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Apr 20, 2011  12:04 PM | Crystal Erickson
Error message
Here is the error .. Seems that it is having trouble finding the log files..How would I fix this. Thanks!



*************************************************************

The pipeline description is now being prepared for execution.

The following folder will be used to store logs and status :

/dagher/dagher3/lauren/niak_output_young/logs/

*************************************************************

Examining the dependencies of the pipeline ...

    Checking that all jobs are associated with a command ...

    Generating dependencies ...

       Reorganizing inputs/outputs ... 2.88 sec

       Analyzing job inputs/outputs, percentage completed :  0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100- 1.54 sec

    Checking if some outputs were not generated twice ...

    Checking if the graph of dependencies is acyclic ...



Loading previous pipeline ...

    Loading old jobs ...

    Loading old status ...

    Loading old logs ...

    Cleaning up job status ...

??? Error using ==> psom_job_status at 115

I am confused : job smooth_pg10_session1_run3 has multiple tags. Sorry dude, I must quit ...



Error in ==> psom_pipeline_init at 517

curr_status = psom_job_status(path_logs,list_jobs_inq,'session');



Error in ==> psom_run_pipeline at 324

    psom_pipeline_init(pipeline,opt_init);   



Error in ==> niak_pipeline_fmri_preprocess at 570

    psom_run_pipeline(pipeline,opt.psom);



>> psom_pipeline_visu('/dagher/dagher3/lauren/niak_output_young/logs/', 'logs', 'smooth_pg10_session1_run3')

??? Error using ==> psom_pipeline_visu at 310

psom:pipeline: unknown action logs



>> psom_pipeline_visu('/dagher/dagher3/lauren/niak_output_young/', 'logs', 'smooth_pg10_session1_run3')     

??? Error using ==> load

Unable to read file /dagher/dagher3/lauren/niak_output_young/PIPE_jobs.mat: No such file or directory.



Error in ==> psom_pipeline_visu at 131

pipeline = load(file_jobs);
 
Apr 20, 2011  06:04 PM | Pierre Bellec
RE: Error message
Dear Crystal,

I checked the history of the pipeline. You ran into a lot of issues ! The latest you got belongs to the same family as the one I fixed recently for you (even though it is different). I applied a similar fix (removed some checking regarding the job status, which was useless in practice and could eventually crash the pipeline). To restart the pipeline, go in the log folder, and remove all *.failed tag files. Everything will then be back to normal. 

I am very sorry you experienced all these difficulties to complete your pipeline. I hope you will soon be able to move on with your analysis. We are currently working on integrating NIAK into the CBRAIN platform, which will provide you with a more user-friendly and stable production environment.

Best regards,

Pierre

PS : BTW, the correct instruction to check the logs of a job is :

>> psom_pipeline_visu('/dagher/dagher3/lauren/niak_output_young/logs/', 'log', 'smooth_pg10_session1_run3')

('log' and not 'logs'). 

In any case the issue here was not with the job itself but with its completion status. The job had completed successfully, but was applied prematurely a "failed" tag for a reason that probably has to do with lags in the disk access. 
Apr 21, 2011  10:04 AM | Crystal Erickson
RE: Error message
It's complete now! Thank you for the help!!