Allow for uncertainties which name does not start with output

[clitk.git] / cluster_tools / gate_run_submit_cluster.sh

diff --git a/cluster_tools/gate_run_submit_cluster.sh b/cluster_tools/gate_run_submit_cluster.sh
index 136a56742ec3985e1eb8d87bba4bc29c0ef02c1a..0248a1ec007262561431d49f9ccf4db00de59f93 100755 (executable)
--- a/cluster_tools/gate_run_submit_cluster.sh
+++ b/cluster_tools/gate_run_submit_cluster.sh
@@ -1,37 +1,48 @@
-#!/bin/bash
+#!/usr/bin/env bash 
 
 set -u
 SCRIPTNAME="$(basename "${0}")"
 
+# -------------------------------------------------
 function error {
-echo "ERROR: $1"
-usage
-exit 1
+    echo "ERROR: $1"
+    usage
+    exit 1
 }
+# -------------------------------------------------
 
-DEFAULTRELEASESUFFIX="06o"
+DEFAULTRELEASESUFFIX="NONE"
 DEFAULTNUMBEROFJOBS="10"
 
+# -------------------------------------------------
 function usage {
-echo "${SCRIPTNAME} mac/main.mac njobs releasesuffix paramtogate"
-echo "default njobs = ${DEFAULTNUMBEROFJOBS}"
-echo "default releasesuffix = ${DEFAULTRELEASESUFFIX}"
+    echo "${SCRIPTNAME} mac/main.mac njobs releasesuffix paramtogate"
+    echo "default njobs = ${DEFAULTNUMBEROFJOBS}"
+    echo "default releasesuffix = ${DEFAULTRELEASESUFFIX} (NONE means use Gate in PATH)"
 }
+# -------------------------------------------------
 
 test $# -eq 0 && usage && exit 0
 
-SCRIPTDIR=~/gate/gate-tests/bin
-RELEASEDIR="${HOME}/gate/release${3:-"${DEFAULTRELEASESUFFIX}"}"
-JOBFILE=~/gate/gate-tests/job_release.job
+SCRIPTDIR="${HOME}/git/gate-tests/bin"
+RELEASESUFFIX=${3:-"${DEFAULTRELEASESUFFIX}"}
+RELEASEDIR="${HOME}/releases/grid_release${RELEASESUFFIX}"
+JOBFILE="$(dirname $0)/gate_job_cluster.job"
 
 echo "Checking stuff"
 test -f ${JOBFILE} || error "can't find job file ${JOBFILE}"
-test -d ${RELEASEDIR} || error "invalid release dir ${RELEASEDIR}"
+if test "${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"
-OUTPUTDIR=$(mktemp --tmpdir=${MACRODIR} -d run.XXXX)
+OUTPUTDIR=$(mktemp --tmpdir=${MACRODIR} -d run.XXXX || error "can't create temp dir")
 test -d ${OUTPUTDIR} || error "can't locate output dir"
 RUNID=${OUTPUTDIR##*.}
 NJOBS=${2:-"${DEFAULTNUMBEROFJOBS}"}
@@ -40,15 +51,42 @@ 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}"
-echo "using release $(basename ${RELEASEDIR})"
+if test "$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}"
+
 while test $NJOBS -gt 0; do
-       qsub -N "gatejob.${RUNID}" -o "${OUTPUTDIR}" \
-       -v "PARAM=\"${PARAM}\",INDEX=${NJOBS},INDEXMAX=${NJOBSMAX},SCRIPTDIR=${SCRIPTDIR},OUTPUTDIR=${OUTPUTDIR},RELEASEDIR=${RELEASEDIR},MACROFILE=${MACROFILE},MACRODIR=${MACRODIR}" \
-       ${JOBFILE} || error "submission error"
-       let NJOBS--
+
+    if test "${QSUB}" = "noqsub"
+    then 
+        echo "Launching Gate log in ${OUTPUTDIR}/gate_${NJOBS}.log"
+        PARAM=\"${PARAM}\" INDEX=${NJOBS} INDEXMAX=${NJOBSMAX} SCRIPTDIR=${SCRIPTDIR} OUTPUTDIR=${OUTPUTDIR}  RELEASEDIR=${RELEASEDIR} MACROFILE=${MACROFILE} MACRODIR=${MACRODIR} PBS_JOBID="local_${NJOBS}" bash "${JOBFILE}" > ${OUTPUTDIR}/gate_${NJOBS}.log &
+    else
+        qsub -N "gatejob.${RUNID}" -o "${OUTPUTDIR}" \
+           -v "PARAM=\"${PARAM}\",INDEX=${NJOBS},INDEXMAX=${NJOBSMAX},SCRIPTDIR=${SCRIPTDIR},OUTPUTDIR=${OUTPUTDIR},RELEASEDIR=${RELEASEDIR},MACROFILE=${MACROFILE},MACRODIR=${MACRODIR}" \
+           "${JOBFILE}" || error "submission error"
+    fi
+
+    let NJOBS--
 done
 
 echo "runid is ${RUNID}"