Différences

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

--- faq:chimie:namd [2018/07/23 13:43] – créée tjiang
+++ faq:chimie:namd [2022/03/03 16:30] (Version actuelle) – [Submission script NAMD] tjiang
@@ Ligne 1: / Ligne 1: @@
 ====== NAMD ======
+===== Submission script NAMD =====
+<code bash sub_namd.sh>
+#!/bin/bash
+#$ -S /bin/bash
+#$ -N  mutm_ap-oxog
+#$ -q  E5-2670gpuK20deb128
+#$ -pe mpi_debian 16
+#$ -cwd
+#$ -V
+# Loading modules to set up environment
+module load NAMD/multicore+CUDA/2.12
+# Setting up home and scratch directories
+HOMEDIR="${SGE_O_WORKDIR}"
+cd "${HOMEDIR}" || { echo "cannot cd to ${HOMEDIR}"; exit 1; }
+if [[ -d "/scratch/Chimie" ]]
+then
+    SCRATCHDIR="/scratch/Chimie/${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
+echo "Creating scratch for this job: ${SCRATCHDIR}"
+/bin/mkdir -p "${SCRATCHDIR}"
+HOSTFILE="${TMPDIR}/machines"
+cp "${HOSTFILE}" .  # we are supposed to be in ${HOMEDIR}
+sed -i -e 's/^/host\ /' machines
+# Please provide the following files for namd
+CONFIGFILE="run2.namd"
+TOPFILE="DDB2_CT_hmr.prmtop"
+PDBFILE="DDB2_CT_run1_0.coor"
+FIXFILE="DDB2_CT_new.fix"
+COLVARSFILE="dihedral_run1.in"
+LOGFILE="run2.out"
+# Copying files to scratchdir
+rsync -c "${CONFIGFILE}" "${TOPFILE}" "${PDBFILE}" "${FIXFILE}" "${COLVARSFILE}" machines runscript "${SCRATCHDIR}"
+# The executables for mpirun and namd2
+MPIRUN="mpirun"
+# Go to scratch directory and run calculation there
+cd "${SCRATCHDIR}" || { echo "cannot cd to ${SCRATCHDIR}"; exit 1; }
+echo 'group main ++shell ssh' > nodelist
+cat machines >> nodelist
+namd2 +idlepoll +p "${NSLOTS}" +devices 0,1 "${CONFIGFILE}" > "${LOGFILE}"
+# Copy back data
+rsync -c --exclude "${CONFIGFILE} ${TOPFILE} ${PDBFILE} ${COLVARSFILE}" -- * "${HOMEDIR}"
+cd "${HOMEDIR}" || { echo "cannot cd to ${HOMEDIR}"; exit 1; }
+# Cleaning up scratch directory and hostfile
+rm -fr "${SCRATCHDIR}"
+</code>

faq/chimie/namd.1532353384.txt.gz · Dernière modification : 2020/08/25 15:58 (modification externe)

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