bedpostx script for PBS/Torque GPU cluster

CUDA/bedpostx_multigpu_PBS.sh

+#!/bin/sh
+
+#   Copyright (C) 2004 University of Oxford
+#
+#   SHCOPYRIGHT
+
+export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${FSLDIR}/lib:${CUDA}/lib64:
+export DYLD_LIBRARY_PATH=$LD_LIBRARY_PATH
+
+Usage() {
+    echo ""
+    echo "Usage: bedpostx <subject directory> [options]"
+    echo ""
+    echo "expects to find bvals and bvecs in subject directory"
+    echo "expects to find data and nodif_brain_mask in subject directory"
+    echo "expects to find grad_dev in subject directory, if -g is set"
+    echo ""
+    echo "<options>:"
+    echo "-NJOBS (number of jobs to queue, the data is divided in NJOBS parts, usefull for a GPU cluster, default 1)"
+    echo "-n (number of fibres per voxel, default 2)"
+    echo "-w (ARD weight, more weight means less secondary fibres per voxel, default 1)"
+    echo "-b (burnin period, default 1000)"
+    echo "-j (number of jumps, default 1250)"
+    echo "-s (sample every, default 25)"
+    echo "-model (1 for monoexponential, 2 for multiexponential, default 1)"
+    echo "-g (consider gradient nonlinearities, default off)"
+    echo ""
+    echo ""
+    echo "ALTERNATIVELY: you can pass on xfibres options onto directly bedpostx"
+    echo " For example:  bedpostx <subject directory> --noard --cnonlinear"
+    echo " Type 'xfibres --help' for a list of available options "
+    echo " Default options will be bedpostx default (see above), and not xfibres default."
+    echo ""
+    echo "Note: Use EITHER old OR new syntax."
+    exit 1
+}
+
+make_absolute(){
+    dir=$1;
+    if [ -d ${dir} ]; then
+	OLDWD=`pwd`
+	cd ${dir}
+	dir_all=`pwd`
+	cd $OLDWD
+    else
+	dir_all=${dir}
+    fi
+    echo ${dir_all}
+}
+
+[ "$1" = "" ] && Usage
+
+subjdir=`make_absolute $1`
+subjdir=`echo $subjdir | sed 's/\/$/$/g'`
+
+echo subjectdir is $subjdir
+
+#parse option arguments
+njobs=1
+nfibres=2
+fudge=1
+burnin=1000
+njumps=1250
+sampleevery=25
+model=1
+gflag=0
+
+shift
+while [ ! -z "$1" ]
+do
+  case "$1" in
+      -NJOBS) njobs=$2;shift;;
+      -n) nfibres=$2;shift;;
+      -w) fudge=$2;shift;;
+      -b) burnin=$2;shift;;
+      -j) njumps=$2;shift;;
+      -s) sampleevery=$2;shift;;
+      -model) model=$2;shift;;
+      -g) gflag=1;; 
+      *) break;;
+  esac
+  shift
+done
+opts="--nf=$nfibres --fudge=$fudge --bi=$burnin --nj=$njumps --se=$sampleevery --model=$model"
+defopts="--cnonlinear"
+opts="$opts $defopts $*"  
+
+#check that all required files exist
+
+if [ ! -d $subjdir ]; then
+	echo "subject directory $1 not found"
+	exit 1
+fi
+
+if [ ! -e ${subjdir}/bvecs ]; then
+	echo "${subjdir}/bvecs not found"
+	exit 1
+fi
+
+if [ ! -e ${subjdir}/bvals ]; then
+	echo "${subjdir}/bvals not found"
+	exit 1
+fi
+
+if [ `${FSLDIR}/bin/imtest ${subjdir}/data` -eq 0 ]; then
+	echo "${subjdir}/data not found"
+	exit 1
+fi
+
+if [ ${gflag} -eq 1 ]; then
+    if [ `${FSLDIR}/bin/imtest ${subjdir}/grad_dev` -eq 0 ]; then
+	echo "${subjdir}/grad_dev not found"
+	exit 1
+    fi
+fi
+
+if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif_brain_mask` -eq 0 ]; then
+	echo "${subjdir}/nodif_brain_mask not found"
+	exit 1
+fi
+
