Merge branch 'master' of https://gitlab.in2p3.fr/cosmotools/CAMEL

Conflicts:
	cmt/requirements-icc

cmt/requirements-lsst

@@ -5,6 +5,7 @@ use class *
 #compiler options
 macro cpp "icpc"
 macro cppflags " -O2 -ip -ansi_alias -align -Wbrief -Wdeprecated -Wuninitialized -align -Wbrief -Wunused-function  -Wpointer-arith -Wreturn-type"
+macro_append cppflags " -g "
 
 #CAMEL includes
 include_dirs " $(CAMELROOT)/src"
@@ -27,6 +28,8 @@ application test_jla -group=test -s=$(CAMELROOT)/src/camel test/test_jla.cc
 #include_dirs "$(CLIKDIR)/include"
 #macro_append  CAMEL_linkopts " -L$(CLIKDIR)/lib -lcfitsio "
 
+#include_dirs "$(CFITSIODIR)/include"
+#macro_append  CAMEL_linkopts " -L$(CFITSIODIR)/lib -lcfitsio "
 include_dirs "/usr/include/cfitsio"
 macro_append  CAMEL_linkopts " -lcfitsio "
 #PLANCK

work/batch/cc/Minimize5.sh

+#!/bin/bash
+
+#script to embed Minimize executable in batch at cc-in2p3
+#optionally you can pecify a range for runs with different starting  points (as "1-5" for 5 points)
+
+#arguments
+nargs=$#
+if ! [ $nargs -eq 1 -o $nargs -eq 2 ]; then
+echo "usage: Minimize.sh parFile (range) "
+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
+fi
+
+parFile=$1
+
+range="1-1"
+if [ $# -eq 2 ] ; then
+range=$2
+fi
+
+#default is running on 8 cores.
+#if you wish to change it, set the environment variable NCORES to another value.
+if [ -z "$NCORES" ] ; then 
+NCORES=8
+fi
+
+##some checks
+if [ -z "${CAMELROOT}" ] ; then
+echo "CAMELROOT undefined: did you sourced camel_setup.sh?"
+exit
+fi
+if [ -z "$CLIKDIR" ] ; then
+echo "miss CLIKDIR"
+fi
+if ! [ -f $CAMELROOT/$CMTCONFIG/Minimize ] ; then
+echo "missing Minimize executable: rum make exec in cmt/"
+fi
+
+
+file=$(readlink -e $parFile)
+
+if [ ! -f  "$file" ] ; then
+echo "no parfile=$file"
+exit
+fi
+
+
+parbase=$(basename $file)
+
+dirout=${parbase%".par"}_"min"
+OUTDIR=$PWD/$dirout
+
+
+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
+
+
+
+#
+cd $OUTDIR
+
+###################################################
+cat > camelrun  <<EOBATCH
+#!/bin/bash
+
+cd \$TMPDIR
+
+uname -a
+echo "NSLOTS=\$NSLOTS"
+
+source /sps/lsst/Library/CMT/v1r26/mgr/setup.sh
+
+#mes compilos
+source /usr/local/shared/bin/gcc_env.sh 5.2.0
+
+COMPILERVARS_ARCHITECTURE=intel64
+COMPILERVARS_PLATFORM=linux
+source /usr/local/intel/icc/bin/iccvars.sh
+
+gcc --version | grep gcc
+icc --version | grep icc
+
+# copies localeS
+cp $CAMELROOT/\$CMTCONFIG/Minimize .
+cp $CAMELROOT/work/tools/awk/genrand.awk .
+#
+#input file
+# enleve lo:w-l
+
+cp $file 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 $OUTDIR/camel\${SGE_TASK_ID}.par
+echo "***************************************************************"
+  #================================
+  # Camel run
+  #================================
+export PYTHONPATH="${PICO_CODE}"
+export OMP_NUM_THREADS=$NCORES
+./Minimize parfile bestfit covmat
+cp -f bestfit $OUTDIR/best_fit\${SGE_TASK_ID}
+cp -f covmat $OUTDIR/covmat\${SGE_TASK_ID}.dat
+EOBATCH
+
+##############################################################################################
+if [ -z "${QSUB_CMD}" ] ; then
+QSUB_CMD="qsub -P P_$GROUP -pe multicores $NCORES -q mc_long -R y -j y -l sps=1,os=\"sl6|cl7\""
+fi
+jobsub="${QSUB_CMD} -o $PWD -N $(basename $dirout) -t $range camelrun"
+
+echo "about to run : $jobsub"
+echo "OK? [y/n]"
+read answer
+if [ $answer != 'y' ] ; then
+echo "exiting"
+exit 1
+fi
+
+eval $jobsub
+
+echo ">>>> Ouptuts in: $OUTDIR"
+