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Subject:

Re: matlab compiler (mcc) & spm batch scripts

From:

Christian Gaser <[log in to unmask]>

Reply-To:

Christian Gaser <[log in to unmask]>

Date:

Fri, 24 Feb 2012 16:38:38 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (103 lines)

Dear Jen,

an alternative approach is to call a batch file with cg_spm8_batch.sh, that is provided with my VBM8 toolbox. This should work for most batch files.

Regards,

Christian
____________________________________________________________________________

Christian Gaser, Ph.D.
Departments of Psychiatry and Neurology
Friedrich-Schiller-University of Jena
Jahnstrasse 3, D-07743 Jena, Germany
Tel: ++49-3641-934752	Fax:   ++49-3641-934755
e-mail: [log in to unmask]
http://dbm.neuro.uni-jena.de


On Thu, 16 Feb 2012 15:28:59 -0800, s pm <[log in to unmask]> wrote:

>I am trying to compile an spm8 batch script as a shell script to be run
>from the linux command prompt, so that it can be run on a remote server in
>a high-performance computing environment. I have done this successfully
>with other matlab scripts using the mcc command (matlab 2010a). The spm8
>batch script (for normalization) that I'm trying to compile runs fine from
>the matlab command prompt. The process of compiling this script runs
>smoothly, but when I try to run the compiled version I get error messages
>regarding cfg_mlbatch_appcfg_master and local_initapps (full output pasted
>below).
>
>I'm actually compiling a script which calls the normalization batch script.
>The relevant lines in that (the lines it gets to when the error output
>appears) are:
>
>spm('Defaults','fmri')
>spm_jobman('initcfg'); % recommended by the ouput from running
>normalize_batchscript_generic from mlab command prompt
>normalize_batchscript_generic % line 74
>
>I've been attempting to fix the problem by adding spm scripts mentioned in
>error outputs to the list of scripts to compile in my mcc command:
>mcc -C -R -nodisplay -R -nojvm -R -singleCompThread  -m -v -w enable -d
>./compilenormsmoothdeploydir fieldtriptocpcaimageprep.m spm_jobman.m
>cfg_util.m cfg_mlbatch_appcfg.m
>
>However, I have no way around the cfg_mlbatch_appcfg_master and
>local_initapps errors below. I tried downloading the latest spm8 updates
>but the only difference that made was to change the line numbers in the
>error message. I tried entering 'run_nogui' instead of 'serial' in the
>first option when calling spm_jobman:
>
>spm_jobman('serial', jobs, '', inputs{:}); % line 14.
>
>but that didn't make any difference.
>
>Any suggestions, anyone?
>
>Jen Whitman
>
>error output when trying to run compiled script from linux command prompt:
>
>------------------------------------------
>Setting up environment variables
>---
>LD_LIBRARY_PATH is
>.:/opt/MATLAB_Compiler_Runtime/v713//runtime/glnxa64:/opt/MATLAB_Compiler_Runtime/v713//bin/glnxa64:/opt/MATLAB_Compiler_Runtime/v713//sys/os/glnxa64:/opt/MATLAB_Compiler_Runtime/v713//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/opt/MATLAB_Compiler_Runtime/v713//sys/java/jre/glnxa64/jre/lib/amd64/server:/opt/MATLAB_Compiler_Runtime/v713//sys/java/jre/glnxa64/jre/lib/amd64/client:/opt/MATLAB_Compiler_Runtime/v713//sys/java/jre/glnxa64/jre/lib/amd64
>Extracting CTF archive. This may take a few seconds, depending on the
> size of your application. Please wait...
>...CTF archive extraction complete.
>run 1 of 1
>Warning: Run spm_jobman('initcfg'); beforehand
>> In spm_jobman at 107
>  In normalize_batchscript_generic at 14
>??? Undefined function or variable 'cfg_mlbatch_appcfg_master'.
>
>Error in ==> cfg_util>local_initapps at 1283
>
>
>
>Error in ==> cfg_util at 619
>
>
>
>Error in ==> spm_jobman at 160
>
>
>
>Error in ==> spm_jobman at 109
>
>
>
>Error in ==> normalize_batchscript_generic at 14
>
>
>
>Error in ==> imageprep at 74
>
>
>
>
>MATLAB:UndefinedFunction
>

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