[Neurodebian-users] matlab-support issues

Tue Apr 24 18:17:59 BST 2018

Hey,

on (1): I am using "The Plot" (https://www.jonathanpower.net/2017-ni-the-plot.html) calling it from MATLAB to integrate it into my SPM pipeline. This caused  (random, not reproducable) crashes when printing the figure using a MATLAB command. Withput being an expert, this hints me to the same problem. I contacted the MATLAB support and calling matlab with the "-noopenfg" flag solved my problem. I did not have this issue with any pre-2017 release of MATLAB.Perhaps this information helps.

Cheers,

Arne

Arne Hartz, M.Sc.-Phys., PhD Candidate
Child Neuropsychology Section/Translational Brain Medicine in Psychiatry and Neurology
Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy
Uniklinik RWTH Aachen/JARA Brain Translational Medicine
Neuenhofer Weg 21
52074 Aachen
Germany

phone: +49 241 80-89892
fax: +49 241 80-3389892
ahartz at ukaachen.de

________________________________________
Von: Neurodebian-users [neurodebian-users-bounces+ahartz=ukaachen.de at alioth-lists.debian.net]" im Auftrag von "Andreas Widmann [widmann at uni-leipzig.de]
Gesendet: Dienstag, 24. April 2018 17:17
An: neurodebian-users at alioth-lists.debian.net
Cc: iandol at gmail.com; tbc.class at gmail.com
Betreff: [Neurodebian-users] matlab-support issues

May I report one issue and one feature request for the matlab-support package? Currently both issues may only affect Ubuntu users but on the longer run I think most Debian versions will be affected.

(1) MATLAB R2018a compatibility
MATLAB R2018a depends on GLIBCXX_3.4.22 or newer to be included in libstdc++.so.6. Ubuntu 16.04.4 LTS only includes GLIBCXX up to 3.4.21 in libstdc++.so.6. That is, MATLAB will not start if MATLAB included libstdc++.so.6 is renamed during the matlab-support package installation.

The error message is:
/usr/local/MATLAB/R2018a/bin/glnxa64/MATLAB: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.22' not found (required by /usr/local/MATLAB/R2018a/bin/glnxa64/libCppMicroServices.so.3.1.1)

Maybe it would be good to check for GLIBCXX_3.4.22 or newer version before renaming the MATLAB included libstdc++.so.6?

Good part is that MATLAB included libstdc++.so.6 apparently no longer breaks hardware opengl support.

(2) libjogl incompatibility
Newer versions of Mesa no longer including the string "Gallium" in the version name break hardware opengl support in MATLAB (tested from R2016a to R2018a). This is the case on newer Ubuntu versions starting from 16.04.3 LTS including 18.04 LTS.

The underlying bug was reported here:
https://jogamp.org/bugzilla/show_bug.cgi?id=1357
and is actually already fixed in all affected Ubuntu versions.

Unfortunately the MATLAB included jogl libraries are not fixed and I assume they will probably not be fixed in the foreseeable future. There is also a thread on MATLAB central discussing the effects of the bug:
https://de.mathworks.com/matlabcentral/answers/377644-hardware-opengl-failure-on-ubuntu-16-04-3-can-not-initialize-shared-resources

A simple workaround would be to use the fixed OS provided jogl libraries and remove the MATLAB provided libraries. I figured out how to do this and reported the necessary steps on the psychtoolbox forum:
https://groups.yahoo.com/neo/groups/psychtoolbox/conversations/messages/22687

Thad from psychtoolbox forum wrote a shell script automatizing the necessary steps and made it available on Github:
https://raw.githubusercontent.com/czuba/sysconfig/master/ubuntuFixJogl_ML2018a.sh

As this issue might on the long run affect most new Debian and derived distributions installations I would like to suggest to include Thad's script in the matlab-support package. Thad would be a happy with this.

See also this thread of the psychtoolbox forum for extended discussion of the issue and the suggested workaround:
https://groups.yahoo.com/neo/groups/PSYCHTOOLBOX/conversations/topics/22674

Thank you! Best,
Andreas
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