genomix » matlab-genomix

I can't reproduce this, i.e. it works well for me (matlab-2018b,
ubuntu-20.04).

First, can you make sure that the genomix_block.mexa64 library is
dynamically linked with the correct libraries?
The genomix_block.mexa64 is located in
<prefix>/lib/matlab/simulink/genomix and you can check with `ldd` that
all dependencies are fetched in the correct matlab installation
prefix.

Thanks for your prompt reply.
In the following, the output of the suggested command.
FYI, "/home/dbicego/Work/opt/MATLAB/R2018b/" is indeed the path where my Matlab instance is installed (as well as the other version "/home/dbicego/Work/opt/MATLAB/R2020a/").

dbicego@prometheus:~/Work/openrobots/lib/matlab/simulink/genomix$ ldd genomix_block.mexa64
linux-vdso.so.1 (0x00007ffef475f000)
libmex.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmex.so (0x00007fb766cd4000)
libmx.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmx.so (0x00007fb7668eb000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fb7664fa000)
libmwfl.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwfl.so (0x00007fb766142000)
libut.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libut.so (0x00007fb765e61000)
libmwservices.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwservices.so (0x00007fb7658c0000)
libmwfoundation_matlabdata_matlab.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwfoundation_matlabdata_matlab.so (0x00007fb7655ae000)
libmwfoundation_extdata_array.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwfoundation_extdata_array.so (0x00007fb765288000)
libmwmvm.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwmvm.so (0x00007fb764c37000)
libmwmpath.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwmpath.so (0x00007fb764a17000)
libmwm_dispatcher_interfaces.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwm_dispatcher_interfaces.so (0x00007fb764811000)
libmwm_dispatcher.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwm_dispatcher.so (0x00007fb7644d7000)
libmwi18n.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwi18n.so (0x00007fb764182000)
libmwmlutil.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwmlutil.so (0x00007fb7636f5000)
libmwfoundation_usm.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwfoundation_usm.so (0x00007fb7634ca000)
libmwgenerate_diag_message.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwgenerate_diag_message.so (0x00007fb7632c1000)
libmwmcos.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwmcos.so (0x00007fb76305b000)
libmwboost_date_time.so.1.65.1 => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwboost_date_time.so.1.65.1 (0x00007fb762e4b000)
libmwboost_log.so.1.65.1 => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwboost_log.so.1.65.1 (0x00007fb762b74000)
libmwboost_system.so.1.65.1 => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwboost_system.so.1.65.1 (0x00007fb762970000)
libmwboost_thread.so.1.65.1 => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwboost_thread.so.1.65.1 (0x00007fb762748000)
libmwcpp11compat.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwcpp11compat.so (0x00007fb762527000)
libstdc++.so.6 => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6 (0x00007fb7621a6000)
libgcc_s.so.1 => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/../../sys/os/glnxa64/libgcc_s.so.1 (0x00007fb761f8f000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fb761d70000)
libmwmfl_permute.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwmfl_permute.so (0x00007fb761b5d000)
libmwindexingapimethods.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwindexingapimethods.so (0x00007fb761950000)
libicuuc.so.59 => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libicuuc.so.59 (0x00007fb76159d000)
libtbbmalloc.so.2 => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libtbbmalloc.so.2 (0x00007fb761349000)
libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007fb76112c000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fb760d8e000)
/lib64/ld-linux-x86-64.so.2 (0x00007fb767199000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fb760b8a000)
libcrypt.so.1 => /lib/x86_64-linux-gnu/libcrypt.so.1 (0x00007fb760952000)
libpam.so.0 => /lib/x86_64-linux-gnu/libpam.so.0 (0x00007fb760744000)
libmwboost_filesystem.so.1.65.1 => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwboost_filesystem.so.1.65.1 (0x00007fb76052a000)
libmwboost_regex.so.1.65.1 => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwboost_regex.so.1.65.1 (0x00007fb760215000)
libmwboost_serialization.so.1.65.1 => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwboost_serialization.so.1.65.1 (0x00007fb75ffd7000)
libunwind.so.8 => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libunwind.so.8 (0x00007fb75fdb9000)
libicuio.so.59 => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libicuio.so.59 (0x00007fb75fbac000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007fb75f9a4000)
libmwlivecode.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwlivecode.so (0x00007fb75f75e000)
libmwcppmicroservices.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwcppmicroservices.so (0x00007fb75f531000)
libmwregexp.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwregexp.so (0x00007fb75f2e9000)
libmwsearch_path_utilities.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwsearch_path_utilities.so (0x00007fb75f0c3000)
