Our shipping fsl_sub is Grid Engine only. I’m aware that several people have discussed this and provided patches/variations on the fsl_sub script for Torque/PBS etc, so a search of the archives should be useful.
As for whether this would get integrated into the default fsl_sub, I don’t know.
Duncan
On 14 Apr 2014, at 23:17, Yang, Daniel <[log in to unmask]> wrote:
> Hi Duncan,
>
> Thanks a lot! It works like a charm!
>
> One thing I am wondering if you also know -- does fsl_sub support the torque cluster system, in addition to SGE? If not, do you know if the next version of fsl_sub would support it?
>
> Best,
> Daniel
>
> --
> Daniel (Yung-Jui) Yang, Ph.D.
> Postdoctoral Researcher
> Yale Child Study Center
> New Haven, CT
> Tel: (203) 737-5454
> E-mail: [log in to unmask]
>
> On 4/14/14 10:29 AM, "Duncan Mortimer" <[log in to unmask]> wrote:
>
> Hi Daniel,
>
> You are correct, the fsl_sub script is at fault, something we identified independently a short while ago. The updated version will be included in the next FSL release, but in the meantime, please find attached the very latest version.
>
> To install the patched version…
>
> cd $FSLDIR
> sudo tar zxf ~/Downloads/fsl_sub_apr_2014.tar.gz
>
> assuming that the tar.gz file is in your ~/Downloads folder. You don’t need sudo if you installed FSL to a user-writeable location (e.g. not /usr/local).
>
> Duncan
>
> On 13 Apr 2014, at 03:36, Yang, Daniel <[log in to unmask]> wrote:
>
> Hi Steve,
> The system is a standalone MacOS and $SGE_ROOT is not specified (thus, I get blank by echo $SGE_ROOT)
> I took a look at fsl_sub script. It appears that METHOD is set to be NONE in such situation and qconf is not supposed to be called. However, fsl_sub -q would still always call qconf, regardless of whether $SGE_ROOT is set, which leads to error message because I don't have qconf.
> Best,
> Daniel
> --
> Daniel (Yung-Jui) Yang, Ph.D.
> Postdoctoral Researcher
> Yale Child Study Center
> New Haven, CT
> Tel: (203) 737-5454
> E-mail: [log in to unmask]
> On 4/12/14 6:14 AM, "Stephen Smith" <[log in to unmask]> wrote:
> Hi - what do you get from
> echo $SGE_ROOT
> Cheers.
> On 12 Apr 2014, at 11:11, Yang, Daniel <[log in to unmask]> wrote:
> Hi Steve,
> Yes, I understand that SGE_ROOT must be properly specified in order to use fsl -l on a cluster.
> However, the fix v1.06 script, it is not working properly for computers not on a cluster.
> For example, using Mac OS, I will receive error message because the code (as following) calls qsub -q short.q (which in turn forces qsub to call qconf, which is not existing in Mac OS).
