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faq:chimie:namd [2018/07/23 13:43] – créée tjiangfaq:chimie:namd [2022/03/03 16:30] (Version actuelle) – [Submission script NAMD] tjiang
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 ====== NAMD ====== ====== 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.txt · Dernière modification : 2022/03/03 16:30 de tjiang