Clean up of David's commits

diff --git a/cluster_tools/gate_job_ccin2p3.job b/cluster_tools/gate_job_ccin2p3.job
index 016b2368de00972fc3348668de2b7d56489b048d..c7abaacb11eb6d62d3ef05ca1da5e5735ce725a9 100644 (file)
--- a/cluster_tools/gate_job_ccin2p3.job
+++ b/cluster_tools/gate_job_ccin2p3.job
@@ -17,8 +17,6 @@
 
 function transferJobData {
     echo "Copying data back"
-    #ssh -i ${HOME}/.ssh/ccin2p3 linux1.dg.creatis.insa-lyon.fr "mkdir cc/$(basename ${OUTPUTDIR})/output.${JOB_ID%%.*}"
-    #rsync -av --remove-source-files -e "ssh -i ${HOME}/.ssh/ccin2p3" output/ "linux1.dg.creatis.insa-lyon.fr:./cc/$(basename ${OUTPUTDIR})/output.${JOB_ID%%.*}"
     pwd
     echo ${OUTPUTDIR}
     mkdir "${OUTPUTDIR}/output.${JOB_ID%%.*}"
@@ -76,7 +74,7 @@ test -d "${MACRODIR}" && test -d "${MACRODIR}/mac" || error "invalid macro"
 
 echo "Copying inputs"
 LOCALMACRODIR=$(mktemp -d)
-trap "wait ; transferJobData ; exit 1" 137 138 152 153
+trap "wait ; transferJobData ; exit 1" 1 2 3 15
 cd ${LOCALMACRODIR}
 cp -r -L "${MACRODIR}"/{data,mac} .
 mkdir output

diff --git a/cluster_tools/gate_power_merge.sh b/cluster_tools/gate_power_merge.sh
index fa2904a5a33855557dff6e68c221858a3152173c..aaf063b18d4f8cc85be856ef0f19df1087c1570d 100755 (executable)
--- a/cluster_tools/gate_power_merge.sh
+++ b/cluster_tools/gate_power_merge.sh
@@ -51,9 +51,9 @@ END { print xsize * ysize * zsize * byte_per_pixel; }' "${input_interfile}")
 
 function write_mhd_header {
     local input_interfile="${1:?"provide input interfile"}"
-    local output_mhd="$(dirname "${input_interfile}")/$(basename "${input_interfile}" ".hdr").hdr.mhd"
+    local output_mhd="$(dirname "${input_interfile}")/$(basename "${input_interfile}" ".hdr").mhd"
 
-    check_interfile "${input_interfile}" || warning "${input_interfile} isn't an interfile image (or unknown format)"
+    check_interfile "${input_interfile}" || error "${input_interfile} isn't an interfile image"
 
     local header_start='ObjectType = Image
 NDims = 3
@@ -334,8 +334,8 @@ function merge_dispatcher {
         echo "${indent}this is a interfile image"
         echo "${indent}creating mhd headers"
         for partialoutputfile in $partialoutputfiles; do write_mhd_header "${partialoutputfile}"; done
-        local mhd_partialoutputfiles="$(for partialoutputfile in $partialoutputfiles; do echo "${partialoutputfile%.*}.hdr.mhd"; done)"
-        local mhd_mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}" ".hdr").hdr.mhd"
+        local mhd_partialoutputfiles="$(for partialoutputfile in $partialoutputfiles; do echo "${partialoutputfile%.*}.mhd"; done)"
+        local mhd_mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}" ".hdr").mhd"
         merge_mhd_image "${mhd_mergedfile}" ${mhd_partialoutputfiles} || error "error while merging"
         echo "${indent}cleaning mhd headers"
         for mhd_partialoutputfile in $mhd_partialoutputfiles; do rm "${mhd_partialoutputfile}"; done

diff --git a/cluster_tools/gate_run_submit_cluster.sh b/cluster_tools/gate_run_submit_cluster.sh
index 2ae6186bcfc38a27bfc230d4052d6c4f338e16e6..edd798bf62839fdbaccd39d28e828be2086d808e 100755 (executable)
--- a/cluster_tools/gate_run_submit_cluster.sh
+++ b/cluster_tools/gate_run_submit_cluster.sh
@@ -1,4 +1,4 @@
-#!/bin/bash -l
+#! /bin/bash -lx
 
 set -u
 SCRIPTNAME="$(basename "${0}")"
@@ -91,7 +91,6 @@ 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
 
@@ -105,11 +104,12 @@ while test $NJOBS -gt 0; do
     then
         PROJECTGROUP=creatis
         qsub -o "${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 "${OUTPUTDIR}" \
+        qsub -N "gatejob.${RUNID}" -o "${OUTPUTDIR}" \
            -v "PARAM=${PARAM},INDEX=${NJOBS},INDEXMAX=${NJOBSMAX},OUTPUTDIR=${OUTPUTDIR},RELEASEDIR=${RELEASEDIR},MACROFILE=${MACROFILE},MACRODIR=${MACRODIR}" \
            "${JOBFILE}" || error "submission error"
     fi
@@ -118,7 +118,3 @@ while test $NJOBS -gt 0; do
 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

diff --git a/cluster_tools/gate_run_submit_cluster_sps.sh b/cluster_tools/gate_run_submit_cluster_sps.sh
deleted file mode 100755 (executable)
index ddc48ca..0000000
--- a/cluster_tools/gate_run_submit_cluster_sps.sh
+++ /dev/null
@@ -1,125 +0,0 @@
-#! /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