[Neurodebian-users] fsl is not paralelized with condor

[Michael Hanke]

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" <xlabou01 at stud.feec.vutbr.cz>
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 at magellan:~$ condor_status
> Name               OpSys      Arch   State     Activity LoadAv Mem
>  ActvtyTime
>
> slot10 at emperor.fno LINUX      X86_64 Unclaimed Idle      0.470 2682 14
> +02:32:15
> slot11 at emperor.fno LINUX      X86_64 Unclaimed Idle      0.000 2682
> 14+02:32:16
> slot12 at emperor.fno LINUX      X86_64 Unclaimed Idle      0.000 2682
> 14+02:32:17
> slot1 at emperor.fnol LINUX      X86_64 Unclaimed Idle      1.000 2682
> 14+02:32:12
> slot2 at emperor.fnol LINUX      X86_64 Unclaimed Idle      1.000 2682
> 14+02:32:15
> slot3 at emperor.fnol LINUX      X86_64 Unclaimed Idle      1.000 2682
> 14+02:32:16
> slot4 at emperor.fnol LINUX      X86_64 Unclaimed Idle      1.000 2682
> 14+02:32:17
> slot5 at emperor.fnol LINUX      X86_64 Unclaimed Idle      1.000 2682
> 14+02:32:18
> slot6 at emperor.fnol LINUX      X86_64 Unclaimed Idle      1.000 2682
> 14+02:32:19
> slot7 at emperor.fnol LINUX      X86_64 Unclaimed Idle      1.000 2682
> 14+02:32:20
> slot8 at emperor.fnol LINUX      X86_64 Unclaimed Idle      1.000 2682
> 14+02:32:13
> slot9 at emperor.fnol LINUX      X86_64 Unclaimed Idle      1.000 2682
> 14+02:32:14
> slot1 at magellan.fno LINUX      X86_64 Unclaimed Idle      0.990 1333 0
> +02:44:39
> slot2 at magellan.fno LINUX      X86_64 Unclaimed Idle      0.000 1333
> 0+02:45:06
> slot3 at magellan.fno LINUX      X86_64 Unclaimed Idle      0.000 1333
> 0+02:45:07
> slot4 at magellan.fno LINUX      X86_64 Unclaimed Idle      0.000 1333
> 0+02:45:08
> slot5 at magellan.fno LINUX      X86_64 Unclaimed Idle      0.000 1333
> 0+02:45:09
> slot6 at magellan.fno 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 at 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 at 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
>
>
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>
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