[Neurodebian-users] fsl is not paralelized with condor

[Chase,Philip B]

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: pbc at ufl.edu<mailto:pbc at ufl.edu>
Phone: (352) 575-0705

On Feb 29, 2016, at 9:29 AM, Labounek René <xlabou01 at stud.feec.vutbr.cz<mailto: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<mailto:slot10 at emperor.fno> LINUX      X86_64 Unclaimed Idle      0.470 2682 14+02:32:15
slot11 at emperor.fno<mailto:slot11 at emperor.fno> LINUX      X86_64 Unclaimed Idle      0.000 2682 14+02:32:16
slot12 at emperor.fno<mailto:slot12 at emperor.fno> LINUX      X86_64 Unclaimed Idle      0.000 2682 14+02:32:17
slot1 at emperor.fnol<mailto:slot1 at emperor.fnol> LINUX      X86_64 Unclaimed Idle      1.000 2682 14+02:32:12
slot2 at emperor.fnol<mailto:slot2 at emperor.fnol> LINUX      X86_64 Unclaimed Idle      1.000 2682 14+02:32:15
slot3 at emperor.fnol<mailto:slot3 at emperor.fnol> LINUX      X86_64 Unclaimed Idle      1.000 2682 14+02:32:16
slot4 at emperor.fnol<mailto:slot4 at emperor.fnol> LINUX      X86_64 Unclaimed Idle      1.000 2682 14+02:32:17
slot5 at emperor.fnol<mailto:slot5 at emperor.fnol> LINUX      X86_64 Unclaimed Idle      1.000 2682 14+02:32:18
slot6 at emperor.fnol<mailto:slot6 at emperor.fnol> LINUX      X86_64 Unclaimed Idle      1.000 2682 14+02:32:19
slot7 at emperor.fnol<mailto:slot7 at emperor.fnol> LINUX      X86_64 Unclaimed Idle      1.000 2682 14+02:32:20
slot8 at emperor.fnol<mailto:slot8 at emperor.fnol> LINUX      X86_64 Unclaimed Idle      1.000 2682 14+02:32:13
slot9 at emperor.fnol<mailto:slot9 at emperor.fnol> LINUX      X86_64 Unclaimed Idle      1.000 2682 14+02:32:14
slot1 at magellan.fno<mailto:slot1 at magellan.fno> LINUX      X86_64 Unclaimed Idle      0.990 1333  0+02:44:39
slot2 at magellan.fno<mailto:slot2 at magellan.fno> LINUX      X86_64 Unclaimed Idle      0.000 1333  0+02:45:06
slot3 at magellan.fno<mailto:slot3 at magellan.fno> LINUX      X86_64 Unclaimed Idle      0.000 1333  0+02:45:07
slot4 at magellan.fno<mailto:slot4 at magellan.fno> LINUX      X86_64 Unclaimed Idle      0.000 1333  0+02:45:08
slot5 at magellan.fno<mailto:slot5 at magellan.fno> LINUX      X86_64 Unclaimed Idle      0.000 1333  0+02:45:09
slot6 at magellan.fno<mailto: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


_______________________________________________
Neurodebian-users mailing list
Neurodebian-users at lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/neurodebian-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.alioth.debian.org/pipermail/neurodebian-users/attachments/20160308/7024025b/attachment.html>