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 https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=693373
Regards, Philip Philip B. Chase Assistant Director Clinical and Translational Science IT University of Florida PO Box 103700 Gainesville, Florida 32610 Email: [email protected]<mailto:[email protected]> Phone: (352) 575-0705 On Feb 29, 2016, at 9:29 AM, Labounek René <[email protected]<mailto:[email protected]>> wrote: Dear Neurodebian users, I am not able to paralelize fsl via condor. I have installed condor based grid of 2 computers (called emperor and magellan). On emperor: condor_master, condor_startd, condor_shedd, condor_collector, condor_negotiator and condor_procd are running On magellan: condor_master, condor_startd and condor_procd are running. condor_status output looks ok: labounek@magellan:~$ condor_status Name OpSys Arch State Activity LoadAv Mem ActvtyTime [email protected]<mailto:[email protected]> LINUX X86_64 Unclaimed Idle 0.470 2682 14+02:32:15 [email protected]<mailto:[email protected]> LINUX X86_64 Unclaimed Idle 0.000 2682 14+02:32:16 [email protected]<mailto:[email protected]> LINUX X86_64 Unclaimed Idle 0.000 2682 14+02:32:17 [email protected]<mailto:[email protected]> LINUX X86_64 Unclaimed Idle 1.000 2682 14+02:32:12 [email protected]<mailto:[email protected]> LINUX X86_64 Unclaimed Idle 1.000 2682 14+02:32:15 [email protected]<mailto:[email protected]> LINUX X86_64 Unclaimed Idle 1.000 2682 14+02:32:16 [email protected]<mailto:[email protected]> LINUX X86_64 Unclaimed Idle 1.000 2682 14+02:32:17 [email protected]<mailto:[email protected]> LINUX X86_64 Unclaimed Idle 1.000 2682 14+02:32:18 [email protected]<mailto:[email protected]> LINUX X86_64 Unclaimed Idle 1.000 2682 14+02:32:19 [email protected]<mailto:[email protected]> LINUX X86_64 Unclaimed Idle 1.000 2682 14+02:32:20 [email protected]<mailto:[email protected]> LINUX X86_64 Unclaimed Idle 1.000 2682 14+02:32:13 [email protected]<mailto:[email protected]> LINUX X86_64 Unclaimed Idle 1.000 2682 14+02:32:14 [email protected]<mailto:[email protected]> LINUX X86_64 Unclaimed Idle 0.990 1333 0+02:44:39 [email protected]<mailto:[email protected]> LINUX X86_64 Unclaimed Idle 0.000 1333 0+02:45:06 [email protected]<mailto:[email protected]> LINUX X86_64 Unclaimed Idle 0.000 1333 0+02:45:07 [email protected]<mailto:[email protected]> LINUX X86_64 Unclaimed Idle 0.000 1333 0+02:45:08 [email protected]<mailto:[email protected]> LINUX X86_64 Unclaimed Idle 0.000 1333 0+02:45:09 [email protected]<mailto:[email protected]> LINUX X86_64 Unclaimed Idle 0.000 1333 0+02:45:10 Total Owner Claimed Unclaimed Matched Preempting Backfill X86_64/LINUX 18 0 0 18 0 0 0 Total 18 0 0 18 0 0 0 labounek@magellan:~$ 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: http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html 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. Does somebody has an idea what is wrong? Here is the terminal output and now is running xfibers on one core for labounek user. labounek@emperor:~/test$ bedpostx dti/ subjectdir is /home/labounek/test/dti Making bedpostx directory structure Queuing preprocessing stages Queuing parallel processing stage ----- Bedpostx Monitor ----- Regards, Rene Labounek _______________________________________________ Neurodebian-users mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/neurodebian-users
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