> 2)
> echo "FIX Training classifier with output training file: $TRAIN and Melodic outputs list: $MELOUT"
> echo " copy true labels and features into training directory"
> /bin/rm -rf $TRAIN ${TRAIN}.RData
> mkdir -p $TRAIN; mycwd=`pwd`; cd $TRAIN; TRAIN=`pwd`; cd $mycwd
> j=1
> for i in $MELOUT ; do
> CheckFeatures $i
> jj=`zeropad $j 5`
> cp $i/hand_labels_noise.txt $TRAIN/${jj}.txt
> cp $i/fix/features.csv $TRAIN/${jj}.csv
> j=`echo "$j 1 + p" | dc -`
> done
> i=1
> while [ $i -lt 11 ] ; do
> echo " running classifier training"
> R CMD BATCH "--no-restore --no-save --args ${FSL_FIXDIR} ${TRAIN} ${TRAIN}.RData" ${FSL_FIXDIR}/fix_2a_train.R ${TRAIN}/.Rlog$i
> [ -f ${TRAIN}.RData ] && i=10000
> i=`echo "$i 1 + p" | dc -`
> done
> if [ $loo = 1 ] ; then
> echo $MELOUT > $TRAIN/.fixlist
> echo " running LOO accuracy testing"
> LOO=${TRAIN}_LOO
> bLOO=`basename $LOO`
> /bin/rm -rf $LOO ${LOO}results; mkdir -p $LOO
> echo $MELOUT > $LOO/.fixlist
> j=1
> for f in $MELOUT ; do
> echo leaving-out: $f
> loof=`echo $MELOUT | awk '{$'$j'=""; print $0}'`
> jid=`fsl_sub -q short.q -l $LOO/$j ${FSL_FIXDIR}/fix -t $LOO/$j/$bLOO $loof`
> for d in 1 2 5 10 20 30 40 50 ; do
> jidd=`fsl_sub -j $jid -q short.q -l $LOO/${j}_$d ${FSL_FIXDIR}/fix -c $f $LOO/$j/${bLOO}.RData $d`
> if [ "$jids" = "" ] ; then
> jids="-j $jidd"
> else
> jids="${jids},$jidd"
> fi
> done
> j=`echo "$j 1 + p" | dc -`
> done
> jidf=`fsl_sub $jids -q short.q -l $LOO ${FSL_FIXDIR}/call_matlab.sh -f fix_2c_loo_results $LOO`
> fi
> ;;
> --
> Daniel (Yung-Jui) Yang, Ph.D.
> Postdoctoral Researcher
> Yale Child Study Center
> New Haven, CT
> Tel: (203) 737-5454
> E-mail: [log in to unmask]
> On 4/12/14 3:42 AM, "Stephen Smith" <[log in to unmask]> wrote:
> Hi - you should not need that - this problem should only arise if you have SGE_ROOT incorrectly set when SGE has not been setup.
> Cheers.
> On 12 Apr 2014, at 08:26, Yang, Daniel <[log in to unmask]> wrote:
> Hi all,
> It turns out that this problem can be solved by the following:
> replace all texts of "-q short.q" with blank in the "fix" script
> It will force fix to do LOO sequentially rather than in parallel.
> Hope this helps!
> Daniel
> On 4/11/14 10:19 PM, "Yang, Daniel" <[log in to unmask]> wrote:
> Hi all,
> Upon further examination, I can see where the problem is rooted.
> fix -l called fsl_sub -q ...
> and fsl_sub -q called qconf …
> However, there is no qconf installed in the system. Thus, the error message.
> Does anyone know how to fix this problem (e.g., let fix -l bypass fsl_sub -q)?
> Best,
> Daniel
> --
> Daniel (Yung-Jui) Yang, Ph.D.
> Postdoctoral Researcher
> Yale Child Study Center
> New Haven, CT
> Tel: (203) 737-5454
> E-mail: [log in to unmask]
> On 4/7/14 8:12 AM, "Yang, Daniel" <[log in to unmask]> wrote:
> Hi Fsl list,
> I am trying to trace down the problem by adding an alias line='head -1' in the fix script
> Then I saw new error message when doing LOO: qconf command not found…
> I can't find qconf in my cluster either. By the way, I didn't set up the following two commands because I cannot find them in my systems. Would these be causing problems?
> FSL_FIX_CIFTIRW='/vols/Data/HCP/workbench/CIFTIMatlabReaderWriter';
> FSL_FIX_WBC='/vols/Data/HCP/workbench/bin_linux64/wb_command';
> Thanks, Daniel
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
> Stop the cultural destruction of Tibet
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
> Stop the cultural destruction of Tibet
>
> --
> Duncan A B Mortimer DPhil MChem
> Computing Officer, FMRIB Centre, University of Oxford,
> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.
>
>
>
--
Duncan Mortimer
Computing Officer, FMRIB Centre, University of Oxford
John Radcliffe Hospital, Oxford, UK
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