Hi Alfonso,

I am trying to run the default preprocessing pipeline through the GUI on one subject using CONN v20b on my University's cluster. However, it appears to be getting "stuck" at the Outlier detection stage. That is, MATLAB does not throw an error, but the program will not move on from this step, even after the art_screenshot.jpg file is saved. I am not sure what to do, because MATLAB is not throwing an error, so I cannot diagnose the actual problem. 

I have successfully run this pipeline on my local computer, with the same subject, so I am pretty confident that it is not an issue with my data. I am curious if you have come across this issue before when people try to run this version of the toolbox on a cluster?

I am using the following programs:
- CONN v20b
- SPM12 v7771

Any advice would be greatly appreciated!

Thanks,
Ryan

Hi Ryan,
Can you please take a look at the log file in your project conn_*.qlog/ID/node.*.stdout file (ID's are dates, so just select the last folder there) to try to see where the code is getting stuck?
Thanks
Alfonso
Originally posted by Ryan Daley:

Hi Alfonso,

After receiving your response, I went to cancel a job that was running by hitting "ctl + c". This provided the following MATLAB error message:

"Operation terminated by user during dos (line 67)

Error using close
Interrupt while evaluating Figure CloseRequestFcn."

The program then went on to perform Direct Segmentation & Normalization and successfully ran the rest of the preprocessing pipeline. All of the files were present that I would have expected in the output.  However, there were also 6 files in the output that I did not expect to see including the following:

art_mask_temporalfile20210409094858825.mat
art_mask_temporalfile202104090948588251.mat
art_mask_temporalfile202104090948588252.mat
art_mask_temporalfile202104090948588253.mat
art_mask_temporalfile202104090948588254.mat
art_mask_temporalfile202104090948588255.mat

I had never tried to close out a job this way before, because I had let the walltime expire on previous jobs.

That said, it seems odd that I would need to cancel a process in order for the pipeline to continue running.

Also, it doesn't appear as though a qloq was created for this project. I'm wondering if this is because I opened a node, then opened the Conn project, and then "ran locally" within the node.

Thanks,
Ryan

Hi Ryan, 

Thanks for the detailed feedback, my guess is that the procedure may have got stuck trying to delete those files and likely waiting for user-confirmation as some of those may have been marked as read-only. Could you please try the attached patch and let me know if that seems to fix this issue? (this patch is for release 20b, to install it simply copy this file to your conn distribution folder overwriting the file with the same name there). 

Thanks again!
Alfonso
 
Originally posted by Ryan Daley:

Hi Alfonso,

Thanks for the patch!

I just ran a couple of tests and unfortunately this didn't appear to fix the issue. Again, no error was thrown, but the pipeline appears to get hung up after the art_screenshot.jpg was saved.

Thanks,
Ryan

Hi,
I had the exact same issue and the patch fixed it.

Thank you so much!
Giuseppe


Originally posted by Alfonso Nieto-Castanon: