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Bug 2637 - *_ouput.mat file not found (yet)
| Status | CLOSED WONTFIX |
| Reported | 2014-07-05 10:22:00 +0200 |
| Modified | 2015-02-11 10:40:33 +0100 |
| Product: | FieldTrip |
| Component: | qsub |
| Version: | unspecified |
| Hardware: | PC |
| Operating System: | Windows |
| Importance: | P5 normal |
| Assigned to: | Robert Oostenveld |
| URL: | |
| Tags: | |
| Depends on: | |
| Blocks: | |
| See also: |
Marcel Zwiers - 2014-07-05 10:22:08 +0200
Occasionally, I get the following concurrency error: [..] job marzwi_dccn_c355_p1919_b7_j219 returned, it required 11.5 minutes and 2.1 GB job marzwi_dccn_c355_p1919_b7_j212 returned, it required 11.8 minutes and 2.1 GB Warning: File '/home/mrphys/marzwi/marzwi_dccn_c355_p1919_b7_j301_output.mat' not found. > In qsubget at 105 In qsubcellfun at 362 In dd_basicproc>run_job at 1486 In dd_basicproc>jobman at 1199 In gui_mainfcn at 94 In dd_basicproc at 193 In ni_nifti_job>run_dd_basicproc at 736 In ni_nifti_job at 301 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % an error was detected, the output of the remote execution follows %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ---------------------------------------- Begin PBS Prologue Sat Jul 5 10:00:26 CEST 2014 1404547226 Job ID: 6098518.dccn-l029.dccn.nl Username: marzwi Group: mrphys Asked resources: mem=3800039424b,neednodes=matlab,walltime=01:08:00 Queue: matlab Nodes: dccn-c007 End PBS Prologue Sat Jul 5 10:00:26 CEST 2014 1404547226 ---------------------------------------- -------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /opt/freesurfer-v5.3 FSFAST_HOME /opt/freesurfer-v5.3/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /opt/freesurfer-v5.3/subjects MNI_DIR /opt/freesurfer-v5.3/mni FSL_DIR /opt/fsl Starting version 2011a of MATLAB Executing /opt/matlab2011a/bin/matlab -singleCompThread -nodisplay -singleCompThread -nosplash -nodisplay -r restoredefaultpath;addpath('/home/common/matlab/fieldtrip/qsub');qsubexec('/home/mrphys/marzwi/marzwi_dccn_c355_p1919_b7_j301');exit < M A T L A B (R) > Copyright 1984-2010 The MathWorks, Inc. Version 7.12.0.635 (R2011a) 64-bit (glnxa64) March 18, 2011 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. adding user Matlab-paths... ++ marcel ++ fsfast toolbox ++ SPM8 Your version of SPM is up to date. dccn-c007 (05-Jul-2014 10:00:30) current directory: /home/mrphys/marzwi Warning: the input file /home/mrphys/marzwi/marzwi_dccn_c355_p1919_b7_j301_input.mat does not yet exist > In qsubexec at 52 Warning: the input file /home/mrphys/marzwi/marzwi_dccn_c355_p1919_b7_j301_input.mat does not yet exist > In qsubexec at 52 Warning: the input file /home/mrphys/marzwi/marzwi_dccn_c355_p1919_b7_j301_input.mat does not yet exist > In qsubexec at 52 Warning: the input file /home/mrphys/marzwi/marzwi_dccn_c355_p1919_b7_j301_input.mat does not yet exist > In qsubexec at 52 Warning: the input file /home/mrphys/marzwi/marzwi_dccn_c355_p1919_b7_j301_input.mat does not yet exist > In qsubexec at 52 Warning: the input file /home/mrphys/marzwi/marzwi_dccn_c355_p1919_b7_j301_input.mat does not yet exist > In qsubexec at 52 MException Properties: identifier: '' message: [1x101 char] cause: {0x1 cell} stack: [1x1 struct] Warning: an error was caught > In qsubexec at 110 ---------------------------------------- Begin PBS Epilogue Sat Jul 5 10:01:36 CEST 2014 1404547296 Job ID: 6098518.dccn-l029.dccn.nl Username: marzwi Group: mrphys Job Name: marzwi_dccn_c355_p1919_b7_j301 Session: 56013 Asked resources: mem=3800039424b,neednodes=matlab,walltime=01:08:00 Used resources: cput=00:00:00,mem=128040kb,vmem=4137044kb,walltime=00:00:26 Queue: matlab Nodes: dccn-c007 End PBS Epilogue Sat Jul 5 10:01:36 CEST 2014 1404547296 ---------------------------------------- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Warning: error during remote execution: Error in job execution > In qsubget at 204 In qsubcellfun at 362 In dd_basicproc>run_job at 1486 