Dear FSL experts,
I am trying to run PALM on a Linux cluster and I am running into some issues. I know that cluster configurations are very site-specific, but I still hope you can help or at least tell me that the problem is not due to PALM.
I am using palm-alpha111 in stand-alone mode, and I have edited the PALM startup script to point to the correct Octave executable location and to use Octave instead of Matlab (settings WHICH_TO_RUN and OCTAVEPATH). I have also confirmed that I can successfully start octave after loading the required modules, and that I can use it interactively. The full PALM command line I am runnning is:
palm -i lh.concat.surface.fwhm15.fsaverage.mgh -s ${FSAVERAGE_DIR}/surf/lh.white ${FSAVERAGE_DIR}/surf/lh.area -d design.mat -t design.con -n 1000 -T -C 2.6 -tfce2D -fdr -o ${PALM_OUTPUT_PREFIX}
The settings which are giving me trouble are IS_CLUSTER and TEMP_DIR.
1) When I set IS_CLUSTER=0, I get the following error when running PALM:
octave: X11 DISPLAY environment variable not set
octave: disabling GUI features
which: no wb_command in (/shared/apps/octave/intel/4.2.1/2018u1/bin:/shared/apps/gcc/4.9.4/bin:/shared/apps/intel/2018u1/inspector_2018.1.1.535159/bin64:/shared/apps/intel/2018u1/advisor_2018.1.1.535164/bin64:/shared/apps/intel/2018u1/compilers_and_libraries_2018.1.163/linux/bin/intel64:/shared/apps/intel/2018u1/itac/2018.1.017/intel64/bin:/shared/apps/intel/2018u1/vtune_amplifier_2018.1.0.535340/bin64:/shared/apps/intel/2018u1/clck/2018.1/bin/intel64:/shared/apps/intel/2018u1/parallel_studio_xe_2018.1.038/bin:/shared/apps/svn/1.9.6/bin:/opt/xcat/bin:/opt/xcat/sbin:/opt/xcat/share/xcat/tools:/shared/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ibutils/bin:/opt/slurm/current/bin:/usr/lpp/mmfs/bin:/opt/singularity/bin:/shared/apps/octave/intel/4.2.1/2018u1/libexec/octave/4.2.1/site/exec/x86_64-pc-linux-gnu:/shared/apps/octave/intel/4.2.1/2018u1/libexec/octave/api-v51/site/exec/x86_64-pc-linux-gnu:/shared/apps/octave/intel/4.2.1/2018u1/libexec/octave/site/exec/x86_64-pc-linux-gnu:/shared/apps/octave/intel/4.2.1/2018u1/libexec/octave/4.2.1/exec/x86_64-pc-linux-gnu:/shared/apps/octave/intel/4.2.1/2018u1/bin)
or 2) When I set IS_CLUSTER=1 and specify a valid temp dir like this: TEMP_DIR=/tmp, I get this error instead:
octave: X11 DISPLAY environment variable not set
octave: disabling GUI features
parse error:
syntax error
>>> /tmp/palm_temp_7lzj6ZRv5z.m
^
What should I do?
At first glance, it seems that to fix error 1, it seems I should get a `wp_command` executable (I found https://www.humanconnectome.org/software/workbench-command which may be that executable). But strangely, I do not have that executable on my local box that runs PALM without issues.
Maybe I am missing something very obvious? Do I have to install FSL and / or FreeSurfer? Neither of them seems to have a `wb_command` executable though, as both are installed on my client box and it has none.
Thanks in advance,
Tim
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