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---------- Forwarded message --------- From: freesurfer-bounces@nmr.mgh.harvard.edu Date: Fri, May 26, 2023 at 11:25 AM Subject: The results of your email commands To: rk3199@columbia.edu
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---------- Forwarded message ---------- From: Rob Kudyba rk3199@columbia.edu To: Freesurfer-request@nmr.mgh.harvard.edu Cc: Bcc: Date: Fri, 26 May 2023 11:24:40 -0400 Subject: FS in a HPC cluster via module file: ERROR: Environment variable FREESURFER_HOME must be defined prior to sourcing Freesurfer
External Email - Use Caution
In. HPC cluster where Freesurfer is loaded ad hoc as a module. Running module avail results in the following warnings:
/path/to/anaconda3-2021.11/bin/mpicc: line 285: x86_64-conda_cos6-linux-gnu-cc: command not found ERROR: Environment variable FREESURFER_HOME must be defined prior to sourcing Freesurfer. /path/to/anaconda3-2021.11/bin/mpicc: line 285: x86_64-conda_cos6-linux-gnu-cc: command not found ERROR: Environment variable FREESURFER_HOME must be defined prior to sourcing Freesurfer.
In my .bashrc file:
conda initialize >>>
!! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/path/to/anaconda3-2021.11/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__conda_setup"
else
if [ -f "/path/to/anaconda3-2021.11/etc/profile.d/conda.sh" ]; then
. "/path/to/anaconda3-2021.11/etc/profile.d/conda.sh"
else
export PATH="/path/to/anaconda3-2021.11/bin:$PATH"
fi
fi
unset __conda_setup
The modulefile for Freesurfer contains:
module-whatis "adds freesurfer to your environment variables"
set root /path/to/freesurfer
setenv "FREESURFER_HOME" "/path/to/freesurfer"
setenv "SUBJECTS_DIR" "/path/to/freesurfer/subjects"
prepend-path PATH $root/bin
if { [ module-info mode load ] } {
system "source /path/to/freesurfer/SetUpFreeSurfer.sh"
}
I see that SetUpFreeSurfer.sh has this:
# Call configuration script:
source $FREESURFER_HOME/FreeSurferEnv.sh
After running module unload freesurfer several directories remain in $PATH:
echo $PATH /path/to/freesurfer/fsfast/bin:/path/to/freesurfer/tktools:/path/to/freesurfer/mni/bin:/path/to/freesurfer/fsfast/bin:/path/to/freesurfer/tktools:/path/to/freesurfer/mni/bin
So $FREESURFER_HOME and $SUBJECTS_DIR are being unset but all of the other env vars are not. Is there a way to unset the vars from FreeSurferEnv.sh? A thread on SO https://secure-web.cisco.com/1r8-C-he2TdIjGUEFvriv0MeCNYVOFUUqm9zHSNCvE844JRdcDiH-zTozS1MK4YmLYbWW5owRn1_jG2pI7aRGML1VxZ6MwPyyX-l68SVs8CLh_OgXbNvqqbbKxc6H2wJOrR2lFw88J7e0uHHoheCpWptWc1c6Th6ZC3Whenq1oL2p0WFqeZ8Q4D1fzn1lVV4VcGrJifg3mWJAVj2aOc99MSR3rTJ_uaL_2kGcfPb8Ise9by7L3ccksmUQnGpVqZLXUOa2yx1QgokGaSQX04nJSeEbll11q-KQNwuX3qrnk2rbjZTPaJsLJ-dHCFItgVc6Ey2edjW1j1ABISrh-M2IAA/https%3A%2F%2Fstackoverflow.com%2Fquestions%2F69274347%2Foverwrite-and-restore-environment-variables-in-bash-with-environment-modules mentions using unsetenv but perhaps there's an elseif that can be added to the modulefile?
freesurfer@nmr.mgh.harvard.edu
-
Rob Kudyba