So I peaked in archive and did not get a hit.
The situation is that the University of Wisconsin Madison site license prohibits us running Matlab in a cluster unless it is compiled.
I am assisting a Neurology lab with having a Condor workflow which this time round will do both Matlab and FSL post processing.
To compile the Matlab one needs to compile the entry points. But to run it, we'd have to change how it is called.
Anyone have pointers for me?
Bill Taylor Center for High Throughput Computing Condor Project Computer Sciences University of Wisconsin, Madison 608-219-4430
Hi Bill, what portions are you talking about? recon-all shouldn't use any matlab.
cheers Bruce On Tue, 19 Jul 2011, Bill Taylor wrote:
So I peaked in archive and did not get a hit.
The situation is that the University of Wisconsin Madison site license prohibits us running Matlab in a cluster unless it is compiled.
I am assisting a Neurology lab with having a Condor workflow which this time round will do both Matlab and FSL post processing.
To compile the Matlab one needs to compile the entry points. But to run it, we'd have to change how it is called.
Anyone have pointers for me?
Bill Taylor Center for High Throughput Computing Condor Project Computer Sciences University of Wisconsin, Madison 608-219-4430
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
This is the proposed workflow and some latter parts are done with Matlab.
I assist is masses of Matlab jobs using compiled Matlab and run thousands of jobs both in on center, on our campus and out in to other resources in the GRID.
My problem is not how to run a compiled Matlab job, but how to interface the Matlab portion perhaps invisibly and perhaps not to running with compiled matlab code.
I know and will never be a freesurfer person. I am only trying to automate more of it. Is there perhaps a single script which matches up to calls to Matlab entry points?
processed in parallel for two subjects three time points example; recon-all -autorecon1 -subjid 1001a recon-all -autorecon1 -subjid 1001b recon-all -autorecon1 -subjid 1001c recon-all -autorecon1 -subjid 1002a recon-all -autorecon1 -subjid 1002b recon-all -autorecon1 -subjid 1002c
. . . After completion of -autorecon1
recon-all -autorecon2 -subjid 1001a recon-all -autorecon2 -subjid 1001b recon-all -autorecon2 -subjid 1001c recon-all -autorecon2 -subjid 1002a recon-all -autorecon2 -subjid 1002b recon-all -autorecon2 -subjid 1002c . . . After completion of -autorecon2
recon-all -autorecon3 -subjid 1001a recon-all -autorecon3 -subjid 1001b recon-all -autorecon3 -subjid 1001c recon-all -autorecon3 -subjid 1002a recon-all -autorecon3 -subjid 1002b recon-all -autorecon3 -subjid 1002c . .
After completion of -autorecon3 OPTIONAL COMPUTATION OF LGI WHICH REQUIRES MATLAB ~3 hours recon-all -s 1001a -localGI recon-all -s 1001b -localGI recon-all -s 1001c -localGI recon-all -s 1002a -localGI recon-all -s 1002b -localGI recon-all -s 1002c -localGI recon-all -base 1001base3 -tp 1001a -tp 1001b -tp 1001c -all recon-all -base 1002base3 -tp 1002a -tp 1002b -tp 1002c -all . . . After completion of -base runs recon-all -long 1001a 1001base3 -all recon-all -long 1001b 1001base3 -all recon-all -long 1001c 1001base3 -all recon-all -long 1002a 1002base3 -all recon-all -long 1002b 1002base3 -all recon-all -long 1001c 1002base3 -all
On 7/19/2011 2:03 PM, Bruce Fischl wrote:
Hi Bill, what portions are you talking about? recon-all shouldn't use any matlab.
cheers Bruce On Tue, 19 Jul 2011, Bill Taylor wrote:
So I peaked in archive and did not get a hit.
The situation is that the University of Wisconsin Madison site license prohibits us running Matlab in a cluster unless it is compiled.
I am assisting a Neurology lab with having a Condor workflow which this time round will do both Matlab and FSL post processing.
To compile the Matlab one needs to compile the entry points. But to run it, we'd have to change how it is called.
Anyone have pointers for me?
Bill Taylor Center for High Throughput Computing Condor Project Computer Sciences University of Wisconsin, Madison 608-219-4430
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Bill,
you want to look at mcc (http://www.mathworks.com/help/toolbox/compiler/mcc.html )
Usually what works for me is something like:
mcc -m -v matlab_file.m
This will generate a console executable "matlab_file"
--Thomas
On Jul 19, 2011, at 3:02 PM, Bill Taylor wrote:
So I peaked in archive and did not get a hit.
The situation is that the University of Wisconsin Madison site license prohibits us running Matlab in a cluster unless it is compiled.
I am assisting a Neurology lab with having a Condor workflow which this time round will do both Matlab and FSL post processing.
To compile the Matlab one needs to compile the entry points. But to run it, we'd have to change how it is called.
Anyone have pointers for me?
Bill Taylor Center for High Throughput Computing Condor Project Computer Sciences University of Wisconsin, Madison 608-219-4430
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
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B.T. Thomas Yeo -
Bill Taylor -
Bruce Fischl