External Email - Use Caution
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
External Email - Use Caution
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
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Dr Roberto Scipioni Senior HPC Specialist, Red Oak Managed Services
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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
External Email - Use Caution
Dear Sir or Madam,
Indeed we run into the same issues again:
mri_convert /campaign/VB-FM5HPC-001/Marlene/data_tmp/input/sub-315A_T1w.nii /campaign/VB-FM5HPC-001/Marlene/data_tmp/output/sub-315A_T1w/mri/orig/001.mgz reading from /campaign/VB-FM5HPC-001/Marlene/data_tmp/input/sub-315A_T1w.nii... TR=7.80, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 0.999974, 0.00720242) k_ras = (0, -0.00720242, 0.999974) writing to /campaign/VB-FM5HPC-001/Marlene/data_tmp/output/sub-315A_T1w/mri/orig/001.mgz... @#@FSTIME 2025:06:19:12:23:46 mri_convert N 2 e 5.96 S 0.03 U 5.86 P 98% M 54352 F 0 R 1082 W 0 c 22 w 164 I 0 O 30376 L 32.16 32.15 32.10 @#@FSLOADPOST 2025:06:19:12:23:52 mri_convert N 2 32.22 32.16 32.10 #-------------------------------------------- #@# MotionCor Thu Jun 19 12:23:52 BST 2025 Found 1 runs /campaign/VB-FM5HPC-001/Marlene/data_tmp/output/sub-315A_T1w/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... UpdateNeeded: Command not found. if: Expression Syntax.
It looks like the code may use bash,csh and tcsh at different stages and therefore the scripts get confused and do not run properly. Also, the UpdateNeeded is NOT found in the FreeSurfer/bin directory although it IS there!
Why does the code not find it? Any suggestion?
Kind regards
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Dr Roberto Scipioni Senior HPC Specialist, Red Oak Managed Services
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T: +44 (0) 1242 806188 M: +44 (0) 7821 656925 E: roberto.scipioni@redoakconsulting.co.ukmailto:roberto.scipioni@redoakconsulting.co.uk W: https://secure-web.cisco.com/17dtTuTXdEem4WdLvQgWdZPyvdi22J3ex3JeJYzMAeiFoWk...https://secure-web.cisco.com/1kYG9MeyeyXAU2Lk9zISt1TqSPP-s0I_hR0cvauocEerLOIOihl8dHB6FZLs6GRFU256fIkWYUgHnJLTDGyOYiZLGdz2gKg2fN1Gd1zWxJk5WuTK9fSlXi7vpSVrLRVu5QmQVyZD4VXtNWfEeCBR00KgWXl8jPCs2-tQ1hQ1naUSlxOrvRThZPReEq456ECCHdj5vFw1V40UakI5aEHCK8_-M_fVnSr5PxyxeMNhLXerZ0738nyZIZUhwXrFxP-bYPFobUUf0YWrCsRkcZr4HTg2hxBwCAc1kUzDN07j5hNpvwkzGRvntTJ-U0QE7Kofc/https%3A%2F%2Fwww.redoakconsulting.co.uk%2F [A white x on a black background Description automatically generated]https://secure-web.cisco.com/1L8r2wmS4jKki9_Ardvl-FHMJbOOTCnVvrtK6Kinuc4dZBPToSV_tHAQeqPJwXEycRSA9sLpTtz_d_cwGGScTUP27uEmEEsj6xDrSTAgMDMTxglnnHikNqOjo-JpUPGHRi6jSyEYuaEyOAFvNv3HQEbB_OEIgI8jwfroBE4Y4ETk9c_k2ccHj-WXLlJ5jq7QffM9aDqoPqibBN30tB03mdjapAKVkGrpgNUSDgdLy4Nj3JEvoEvPaK7hZLPG1CYWTNOzDZs6Fj1oj4RNRAsdi-zHu9-TZSK1hz_gYY13C6gU5Em2L7YpLrFIHWOJFRivV-4IsXSVOLkjf04uoDAnVLg/https%3A%2F%2Ftwitter.com%2Fredoakhpc[Linked in photo]https://secure-web.cisco.com/1opPwWoHrCTuJtmqIZ-VXotnGINIscX-ggT3TURfoqpzh0UlKP8L6IEAtMNZubIin1T4ALfkWvpWJpWDW70GWMYcHqDh97-kiF2GyBxSy87_HGa2Sla-GbBZ9sp2Xdb0kW1y2zUaPCF8VpDzpPLen7DCd51PHmBwx3o-gBx16r1LMbsHJQX2ZK1S5rZE8sOlWjsDzxian3ltExPul910LdRjGmx-CNDQBP-Sg0Du59ZEv3wN56sUAMqrActX1800i5G6duoPjruPzIJqlv8BErHA812wpE6Qt3_Zj5OzWY3zwqLpT522vIEsP9AQLfVVjXXdI-MR0ofZ0Oc4XVz2kgA/https%3A%2F%2Fwww.linkedin.com%2Fin%2Fowen-thomas-3a928732%2F The information in this e-mail is confidential and solely for the use of the intended recipient(s). If you receive this e-mail in error, please notify the sender and delete the e-mail from your system immediately. In such circumstances, you must not make any use of the e-mail or its contents. Views expressed by an individual in this e-mail do not necessarily reflect the views of Red Oak Consulting. Computer viruses may be transmitted by e-mail. Red Oak Consulting accepts no liability for any damage caused by any virus transmitted by this e-mail. Email transmission cannot be guaranteed to be secure or error-free. It is possible that information may be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. Red Oak Consulting is registered in England and Wales, Registration No. OC313216 Registered Office Pure Offices, Hatherley Lane, Cheltenham, Gloucestershire, GL51 6SH
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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
freesurfer@nmr.mgh.harvard.edu
-
fsbuild -
Roberto Scipioni