Hi Chris,
That worked perfectly! With hindsight it seems rather obvious that
there must be some sort of include option, as with most other
compilers.
I see there is also an option '-a' to add directories recursively, but
just adding the top-level SPM8 directory gives me the following error on
compilation:
Unexpected error while determining required deployable files. Compilation terminated.
I suppose I could identify the specific directories needed by
trial-and-error, but I think I'll go with your solution for the time
being. Ultimately I might need a more user-friendly solution for our
less computer-savvy users, but currently I'm just doing this for one
person.
Thanks for the help,
Loris
Christopher Cox <[log in to unmask]> writes:
> 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]
--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin Email [log in to unmask]
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