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Bug 1680 - qsubcellfun fails if you change directory in startup.m

Reported 2012-08-29 15:33:00 +0200
Modified 2012-12-31 11:46:22 +0100
Product: FieldTrip
Component: qsub
Version: unspecified
Hardware: PC
Operating System: Windows
Importance: P3 normal
Assigned to: Robert Oostenveld
Depends on:
See also:

Marcel Zwiers - 2012-08-29 15:33:56 +0200

The following is an example but this behaviour happens with every call >>n = 10; qsubcellfun(@rand, repmat({10},1,n), 'timreq', 600, 'memreq', 100e6) submitting job marzwi_mentat318_p11766_b3_j001... qstat job id submitting job marzwi_mentat318_p11766_b3_j002... qstat job id submitting job marzwi_mentat318_p11766_b3_j003... qstat job id submitting job marzwi_mentat318_p11766_b3_j004... qstat job id submitting job marzwi_mentat318_p11766_b3_j005... qstat job id submitting job marzwi_mentat318_p11766_b3_j006... qstat job id submitting job marzwi_mentat318_p11766_b3_j007... qstat job id submitting job marzwi_mentat318_p11766_b3_j008... qstat job id submitting job marzwi_mentat318_p11766_b3_j009... qstat job id submitting job marzwi_mentat318_p11766_b3_j010... qstat job id It waits for ever for answers but the Torque says the jobs have been completed: 676227.dccn-l014 ...11766_b3_j001 marzwi 00:00:00 C matlab 676228.dccn-l014 ...11766_b3_j002 marzwi 00:00:00 C matlab 676229.dccn-l014 ...11766_b3_j003 marzwi 00:00:00 C matlab 676230.dccn-l014 ...11766_b3_j004 marzwi 00:00:00 C matlab 676231.dccn-l014 ...11766_b3_j005 marzwi 00:00:00 C matlab 676232.dccn-l014 ...11766_b3_j006 marzwi 00:00:00 C matlab 676233.dccn-l014 ...11766_b3_j007 marzwi 00:00:00 C matlab 676234.dccn-l014 ...11766_b3_j008 marzwi 00:00:00 C matlab 676235.dccn-l014 ...11766_b3_j009 marzwi 00:00:00 C matlab 676236.dccn-l014 ...11766_b3_j010 marzwi 00:00:00 C matlab >>ver ------------------------------------------------------------------------------------- MATLAB Version (R2010b) MATLAB License Number: 38957 Operating System: Linux 2.6.18-308.4.1.el5 #1 SMP Tue Apr 17 17:08:00 EDT 2012 x86_64 Java VM Version: Java 1.6.0_17-b04 with Sun Microsystems Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode -------------------------------------------------------------------------------------

Marcel Zwiers - 2012-08-30 09:06:19 +0200

I managed to catch the output file (before it was deleted): -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /opt/freesurfer FSFAST_HOME /opt/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /opt/freesurfer/subjects MNI_DIR /opt/freesurfer/mni FSL_DIR /opt/fsl Starting version 2010b of MATLAB Executing /opt/matlab2010b/bin/matlab -singleCompThread -nodisplay -singleCompThread -nosplash -nodisplay -r restoredefaultpath;addpath('/home/common/matlab/fieldtrip/qsub');qsubexec('marzwi_mentat318_p11766_b6_j003');exit < M A T L A B (R) > Copyright 1984-2010 The MathWorks, Inc. Version (R2010b) 64-bit (glnxa64) August 16, 2010 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit adding user Matlab-paths... ++ marcel ++ SPM8 ++ fsfast toolbox current directory: /home/mrphys/marzwi/mridata MException Properties: identifier: 'MATLAB:load:couldNotReadFile' message: [1x117 char] cause: {0x1 cell} stack: [1x1 struct] {Warning: an error was caught} > In qsubexec at 75

Marcel Zwiers - 2012-08-30 09:09:10 +0200

Mhh, the problem has now been fixed it seems?

Marcel Zwiers - 2012-08-30 09:50:29 +0200

I discovered what the problem was: A cd command in my startup.m that aparently interfered with qsubcellfun's working

Robert Oostenveld - 2012-08-30 10:05:56 +0200

Thanks for digging into this. This is a bug in the cosde, because the case was not correctly caught and transferred ro the end user. I cannot grasp it yet, but let's discuss when i am back from the biomag conference.

Robert Oostenveld - 2012-09-19 22:25:05 +0200

(In reply to comment #3) Hi Marcel, Can you provide a piece of code that allows to replicate the problem? In case it is not reproducible, please close the bug. Robert

Marcel Zwiers - 2012-09-20 13:55:00 +0200

To reproduce the bug add the following line to your startup.m file: cd('The-name-of-any-folder-in-your-home-directory') And run: >>n = 10; qsubcellfun(@rand, repmat({10},1,n), 'timreq', 600, 'memreq', 100e6) And then wait for ever...

Marcel Zwiers - 2012-09-20 13:56:51 +0200

Oh yeah, run that command from a different location. E.g. run: >>cd('~'); n = 10; qsubcellfun(@rand, repmat({10},1,n), 'timreq', 600, 'memreq', 100e6)

Robert Oostenveld - 2012-12-17 12:08:09 +0100

It was easy to fix by passing the full filename of the job mat file in the script. roboos@mentat002> svn commit Sending qsub/qsubfeval.m Transmitting file data . Committed revision 7210.

Robert Oostenveld - 2012-12-31 11:46:22 +0100

closed several bugs that have been resolved for some time. Feel free to reopen the bug if you disagree.