Version used for Mnu

work/batch/cc/runProfile.sh

+#!/bin/bash
+
+nargs=$#
+if ! [ $nargs -eq 2 -o $nargs -eq 3 ]; then
+  echo "***************************************************"
+  echo ">>>> Usage: `basename $0` parfile scanfile (range)"
+  echo "***************************************************"
+  echo "* \"scanfile\" must be provided as a text file with the name and values of the profiled parameter."
+  echo "For instance var=\"omega_b\" && val=(0.02 0.025 0.030)" 
+ echo "* The optional \"range\" parameter can be used to specify different starting points "
+echo "It must be given in the form: begin-end (eg. 1-5 for jobs 1 to 5)"
+echo "Job 1 corresponding to not changing the parFile starting values, while other values"
+echo "will send jobs shuffling the parameters randomly within the min-max bounds of the parFile"
+  exit 1
+fi
+
+parFile=$1
+scanFile=$2
+range="1-1"
+if [ $nargs -eq 3 ] ; then
+range="$3"
+fi
+
+HERE=$PWD
+
+#check environment
+if [ -z "${CAMELROOT}" ] ; then
+echo "CAMELROOT undefined: did you sourced camel_setup.sh?"
+exit
+fi
+if ! [ -f $CAMELROOT/$CMTCONFIG/Minimize ] ; then
+echo "missing Minimize executable: rum make exec in cmt/"
+fi
+
+
+if [ ! -f  "$parFile" ] ; then
+echo "Missing parfile=$parFile"
+exit
+fi
+if [ ! -f  "$scanFile" ] ; then
+echo "Missing scanfile=$scanFile"
+exit
+fi
+##############define the scanned variable###############
+source $scanFile
+if [ -z "$var" ] ; then
+echo "missing profile variable name: define var=\"...\" in the scan file"
+fi
+if [ -z "$val" ] ; then
+echo "missing profile variable values: define val=( v1 v2 ...)  in the scan file"
+fi
+
+######################################################
+echo "Profile variable= $var"
+echo "values=${val[*]}"
+
+#fix number of cores for openMP
+#default is running on 8 cores.
+#if you wish to change it, set the environment variable NCORES to another value.
+if [ -z "$NCORES" ] ; then 
+NCORES=8
+fi
+#default QSUB command (if not overriden by user)
+if [ -z "${QSUB_CMD}" ] ; then
+QSUB_CMD="qsub -P P_$GROUP -pe multicores $NCORES -q mc_long -l sps=1"
+fi
+echo "About to run ${#val[@]} array-jobs (each with range=$range)" 
+echo "QSUB command will be: ${QSUB_CMD} -t $range"
+echo "Is this OK? [y/n]"
+read answer
+if [ $answer != 'y' ] ; then
+echo "exiting"
+exit 1
+fi
+
+######################################
+
+file=$(readlink -e $parFile)
+parbase=$(basename $file)
+dirout=$PWD/${parbase%".par"}_prof_"$var"
+
+if [ -d  "$dirout" ] ; then
+echo "Output directory $dirout already exists: still want to run? (y/n)"
+read answer
+if [ $answer != 'y' ] ; then
+echo "exiting"
+exit 1
+fi
+else
+mkdir $dirout
+fi
+#cp $scanFile $dirout/
+cp $parFile $dirout/
+
+##########LOOP################################
+for i in $(seq 0 $((${#val[@]}-1))) ; do
+zeval=${val[$i]}
+
+OUTDIR=$dirout/"$var"_${zeval}
+mkdir $OUTDIR
+
+cd $OUTDIR
+
+jobname=${parbase%".par"}_prof_"$var"_${zeval}
+########################################################
+cat > camelrun_$zeval  <<EOBATCH
+#!/bin/env bash
+#$  -N  ${jobname}
+#$  -R y
+#$  -j y
+#$  -o $PWD
+#$  -e $PWD
+
+cd \$TMPDIR
+
+uname -a
+echo "NSLOTS=\$NSLOTS"
+
+export OMP_NUM_THREADS=$NCORES
+
+export PYTHONPATH=${PICO_CODE}
+
+# copies locales
+cp $CAMELROOT/$CMTCONFIG/Minimize .
+cp $CAMELROOT/work/tools/awk/genrand.awk .
+
+#
+#input file: rm variable from it
+#need to escape the * for grep command
+awk '{if ((\$1 == "par" || \$1 == "fix" || \$1 == "class") && \$2 == "${var/\*/\\*}") print ""; else print \$0}' ${dirout}/${parbase} > parfile_in
+#grep -v "${var/\*/\\*}" $file > parfile_in
+
+#compute var: here no escape
+echo "fix  $var  cosmo  $zeval" >>   parfile_in
+
+#special case of degenerate neutrinos (need to decrement Neff by 1 when mass=0)
+if [ "$var" == "m_ncdm" ] ; then
+    grep -v ncdm parfile_in | grep -v N_eff > tmp
+    if [ "$zeval" == "0" ] ; then
+	echo "fix  N_ncdm  cosmo  0" >> tmp
+	echo "class N_eff   3.046" >> tmp
+    else
+	echo "class  N_ncdm    1" >>  tmp
+	echo "fix  m_ncdm  cosmo $zeval" >> tmp
+	echo "class N_eff   2.046" >> tmp
+    fi
+    cp -f tmp parfile_in
+fi
+
+#force Profile parameters
+grep -v nitermax parfile_in | grep -v set_tol | grep -v remove_cosmo_limits | grep -v doHesse > tmp
+echo "nitermax=100000" >> tmp
+echo "set_tol=0.0001" >> tmp
+echo "remove_cosmo_limits=true" >> tmp
+echo "doHesse=false" >> tmp
+cp -f tmp parfile_in
+
+
+echo "init par:"
+cat parfile_in
+ #================================
+#randomize si id ne 1
+ #================================
+echo "***************************************************************"
+
+if [ \${SGE_TASK_ID} -eq 1 ] ; then
+cp parfile_in parfile
+else
+RANDOM=\${SGE_TASK_ID}
+awk -v seed=\$RANDOM -f genrand.awk parfile_in > parfile
+fi
+
+cp parfile "$OUTDIR"/camel\${SGE_TASK_ID}.par
+echo "***************************************************************"
+  #================================
+  # Camel run
+  #================================
+
+#PICO RUN
+./Minimize parfile best_fit #covmat
+cp -f best_fit "$OUTDIR"/best_fit\${SGE_TASK_ID}
+#cp -f covmat "$OUTDIR"/covmat\${SGE_TASK_ID}
+
+EOBATCH
+###################################################################
+#submit an array job for this scanned value
+jobsub="${QSUB_CMD} -t $range camelrun_$zeval"
+eval $jobsub
+##################################################################
+done
+echo ">>>> Outputs in: $dirout"