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UAB Research Computing Documentation
https://docs.rc.uab.edu
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Freesufer and Matlab Documentation #359

Closed jgordini closed 2 years ago

jgordini commented 2 years ago

Freesurfer and Matlab documentation on the orginal site https://docs.uabgrid.uab.edu/wiki/FreeSurfer https://docs.uabgrid.uab.edu/wiki/MATLAB

are more comprehensive

but not sure how outdated those docs are.

wwarriner commented 2 years ago

Hi @jgordini! Thanks for bringing these to our attention.

At a glance, a lot of the linked MATLAB page is obsolete. We don't support user installation on personal/lab devices anymore. Integration is out, because folks should be using Open OnDemand MATLAB jobs, and git to move their code around (ideally). I'm not sure vo.uabgrid exists anymore (for the mailing list, user group, etc). If it does still exist it probably won't for too much longer based on my understanding. Happy to be wrong on this part, but now the preferred message for user questions would be our support email. Though the idea of maintaining user-centric forums is interesting. I'll bring it up with our group. I'd prefer a website to an email list for moderated user-user discussions.

FreeSurfer I know much less about. From some quick research, it's two major versions ahead of the 5.3.0 mentioned on that page. Most of that page talks about Cheaha-related stuff that is available on these docs (how to write job scripts, what modules do/how they work). The job script method on that page is obsolete, we would now recommend and teach using --array jobs. We now recommend using rclone (didn't exist in 2013) instead of psftp.

I'm comfortable with starting over on these two if we start getting tickets for these or if users start requesting we discuss them.

If you spot any more that you think might be good to keep around, let us know. Or if you think something specific is missing from our new docs, please let us know!

wwarriner commented 2 years ago

Thinking about it for a moment, we have a user discussion forum, sort of. Check out https://ask.cyberinfrastructure.org/c/locales-data-centers-and-campus-rc/uab/52

I put in a pull request recently to move our FAQ to that site.

jgordini commented 2 years ago

Sounds good. I am cc'ing Kristina Visscher as she is much more familiar with these programs than I am.

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jgordini commented 2 years ago

These are just observations as I was helping to migrate the Visual Brain Core page #358 to the new documentation site.

wwarriner commented 2 years ago

Adding to this based on office hours today, courtesy of @mdefende

https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all https://docs.rc.uab.edu/cheaha/slurm/submitting_jobs/#batch-job

Basically, it may be best to have a short section that points out and links to these two pages (or similar) and ties them together.

mdefende commented 2 years ago

For both MATLAB and Cheaha (and pretty much all other software), we are not going to host pages on how to use them on the Research Computing docs. Starting MATLAB is self-explanatory when starting a job on the website, and Freesurfer has their own documentation that users should go to. This should be the same for all other software. The only exceptions would be if there is a Cheaha specific issue with some software, but that should be handled in our FAQ at https://ask.cyberinfrastructure.org/c/locales-data-centers-and-campus-rc/uab/52