FSL配置GPU环境运行bedpostx以及probtrackx

  之间因为电脑没有显卡，所以为了加快程序速度，配置了condor作业处理系统，本来处理288方向的数据可能会花上7，8天，4核cpu并行了以后时间降为2天。condor的配置步骤另有介绍。

  这里介绍的是配置FSL的GPU环境，FSL wiki官网上也说了FSL bedpostx支持GPU并行计算，不过后来发现probtrackx也可以用GPU跑。

  这里主要是两个步骤bedpostx以及probtrackx。

  首先安装CUDA环境，这个网上步骤较多，这里就不写了，我自己配的是CUDA8.0.我的显卡是nvidia 1080ti。

  一。bedpostx

             关键文件：bedpostx_gpu bedpostx_procpost_gpu xfibres_gpu

            首先根据FSL wiki，在ubantu16.04环境下安装FSL，应该是5.0.8版本，这个版本是没有上述GPU版本文件的，也缺少一些共享库。到FSL Archive里查询可以得到GPU版本下载地址 注意我的cuda后来装的是8.0版本，所以这里下载8.0版本匹配的bedpostx，然后文件保存到/usr/lib/fsl/5.0/ 和/usr/share/fsl/5.0/bin/里去，还有其他文件也要一一下载GPU版本，此外FSL要升级到5.0.9,下载官网的patch包，把里面的bin文件里全部拷贝到/usr/lib/fsl/5.0/ 和/usr/share/fsl/5.0/bin/里去，lib文件有一些库要转移到/usr/lib下面，这个如果有问题，会有log信息提示，可按要求改正，基本上是做软连接。

             另外一些GPU脚本文件有需要修正的地方。

            

