recent versions of FreeSurfer depend on a more recent MCR than documented

[migueldiascosta]

Using FreeSurfer 7.3.2 we got this error

$eb_prefix/software/FreeSurfer/7.3.2-centos7_x86_64/MCRv97

It is looking for either:
  bin/glnxa64/libmwlaunchermain.so    (Linux 64b) or
  bin/maci64/libmwlaunchermain.dylib (Mac 64b)

The hippocampal/amygdala and brainstem modules require the (free) Matlab runtime.
You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2019b.
To do so, please run the following command (you might need root permissions):

fs_install_mcr R2019b

For further details, please visit https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime

The easyconfig in eb uses the MCR that is recommended in that page, MCR 8.4 (R2014b), but it seems at some point that changed and the documentation was not updated. It works for us if we use MCR 9.7 (R2019b) as an easybuild dependency and create a link to it in the FreeSurfer install dir.

Does anyone with knowledge of FreeSurfer know the exact mapping of FreeSurfer and MCR versions so we can fix the relevant easyconfigs?

cc @sassy-crick, @maxim-masterov, @btlindert

[branfosj]

For FreeSurfer 7.2.0, running the grep command from the top level of the install:

$ grep MCRv -r .
./bin/segmentHA_T1_long.sh:set RUNTIME="$FREESURFER_HOME/MCRv84/";
./bin/checkMCR.sh:if ( ! -e ${FREESURFER_HOME}/MCRv84/bin/glnxa64/libmwlaunchermain.so \
./bin/checkMCR.sh:  && ! -e ${FREESURFER_HOME}/MCRv84/bin/maci64/libmwlaunchermain.dylib  ) then
./bin/checkMCR.sh:  echo "${FREESURFER_HOME}/MCRv84"
./bin/segmentBS.sh:set RUNTIME="$FREESURFER_HOME/MCRv84/";
./bin/segmentThalamicNuclei.sh:set RUNTIME="$FREESURFER_HOME/MCRv84/";
./bin/segmentHA_T1.sh:set RUNTIME="$FREESURFER_HOME/MCRv84/";
./bin/segmentHA_T2.sh:set RUNTIME="$FREESURFER_HOME/MCRv84/";
Binary file ./average/SVIP_Adult_Comp_N24_as_orig.4dfp.img matches
Binary file ./average/711-2C_as_mni_average_305.4dfp.img matches
./fsfast/bin/mkcontrast2:if(! $?FS_MCRROOT) setenv FS_MCRROOT $FREESURFER_HOME/MCRv84
./fsfast/bin/selxavg3-sess:if(! $?FS_MCRROOT) setenv FS_MCRROOT $FREESURFER_HOME/MCRv84
./subjects/fsaverage/xhemi/scripts/recon-all.local-copy:  if ( ! -e ${FREESURFER_HOME}/MCRv80/bin/glnxa64/libdctprocess.so \
./subjects/fsaverage/xhemi/scripts/recon-all.local-copy:    && ! -e ${FREESURFER_HOME}/MCRv80/bin/maci64/libdctprocess.jnilib  ) then
./subjects/fsaverage/xhemi/scripts/recon-all.local-copy:    echo "${FREESURFER_HOME}/MCRv80"
./subjects/fsaverage/xhemi/scripts/recon-all.local-copy:    ${FREESURFER_HOME}/MCRv80 \
./subjects/fsaverage/xhemi/scripts/recon-all.local-copy:      ${FREESURFER_HOME}/MCRv80 \
./subjects/fsaverage/xhemi/scripts/recon-all.local-copy:      ${FREESURFER_HOME}/MCRv80 \
./subjects/fsaverage/xhemi/scripts/recon-all.local-copy:      ${FREESURFER_HOME}/MCRv80 \
./easybuild/easybuild-FreeSurfer-7.2.0-20220325.162117.log:== 2022-03-25 16:11:28,340 run.py:233 INFO running cmd: cp -a /dev/shm/carpenjj-admin-2021a-EL8/FreeSurfer/7.2.0/system-system-centos8_x86_64/MCRv84/ /rds/bear-apps/2021a/EL8-has/software/FreeSurfer/7.2.0-centos8_x86_64
./easybuild/easybuild-FreeSurfer-7.2.0-20220325.162117.log:== 2022-03-25 16:12:35,991 run.py:582 INFO cmd "cp -a /dev/shm/carpenjj-admin-2021a-EL8/FreeSurfer/7.2.0/system-system-centos8_x86_64/MCRv84/ /rds/bear-apps/2021a/EL8-has/software/FreeSurfer/7.2.0-centos8_x86_64" exited with exit code 0 and output:
./easybuild/FreeSurfer-7.2.0-centos8_x86_64.eb:postinstallcmds = ['cp -a %(builddir)s/MCRv84/ %(installdir)s']
./easybuild/reprod/FreeSurfer-7.2.0-centos8_x86_64.eb:postinstallcmds = ['cp -a %(builddir)s/MCRv84/ %(installdir)s']
Binary file ./MCRv84/bin/glnxa64/libmwmcr.so matches

I'm currently test installing FreeSurfer-7.3.2-centos8_x86_64.eb and FreeSurfer-7.4.0-centos8_x86_64.eb to look at similar information.

However, I suspect that we can add checkMCR.sh as a sanity check to tell us if all is fine.

$ checkMCR.sh
$ echo $?
0

[branfosj]

See easybuilders/easybuild-easyblocks#2962 for adding checkMCR.sh to the sanity check for recent FreeSurfer.

That check fails on FreeSurfer-7.3.2-centos8_x86_64.eb and passes on FreeSurfer-7.2.0-centos8_x86_64.eb.

[branfosj]

I attempted to fix the easyconfigs in #18302, but it is no longer a case of just copying the MCR files over.

Choices:

• install MCR as a component
• symlink to an existing MCR installation

[migueldiascosta]

symlinking worked for me, with

dependencies = [('MCR', 'R2019b.8')]

postinstallcmds = ["ln -s $EBROOTMCR/v97 %(installdir)s/MCRv97"]

is there a reason to prefer installing MCR as a component?

[branfosj]

is there a reason to prefer installing MCR as a component?

No, but I'm unsure why we have not already changed to having MCR as a dependency.

[branfosj]

I've created #18303 for using MCR as a dependency.

[migueldiascosta]

fixed by easybuilders/easybuild-easyblocks#2962 and #18303, thanks @branfosj!