From 6aec27678d61269347c9fb6eed0ff270711777a2 Mon Sep 17 00:00:00 2001 From: David Sarrut Date: Thu, 9 Feb 2017 10:08:34 +0100 Subject: [PATCH] change path to usr/local + sps option --- cluster_tools/gate_run_submit_cluster.sh | 5 +- cluster_tools/gate_run_submit_cluster_sps.sh | 125 +++++++++++++++++++ 2 files changed, 128 insertions(+), 2 deletions(-) create mode 100755 cluster_tools/gate_run_submit_cluster_sps.sh diff --git a/cluster_tools/gate_run_submit_cluster.sh b/cluster_tools/gate_run_submit_cluster.sh index 9112050..2ae6186 100755 --- a/cluster_tools/gate_run_submit_cluster.sh +++ b/cluster_tools/gate_run_submit_cluster.sh @@ -1,4 +1,4 @@ -#! /usr/local/bin/bash -lx +#!/bin/bash -l set -u SCRIPTNAME="$(basename "${0}")" @@ -91,6 +91,7 @@ cp ${MACROFILE} ${OUTPUTDIR}/mac files=`grep "control/execute" ${MACROFILE} | cut -d " " -f 2` for i in $files do + echo $i cp $i ${OUTPUTDIR}/mac done @@ -102,7 +103,7 @@ while test $NJOBS -gt 0; do PARAM=\"${PARAM}\" INDEX=${NJOBS} INDEXMAX=${NJOBSMAX} OUTPUTDIR=${OUTPUTDIR} RELEASEDIR=${RELEASEDIR} MACROFILE=${MACROFILE} MACRODIR=${MACRODIR} PBS_JOBID="local_${NJOBS}" bash "${JOBFILE}" > ${OUTPUTDIR}/gate_${NJOBS}.log & elif test "$(dnsdomainname)" = "in2p3.fr" then - PROJECTGROUP=creatis + PROJECTGROUP=creatis qsub -o "${OUTPUTDIR}" \ -N "gate.${RUNID}" \ -v "PARAM=\"${PARAM}\",INDEX=${NJOBS},INDEXMAX=${NJOBSMAX},OUTPUTDIR=${OUTPUTDIR},RELEASEDIR=${RELEASEDIR},MACROFILE=${MACROFILE},MACRODIR=${MACRODIR}" \ diff --git a/cluster_tools/gate_run_submit_cluster_sps.sh b/cluster_tools/gate_run_submit_cluster_sps.sh new file mode 100755 index 0000000..ddc48ca --- /dev/null +++ b/cluster_tools/gate_run_submit_cluster_sps.sh @@ -0,0 +1,125 @@ +#! /usr/local/bin/bash -lx + +set -u +SCRIPTNAME="$(basename "${0}")" + +# ------------------------------------------------- +function error { + echo "ERROR: $1" + usage + exit 1 +} +# ------------------------------------------------- + +DEFAULTRELEASESUFFIX="NONE" +DEFAULTNUMBEROFJOBS="10" + +# ------------------------------------------------- +function usage { + echo "${SCRIPTNAME} mac/main.mac njobs releasesuffix paramtogate" + echo "default njobs = ${DEFAULTNUMBEROFJOBS}" + echo "default releasesuffix = ${DEFAULTRELEASESUFFIX} (NONE means use Gate in PATH)" + echo "default paramtogate = \"\" (use \"\" around params and \\ in front of commas)" +} +# ------------------------------------------------- + +test $# -eq 0 && usage && exit 0 + +RELEASESUFFIX=${3:-"${DEFAULTRELEASESUFFIX}"} +RELEASEDIR="${HOME}/releases/grid_release${RELEASESUFFIX}" +if test "$(dnsdomainname)" = "in2p3.fr" +then + JOBFILE="$(dirname $0)/gate_job_ccin2p3.job" +else + JOBFILE="$(dirname $0)/gate_job_cluster.job" +fi + +echo "Checking stuff" +test -f ${JOBFILE} || error "can't find job file ${JOBFILE}" +if test "${RELEASESUFFIX}" = "${DEFAULTRELEASESUFFIX}" +then + RELEASEDIR="NONE" + which Gate 2>&1 >/dev/null || error "there is no Gate in the