Merge pull request #246 from RoanKanninga/master

added custom header (containing projectname in the submitted job)

Author: Gerbenvandervries

molgenis-compute-core/src/main/resources/templates/slurm/header_gaf.ftl

@@ -0,0 +1,54 @@
+#!/bin/bash
+#SBATCH --job-name=${project}_${taskId}
+#SBATCH --output=${taskId}.out
+#SBATCH --error=${taskId}.err
+#SBATCH --partition=${queue}
+#SBATCH --time=${walltime}
+#SBATCH --cpus-per-task ${ppn}
+#SBATCH --mem ${mem}
+#SBATCH --nodes ${nodes}
+#SBATCH --open-mode=append
+
+ENVIRONMENT_DIR="."
+set -e
+set -u
+#-%j
+
+function errorExitandCleanUp()
+{
+        echo "TRAPPED"
+	printf "${taskId}\n" > /groups/umcg-gaf/tmp05/logs/${project}.failed
+	tail -50 ${taskId}.err >> /groups/umcg-gaf/tmp05/logs/${project}.failed
+	rm /groups/umcg-gaf/tmp05/tmp/${project}/*/tmp_${taskId}*
+}
+
+declare MC_tmpFolder="tmpFolder"
+declare MC_tmpFile="tmpFile"
+
+function makeTmpDir {
+        base=$(basename $1)
+        dir=$(dirname $1)
+        echo "dir $dir"
+        echo "base $base"
+        if [[ -d $1 ]]
+        then
+            	dir=$dir/$base
+        fi
+	myMD5=$(md5sum $0)
+        IFS=' ' read -a myMD5array <<< "$myMD5"
+        MC_tmpFolder=$dir/tmp_${taskId}_$myMD5array/
+        mkdir -p $MC_tmpFolder
+        if [[ -d $1 ]]
+        then
+            	MC_tmpFile="$MC_tmpFolder"
+        else
+            	MC_tmpFile="$MC_tmpFolder/$base"
+        fi
+}
+
+trap "errorExitandCleanUp" ERR
+
+# For bookkeeping how long your task takes
+MOLGENIS_START=$(date +%s)
+
+touch ${taskId}.sh.started

molgenis-compute-core/src/main/resources/templates/slurm/submit_gaf.ftl

@@ -0,0 +1,64 @@
+# First cd to the directory with the *.sh and *.finished scripts
+<#noparse>
+MOLGENIS_scriptsDir=$( cd -P "$( dirname "$0" )" && pwd )
+echo "cd $MOLGENIS_scriptsDir"
+cd $MOLGENIS_scriptsDir
+cd ../
+runnumber=`pwd`
+echo basename $runnumber
+run=$(basename $runnumber)
+
+cd ..
+project=`pwd`
+projectName=$(basename $project)
+cd $MOLGENIS_scriptsDir
+if [ -f /groups/umcg-gaf/tmp05/logs/${projectName}.failed ]
+then
+	rm /groups/umcg-gaf/tmp05/logs/${projectName}.failed
+	rm /groups/umcg-gaf/tmp05/logs/${projectName}.mailed.failed
+fi
+
+</#noparse>
+
+touch molgenis.submit.started
+
+
+# Use this to indicate that we skip a step
+skip(){
+echo "0: Skipped --- TASK '$1' --- ON $(date +"%Y-%m-%d %T")" >> molgenis.skipped.log
+}
+
+<#foreach t in tasks>
+#
+##${t.name}
+#
+
+# Skip this step if step finished already successfully
+if [ -f ${t.name}.sh.finished ]; then
+skip ${t.name}.sh
+echo "Skipped ${t.name}.sh"
+else
+# Build dependency string
+dependenciesExist=false
+dependencies="--dependency=afterok"
+    <#foreach d in t.previousTasks>
+    if [[ -n "$${d}" ]]; then
+    dependenciesExist=true
+    dependencies="<#noparse>${dependencies}</#noparse>:$${d}"
+    fi
+    </#foreach>
+if ! $dependenciesExist; then
+unset dependencies
+fi
+output=$(sbatch $dependencies ${t.name}.sh)
+id=${t.name}
+${t.name}=<#noparse>${output##"Submitted batch job "}</#noparse> 
+echo "$id:$${t.name}"
+echo "$id:$${t.name}" >> submitted_jobIDs.txt
+fi
+
+
+
+</#foreach>
+chmod g+w submitted_jobIDs.txt
+touch molgenis.submit.finished