libmwflstoragevfs.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwflstoragevfs.so (0x00007fb75edd5000)
libmwcwf_interface.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwcwf_interface.so (0x00007fb75eb69000)
libmwsettingscore.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwsettingscore.so (0x00007fb75e70a000)
libmwms.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwms.so (0x00007fb75e1ea000)
libmwopccore.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwopccore.so (0x00007fb75df92000)
libmwopcmodel.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwopcmodel.so (0x00007fb75dcc2000)
libmwopczippackage.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwopczippackage.so (0x00007fb75da9c000)
libmwstring_matrix.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwstring_matrix.so (0x00007fb75d866000)
libmwkeybrd.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwkeybrd.so (0x00007fb75d662000)
libmwboost_chrono.so.1.65.1 => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwboost_chrono.so.1.65.1 (0x00007fb75d45b000)
libmwboost_iostreams.so.1.65.1 => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwboost_iostreams.so.1.65.1 (0x00007fb75d247000)
libCppMicroServices.so.3.3.1 => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libCppMicroServices.so.3.3.1 (0x00007fb75cf3f000)
libtbb.so.2 => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libtbb.so.2 (0x00007fb75cce7000)
libmwfoundation_matlabdata_standalone.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwfoundation_matlabdata_standalone.so (0x00007fb75ca47000)
libmwmst.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwmst.so (0x00007fb75c6e3000)
libmwstartupplugin.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwstartupplugin.so (0x00007fb75c4d3000)
libmwstartup_plugin_initializer.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwstartup_plugin_initializer.so (0x00007fb75c23b000)
libmvmtransportapi.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmvmtransportapi.so (0x00007fb75c034000)
libmwmatlab_toolbox_events.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwmatlab_toolbox_events.so (0x00007fb75bd15000)
libmwexecution_events.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwexecution_events.so (0x00007fb75b7db000)
libxerces-c-3.1.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libxerces-c-3.1.so (0x00007fb75b14f000)
libmwcwf_implementation.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwcwf_implementation.so (0x00007fb75af43000)
libmwmatlabstoragesystem.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwmatlabstoragesystem.so (0x00007fb75ad3d000)
libmwmodule_feature.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwmodule_feature.so (0x00007fb75ab3a000)
libmwsearch_path_events.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwsearch_path_events.so (0x00007fb75a8f4000)
libmwsearch_path_impl.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwsearch_path_impl.so (0x00007fb75a631000)
libmwsearch_path_interfaces.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwsearch_path_interfaces.so (0x00007fb75a429000)
libmwddux.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwddux.so (0x00007fb75a208000)
libmwbuiltin.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwbuiltin.so (0x00007fb75a006000)
libmwresource_core.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwresource_core.so (0x00007fb759e03000)
libexpat.so.1 => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libexpat.so.1 (0x00007fb759bd8000)
libicui18n.so.59 => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libicui18n.so.59 (0x00007fb759758000)
libmwboost_atomic.so.1.65.1 => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwboost_atomic.so.1.65.1 (0x00007fb759556000)
libicudata.so.59 => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libicudata.so.59 (0x00007fb757a41000)
libaudit.so.1 => /lib/x86_64-linux-gnu/libaudit.so.1 (0x00007fb757818000)
libmwopcmwservices.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwopcmwservices.so (0x00007fb7575a7000)
libmwstoragefilefolderobserver.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwstoragefilefolderobserver.so (0x00007fb757327000)
libmwflnetwork.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwflnetwork.so (0x00007fb75707b000)
libmwflstorageprovider.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwflstorageprovider.so (0x00007fb756e32000)
libmwflstorageevents.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwflstorageevents.so (0x00007fb756c15000)
libmwxmlcore.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwxmlcore.so (0x00007fb7569a2000)
libmwflcrypto.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwflcrypto.so (0x00007fb75676c000)
libmwflcryptoutils.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwflcryptoutils.so (0x00007fb75655e000)
libmwflcryptocryptopp.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwflcryptocryptopp.so (0x00007fb7560d1000)
libminizip.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libminizip.so (0x00007fb755ec3000)
libmwmodule_descriptor_implementation.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwmodule_descriptor_implementation.so (0x00007fb755c91000)
libcap-ng.so.0 => /lib/x86_64-linux-gnu/libcap-ng.so.0 (0x00007fb755a8c000)
libmwmodule_descriptor_interface.so => /home/dbicego/Work/opt/MATLAB/R2018b/bin/glnxa64/libmwmodule_descriptor_interface.so (0x00007fb755888000)
dbicego@prometheus:~/Work/openrobots/lib/matlab/simulink/genomix$

