Hi I am a graduate student from biomedical department of McGill who use psom ( last released version on unix system) to lauch some simulations in session mode:
opt.path_logs = [resultPath 'logs'];                
opt.mode = 'session';                              
opt.mode_pipeline_manager = 'session';              
opt.time_between_checks = 0.5;                     
opt.max_queued = 2;                                 


My pipeline has 3 jobs
 job 1 and 2 are independant
job 3 call output from job 1 and 2


Psom Process my job 1 and 2 sicessfully ("The job was successfully completed") but stay busy after and doesnt attempt to start the job 3
However  the message the job has been sucessfully completed ( 0
in queue) doesnt appear for any job as if psom is a not able to
finalize the process.

When i press Crtl+C I get:
??? Operation terminated by user during ==> psom_pipeline_process at 679

In ==> psom_run_pipeline at 351
    psom_pipeline_process(file_pipeline,opt_proc);

In ==> pipeline_wgls at 241
psom_run_pipeline(pipeline,opt);

The corresponding line (679) is: pause(time_between_checks); % To avoid wasting resources, wait a bit before re-trying to submit jobs





With an old version of psom  there are no problems.
Any Idea ?

Thank you
Alexis

Dear Alexis,

All my apologies for letting two months pass before answering ! Silly me, I did not register to monitor this forum ... Anyway, do you still have this problem ? It seems that the jobs do not complete "cleanly" (i.e. generating .finshed tags). Would you mind checking the contents of the logs folder while PSOM is stuck (and check the content of any .log file in there). This may give us an indication of what is blocking the pipeline.

Best,

Pierre