#!/bin/sh#   Copyright (C) 2004 University of Oxford##   SHCOPYRIGHTexport LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${FSLDIR}/lib  %%这里是需要修改的，应该是FSL环境版本的问题，5.0.8终端命令安装版本并没有${FSLDIR}/lib这个文件夹，                                                         %%经修改为/bin,能够运行。否则会报错xfibres_gpu：symbol lookup errorUsage() {    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 "-QSYS (Queue System, 0 use fsl_sub: FMRIB, 1 TORQUE (default): WashU)"    echo "-Q (name of the GPU(s) queue, default cuda.q (defined in environment variable: FSLGECUDAQ)"    #echo "-Q (name of the GPU(s) queue, default cuda.q for QSYS=0 and no queue for QSYS=1)"    echo "-NJOBS (number of jobs to queue, the data is divided in NJOBS parts, usefull for a GPU cluster, default 4)"    echo "-n (number of fibres per voxel, default 3)"    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 (Deconvolution model. 1: with sticks, 2: with sticks with a range of diffusivities (default), 3: with zeppelins)"    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}monitor(){    cat <<EOM > ${subjdir}.bedpostX/monitor#!/bin/shnparts=0if [ $njobs -eq 1 ]; then#1 part (GPU) and several subparts#voxels processed in each subpart are 12800 or more if the last one is less than 6400 (1 part less)nparts=\$(($nvox/12800))if [ \$nparts%12800 != 0 ];then nparts=\$((\$nparts + 1)) filast_part=\$(($nvox-(((\$nparts-1))*12800)))if [ \$last_part -lt 6400 ];then nparts=\$((\$nparts - 1)) fielsenparts=$njobsfiechoecho "----- Bedpostx Monitor -----"finished=0lastprinted=0havedad=2while [ \$finished -eq 0 ] ; do    nfin=0    part=0    errorFiles=\`ls ${subjdir}.bedpostX/logs/*.e* 2> /dev/null \`    for errorFile in \$errorFiles    do        if [ -s \$errorFile ]; then            echo An error ocurred. Please check file \$errorFile            kill -9 $$            exit 1        fi    done    while [ \$part -le \$nparts ];do        if [ -e ${subjdir}.bedpostX/logs/monitor/\$part ]; then            nfin=\$((\$nfin + 1))        fi        part=\$((\$part + 1))    done    newmessages=\$((\$nfin - \$lastprinted))    while [ "\$newmessages" -gt 0 ];do        lastprinted=\$((\$lastprinted + 1))        echo \$lastprinted parts processed out of \$nparts        newmessages=\$((\$newmessages - 1))    done    if [ -f ${subjdir}.bedpostX/xfms/eye.mat ] ; then        finished=1        echo "All parts processed"exit     fi    if [ ! \$havedad -gt 0 ]; then       exit 0    fi    if [ "x$SGE_ROOT" = "x" ]; then        havedad=\`ps -e -o pid 2>&1| grep "$$\\b" | wc -l\`    fi    sleep 50;doneEOM    chmod +x ${subjdir}.bedpostX/monitor}make_absolute(){    dir=$1;    if [ -d ${dir} ]; thenOLDWD=`pwd`cd ${dir}dir_all=`pwd`cd $OLDWD    elsedir_all=${dir}    fi    echo ${dir_all}}[ "$1" = "" ] && Usagesubjdir=`make_absolute $1`subjdir=`echo $subjdir | sed 's/\/$/$/g'`echo "---------------------------------------------"echo "------------ BedpostX GPU Version -----------"echo "---------------------------------------------"echo subjectdir is $subjdir#parse option argumentsqsys=0njobs=4nfibres=3fudge=1burnin=1000njumps=1250sampleevery=25model=2gflag=0other=""queue=""if [ $qsys -eq 0 ] && [ "x$SGE_ROOT" != "x" ]; thenqueue="-q $FSLGECUDAQ"fishiftwhile [ ! -z "$1" ]do  case "$1" in      -QSYS) qsys=$2;shift;;      -Q) queue="-q $2";shift;;      -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=$2;shift;;      -g) gflag=1;;       *) other=$other" "$1;;  esac  shiftdoneopts="--nf=$nfibres --fudge=$fudge --bi=$burnin --nj=$njumps --se=$sampleevery --model=$model"defopts="--cnonlinear"opts="$opts $defopts $other"#check that all required files existif [ ! -d $subjdir ]; thenecho "subject directory $1 not found"exit 1fiif [ ! -e ${subjdir}/bvecs ]; then    if [ -e ${subjdir}/bvecs.txt ]; thenmv ${subjdir}/bvecs.txt ${subjdir}/bvecs    elseecho "${subjdir}/bvecs not found"exit 1    fifiif [ ! -e ${subjdir}/bvals ]; then    if [ -e ${subjdir}/bvals.txt ]; thenmv ${subjdir}/bvals.txt ${subjdir}/bvals    elseecho "${subjdir}/bvals not found"exit 1    fifiif [ `${FSLDIR}/bin/imtest ${subjdir}/data` -eq 0 ]; thenecho "${subjdir}/data not found"exit 1fiif [ ${gflag} -eq 1 ]; then    if [ `${FSLDIR}/bin/imtest ${subjdir}/grad_dev` -eq 0 ]; thenecho "${subjdir}/grad_dev not found"exit 1    fifiif [ `${FSLDIR}/bin/imtest ${subjdir}/nodif_brain_mask` -eq 0 ]; thenecho "${subjdir}/nodif_brain_mask not found"exit 