NITRC Pipeline system for Octave and Matlab Forum: help

RE: psom_pipeline_process error with /bin/bash

Pierre Bellec — Mon, 27 Feb 2017 4:21:55 GMT

Hi Casey,

Looks like recent ubuntu does not include the `at` command by default. You can install it using:

`sudo apt-get install at`

Alternatively you can use the 'background' execution mode, which should work on most systems (it's the default). Not sure how panda has set up it's configuration, but in psom it looks something like:

`opt.mode = 'background';`

You may want to get in touch with the PANDA developers on their dedicated forum:
http://www.nitrc.org/forum/forum.php?forum_id=2731

Best,

Pierre

psom_pipeline_process error with /bin/bash

Casey Paquola — Wed, 22 Feb 2017 7:56:45 GMT

Hello,

I am using psom1-2.0 within the GRETNA toolbox on an ubuntu 16.04 system. I am running into the following error when I try to run the network analysis:

Error using psom_pipeline_process (line 339)
Something went bad when sending the pipeline in the background. The error message was : /bin/bash: at: command not found

I noticed on another forum entry that psom was working on other /bin/bash systems (http://www.nitrc.org/forum/forum.php?thread_id=3371&forum_id=1316), which leaves me more confused about what this particular error means. Could you please give me any advice on how I may fix this problem?

Thanks for your help,
Casey

RE: PSOM stay busy

Pierre Bellec — Wed, 15 Jun 2011 14:28:11 GMT

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

PSOM stay busy

Alexis Machado — Wed, 27 Apr 2011 15:03:39 GMT

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

Welcome to Help

Christian Haselgrove — Mon, 21 Dec 2009 17:05:28 GMT

Welcome to Help