+echo Making bedpostx directory structure
+
+mkdir -p ${subjdir}.bedpostX/
+mkdir -p ${subjdir}.bedpostX/diff_parts
+mkdir -p ${subjdir}.bedpostX/logs
+mkdir -p ${subjdir}.bedpostX/logs/logs_gpu
+mkdir -p ${subjdir}.bedpostX/logs/pid_${$}
+mkdir -p ${subjdir}.bedpostX/xfms
+
+if [ ${gflag} -eq 1 ]; then
+    echo "bedpostx_multigpu_LSF "${subjdir}  $opts "-g" >> ${subjdir}.bedpostX/commands.txt
+else
+    echo "bedpostx_multigpu_LSF "${subjdir}  $opts >> ${subjdir}.bedpostX/commands.txt
+fi
+
+echo Copying files to bedpost directory
+cp ${subjdir}/bvecs ${subjdir}/bvals ${subjdir}.bedpostX
+${FSLDIR}/bin/imcp ${subjdir}/nodif_brain_mask ${subjdir}.bedpostX
+if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif` = 1 ] ; then
+    ${FSLDIR}/bin/fslmaths ${subjdir}/nodif -mas ${subjdir}/nodif_brain_mask ${subjdir}.bedpostX/nodif_brain
+fi
+
+part=0
+echo "Submitting parts (jobs) to GPUs"
+
+post="qsub -V -l nodes=1:ppn=1:gpus=1,walltime=8:00:00 -q dque_gpu -W depend=afterok"
+while [ $part -lt $njobs ];do
+	partzp=`$FSLDIR/bin/zeropad $part 4`
+	
+	if [ ${gflag} -eq 1 ]; then
+	    	gopts="$opts --gradnonlin=${subjdir}/grad_dev"
+	else
+	    	gopts=$opts
+	fi    
+	echo "#!/bin/sh" > ${subjdir}.bedpostX/xfibres.sh
+	echo "#PBS -e ${subjdir}.bedpostX/logs/error$partzp" >> ${subjdir}.bedpostX/xfibres.sh
+ 	echo "#PBS -o ${subjdir}.bedpostX/logs/log$partzp" >> ${subjdir}.bedpostX/xfibres.sh
+	echo "${FSLDIR}/bin/xfibres_gpu --data=${subjdir}/data --mask=$subjdir.bedpostX/nodif_brain_mask -b ${subjdir}.bedpostX/bvals -r ${subjdir}.bedpostX/bvecs --forcedir --logdir=$subjdir.bedpostX/diff_parts/data_part_$partzp $gopts ${subjdir} $part $njobs" >> ${subjdir}.bedpostX/xfibres.sh
+	jobid=`qsub -V -l nodes=1:ppn=1:gpus=1,walltime=8:00:00 -q dque_gpu ${subjdir}.bedpostX/xfibres.sh`
+    
+    	#echo $jobid
+     	post=$post":${jobid}"
+	
+	part=$(($part + 1))
+done
+rm ${subjdir}.bedpostX/xfibres.sh
+nvox=`${FSLDIR}/bin/fslstats $subjdir.bedpostX/nodif_brain_mask -V   | cut -d ' ' -f1 `
+echo "#!/bin/sh" > ${subjdir}.bedpostX/post_proc.sh
+echo "#PBS -e ${subjdir}.bedpostX/logs/error_post_proc.log" >> ${subjdir}.bedpostX/post_proc.sh
+echo "#PBS -o ${subjdir}.bedpostX/logs/log_post_proc.log" >> ${subjdir}.bedpostX/post_proc.sh
+echo "${FSLDIR}/bin/bedpostx_postproc_gpu.sh --data=${subjdir}/data --mask=$subjdir.bedpostX/nodif_brain_mask -b ${subjdir}.bedpostX/bvals -r ${subjdir}.bedpostX/bvecs  --forcedir --logdir=$subjdir.bedpostX/diff_parts $opts $nvox $njobs ${subjdir}" >> ${subjdir}.bedpostX/post_proc.sh
+post=$post" "${subjdir}.bedpostX/post_proc.sh
+#echo $post
+$post
+rm ${subjdir}.bedpostX/post_proc.sh
+echo "All parts (jobs) submitted"
+
+finished=0
+logdir=${subjdir}.bedpostX/logs
+
+while [ $finished -eq 0 ] ; do
+    nfin=0
+    part=0
+    while [ $part -lt $njobs ];do
+        partzp=`${FSLDIR}/bin/zeropad $part 4`
+        if [ -f ${subjdir}.bedpostX/diff_parts/data_part_$partzp/mean_S0samplesJ ];then
+          nfin=$(($nfin + 1))
+        fi
+        part=$(($part + 1))
+    done
+    echo $nfin "parts processed of "$njobs
+
+    if [ -f ${subjdir}.bedpostX/xfms/eye.mat ] ; then
+        finished=1
+        echo "All parts processed"
+    fi
+    sleep 60;
+done
+