PATH" +else + test -d ${RELEASEDIR} || error "invalid release dir ${RELEASEDIR}" +fi +MACRODIR=$(pwd) +test -d ${MACRODIR}/mac && test -d ${MACRODIR}/data || error "invalid path" +MACROFILE=${1:?"provide relative macro path"} +test -f ${MACRODIR}/${MACROFILE} || error "invalid macro" +if test "$(dnsdomainname)" = "in2p3.fr" +then + OUTPUTDIR=$(mktemp -d -p "${MACRODIR}" run.XXXX || error "can't create temp dir") + ssh -i ${HOME}/.ssh/ccin2p3 linux1.dg.creatis.insa-lyon.fr mkdir -p "cc/$(basename ${OUTPUTDIR})" +else + OUTPUTDIR=$(mktemp --tmpdir=${MACRODIR} -d run.XXXX || error "can't create temp dir") +fi +test -d ${OUTPUTDIR} || error "can't locate output dir" +RUNID=${OUTPUTDIR##*.} +NJOBS=${2:-"${DEFAULTNUMBEROFJOBS}"} +NJOBSMAX=${NJOBS} +PARAM="${4:-""}" + +echo "Lets roll!!" +echo "runid is ${RUNID}" + +QSUB=$(which qsub 2> /dev/null) +# echo "qsub is $(which qsub)" +test -z "${QSUB}" && QSUB="noqsub" +if test "${QSUB}" = "noqsub" +then + echo "qsub is not found. Simply run Gate on multiple cores." +fi + +test -z "${PARAM}" && echo "no param" || echo "param is ${PARAM}" +if test "$RELEASESUFFIX" = "$DEFAULTRELEASESUFFIX" +then + echo "Gate is $(which Gate)" +else + echo "Gate release is $(basename ${RELEASEDIR})" +fi +echo "submitting ${NJOBS} jobs" + +PARAMFILE="${OUTPUTDIR}/params.txt" +echo "njobs = ${NJOBS}" >> "${PARAMFILE}" +echo "macro = ${MACROFILE}" >> "${PARAMFILE}" +test -z "${PARAM}" || echo "param = ${PARAM}" >> "${PARAMFILE}" + +# Copy macros files (for log) +mkdir ${OUTPUTDIR}/mac +cp ${MACROFILE} ${OUTPUTDIR}/mac +files=`grep "control/execute" ${MACROFILE} | cut -d " " -f 2` +for i in $files +do + cp $i ${OUTPUTDIR}/mac +done + +while test $NJOBS -gt 0; do + + if test "${QSUB}" = "noqsub" + then + echo "Launching Gate log in ${OUTPUTDIR}/gate_${NJOBS}.log" + PARAM=\"${PARAM}\" INDEX=${NJOBS} INDEXMAX=${NJOBSMAX} OUTPUTDIR=${OUTPUTDIR} RELEASEDIR=${RELEASEDIR} MACROFILE=${MACROFILE} MACRODIR=${MACRODIR} PBS_JOBID="local_${NJOBS}" bash "${JOBFILE}" > ${OUTPUTDIR}/gate_${NJOBS}.log & + elif test "$(dnsdomainname)" = "in2p3.fr" + then + PROJECTGROUP=creatis + qsub -o "${OUTPUTDIR}" \ + -l sps=1 \ + -N "gate.${RUNID}" \ + -v "PARAM=\"${PARAM}\",INDEX=${NJOBS},INDEXMAX=${NJOBSMAX},OUTPUTDIR=${OUTPUTDIR},RELEASEDIR=${RELEASEDIR},MACROFILE=${MACROFILE},MACRODIR=${MACRODIR}" \ + "${JOBFILE}" || error "submission error" + else + qsub -N "gatejob.${RUNID}" -o "${OUTPUTDIR}" \ + -l sps=1 \ + -v "PARAM=\"${PARAM}\",INDEX=${NJOBS},INDEXMAX=${NJOBSMAX},OUTPUTDIR=${OUTPUTDIR},RELEASEDIR=${RELEASEDIR},MACROFILE=${MACROFILE},MACRODIR=${MACRODIR}" \ + "${JOBFILE}" || error "submission error" + fi + + let NJOBS-- +done + +echo "runid is ${RUNID}" +if test "$(dnsdomainname)" = "in2p3.fr" +then + rsync -av --remove-source-files -e "ssh -i ${HOME}/.ssh/ccin2p3" ${OUTPUTDIR}/ "linux1.dg.creatis.insa-lyon.fr:./cc/$(basename ${OUTPUTDIR})" --exclude '.__afs*' --exclude "${OUTPUTDIR}/gatejob.*.o*" +fi -- 2.47.1