general-discussion > NIAK running REALLY slow?
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Dec 30, 2010  05:12 PM | Deborah Tang
NIAK running REALLY slow?
Hi Pierre,

Just started running Niak, and after 6 hours, it is still processing subject 1. Is this normal? And will it completely finish processing subject 1 before it starts on the other subjects?

Since I have 30 subjects, by my calculations it will take more than 180 hours before it finishes...

Thanks!
Deb

PS See below for an excerpt of the log file:

30-Dec-2010 14:03:10 - The job slice_timing_subject1_session1_run1 has been submitted to the queue (1 jobs in queue).
...
30-Dec-2010 20:28:29 - The job smooth_subject1_run2 has been submitted to the queue (2 jobs in queue).
Dec 30, 2010  06:12 PM | Pierre Bellec
RE: NIAK running REALLY slow?
Dear Deborah,

I had to go directly check on the BIC server for that one. So, you have in your script the following lines :

opt.psom.mode = 'batch';
opt.psom.mode_pipeline_manager = 'batch';
opt.psom.max_queued = 2;

This is telling NIAK to process on your local machine only, using two CPUs. You have 30 subjects, and 10 runs per subject (two acquisitions, this counts more like 60 subjects), so indeed this is going to take a while. 1-2 weeks of processing sounds about right.

What you have to do is delete the file PIPE.lock in your log folder. This will kill the pipeline. Just wait for the two jobs to finish. Then comment this part of your script and restart the pipeline. It will send the pipeline for execution on the linux64bit queue using 20 cores. This should cut down the computation time to something more amenable, like one day. Note that the pipeline will start again where it stopped, i.e. it won't reprocess subject 1.

Good luck with your analysis,

Pierre
Jul 12, 2013  08:07 AM | Debra Dawson
RE: NIAK running REALLY slow?
Hi Pierre,

I am having a similar issue, but I have tried the fix you suggested in your reply with no change in progress.

I have only 5 subjects to analyze, however the pipeline has been analyzing subject 1 for over a week now.
All directories have been created for subject one, however all but the log directory are empty.  Here is the last text from the PIPE_history file:

The pipeline PIPE is now being processed.
Started on 05-Jul-2013 12:19:40
user: ddawson, host: william, system: unix
******************************************
05-Jul-2013 12:19:42 - The job slice_timing_subject1_session1_run1 has been submitted to the queue (1 jobs in queue).
05-Jul-2013 12:19:42 - The job slice_timing_subject1_session1_run2 has been submitted to the queue (2 jobs in queue).
05-Jul-2013 12:19:42 - The job slice_timing_subject1_session1_run3 has been submitted to the queue (3 jobs in queue).
05-Jul-2013 12:19:42 - The job slice_timing_subject1_session1_run4 has been submitted to the queue (4 jobs in queue).
.........................................................................................................


Do you  have any ideas on how to fix this?

Thank you,

Debbie