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There was a dash-vs-bash bug in FSL that adversely effected condor. It was fixed in FSL 5.0.7-2. If you’re not running 5.0.7-2 or higher take a look at <a href="https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=693373" class="">https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=693373</a>
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<div class="">Regards,</div>
<div class="">Philip</div>
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<div apple-content-edited="true" class="">Philip B. Chase<br class="">
Assistant Director<br class="">
Clinical and Translational Science IT<br class="">
University of Florida<br class="">
PO Box 103700<br class="">
Gainesville, Florida 32610<br class="">
Email: <a href="mailto:pbc@ufl.edu" class="">pbc@ufl.edu</a><br class="">
Phone: (352) 575-0705 </div>
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<div class="">On Feb 29, 2016, at 9:29 AM, Labounek René <<a href="mailto:xlabou01@stud.feec.vutbr.cz" class="">xlabou01@stud.feec.vutbr.cz</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">Dear Neurodebian users,<br class="">
<br class="">
I am not able to paralelize fsl via condor. I have installed condor based grid of 2 computers (called emperor and magellan).<br class="">
<br class="">
On emperor: condor_master, condor_startd, condor_shedd, condor_collector, condor_negotiator and condor_procd are running<br class="">
<br class="">
On magellan: condor_master, condor_startd and condor_procd are running.<br class="">
<br class="">
condor_status output looks ok:<br class="">
<br class="">
labounek@magellan:~$ condor_status<br class="">
Name OpSys Arch State Activity LoadAv Mem ActvtyTime<br class="">
<br class="">
<a href="mailto:slot10@emperor.fno" class="">slot10@emperor.fno</a> LINUX X86_64 Unclaimed Idle 0.470 2682 14+02:32:15<br class="">
<a href="mailto:slot11@emperor.fno" class="">slot11@emperor.fno</a> LINUX X86_64 Unclaimed Idle 0.000 2682 14+02:32:16<br class="">
<a href="mailto:slot12@emperor.fno" class="">slot12@emperor.fno</a> LINUX X86_64 Unclaimed Idle 0.000 2682 14+02:32:17<br class="">
<a href="mailto:slot1@emperor.fnol" class="">slot1@emperor.fnol</a> LINUX X86_64 Unclaimed Idle 1.000 2682 14+02:32:12<br class="">
<a href="mailto:slot2@emperor.fnol" class="">slot2@emperor.fnol</a> LINUX X86_64 Unclaimed Idle 1.000 2682 14+02:32:15<br class="">
<a href="mailto:slot3@emperor.fnol" class="">slot3@emperor.fnol</a> LINUX X86_64 Unclaimed Idle 1.000 2682 14+02:32:16<br class="">
<a href="mailto:slot4@emperor.fnol" class="">slot4@emperor.fnol</a> LINUX X86_64 Unclaimed Idle 1.000 2682 14+02:32:17<br class="">
<a href="mailto:slot5@emperor.fnol" class="">slot5@emperor.fnol</a> LINUX X86_64 Unclaimed Idle 1.000 2682 14+02:32:18<br class="">
<a href="mailto:slot6@emperor.fnol" class="">slot6@emperor.fnol</a> LINUX X86_64 Unclaimed Idle 1.000 2682 14+02:32:19<br class="">
<a href="mailto:slot7@emperor.fnol" class="">slot7@emperor.fnol</a> LINUX X86_64 Unclaimed Idle 1.000 2682 14+02:32:20<br class="">
<a href="mailto:slot8@emperor.fnol" class="">slot8@emperor.fnol</a> LINUX X86_64 Unclaimed Idle 1.000 2682 14+02:32:13<br class="">
<a href="mailto:slot9@emperor.fnol" class="">slot9@emperor.fnol</a> LINUX X86_64 Unclaimed Idle 1.000 2682 14+02:32:14<br class="">
<a href="mailto:slot1@magellan.fno" class="">slot1@magellan.fno</a> LINUX X86_64 Unclaimed Idle 0.990 1333 0+02:44:39<br class="">
<a href="mailto:slot2@magellan.fno" class="">slot2@magellan.fno</a> LINUX X86_64 Unclaimed Idle 0.000 1333 0+02:45:06<br class="">
<a href="mailto:slot3@magellan.fno" class="">slot3@magellan.fno</a> LINUX X86_64 Unclaimed Idle 0.000 1333 0+02:45:07<br class="">
<a href="mailto:slot4@magellan.fno" class="">slot4@magellan.fno</a> LINUX X86_64 Unclaimed Idle 0.000 1333 0+02:45:08<br class="">
<a href="mailto:slot5@magellan.fno" class="">slot5@magellan.fno</a> LINUX X86_64 Unclaimed Idle 0.000 1333 0+02:45:09<br class="">
<a href="mailto:slot6@magellan.fno" class="">slot6@magellan.fno</a> LINUX X86_64 Unclaimed Idle 0.000 1333 0+02:45:10<br class="">
Total Owner Claimed Unclaimed Matched Preempting Backfill<br class="">
<br class="">
X86_64/LINUX 18 0 0 18 0 0 0<br class="">
<br class="">
Total 18 0 0 18 0 0 0<br class="">
labounek@magellan:~$<br class="">
<br class="">
<br class="">
I have set FSLPARALLEL=condor in /etc/fsl/fsl.sh file (symbolic link to /etc/fsl/5.0/fsl.sh) as it is written here:<br class="">
<br class="">
<a href="http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html" class="">http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html</a><br class="">
<br class="">
I have tried to run bedpostx but it is still running on one core under my_user_account (labounek) and not under condor_account at multiple-cores.<br class="">
<br class="">
Does somebody has an idea what is wrong?<br class="">
<br class="">
Here is the terminal output and now is running xfibers on one core for labounek user.<br class="">
<br class="">
labounek@emperor:~/test$ bedpostx dti/<br class="">
subjectdir is /home/labounek/test/dti<br class="">
Making bedpostx directory structure<br class="">
Queuing preprocessing stages<br class="">
Queuing parallel processing stage<br class="">
<br class="">
----- Bedpostx Monitor -----<br class="">
<br class="">
Regards,<br class="">
Rene Labounek<br class="">
<br class="">
<br class="">
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Neurodebian-users mailing list<br class="">
Neurodebian-users@lists.alioth.debian.org<br class="">
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/neurodebian-users<br class="">
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