1fiif [ -e ${subjdir}.bedpostX/xfms/eye.mat ]; thenecho "${subjdir} has already been processed: ${subjdir}.bedpostX." echo "Delete or rename ${subjdir}.bedpostX before repeating the process."exit 1fiecho Making bedpostx directory structuremkdir -p ${subjdir}.bedpostX/mkdir -p ${subjdir}.bedpostX/diff_partsmkdir -p ${subjdir}.bedpostX/logsmkdir -p ${subjdir}.bedpostX/logs/logs_gpumkdir -p ${subjdir}.bedpostX/logs/monitorrm -f ${subjdir}.bedpostX/logs/monitor/*mkdir -p ${subjdir}.bedpostX/xfms#mailto=`whoami`@fmrib.ox.ac.ukecho Copying files to bedpost directorycp ${subjdir}/bvecs ${subjdir}/bvals ${subjdir}.bedpostX${FSLDIR}/bin/imcp ${subjdir}/nodif_brain_mask ${subjdir}.bedpostXif [ `${FSLDIR}/bin/imtest ${subjdir}/nodif` = 1 ] ; then    ${FSLDIR}/bin/fslmaths ${subjdir}/nodif -mas ${subjdir}/nodif_brain_mask ${subjdir}.bedpostX/nodif_brainfi# Split the dataset in parts echo Pre-processing stageif [ ${gflag} -eq 1 ]; thenpre_command="$FSLDIR/bin/split_parts_gpu ${subjdir}/data ${subjdir}/nodif_brain_mask ${subjdir}.bedpostX/bvals ${subjdir}.bedpostX/bvecs ${subjdir}/grad_dev 1 $njobs ${subjdir}.bedpostX"elsepre_command="$FSLDIR/bin/split_parts_gpu ${subjdir}/data ${subjdir}/nodif_brain_mask ${subjdir}.bedpostX/bvals ${subjdir}.bedpostX/bvecs NULL 0 $njobs ${subjdir}.bedpostX"fiif [ $qsys -eq 0 ]; then#SGEsplitID=`${FSLDIR}/bin/fsl_sub -T 40 -l ${subjdir}.bedpostX/logs -N bedpostx_preproc_gpu $pre_command`else#TORQUEecho $pre_command > ${subjdir}.bedpostX/temptorque_command="qsub -V $queue -l nodes=1:ppn=1:gpus=1,walltime=00:40:00 -N bedpostx_preproc_gpu -o ${subjdir}.bedpostX/logs -e ${subjdir}.bedpostX/logs"splitID=`exec $torque_command ${subjdir}.bedpostX/temp | awk '{print $1}' | awk -F. '{print $1}'`        rm ${subjdir}.bedpostX/tempsleep 10finvox=`${FSLDIR}/bin/fslstats $subjdir.bedpostX/nodif_brain_mask -V  | cut -d ' ' -f1 `echo Queuing parallel processing stage[ -f ${subjdir}.bedpostX/commands.txt ] && rm ${subjdir}.bedpostX/commands.txtmonitorif [ "x$SGE_ROOT" = "x" ]; then    ${subjdir}.bedpostX/monitor&fipart=0while [ $part -lt $njobs ]do    partzp=`$FSLDIR/bin/zeropad $part 4`    if [ ${gflag} -eq 1 ]; then    gopts="$opts --gradnonlin=${subjdir}.bedpostX/grad_dev_$part"else    gopts=$optsfi    echo "${FSLDIR}/bin/xfibres_gpu --data=${subjdir}.bedpostX/data_$part --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 $nvox" >> ${subjdir}.bedpostX/commands.txt        part=$(($part + 1))doneif [ $qsys -eq 0 ]; then#SGEbedpostid=`${FSLDIR}/bin/fsl_sub $queue -l ${subjdir}.bedpostX/logs -N bedpostx_gpu -j $splitID -t ${subjdir}.bedpostX/commands.txt`else#TORQUEtaskfile=${subjdir}.bedpostX/commands.txtecho "command=\`cat "$taskfile" | head -\$PBS_ARRAYID | tail -1\` ; exec \$command" > ${subjdir}.bedpostX/temptasks=`wc -l $taskfile | awk '{print $1}'`sge_tasks="-t 1-$tasks"#PBS -t x-y: x and y are the array boundstorque_command="qsub -V $queue -l nodes=1:ppn=1:gpus=1,walltime=3:00:00,pmem=16gb -N bedpostx_gpu -o ${subjdir}.bedpostX/logs -e ${subjdir}.bedpostX/logs -W depend=afterok:$splitID $sge_tasks"bedpostid=`exec $torque_command ${subjdir}.bedpostX/temp | awk '{print $1}' | awk -F. '{print $1}'`        rm ${subjdir}.bedpostX/tempsleep 10fiecho Queuing post processing stage    %%这里可能涉及到bash dash等shell版本区别，不一一解释，要将sh脚本前面bash执行。post_command="${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 $gopts $nvox $njobs ${subjdir} ${FSLDIR}"if [ $qsys -eq 0 ]; then#SGEmergeid=`${FSLDIR}/bin/fsl_sub -T 120 -j $bedpostid -N bedpostx_postproc_gpu -l ${subjdir}.bedpostX/logs $post_command`else#TORQUEecho $post_command > ${subjdir}.bedpostX/temptorque_command="qsub -V $queue -l nodes=1:ppn=1:gpus=1,walltime=00:40:00 -N bedpostx_postproc_gpu -o ${subjdir}.bedpostX/logs -e ${subjdir}.bedpostX/logs -W depend=afterokarray:$bedpostid"mergeid=`exec $torque_command ${subjdir}.bedpostX/temp | awk '{print $1}' | awk -F. '{print $1}'`        rm ${subjdir}.bedpostX/tempsleep 10fiecho $mergeid > ${subjdir}.bedpostX/logs/postproc_IDif [ "x$SGE_ROOT" != "x" ]; then    echo    echo Type ${subjdir}.bedpostX/monitor to show progress.    echo Type ${subjdir}.bedpostX/cancel to terminate all the queued tasks.    cat <<EOC > ${subjdir}.bedpostX/cancel#!/bin/shqdel $mergeid $bedpostidEOC    chmod +x ${subjdir}.bedpostX/cancel    echo    echo You will get an email at the end of the post-processing stage.    echoelse    sleep 60fi

