Dear Tianyi,
If you want to compile SPM yourself, please use spm_make_standalone
(from the config directory) instead of calling mcc directly - it will
take care specifically of some specificities of the batch interface.
Note that if you just want to execute a script (i.e. you didn't define
any extra functions), then you could use the SPM Standalone that we
provide precompiled with the syntax:
./spm12 script template_job.m
It does not contain the cat12 toolbox though - I don't know if the
distributed compiled cat12 allows for this syntax.
Best regards,
Guillaume.
On 14/06/2022 20:42, Wang, Tianyi (Erik) wrote:
> ⚠ Caution: External sender
>
>
> Dear SPM experts,
>
> I'm trying to deploy my script to our university's computing cluster.
> Here is my batch shell script:
> export MATLABPATH=/blue/rachaelseidler/wangtianyi/
> mkdir temp
> cd temp
> cp ../template_job.m .
> module load matlab
> mcc -R -singleCompThread -m template_job.m
> ./template_job
>
> And these are the errors that I got:
>
> [Warning: Name is nonexistent or not a directory:
> /scratch/local/10533627/Editor_cijnl]
> Initialising batch system... Undefined function 'cfg_getfile' for input
> arguments of type 'cell'.
>
> Error in spm_select (line 115)
>
> Error in spm_select (line 110)
>
> Error in spm_select (line 97)
>
> Error in spm_jobman (line 173)
>
> Error in spm_jobman (line 108)
>
> Error in template_job (line 118)
>
> MATLAB:UndefinedFunction
>
>
> It seems some files from spm are missing so I ran spm_check_installation
> full. Here are the errors I got:
>
>
> SPM is installed in: /blue/rachaelseidler/wangtianyi/spm12
> SPM version is SPM12 (7771, 13 Jan 20)
> SPM toolboxes: cat12
> MATLAB is installed in: /apps/matlab/r2020b
> MATLAB version is 9.9.0.1467703 (R2020b)
> MATLAB toolboxes: signal (v8.5) images (v11.2) stats (v12.0)
> Platform: GLNXA64 (maxsize=281474976710655)
> OS: Linux 3.10.0-1062.18.1.el7.x86_64 #1 SMP Wed Feb 12 14:08:31 UTC
> 2020 x86_64
> Java 1.8.0_202-b08 with Oracle Corporation Java HotSpot(TM) 64-Bit
> Server VM mixed mode
> Java support: jvm
> Monitor(s): [1 1 1024 768] (32bit)
> OpenGL version: (Software)
> OpenGL renderer: (None)
> MEX extension: mexa64
> C Compiler: gcc (4.8.5).
> C Compiler settings: /usr/bin/gcc ('-O2 -fwrapv -DNDEBUG')
> C Source code permissions: dir rwxr-xr-x, file rw-r--r--
> ----------------------------------------------------------------------
> Directory : /blue/rachaelseidler/wangtianyi/spm12/toolbox/cat12
> SVN Id does not match filename for file:
> /blue/rachaelseidler/wangtianyi/spm12/toolbox/cat12/Contents.m
>
> SVN Id does not match filename for file:
> /blue/rachaelseidler/wangtianyi/spm12/toolbox/cat12/Contents.txt
>
> SVN Id does not match filename for file:
> /blue/rachaelseidler/wangtianyi/spm12/toolbox/cat12/cat_long_main.txt
> Parsing local installation... ...done
> Downloading SPM information... ...done
> Parsing SPM information...
> Parsing failed
>
> I also tried spm that works for other lab members and it's the same so I
> guess it's not a version issue.
> I will really appreciate it if you have any idea about what's going on.
> Thank you!
>
>
> Best wishes,
> Tianyi Wang
> Doctoral student
> Department of Applied Physiology and Kinesiology
> University of Florida
>
--
Guillaume Flandin, PhD
Wellcome Centre for Human Neuroimaging
UCL Queen Square Institute of Neurology
London WC1N 3BG
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