Script pour VASP-5
#!/bin/bash -x
#SBATCH --account=<id-projet>
#SBATCH --partition=std
#SBATCH --job-name=Test-vasp
#SBATCH --output=slurm-%x.%N.%j.out
#SBATCH --error=slurm-%x.%N.%j.err
#SBATCH --nodes=2
#SBATCH --ntasks=16
#SBATCH --ntasks-per-node=8
#SBATCH --cpus-per-task=1 # always 1 thread
#SBATCH --time=0-04:00:00
#SBATCH --exclude=cnd[01-04,06-12] # IVY nodes are showing issues with VASP
version='std' # gam | ncl
env | grep -i slurm
cd $SLURM_SUBMIT_DIR
## Creating directory in $SCRATCHDIR ################
WORKDIR="$SCRATCHDIR/job.$SLURM_JOB_ID.$USER"
mkdir -p $WORKDIR
if [ -e $WORKDIR ] ; then
cd $WORKDIR
module purge
module load intel/2017.4.196 mkl/2017.4.196 intelmpi/2017.4.196
export PATH='/opt/soft/std/vasp.5.4.4':$PATH
export VASP=$( which vasp_$version )
export OMP_NUM_THREADS=1
export MKL_NUM_THREADS=1
ulimit -s unlimited
unset I_MPI_PMI_LIBRARY
# for IB-INTEL&AMD machine fine tune for the intranode connection
echo $SLURM_TOPOLOGY_ADDR > toptype.txt
grep -i ib toptype.txt >& /dev/null
if [ $? -eq 0 ] ; then
export I_MPI_FABRICS=dapl
fi
grep -i cnj toptype.txt >& /dev/null
if [ $? -eq 0 ]; then
export SLURM_CPU_BIND=none
fi
ffile=(INCAR KPOINTS POSCAR POTCAR WAVECAR CHGCAR)
for ifile in ${ffile[@]}; do
if [ -e $SLURM_SUBMIT_DIR/$ifile ]; then
cp $SLURM_SUBMIT_DIR/$ifile $WORKDIR/$ifile
fi
done
srun --mpi=pmi2 $VASP >& vasp.out 2>&1
# Copying all files to the output directory
OUTDIR="$SLURM_SUBMIT_DIR/outdir.$SLURM_JOB_ID"
mkdir -p "$OUTDIR"
# Move all files to the output directory
cp $WORKDIR/OUTCAR $OUTDIR
cp $WORKDIR/CONTCAR $OUTDIR
cp $WORKDIR/IBZKPT $OUTDIR
else
echo "ERROR: Cannot create the WRK=$WORKDIR"
fi
Script pour VASP-6*
* voir Matériel EXPLOR pour identifier les nodes
- Pour processeurs AMD
#!/bin/bash -x
#SBATCH --account=support
#SBATCH --partition=std
#SBATCH --job-name=vaspAMD
#SBATCH -C EPYC4 # or EPYC3
#SBATCH --output=slurm-%x.%N.%j.out
#SBATCH --error=slurm-%x.%N.%j.err
#SBATCH --nodes=2
#SBATCH --ntasks=16
#SBATCH --ntasks-per-node=8
#SBATCH --cpus-per-task=1 # always 1 thread
#SBATCH --time=2-04:00:00
version='std' # gam | ncl
env | grep -i slurm
echo ""
echo " JOB started: $(date) "
echo ""
cd $SLURM_SUBMIT_DIR
## Creating directory in $SCRATCHDIR ################
WORKDIR="$SCRATCHDIR/job.$SLURM_JOB_ID.$USER"
mkdir -p $WORKDIR
if [ -e $WORKDIR ] ; then
cd $WORKDIR
module purge
module load mcs_mod/softwares/vasp6/gcc-11.2/6.4.3
export VASP=$( which vasp_$version )
export OMP_NUM_THREADS=1
export MKL_NUM_THREADS=1
ulimit -s unlimited
unset I_MPI_PMI_LIBRARY
