[VoxBo] Fwd: spm2_norm_calc through vbprep waiting in queue

[Jarrod Lewis-Peacock]

>
> Hi Jarrod.  Here are a few things to check...
>
>
> It should be defined in your defaults file (VoxBO/etc/defaults).  If
> it's missing, someone from the CfN can forward you a copy of ours
> (someone?).


Thank you for your response. (and we are sorry Dan we disturbed you on your
vacation)

Thanks for pointing that out. We found those missing lines yesterday morning
(from looking at the defaults file in the full 1.8.2 release). I added the
following lines to our defaults file:

# SPM2-related
setenv SPM2_PATH=/share/SPM/spm2
setenv SPM2_MATLAB_CMD=/usr/local/bin/matlab -nodisplay -nojvm

# SPM5-related
setenv SPM5_PATH=/share/SPM/spm5
setenv SPM5_MATLAB_CMD=/usr/local/bin/matlab -nodisplay -nojvm

It might be helpful to take a look at
> the VoxBo/etc/logs/voxbo.log file to see if the job is really not
> running or is just repeatedly getting re-started.  Also keep an eye on
> the queue directory files for that job (.job and .log) to see if
> there's any action.


The log file does not show that the job was ever submitted. I've examined
the .job files in the queue for the jobs that are stalling in Wait (there is
not .log file for them yet since they are not submitted out of the queue).
There is nothing in there that points to any problems.

This doesn't explain why your stripped down version
> didn't work, which is very odd. Also double-check that when
> you put your bogus jobtype in, you didn't have editor backup files in
> the directory and/or multiple jobtypes with the same name.


In my first attempt stripping down the jobtype to debug this problem, I
might have had multiple jobtypes with the same name. That might explain why
those jobs also hung in Wait. However, I've since fixed that and tried it
again. The stripped down jobtypes now submit. With more debugging I think I
found the key line that is causing the spm jobtypes to fail. It is:

"requires matlab"

When I comment that line out, the stripped-down job (without any spm
commands) submits. When it's in the .vjt file, that jobtype hangs in Wait
and is not issued. So it seems like this is a matlab path issue.

I tried looking in the reference manuals and google searches for more
information about the vbprep command and the "requires matlab" line. Didn't
find anything. Apparently the lines I added to the defaults file aren't
sufficient to configure matlab.Can you please help me figure out how to
satisfy this "requires matlab" command for vbprep so it can locate matlab
and submit the jobs?

Thanks,
Jarrod
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