In dd_basicproc>jobman at 1199 In gui_mainfcn at 94 In dd_basicproc at 193 In ni_nifti_job>run_dd_basicproc at 736 In ni_nifti_job at 301 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Warning: File '/home/mrphys/marzwi/marzwi_dccn_c355_p1919_b7_j302_output.mat' not found. > In qsubget at 105 In qsubcellfun at 362 In dd_basicproc>run_job at 1486 In dd_basicproc>jobman at 1199 In gui_mainfcn at 94 In dd_basicproc at 193 In ni_nifti_job>run_dd_basicproc at 736 In ni_nifti_job at 301 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % an error was detected, the output of the remote execution follows %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ---------------------------------------- Begin PBS Prologue Sat Jul 5 10:00:26 CEST 2014 1404547226 Job ID: 6098519.dccn-l029.dccn.nl Username: marzwi Group: mrphys Asked resources: mem=3800039424b,neednodes=matlab,walltime=01:08:00 Queue: matlab Nodes: dccn-c007 End PBS Prologue Sat Jul 5 10:00:26 CEST 2014 1404547226 ---------------------------------------- -------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /opt/freesurfer-v5.3 FSFAST_HOME /opt/freesurfer-v5.3/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /opt/freesurfer-v5.3/subjects MNI_DIR /opt/freesurfer-v5.3/mni FSL_DIR /opt/fsl Starting version 2011a of MATLAB Executing /opt/matlab2011a/bin/matlab -singleCompThread -nodisplay -singleCompThread -nosplash -nodisplay -r restoredefaultpath;addpath('/home/common/matlab/fieldtrip/qsub');qsubexec('/home/mrphys/marzwi/marzwi_dccn_c355_p1919_b7_j302');exit < M A T L A B (R) > Copyright 1984-2010 The MathWorks, Inc. Version 7.12.0.635 (R2011a) 64-bit (glnxa64) March 18, 2011 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. adding user Matlab-paths... ++ marcel ++ fsfast toolbox ++ SPM8 Your version of SPM is up to date. dccn-c007 (05-Jul-2014 10:00:30) current directory: /home/mrphys/marzwi Warning: the input file /home/mrphys/marzwi/marzwi_dccn_c355_p1919_b7_j302_input.mat does not yet exist > In qsubexec at 52 Warning: the input file /home/mrphys/marzwi/marzwi_dccn_c355_p1919_b7_j302_input.mat does not yet exist > In qsubexec at 52 Warning: the input file /home/mrphys/marzwi/marzwi_dccn_c355_p1919_b7_j302_input.mat does not yet exist > In qsubexec at 52 Warning: the input file /home/mrphys/marzwi/marzwi_dccn_c355_p1919_b7_j302_input.mat does not yet exist > In qsubexec at 52 Warning: the input file /home/mrphys/marzwi/marzwi_dccn_c355_p1919_b7_j302_input.mat does not yet exist > In qsubexec at 52 Warning: the input file /home/mrphys/marzwi/marzwi_dccn_c355_p1919_b7_j302_input.mat does not yet exist > In qsubexec at 52 MException Properties: identifier: '' message: [1x101 char] cause: {0x1 cell} stack: [1x1 struct] Warning: an error was caught > In qsubexec at 110 ---------------------------------------- Begin PBS Epilogue Sat Jul 5 10:01:36 CEST 2014 1404547296 Job ID: 6098519.dccn-l029.dccn.nl Username: marzwi Group: mrphys Job Name: marzwi_dccn_c355_p1919_b7_j302 Session: 56035 Asked resources: mem=3800039424b,neednodes=matlab,walltime=01:08:00 Used resources: cput=00:00:00,mem=128104kb,vmem=4137044kb,walltime=00:00:26 Queue: matlab Nodes: dccn-c007 End PBS Epilogue Sat Jul 5 10:01:36 CEST 2014 1404547296 ---------------------------------------- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Warning: error during remote execution: Error in job execution > In qsubget at 204 In qsubcellfun at 362 In dd_basicproc>run_job at 1486 In dd_basicproc>jobman at 1199 In gui_mainfcn at 94 In dd_basicproc at 193 In ni_nifti_job>run_dd_basicproc at 736 In ni_nifti_job at 301 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% job marzwi_dccn_c355_p1919_b7_j010 returned, it required 13.9 minutes and 2.1 GB job marzwi_dccn_c355_p1919_b7_j002 returned, it required 15.9 minutes and 2.1 GB [..]
Robert Oostenveld - 2014-07-15 17:27:05 +0200
I don't think this can be fixed. It seems due to NFS slowness and appears to have happened around the upgrade of the NetApp NAS filer.