Re: [Freesurfer] TRACULA -bedp parallel processing

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Thanks for the reply. I'm not sure if you are looking for this: we use a small cluster with 40 nodes, 512 CPU cores. We are still using PBS.

Thanks, Ela ________________________________ From: Yendiki, Anastasia AYENDIKI@mgh.harvard.edu Sent: Saturday, June 4, 2022 1:05 AM To: Salar Dini, Elaheh elaheh.salardini@yale.edu; Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: TRACULA -bedp parallel processing

What kind of cluster are you running the parallel processes on?

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Salar Dini, Elaheh elaheh.salardini@yale.edu Sent: Friday, June 3, 2022 7:44 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA -bedp parallel processing

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Thank you for the guidance.

When it tries to run pre.ParallelI , I'll get this:

Copying files to bedpost directory

cp: target '/home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX' is not a directory /home1/es2263/fsl//bin/bedpostx_preproc.sh: line 79: [: -eq: unary operator expected Done

This happens for all subjects.

After this, when I check the subject 57 folder in subjects_dir, there is a file named "dmri.bedpostX.nii.gz".

However, when it tries to run Parallel lines, these errors coming up:

/home1/es2263/fsl//bin/bedpostx_single_slice.sh: line 77: /home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX/logs/log0000: No such file or directory /home1/es2263/fsl//bin/bedpostx_single_slice.sh: line 77: /home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX/logs/log0001: No such file or directory

...

If I run trac-all -bedp -c <Cinfig File> , and not try to process parallelly, it runs without any errors to the end.

Do you have any thoughts what goes wrong?

Thanks again,

Ela

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You run them in that order. First the pre, then the parallel, then the post. You can queue them that way, so that the parallel jobs wait for the pre to finish, and the post waits for all the parallel jobs to finish.

________________________________ From: Salar Dini, Elaheh Sent: Friday, June 3, 2022 3:09 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: TRACULA -bedp parallel processing

Hello,

I have tried to create a text file with command lines that can be run in parallel by using trac-all -bedp -c <config file> -jobs Parallel. When I use this command three text files are produced named: pre.Parallel, post.Parallel, and Parallel. Should I just use Parallel as a source for command lines? What are pre.Parallel and post.Parallel for? I am attaching my Configuration file, pre.Parallel, post.Parallel, and Parallel to this message as well.

OS: Centos 7, Freesurfer version: 7.2.0

Thank you for your help. Kindly, Ela

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