TASK -nsteps 20000 -noconfout -s systWT250nsGr2018woEne.tpr  -deffnm bench280 -resethway
+grep Performance slurm* > results

Gromacs/machines/jean-zay-cpu/batch_large_ion_channel.slurm

+#!/bin/bash
+#SBATCH -J gr_ion_channel
+#SBATCH -t 00:30:00
+#SBATCH --hint=nomultithread
+#SBATCH -A qbg@cpu
+#SBATCH --nodes=16
+#SBATCH --ntasks=128
+#SBATCH --ntasks-per-node=8
+#SBATCH --cpus-per-task=5
+
+module purge
+module load intel-compilers/18.0.1 intel-mpi/18.0.1 intel-mkl/18.0.1
+
+export PATH=GROMACS_HOME/bin:$PATH
+export LD_LIBRARY_PATH=GROMACS_HOME/lib64:$LD_LIBRARY_PATH
+export PKG_CONFIG_PATH=GROMACS_HOME/lib64/pkgconfig:$PKG_CONFIG_PATH
+export GMXBIN=GROMACS_HOME/bin
+export GMXLDLIB=GROMACS_HOME/lib64
+export GMXDATA=GROMACS_HOME/share/gromacs
+
+export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
+export KMP_HW_SUBSET=1T
+export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
+export KMP_AFFINITY=compact,1,0,granularity=fine
+
+srun -n $SLURM_NTASKS  gmx_mpi mdrun -pin off -notunepme -maxh 0.5 -ntomp $SLURM_CPUS_PER_TASK -nsteps 1000000 -noconfout -s ion_channel.tpr -resethway
+grep Performance slurm* > results

Gromacs/machines/jean-zay-gpu/batch_large_BSG.slurm

 #!/bin/bash
-#SBATCH -J gr_ion_channel
+#SBATCH -J benchBSG
 #SBATCH -t 00:30:00
 #SBATCH --hint=nomultithread
 # #SBATCH --qos=qos_gpu-dev

Gromacs/machines/jean-zay-gpu/batch_large_ion_channel.slurm

+#!/bin/bash
+#!/bin/bash
+#SBATCH -J gr_ion_channel
+#SBATCH -t 00:30:00
+#SBATCH --hint=nomultithread
+# #SBATCH --qos=qos_gpu-dev
+#SBATCH -A qbg@gpu
+#SBATCH --nodes=2
+#SBATCH --ntasks=8
+#SBATCH --ntasks-per-node=4
+#SBATCH --cpus-per-task=10
+#SBATCH --gres=gpu:4
+
+module purge
+module load intel-compilers/18.0.1 intel-mpi/18.0.1 intel-mkl/18.0.1 gcc/6.5.0 cuda/10.1.1
+
+export PATH=GROMACS_HOME/bin:$PATH
+export LD_LIBRARY_PATH=GROMACS_HOME/lib64:$LD_LIBRARY_PATH
+export PKG_CONFIG_PATH=GROMACS_HOME/lib64/pkgconfig:$PKG_CONFIG_PATH
+export GMXBIN=GROMACS_HOME/bin
+export GMXLDLIB=GROMACS_HOME/lib64
+export GMXDATA=GROMACS_HOME/share/gromacs
+
+export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
+export KMP_HW_SUBSET=1T
+export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
+export KMP_AFFINITY=compact,1,0,granularity=fine
+
+srun -n $SLURM_NTASKS  gmx_mpi mdrun -pin off -notunepme -maxh 0.5 -ntomp $SLURM_CPUS_PER_TASK -nsteps 1000000 -noconfout -s ion_channel.tpr -resethway
+grep Performance slurm* > results

Gromacs/machines/occigen-bdw/batch_large_BSG.slurm

 #!/bin/bash
-#SBATCH -J bench280
+#SBATCH -J benchBSG
 #SBATCH -C BDW28
 #SBATCH -t 00:30:00
-#SBATCH --nodes=10
+#SBATCH --nodes=280
 #SBATCH --ntasks=280
-#SBATCH --ntasks-per-node=28
-#SBATCH --cpus-per-task=1
+#SBATCH --ntasks-per-node=2
+#SBATCH --cpus-per-task=14
 #SBATCH --threads-per-core=1
 
 module purge
@@ -23,5 +23,5 @@ export KMP_HW_SUBSET=1T
 export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
 export KMP_AFFINITY=compact,1,0,granularity=fine
 
-srun -n $SLURM_NTASKS  gmx_mpi mdrun -g -pin off -notunepme -maxh 0.5 -ntomp $SLURM_CPUS_PER_TASK -nsteps 20000 -noconfout -s systWT250nsGr2018woEne.tpr  -deffnm bench280 -resethway
+srun -n $SLURM_NTASKS  gmx_mpi mdrun -g -pin off -notunepme -maxh 0.5 -ntomp $SLURM_CPUS_PER_TASK -nsteps 20000 -noconfout -s systWT250nsGr2018woEne.tpr  -deffnm benchBSG -resethway
 grep Performance slurm* > results