Hi Loris,
If you are only including /path/to/spm8 while compiling, you are probably missing many critical subfolders.
To get a recursive list of folders in the SPM directory, you can run a command like from the unix terminal (which I imagine is how you interact with your cluster):
find /path/to/spm8 -type d > spm8_directories.txt
Open this text file up and remove folders that are named "private" and those that begin with "@", for starters, and then drop anything else you know you don't need to include. Then just prefix each line with -I and add all that to your mcc call. I'll include the list of paths that I came up with when I look on my cluster.
I haven't tried compiling a program using SPM8 (or any SPM), but I do compile Matlab for the cluster routinely. This is how I'd try to solve the problem.
Sorry to not have a more definitive answer... maybe there is someone who has actually done it!
Good luck,
Chris
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8 \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/external \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/external/eeprobe \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/external/fieldtrip \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/external/fieldtrip/plotting \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/external/fieldtrip/specest \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/external/fieldtrip/utilities \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/external/fieldtrip/preproc \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/external/fieldtrip/inverse \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/external/fieldtrip/connectivity \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/external/fieldtrip/trialfun \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/external/fieldtrip/forward \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/external/fieldtrip/fileio \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/external/fieldtrip/statfun \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/external/ctf \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/external/bemcp \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/external/yokogawa \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/matlabbatch \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/matlabbatch/cfg_confgui \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/matlabbatch/examples \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/matlabbatch/cfg_basicio \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/EEGtemplates \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/tpm \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/config \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/templates \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/toolbox \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/toolbox/Neural_Models \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/toolbox/mixture \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/toolbox/spectral \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/toolbox/SRender \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/toolbox/Beamforming \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/toolbox/FieldMap \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/toolbox/MEEGtools \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/toolbox/Seg \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/toolbox/Shoot \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/toolbox/DEM \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/toolbox/DARTEL \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/toolbox/HDW \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/toolbox/dcm_meeg \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/apriori \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/spm_orthviews \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/rend \
-I /opt/gridware/apps/binapps/matlab/third_party_toolboxes/spm/8/canonical
-----Original Message-----
From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On Behalf Of Loris Bennett
Sent: 29 June 2017 16:07
To: [log in to unmask]
Subject: [SPM] Compiling a MATLAB program which uses SPM8
Hi,
I'm trying to help a user to run a compiled version of her MATLAB program, which makes use of SPM8.
The uncompiled version runs fine on our cluster, but the compiled version doesn't. It can be compiled without error, but when it runs I get
Undefined function 'ft_datatype_sens' for input arguments of type
'struct'
The ctf-file created by the compilation contains the SPM8 files but not the FieldTrip files, so I presume this is the problem.
Does any have any idea what I am doing wrong?
Cheers,
Loris
--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin Email [log in to unmask]
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