Dear Sir,

(If I may come in)

“ …, then I recommend analyzing the package files to check all the dependencies are otherwise installed.”

What is that even mean?

Should it not the software have a configure or at least some proper environment options so that the settings can be picked up? Otherwise, is it really fit for purpose for use on an HPC.

On a Cloud HPC, compute nodes are recreated each time they are used and that is why a module environment is used so that the software stack and/or the proper environment is properly loaded on top of an essentially “bare” machine.

I am looking forward to hear your comments

Kind regards


	Dr Roberto Scipioni Senior HPC Specialist, Red Oak Managed Services
	T: +44 (0) 1242 806188 M: +44 (0) 7821 656925 E: roberto.scipioni@redoakconsulting.co.uk W: https://www.redoakconsulting.co.uk

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From: fsbuild <fsbuild@contbay.com>
Sent: 17 June 2025 23:40
To: freesurfer@nmr.mgh.harvard.edu
Cc: Roberto Scipioni <roberto.scipioni@redoakconsulting.co.uk>
Subject: Re: [Freesurfer] Running Freesurfer on HPC (Almalinux OS, CycleCloud Compute nodes)

Currently the tcsh scripts assume a normal Linux .rpm or .deb package installation with a dependency on csh/tcsh being installed under /bin. We do not assume spack, modules, etc. as may be used on clusters is going to configure software images such that it will conflict with that setup. So the tcsh scripts will not run unless /bin/tcsh exists or maybe an alias would work.

If it’s not possible to do a normal install of the .deb or .rpm package to directly install all the system command and library dependencies, then I recommend analyzing the package files to check all the dependencies are otherwise installed.

"If: expression syntax errors" can be from executing the wrong shell. In the case of trying to execute bash scripts, that error might be from running something like “dash” on an Ubuntu flavor of Linux instead of the full-blown “bash" shell.

- R