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Bug 1648 - qsubcellfun fails on matlab version 7.8 (2009a)
| Status | CLOSED FIXED |
| Reported | 2012-08-13 10:56:00 +0200 |
| Modified | 2012-12-31 11:46:25 +0100 |
| Product: | FieldTrip |
| Component: | qsub |
| Version: | unspecified |
| Hardware: | PC |
| Operating System: | Mac OS |
| Importance: | P3 normal |
| Assigned to: | Robert Oostenveld |
| URL: | |
| Tags: | |
| Depends on: | |
| Blocks: | |
| See also: |
Robert Oostenveld - 2012-08-13 10:56:57 +0200
>> n = 20; qsubcellfun(@rand, repmat({10},1,n), 'timreq', 600, 'memreq', 100e6) submitting job roboos_dccn_c315_p11261_b1_j001... qstat job id 610351.dccn-l014.dccn.nl submitting job roboos_dccn_c315_p11261_b1_j002... qstat job id 610352.dccn-l014.dccn.nl submitting job roboos_dccn_c315_p11261_b1_j003... qstat job id 610353.dccn-l014.dccn.nl submitting job roboos_dccn_c315_p11261_b1_j004... qstat job id 610354.dccn-l014.dccn.nl submitting job roboos_dccn_c315_p11261_b1_j005... qstat job id 610355.dccn-l014.dccn.nl submitting job roboos_dccn_c315_p11261_b1_j006... qstat job id 610356.dccn-l014.dccn.nl submitting job roboos_dccn_c315_p11261_b1_j007... qstat job id 610357.dccn-l014.dccn.nl submitting job roboos_dccn_c315_p11261_b1_j008... qstat job id 610358.dccn-l014.dccn.nl submitting job roboos_dccn_c315_p11261_b1_j009... qstat job id 610359.dccn-l014.dccn.nl submitting job roboos_dccn_c315_p11261_b1_j010... qstat job id 610360.dccn-l014.dccn.nl submitting job roboos_dccn_c315_p11261_b1_j011... qstat job id 610361.dccn-l014.dccn.nl submitting job roboos_dccn_c315_p11261_b1_j012... qstat job id 610362.dccn-l014.dccn.nl submitting job roboos_dccn_c315_p11261_b1_j013... qstat job id 610363.dccn-l014.dccn.nl submitting job roboos_dccn_c315_p11261_b1_j014... qstat job id 610364.dccn-l014.dccn.nl submitting job roboos_dccn_c315_p11261_b1_j015... qstat job id 610365.dccn-l014.dccn.nl submitting job roboos_dccn_c315_p11261_b1_j016... qstat job id 610366.dccn-l014.dccn.nl submitting job roboos_dccn_c315_p11261_b1_j017... qstat job id 610367.dccn-l014.dccn.nl submitting job roboos_dccn_c315_p11261_b1_j018... qstat job id 610368.dccn-l014.dccn.nl submitting job roboos_dccn_c315_p11261_b1_j019... qstat job id 610369.dccn-l014.dccn.nl submitting job roboos_dccn_c315_p11261_b1_j020... qstat job id 610370.dccn-l014.dccn.nl which: no shopt in (/home/mrphys/roboos/mpich2/bin:.:/home/mrphys/roboos/bin.linux:/home/mrphys/roboos/sbin:/home/mrphys/roboos/bin:/usr/lib64/qt-3.3/bin:/opt/utilities/bin64:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/cluster:/opt/rrd/bin:/opt/git/bin:/opt/R/bin:/opt/eagle/bin:/opt/fsl/bin:/opt/scopira:/opt/mricro:/opt/brainvoyagerqx:/opt/ctf-5.4.0/bin:/opt/rsi/idl/bin:/opt/freesurfer/bin:/opt/keepassx/bin:/usr/local/maui/bin:/usr/local/maui/sbin:/opt/ganglia/bin:/usr/sbin) Warning: cleaning up all scheduled and running jobs, don't worry if you see warnings from "qdel" > In qsublist at 111 In qsubcellfun>cleanupfun at 430 In onCleanup>onCleanup.delete at 61 qdel: Request invalid for state of job MSG=invalid state for job - EXITING 610359.dccn-l014.dccn.nl qdel 610359.dccn-l014.dccn.nl: Signal 42 qdel: Request invalid for state of job MSG=invalid state for job - EXITING 610358.dccn-l014.dccn.nl qdel 610358.dccn-l014.dccn.nl: Signal 42 qdel: Request invalid for state of job MSG=invalid state for job - EXITING 610357.dccn-l014.dccn.nl qdel 610357.dccn-l014.dccn.nl: Signal 42 qdel: Request invalid for state of job MSG=invalid state for job - EXITING 610356.dccn-l014.dccn.nl