Différences

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

--- faq:chimie:cp2k [2020/06/24 10:19] – créée tjiang
+++ faq:chimie:cp2k [2022/04/22 08:54] (Version actuelle) – [Submission script] tjiang
@@ Ligne 1: / Ligne 1: @@
 ======CP2K======
+===== Submission script =====
+<code bash sub_cp2k.sh>
+#!/bin/bash
+#$ -S /bin/bash
+#$ -N cp2kjob          # The name of the job can be changed here
+#$ -q E5-2667v4deb256A
+#$ -pe mpi16_debian 16
+#$ -V
+#$ -cwd
+module purge
+module use /home/tjiang/modules/lmod
+#choose different versions of cp2k
+#5.1
+module load cp2k/5.1_gcc7.2_avx_pclabaut
+#7.1
+#module load cp2k/7.1_gcc7.2_avx2
+#source /Xnfs/chimie/cp2k/7.1/gcc7.2_avx2/tools/toolchain/install/setup
+cat $TMPDIR/machines
+cd "${SGE_O_WORKDIR}" || { echo "cannot cd to ${SGE_O_WORKDIR}"; exit 1; }
+echo NSLOTS="${NSLOTS}"
+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}/"
+echo "Creating scratch for this job: ${SCRATCHDIR}"
+/bin/mkdir -p "${SCRATCHDIR}"
+cp md.inp "${SCRATCHDIR}"
+cd "${SCRATCHDIR}" || { echo "cannot cd to ${SCRATCHDIR}"; exit 1; }
+mpirun -x LIBRARY_PATH -x CPATH -x LD_LIBRARY_PATH -hostfile $TMPDIR/machines -np $NSLOTS cp2k.popt -i md.inp > md.out
+#Please change the outputfiles_only to the output files you need to copy back
+cp -- outputfiles_only "${SGE_O_WORKDIR}"
+rm -rf "${SCRATCHDIR}"
+</code>

faq/chimie/cp2k.1592993955.txt.gz · Dernière modification : 2020/08/25 15:58 (modification externe)

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