OK, this looks fine (as long as you are effectively using
matlab-2018b, of course).

Next step is to run in debugging mode to help me confirm a potential
issue. Can you :

- update matlab-genomix code with the very last commit (6dd3d26), and
install that (it has some new useful debugging info)
- run matlab with "export GENOMIX_DEBUG=1" set (in the same
terminal were you run matlab)

In the simulink diagnostic window, you should see information like
"DEBUG: new connection 0 at 0x7f61a40f135c, fd [874, 875]"
when you start the simulation.

I'm interrested in the "fd" number, 874 & 875 in the example above. If
they are greater than 1024 then we found the reason of the crash.

Thanks for your prompt reply.

• updated matlab-genomix code with the very last commit (using "make checkout" inside "/robotpkg/supervision/matlab-genomix" and then make update)
• ran matlab with "export GENOMIX_DEBUG=1" set (same terminal)
• when I call "client = genomix.client(host_remote);" from matlab, I receive (Matlab command history) the following:
  INFO: loading matlab-genomix 1.8.4 at 0x7fdfaf63426c
  DEBUG: new connection 0 at 0x7fdfaf63426c, fd [943, 963]
  INFO: locking matlab-genomix 1.8.4
• Just to make it more clear, I only got these messages in the Matlab command history, while on the Simulink Diagnostic Viewer we just got:
  INFO: loading matlab-genomix 1.8.4 at 0x7fdf21f5835c
• when I ran the simulink file, or just tried to fetch the port block, Simulink crashes, as expected

More details from the terminal when I launched the components:
11:16:27.664282:genomixd: sock56264eb12550: get /version
11:16:27.664379:genomixd: sock56264eb12550: status 200 OK
11:16:27.664514:genomixd: sock56264eb12550: get /session/start s=
11:16:27.664589:genomixd: sock56264eb12550: new session s1
11:16:27.664628:genomixd: sock56264eb12550: status 200 OK
11:16:27.664796:genomixd: connection from 127.0.0.1:59048 on sock56264e65c430
11:16:27.664925:genomixd: sock56264e65c430: get /session/listen s=s1
11:16:27.664989:genomixd: sock56264e65c430: listening session s1
11:17:07.990559:genomixd: sock56264eb12550: get /rpath//home/dbicego/Work/openrobots/lib/genom/pocolibs/plugins s=s1
11:17:07.990893:genomixd: sock56264eb12550: status 200 OK

Unfortunately, what matters is the logs before the crash, and
apparently matlab does have the time to print them before crashing,
since the simulink windows does not show the new connections.

I will anyway fix what I think is the cause of the issue and we'll
see.

I was fearing so :/
Thanks a lot for your support.
IF you believe that it could be of any help, I am available tomorrow or next week to have a video call in which I can share my screen.
In that case, we can arrange that via email.
Cheers,
Davide

If you can test the latest commit in matlab-genomix (795123d), this
would help!