qdel 610356.dccn-l014.dccn.nl: Signal 42 qdel: Request invalid for state of job MSG=invalid state for job - COMPLETE 610355.dccn-l014.dccn.nl qdel 610355.dccn-l014.dccn.nl: Signal 42 qdel: Request invalid for state of job MSG=invalid state for job - EXITING 610354.dccn-l014.dccn.nl qdel 610354.dccn-l014.dccn.nl: Signal 42 qdel: Request invalid for state of job MSG=invalid state for job - EXITING 610353.dccn-l014.dccn.nl qdel 610353.dccn-l014.dccn.nl: Signal 42 qdel: Request invalid for state of job MSG=invalid state for job - COMPLETE 610352.dccn-l014.dccn.nl qdel 610352.dccn-l014.dccn.nl: Signal 42 qdel: Request invalid for state of job MSG=invalid state for job - COMPLETE 610351.dccn-l014.dccn.nl qdel 610351.dccn-l014.dccn.nl: Signal 42 ??? Error using ==> qsubget at 76 the batch queue system returned an error for job roboos_dccn_c315_p11261_b1_j005, now aborting Error in ==> qsubcellfun at 322 [argout, options] = qsubget(jobid{collect}, 'output', 'cell', 'diary', diary, 'StopOnError', StopOnError);
Robert Oostenveld - 2012-12-17 12:29:34 +0100
matlab2009a = matlab78
Robert Oostenveld - 2012-12-17 12:30:50 +0100
the problem still exists >> qsubcellfun(@randn, {1, 2, 3}, 'memreq', 1, 'timreq', 1) stacking 3 matlab jobs in each qsub job submitting job roboos_dccn_c012_p1291_b2_j001... qstat job id 1463230.dccn-l014.dccn.nl which: no shopt in (/home/mrphys/roboos/mpich2/bin:.:/home/mrphys/roboos/bin.linux:/home/mrphys/roboos/sbin:/home/mrphys/roboos/bin:/usr/lib64/qt-3.3/bin:/opt/utilities/bin64:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/cluster:/opt/rrd/bin:/opt/git/bin:/opt/openmeeg/bin:/opt/R/bin:/opt/eagle/bin:/opt/fsl/bin:/opt/scopira:/opt/mricro:/opt/brainvoyagerqx:/opt/ctf-5.4.0/bin:/opt/rsi/idl/bin:/opt/freesurfer/bin:/opt/keepassx/bin:/usr/local/maui/bin:/usr/local/maui/sbin:/opt/ganglia/bin:/usr/sbin:/opt/openmeeg/bin) Warning: cleaning up all scheduled and running jobs, don't worry if you see warnings from "qdel" > In qsublist at 113 In qsubcellfun>cleanupfun at 438 In onCleanup>onCleanup.delete at 61 In qsubcellfun at 254 qdel: Request invalid for state of job MSG=invalid state for job - COMPLETE 1463230.dccn-l014.dccn.nl qdel 1463230.dccn-l014.dccn.nl: Signal 42 ??? Error using ==> qsubget at 78 the batch queue system returned an error for job roboos_dccn_c012_p1291_b2_j001, now aborting Error in ==> qsubcellfun at 330 [argout, options] = qsubget(jobid{collect}, 'output', 'cell', 'diary', diary, 'StopOnError', StopOnError); Error in ==> qsubcellfun at 254 [stackargout{:}] = qsubcellfun(@cellfun, stackargin{:}, optarg{:});
Robert Oostenveld - 2012-12-17 12:44:33 +0100
It is easier to follow in MATLAB with jobid = qsubfeval(@randn, 1, 'memreq', 1, 'timreq', 1) this results in -rw------- 1 roboos mrphys 523 Dec 17 12:37 roboos_dccn_c012_p1291_b1_j002.e1463235 -rw------- 1 roboos mrphys 875 Dec 17 12:37 roboos_dccn_c012_p1291_b1_j002.o1463235 -rw-r--r-- 1 roboos mrphys 17064 Dec 17 12:37 roboos_dccn_c012_p1291_b1_j002_output.mat which are perfectly fine results, except that the e-file contains a warning about shopt that was printed to stderr.
Robert Oostenveld - 2012-12-17 12:46:07 +0100
*** Bug 1732 has been marked as a duplicate of this bug. ***
Robert Oostenveld - 2012-12-17 12:48:58 +0100
solution: check not only whether *.e file is non-empty, but also check for existence of output mat file. If there is an output mat file, assume that it ran through properly. roboos@mentat002> svn commit Sending qsub/qsubget.m Transmitting file data . Committed revision 7212.