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Dear Sir or Madam,


I am an HPC admin who has been contacted by a user who has installed the Freesurfer in his local directory. However, she keeps getting errors in using the software., for instance:

  1. tcsh ONLY works if it is actually present in /bin  . This defeats the purpose of using the HPC and its module environment especially using the Cloud as compute nodes are ephemeral.
  2. Update needed is searched in /opt/cycle/jetpack/bin/UpdateNeeded rather than in the Software folder /campaign/VB-FM5HPC-001/Marlene/software/freesurfer/freesurfer_backup/bin where it is.

Is there any obvious reason why this may happen. The user is knowledgeable and she has already trying different environment options like those suggested in:
https://surfer.nmr.mgh.harvard.edu/fswiki/rel6downloads

Your help with this would be greatly appreciated.
Kind regards

Dr Roberto Scipioni
Senior HPC specialist, Red Oak Consulting, UK