Update version used for Mnu paper

work/batch/cc/runMCMC.sh

 #!/bin/env bash
 
-if [ -z "$NCHAINS" ] ; then
-NCHAINS=4
-fi
-
-if [ -z "$NCORES" ] ; then
-NCORES=8
-fi
-
 myexec=$CAMELROOT/$CMTCONFIG/mcmc
 
-if [ $# -ne 2 ]; then
-echo "usage: parFile mcsetup.txt"
-exit
+
+npar=1
+if [ $# -lt 1 ]; then
+	echo "runMCMC.sh parFile"
+	echo "           [Nsamples=500000]"
+	echo "           [Nchain=4]"
+	echo "           [Ncore=8]"
+	echo "           [queue=mc_long]"
+	echo "           [project=P_planck]"
+	echo ""
+	exit
 fi
+parFile=`readlink -f $1`
+
+Nsample=500000
+Nchain=4
+Ncore=8
+queue=mc_long
+project=P_planck
+
+while(( $# > "$npar")); do
+	((npar = npar + 1))
+	eval riri=\$$npar
+	vals=(${riri//=/ })
+	var=${vals[0]}
+	eval old=\$${vals[0]}
+	echo ${vals[0]}=${vals[1]} "( old:"$old")"
+	if [ -z "$old" ]; then
+	    echo "wrong parameter"
+	    exit
+	fi
+	eval ${vals[0]}=${vals[1]}
+done
+
 
 if [ -z "$CLIKDIR" ] ; then
-echo "miss CLIKDIR"
-exit
+    echo "miss CLIKDIR"
+    exit
 fi
 
 if ! [ -f $myexec ] ; then
-echo "missing exec"
-exit
+    echo "missing exec"
+    exit
 fi
 localexec=`basename $myexec`
 
-file=$1
-mcsetup=$(readlink -e $2)
-
-
-parFile=$(readlink -e $file)
-parbase=$(basename $parFile)
-dirout=${parbase%".par"}_"MC"
-zeroot=$PWD/$dirout
+if ! [ -f $parFile ] ; then
+    echo "wrong parFile $parFile"
+    exit
+fi
+#cat $parFile
+dirpar=`dirname $parFile`
+parbase=`basename $parFile`
+zename=${parbase%".par"}
+echo $dirpar
+echo $parFile
 
+ndim=`awk '$1=="par"{n++}; END {print n}' $parFile`
 
-if ! [ -f $parFile ] ; then
-echo "wrong parFile $parFile"
+#MCMC proposal
+cov=${parbase%".par"}.cov
+if ! [ -f $dirpar/$cov ] ; then
+echo "$dirpar/$cov"
+echo "no covariance matrix found ndim=$ndim"
 exit
 fi
+echo `readlink -f $cov`
 
+#create output directory
+zeroot=$PWD/${zename}_MC
 if [ -d  "$zeroot" ] ; then
-echo "directory $zeroot exists: still want to run? (y/n)"
-read answer
-if [ $answer != 'y' ] ; then
-echo "exiting"
-exit 1
-fi
+    echo "directory $zeroot exists: still want to run? (y/N)"
+    read answer
+    if [ "$answer" != 'y' ] ; then
+	exit 1
+    fi
+else
+    mkdir $zeroot
 fi
-
-#
-
-mkdir $zeroot
 cd $zeroot
 
-#MCMC mandatory stuff
-#read mcsetup
-tmp=`mktemp`
-grep proposal_cov $mcsetup >> $tmp
-source $tmp
-
-#checks on covmat
-if [ -z "${proposal_cov}" ] ; then
-echo "missing proposal_cov in mc_setup"
-exit 1
-fi
-
-if [ ! -f ${proposal_cov} ] ; then
-echo "covariance matrix $proposal_cov does not exist"
-exit 1
-fi
-
-#check sizes
-nlines=`wc -l ${proposal_cov} | cut -d " " -f 1`
-ndim=`awk '$1=="par"{n++}; END {print n}' $parFile`
-echo "ndim=$ndim nlines=$nlines"
-if [ $ndim -ne $nlines ] ; then
-echo "covariance matrix not compatible in size with parFile"
-exit 1
-fi
+#generate parbase
+#enleve precision pour MCMC
+grep -v precision $dirpar/$parbase > $parbase
+#cp $dirpar/$parbase .
+cp $dirpar/$cov .
+
+#setup MCMC
+cat > mc_setup <<EOF
+dim=$ndim
+algo=ada
+length=$Nsample
+proposal_cov=./$cov
+ts=10000
+t0=2000
+scale=0.001
+do_move=false
+EOF
+#cat mc_setup
+
+cat mc_setup >> $parbase
+rm -f mc_setup
 
-echo "**************************************"
-cat $mcsetup
-echo "**************************************"
 
 cat > zerun.sh  <<eof
 echo "running on : \$(uname -a)"
-
 export PYTHONPATH=${PICO_CODE}
-export OMP_NUM_THREADS=$NCORES
-
+export OMP_NUM_THREADS=$Ncore
 cd \$TMPDIR
 cp $myexec .
-#enleve precision pour MCMC
-grep -v precision $parFile > $parbase
-cat $mcsetup >>  $parbase
-
-#each job from the array will have different seeds but is repoductible.
+cp $zeroot/$parbase mcmc\${SGE_TASK_ID}.par
+cp $zeroot/$cov .
 RANDOM=\${SGE_TASK_ID}
-echo "seed=\$RANDOM" >>  $parbase
-echo "seedU=\$RANDOM" >>  $parbase
+echo "seed=\$RANDOM" >>  mcmc\${SGE_TASK_ID}.par
 
-cp $parbase $PWD/camel.par
+cp mcmc\${SGE_TASK_ID}.par $PWD/
 
-./$localexec $parbase $PWD/samples\${SGE_TASK_ID}.txt
+./$localexec mcmc\${SGE_TASK_ID}.par $PWD/samples\${SGE_TASK_ID}.txt
 
 cp ar_vs_length.txt $PWD/ar_vs_length\${SGE_TASK_ID}.txt
 cp scale_vs_length.txt $PWD/scale_vs_length\${SGE_TASK_ID}.txt
@@ -113,24 +128,19 @@ cp corr.txt $PWD/corr\${SGE_TASK_ID}.txt
 qstat -j \${JOB_ID} -nenv
 eof
 
+echo "**************************************"
 #cat zerun.sh
-
-#default qsub command (you may override)
-if [ -z "${QSUB_CMD}" ] ; then
-QSUB_CMD="qsub -P P_$GROUP -pe multicores $NCORES -q mc_longlasting -R y -j y -l sps=1"
-fi
-jobsub="${QSUB_CMD} -o $PWD -N $(basename $zeroot) -t 1-$NCHAINS zerun.sh"
-
-echo "about to run : $jobsub"
-echo "OK? [y/n]"
+echo "queue   : $queue"
+echo "nchain  : $Nchain"
+echo "nsamples: $Nsample"
+echo "OK? [y/N]"
 read answer
-if [ $answer != 'y' ] ; then
-echo "exiting"
-exit 1
+if [ "$answer" != 'y' ]; then
+    exit 1
 fi
 
-eval $jobsub
+QSUB_ARGS="-l sps=1 -R y -j y -o $PWD -e $PWD"
+QUEUE_ARGS="-P $project -pe multicores $Ncore"
+qsub ${QUEUE_ARGS} -q $queue ${QSUB_ARGS} -t 1-$Nchain  -N $zename zerun.sh
 
 cd - > /dev/null
-echo "output will be in $zeroot"
-