Différences

Ci-dessous, les différences entre deux révisions de la page.

--- faq:chimie:vasp [2018/07/23 14:56] – [Submission script] tjiang
+++ faq:chimie:vasp [2021/10/08 13:45] – [Submission script] tjiang
@@ Ligne 1: / Ligne 1: @@
 ====== VASP ======
+===== Submission script =====
+<code bash submission_script>
+#!/bin/bash
+#$ -S /bin/bash
+#$ -N vasp_ompi_8
+#$ -q E5-2667v2*
+#$ -pe mpi8_debian 8
+#$ -V
+#$ -cwd
+# Choose the version of vasp by loading the module file accordingly
+module use /home/tjiang/modules/lmod/
+#choose a version of vasp by uncommenting the corresponding section below
+# vasp 5.4.1
+module load vasp/5.4.1_ompi1.8.8_intel15.0.2
+#For vasp 5.4.4, we need to source the intel mpi mpivars script to properly set environment
+#module load vasp/5.4.4_intel_suite2019.5
+#source /applis/PSMN/debian9/software/Compiler/intel/2019.5/impi/2019.5.281/intel64/bin/mpivars.sh
+#For vasp 6.2.0, we need to source the intel mpi mpivars script to properly set environment
+#module load vasp/6.2.0_intel_suite2019.5
+#source /applis/PSMN/debian9/software/Compiler/intel/2019.5/impi/2019.5.281/intel64/bin/mpivars.sh
+# for OpenMP + multithreaded MKL
+export OMP_NUM_THREADS="1"
+export MKL_NUM_THREADS="1"
+#ulimit -l unlimited
+# Where are we
+HOMEDIR="${SGE_O_WORKDIR}"
+# stuff for parallel computing
+HOSTFILE="${TMPDIR}/machines"
+# save nodelist (optional)
+#/bin/cat "${TMPDIR}/machines" > "${HOMEDIR}/tmp"
+# Check which scratch to use
+if [[ -d "/scratch/Chimie" ]]
+then
+    SCRATCHDIR="/scratch/Chimie/${USER}/${JOB_ID}/"
+elif [[ -d "/scratch/Lake" ]]
+then
+    SCRATCHDIR="/scratch/Lake/${USER}/${JOB_ID}/"
+elif [[ -d "/scratch/E5N" ]]
+then
+    SCRATCHDIR="/scratch/E5N/${USER}/${JOB_ID}/"
+else
+    echo "/scratch not found, cannot create ${SCRATCHDIR”}
+    exit 1
+fi
+# Using /tmp as scratch instead
+#SCRATCHDIR="/tmp/${USER}/${JOB_ID}/"
+mkdir -p "${SCRATCHDIR}"
+echo "scratch directory is: ${SCRATCHDIR}"
+cd "${HOMEDIR}" || { echo "cannot cd to ${HOMEDIR}"; exit 1; }
+#for normal calculation
+/bin/cp -f INCAR KPOINTS POTCAR POSCAR WAVECAR "${SCRATCHDIR}/"
+#for neb calculation, numbering depends on the number of images
+#/bin/cp -rf INCAR KPOINTS POTCAR POSCAR WAVECAR 00 01 02 "${SCRATCHDIR}/"
+# If starting wavecar and chgcar exists, uncomment the following line
+#/bin/cp -f -- "${HOMEDIR}/CHG*" "${HOMEDIR}/WAVECAR" "${SCRATCHDIR}/"
+# go to scratch (instead of SGE workdir)
+cd "${SCRATCHDIR}" || { echo "cannot cd to ${SCRATCHDIR}"; exit 1; }
+echo "${HOMEDIR}" > homedir
+# The line for computing
+mpirun  -hostfile "${HOSTFILE}" -np "${NSLOTS}" vasp_std > "${HOMEDIR}/out"
+#mpirun  -hostfile "${HOSTFILE}" -np "${NSLOTS}" vasp_gam > "${HOMEDIR}/out"
+#mpirun  -hostfile "${HOSTFILE}" -np "${NSLOTS}" vasp_ncl > "${HOMEDIR}/out"
+# Get back the results
+# Full copy back
+#cp -- WAVECAR CHG* OUTCAR POSCAR OSZICAR XDATCAR CONTCAR vasprun.xml "${HOMEDIR}/"
+# Minimum copy back
+cp -rf OUTCAR POSCAR OSZICAR XDATCAR CONTCAR "${HOMEDIR}/"
+# copy back for neb calculation, numbering depends on the number of images
+#cp -rf OUTCAR POSCAR OSZICAR XDATCAR CONTCAR 00 01 02 "${HOMEDIR}/"
+# Zip OUTCAR to save space
+cd "${HOMEDIR}/" || { echo "cannot cd to ${HOMEDIR}"; exit 1; }
+bzip2 OUTCAR
+#gzip OUTCAR
+# Cleaning up
+# there should be a test here, what if ${SCRATCHDIR} = ${SGE_O_WORKDIR}?
+rm -rf "${SCRATCHDIR}"
+# The following part is only useful for users from the chemistry lab of ens-lyon.
+# Importing finished calculation into database
+#if [ ! -d "/home/${USER}/.chimie_db/" ]; then
+#    mkdir "/home/${USER}/.chimie_db/"
+#fi
+#export PYTHONPATH="/home/tjiang/usr/lib/python2.7/site-package/:$PYTHONPATH"
+#export PATH="/home/tjiang/chimie4psmn/database/:$PATH"
+#import_vasp_calc -p -u "${USER}" -n 1 -d "/home/${USER}/.chimie_db/${USER}.db" "${HOMEDIR}"
+</code>

faq/chimie/vasp.txt · Dernière modification : 2022/03/01 12:36 de tjiang

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