#!/bin/sh#   Copyright (C) 2012 University of Oxford##   SHCOPYRIGHT# last 2 parameters are subjdir and bindirparameters=""while [ ! -z "$2" ]                                      %%这里可能会报[[错误doif [[ $1 =~ "--nf=" ]]; then                     %% if[[ ]] 代表正则表达式匹配 如果查询到nf变量，将numfib赋值为nf，cut -d 表示将一个字符串切断    numfib=`echo $1 | cut -d '=' -f2`        %%这里'='表示把'--nf=3'切为'--nf'和'3' 而-f后接2表示第二个串，即3赋值给numfib，这里-f与2之间fi                                               %%加个空格，这里如果反复bug，可以echo numfib的值进行观察 all=$all" "$1subjdir=$1shiftdonebindir=$1$bindir/bin/merge_parts_gpu $allfib=1while [ $fib -le $numfib ]do    ${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/merged_th${fib}samples -Tmean ${subjdir}.bedpostX/mean_th${fib}samples    ${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/merged_ph${fib}samples -Tmean ${subjdir}.bedpostX/mean_ph${fib}samples    ${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/merged_f${fib}samples -Tmean ${subjdir}.bedpostX/mean_f${fib}samples    ${FSLDIR}/bin/make_dyadic_vectors ${subjdir}.bedpostX/merged_th${fib}samples ${subjdir}.bedpostX/merged_ph${fib}samples ${subjdir}/nodif_brain_mask ${subjdir}.bedpostX/dyads${fib}    if [ $fib -ge 2 ];then${FSLDIR}/bin/maskdyads ${subjdir}.bedpostX/dyads${fib} ${subjdir}.bedpostX/mean_f${fib}samples${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/mean_f${fib}samples -div ${subjdir}.bedpostX/mean_f1samples ${subjdir}.bedpostX/mean_f${fib}_f1samples${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/dyads${fib}_thr0.05 -mul ${subjdir}.bedpostX/mean_f${fib}_f1samples ${subjdir}.bedpostX/dyads${fib}_thr0.05_modf${fib}${FSLDIR}/bin/imrm ${subjdir}.bedpostX/mean_f${fib}_f1samples    fi    fib=$(($fib + 1))doneif [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/mean_f1samples` -eq 1 ];then    ${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/mean_f1samples -mul 0 ${subjdir}.bedpostX/mean_fsumsamples    fib=1    while [ $fib -le $numfib ]    do${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/mean_fsumsamples -add ${subjdir}.bedpostX/mean_f${fib}samples ${subjdir}.bedpostX/mean_fsumsamplesfib=$(($fib + 1))    donefiecho Removing intermediate filesif [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/merged_th1samples` -eq 1 ];then  if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/merged_ph1samples` -eq 1 ];then    if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/merged_f1samples` -eq 1 ];then      rm -rf ${subjdir}.bedpostX/diff_parts      rm -rf ${subjdir}.bedpostX/data*      rm -rf ${subjdir}.bedpostX/grad_dev*      fi  fifiecho Creating identity xfmxfmdir=${subjdir}.bedpostX/xfmsecho 1 0 0 0 > ${xfmdir}/eye.matecho 0 1 0 0 >> ${xfmdir}/eye.matecho 0 0 1 0 >> ${xfmdir}/eye.matecho 0 0 0 1 >> ${xfmdir}/eye.matecho Done

共享库的问题主要是libcudart,libcuda,libcurand,libbedpostx_cuda 注意如果有地方出问题可以进当前目录用ldd -r *指令查看共享库依赖，注意软链接方法

一切搞定之后，bedpostx_gpu在98个方向上只需要30分钟，在288个方向上需要一个小时多一点。

二。probtrackx

  下载地址,一定要下载，因为FSL就算5.0.9版本也没有GPU版本的probtrackx

然后运行的时候注意 permission问题，加一下权限 chmod +777 /probtrackx2_gpu路径

后面find_the_biggest记得指定output名字，生成在home里面

probtarckx的运行时间，CPU运行大概2小时多，GPU7分钟左右。

整体配置：

1.ubantu16.04

2.cuda8.0

3.FSL5.0.8+后续缺少的GPU版本文件

4.显卡GTX 1080 TI

5.内存32GB

FSL的FDT部分可以完美GPU运行