# for IB-INTEL&AMD machine fine tune for the intranode connection
echo $SLURM_TOPOLOGY_ADDR > toptype.txt
grep -i ib toptype.txt >& /dev/null
if [ $? -eq 0 ] ; then
export I_MPI_FABRICS=dapl
fi
grep -i cnj toptype.txt >& /dev/null
if [ $? -eq 0 ]; then
export SLURM_CPU_BIND=none
fi
ffile=(INCAR KPOINTS POSCAR POTCAR WAVECAR CHGCAR)
for ifile in ${ffile[@]}; do
if [ -e $SLURM_SUBMIT_DIR/$ifile ]; then
cp $SLURM_SUBMIT_DIR/$ifile $WORKDIR/$ifile
fi
done
mpirun -np $SLURM_NTASKS $VASP >& vasp.out 2>&1
# Copying all files to the output directory
OUTDIR="$SLURM_SUBMIT_DIR/outdir.$SLURM_JOB_ID"
mkdir -p "$OUTDIR"
# Move all files to the output directory
cp $WORKDIR/OUTCAR $OUTDIR
cp $WORKDIR/CONTCAR $OUTDIR
cp $WORKDIR/IBZKPT $OUTDIR
else
echo "ERROR: Cannot create the WRK=$WORKDIR"
fi
echo ""
echo " JOB finished: $(date) "
echo ""
- pour processeurs INTEL
#!/bin/bash -x
#SBATCH --account=support
#SBATCH --partition=std
#SBATCH --job-name=vaspINTEL
#SBATCH --output=slurm-%x.%N.%j.out
#SBATCH --error=slurm-%x.%N.%j.err
#SBATCH --nodes=4
#SBATCH --ntasks=32
#SBATCH --ntasks-per-node=8
#SBATCH --cpus-per-task=1 # always 1 thread
#SBATCH --time=2-04:00:00
#SBATCH --exclude=cnd[01-04,06-12],cnl[01-18],cnj[01-64] # to exclude IVY and AMD nodes
version='std' # gam | ncl
env | grep -i slurm
echo ""
echo " JOB started: $(date) "
echo ""
cd $SLURM_SUBMIT_DIR
## Creating directory in $SCRATCHDIR ################
WORKDIR="$SCRATCHDIR/job.$SLURM_JOB_ID.$USER"
mkdir -p $WORKDIR
if [ -e $WORKDIR ] ; then
cd $WORKDIR
module purge
module load mcs_mod/softwares/vasp6/oneapi-2023.0.0/6.4.3
export VASP=$( which vasp_$version )
export OMP_NUM_THREADS=1
export MKL_NUM_THREADS=1
ulimit -s unlimited
unset I_MPI_PMI_LIBRARY
# for IB-INTEL&AMD machine fine tune for the intranode connection
echo $SLURM_TOPOLOGY_ADDR > toptype.txt
grep -i ib toptype.txt >& /dev/null
if [ $? -eq 0 ] ; then
export I_MPI_FABRICS=dapl
fi
grep -i cnj toptype.txt >& /dev/null
if [ $? -eq 0 ]; then
export SLURM_CPU_BIND=none
fi
ffile=(INCAR KPOINTS POSCAR POTCAR WAVECAR CHGCAR)
for ifile in ${ffile[@]}; do
if [ -e $SLURM_SUBMIT_DIR/$ifile ]; then
cp $SLURM_SUBMIT_DIR/$ifile $WORKDIR/$ifile
fi
done
mpirun -np $SLURM_NTASKS $VASP >& vasp.out 2>&1
# Copying all files to the output directory
OUTDIR="$SLURM_SUBMIT_DIR/outdir.$SLURM_JOB_ID"
mkdir -p "$OUTDIR"
# Move all files to the output directory
cp $WORKDIR/OUTCAR $OUTDIR
cp $WORKDIR/CONTCAR $OUTDIR
cp $WORKDIR/IBZKPT $OUTDIR
else
echo "ERROR: Cannot create the WRK=$WORKDIR"
fi
echo ""
echo " JOB finished: $(date) "
echo ""