Hey, maybe a stupid question, but after you edited the config file, did you source it again in the shell where you started bedpost?
Michael On Feb 29, 2016 3:40 PM, "Labounek René" <[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] LINUX X86_64 Unclaimed Idle 0.470 2682 14 > +02:32:15 > [email protected] LINUX X86_64 Unclaimed Idle 0.000 2682 > 14+02:32:16 > [email protected] LINUX X86_64 Unclaimed Idle 0.000 2682 > 14+02:32:17 > [email protected] LINUX X86_64 Unclaimed Idle 1.000 2682 > 14+02:32:12 > [email protected] LINUX X86_64 Unclaimed Idle 1.000 2682 > 14+02:32:15 > [email protected] LINUX X86_64 Unclaimed Idle 1.000 2682 > 14+02:32:16 > [email protected] LINUX X86_64 Unclaimed Idle 1.000 2682 > 14+02:32:17 > [email protected] LINUX X86_64 Unclaimed Idle 1.000 2682 > 14+02:32:18 > [email protected] LINUX X86_64 Unclaimed Idle 1.000 2682 > 14+02:32:19 > [email protected] LINUX X86_64 Unclaimed Idle 1.000 2682 > 14+02:32:20 > [email protected] LINUX X86_64 Unclaimed Idle 1.000 2682 > 14+02:32:13 > [email protected] LINUX X86_64 Unclaimed Idle 1.000 2682 > 14+02:32:14 > [email protected] LINUX X86_64 Unclaimed Idle 0.990 1333 0 > +02:44:39 > [email protected] LINUX X86_64 Unclaimed Idle 0.000 1333 > 0+02:45:06 > [email protected] LINUX X86_64 Unclaimed Idle 0.000 1333 > 0+02:45:07 > [email protected] LINUX X86_64 Unclaimed Idle 0.000 1333 > 0+02:45:08 > [email protected] LINUX X86_64 Unclaimed Idle 0.000 1333 > 0+02:45:09 > [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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