The Linux machines in our department use SuSE, so we don't encounter the
Matlab crashes that occur with RedHat. I have therefore very little idea of
which workarounds we can incorporate into SPM in order to make Matlab run
more smoothly on RedHat systems. We don't get to see what lies under the
hood of Matlab (and wouldn't have time to become as intimately acquainted
with the Linux source code as would be necessary), so it's difficult to
figure out why some fixes seem to help. All I know is that changing the
renderer of the figures sometimes seems to help.
Most of SPM2 was developed using Matlab 6.0 and 6.1. There was some testing
using 6.5 (although not enough to notice the reshape bug). Matlab 7 came
along after SPM2 was released, and I have only just begun to figure out where
the Matlab 7.0.1 problems occur on SuSE linux. Most of the SPM2 functions
should work under 5.3, although there are definately a few functions that
don't (DICOM conversion etc).
If you encounter Segmentation Faults, these are usually to do with Matlab and
the operating system, rather than SPM itself. Apart from possible bugs in
the mexglx files released with SPM or the way that they were compiled, if
there is a Segmentation Fault, then it's not our fault.
I have no idea which Linux kernel is used by RedHat 9/Fedora, but according to
the Mathworks, the following should work for 7.0.1:
http://www.mathworks.com/support/sysreq/current_release/unix.html
RedHat 9 seems to have a few problems with Matlab:
http://www.mathworks.com/support/solutions/data/1-1AY16.html?solution=1-1AY16
http://www.mathworks.com/support/solutions/data/1-QB3JW.html?solution=1-QB3JW
http://www.mathworks.com/support/solutions/data/1-1A523.html?solution=1-1A523
http://www.mathworks.com/support/solutions/data/1-1ATCE.html?solution=1-1ATCE
http://www.mathworks.com/support/solutions/data/1-1BDU5.html?solution=1-1BDU5
etc
A move to Fedora Core 2 is likely to throw up a different bunch of problems.
Some of these may be solved by re-compiling the mex functions (making sure
that a compatible compiler is used). With such a wide number of different
Linux versions appearing, it is difficult to ensure that a version of Matlab
will run on all of them.
Best regards,
-John
> John Ashburner wrote:
> > If you have installed all the patches for SPM2, then Matlab 6.5 should
> > work - although 6.5.1 is slightly better. Matlab 7 should mostly work,
> > although the problems that you encounter will depend on the computer and
> > operating system you have. I've put together a few of my thoughts on
> > Matlab 7 at: http://www.fil.ion.ucl.ac.uk/~john/FAQ/Matlab7.html
>
> But which versions of Matlab were SPM99 and SPM2 primarily written for?
> Having this information would really help us.
>
> From the above I get the impression that SPM2 is not fully compatible
> with either of Matlab 6.5, 6.5.1, 7.0 and 7.0.1. Which versions of
> Matlab are SPM99 and SPM2 fully compatible with?
>
>
> We run SPM99 on Matlab 6.5.0.180913a (R13) and SPM2 on Matlab
> 7.0.1.something (R14SP1).
>
> We are now moving from Red Hat 9 to Fedora Core 2, and see lots of
> erratic crashes or errors.
>
> Moving from Red Hat 7.3 to Red Hat 9 had already been a major source of
> problems with Matlab 6.5. We had set LD_ASSUME_KERNEL to 2.4.1 as
> suggested on the Mathworks site, but I still see Matlab 6.5 freeze one
> out of two times at startup on my Red Hat 9 workstation (even though I
> use -nojvm).
>
> Moving from Red Hat 9 to Fedora Core 2, the situation is even worse.
> Matlab 6.5 + SPM99 and Matlab 7.0.1 + SPM2 crash very often (with X
> errors or segfaults) usually during user interaction. Matlab 7.0.1
> itself outputs wrong results or crashes erratically.
>
> Mathworks won't support use with Matlab 6.5 on any Linux platform but
> Red Hat 7.3 which isn't an option for us.
>
> But even Matlab 7.0.1 crashes erratically, and since the crashes are
> hard to reproduce or depend on SPM, we don't get much help from
> Mathworks support either.
>
> > If you have RedHat Linux, then you may need to change some of the code of
> > SPM slightly. Do a search for the following keywords in the JISCmail
> > archives: renderer and zbuffer and painters
>
> Mmmh... Are you sure this is related to Red Hat Linux specifically? Do
> you know what's happening under the hood and why changing from 'zbuffer'
> to 'painters' could help? Anyway, we've tried this with SPM2 and Matlab
> 7.0.1 and it doesn't help, crashes still occur.
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