Dimitiri,
Dimitri Papadopoulos-Orfanos wrote:
> Hi,
>
>> 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
>
>
> Matlab mainly relies on glibc, the system C library, which shouldn't be
> very different from one Linux distribution to another. It also relies on
> a few other system libraries, such as the thread library which is the
> cause of the compatibility issues with Red Hat 9 and later, which
> require setting LD_ASSUME_KERNEL.
>
> Wether we're running SUSE or Red Hat shouldn't be very important. Apart
> from the thread library issue, ideally only the version of glibc should
> matter, and possibly the version of the X server and associated drivers.
>
> What could be specific to our lab:
> * We have dual-processor Linux workstations.
> * We use Nvidia's proprietary drivers.
> Anyone in the same situation and able to run Matlab without erratic
> errors?
>
That's exactly the system I run on. I didn't even need to recompile to
run SPM2 or SPM99 with Matlab 6.5.1 on SuSE 9.1, with Dual PIII-850MHz
and 2.6 series kernel. We also have an NVIDIA proprietary graphics
driver. The only problem was slower running because of the PIII / NaN
bug. Once we got rid of the NumLock error (by setting it off by
default) things ran fine. I have tried it with Matlab7 under Linux
much. Seems to work fine on my Sun SPARC running Solaris 9.
Cheers,
Mark
>
>> 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).
>
>
> Yes, the problem is that Matlab started officially supporting recent
> Linux distributions only with Matlab 7.0.1. No version of Matlab prior
> to 7.0.1 is supported by Mathworks on modern hardware (such as S-ATA
> disks).
>
> We have no choice, either we run Matlab 7.0.1 and we get at least some
> theoretical support form Mathworks, or we run Matlab 6.5 and we get no
> support at all on any decent Linux distribution :-(
>
> What we'll probably do is run SPM99 on Matlab 6.5 (I'll try convincing
> our sysadmins to upgrade to 6.5.1 since some serious 6.5 bugs seem to
> have been fixed in 6.5.1) and hopefully be able to fix all remaining
> issues without help from Mathworks. We may need to recompile SPM, see
> below.
>
> We'll run SPM2 on Matlab 7.0.1 and try to fix all remaining issues with
> possible help from Mathworks. Please post any fixes that apply to SPM2 +
> Matlab 7 as you find them.
>
>
>> 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.
>
>
> It looks like we have compiled SPM99 with Matlab 6.1 and are running it
> under Matlab 6.5. Also we have compiled SPM2 with Matlab 6.5 (maybe even
> 6.1) and are running it under Matlab 7.0.1.
>
> Mathworks support suggest this could be causing our problems. Is this
> also your experience?
>
> So we'll try recompiling SPM on a Linux distribution with a supported
> compiler + the Matlab version that will be eventually used.
>
>
>> 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
>
>
> Actually the version of the Linux kernel is not very important for
> end-user programs. This list is just a list of systems Mathworks have
> tested Matlab on, but I can see no technical reason why Matlab shouldn't
> work on other systems or should rely on a specific kernel. More
> important is the version of the glibc and the thread library.
>
> Anyway, 7.0.1 is theoretically supported on Red Hat 9 and Fedora Core 2
> according to this list.
>
>
>> 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
>>
>
>
> Mmmh... These issues do not apply to a specific Linux distribution as
> far as I can see. They are not specific to Red Hat, it's just that Red
> Hat is/was more common among Matlab users and is/was perceived as the de
> facto standard Linux distribution.
>
> Note that some of the above "solutions" are plain wrong:
> http://www.mathworks.com/support/solutions/data/1-QB3JW.html
> This one seems to imply that Red Hat 9 runs a 2.6 kernel or glibc 2.3.3.
> That is not the case, Red Hat 9 runs a 2.4 kernel and glibc 2.3.2.
>
>
>> 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.
>
>
> Mmmh... There are also a bunch of Solaris or Windows versions out there.
> Ensuring Matlab works on a variety of platforms and keeps running
> programs written under previous Matlab versions is what we're paying
> Mathworks for - and we're paying a lot. At least I would expect Matlab
> to bail out with a nice error message about incompatible compiler or
> Matlab versions instead of crashing. I'm not saying it's easy, as Linux
> does have its share of problems (compatibility used not to be a concern
> for the GNU/Linux community as much as it has been for Microsoft or
> commercial Unix vendors) but I expect Mathworks to deliver worth the
> money they're given and they don't.
>
> Anyway, we'll try recompiling the mex files as both Mathworks support
> and you suggest, I'm confident this will at least improve the situation.
> I'll keep you informed about our progress.
>
> Dimitri
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