simtk.org

Posted: **Mon Nov 19, 2018 4:33 am**

Hi, I am treating to use OpenSim to scripting in Mathlab 18a on Kubuntu 18.4. I Installed OpenSim 4.0 on Kubuntu 18.04 (as https://github.com/opensim-org/opensim- ... -makefiles). However, when ctest was running, java.TableTest() failed.
Then, I can configure OpenSim with Mathlab well through configureOpenSim.m.

However, I get fatal error (I attach) in Mathlab and it crash when I run setupAndRunIKBatchExample.m.

matlab_crash_dump.txt: (11.86 KiB) Downloaded 24 times

I see in other post that could be a problem of libstddc++.so.6 library, but I have the same library in Mathlab and the system.
Finaly, I have installed Mathlab 18.4 in /usr/local and Opensim 4.0 in /opt/opensim-core. Also, I have included the /opt/opensim-core/lib in LD_LIBRARY_PATH and /opt/opensim-core/lib in PATH.

Any idea?
Thanks for the help!

Posted: **Mon Nov 19, 2018 10:59 am**

What do you plan to do in Matlab? The failure sems to be caused by using Intel's BLAS library instead of the BLAS library with which you compiled Simbody. This only occurs because you are attempting to run IK, an optimization, within Matlab. If you do not plan on running IK within Matlab, then this is no issue. Furthermore, you could simply use `system('opensim-cmd run-tool ik_setup_file.xml')` instead of running the tool within Matlab.

You could try using RPATH when building Simbody to force Simbody to use the correct BLAS.

Posted: **Tue Nov 20, 2018 2:49 pm**

Hi Christopher,
Thanks for you response. I have the idea to perform a sensitivity study of a custom model within Matlab.

So, I run again setupAndRunIKBatchExample.m using `system('opensim-cmd run-tool ik_setup_file.xml')` but I have a new error message in Matlab:

Code: Select all

 Updating Model file from 20303 to latest format...
Loaded model subject01 from file /home/emi/Documentos/Investigacion/Biomecanica/OpenSim/Resources/Code/Matlab/testData/Subject01/subject01_gait2392_scaled.osim

fullpath =

    '/home/emi/Documentos/Investigacion/Biomecanica/OpenSim/Resources/Code/Matlab/testData/Subject01/MarkerData/walk_free_01.trc'

Loaded marker file /home/emi/Documentos/Investigacion/Biomecanica/OpenSim/Resources/Code/Matlab/testData/Subject01/MarkerData/walk_free_01.trc (41 markers, 73 frames)
Performing IK on cycle # 1
SimTK Exception thrown at Xml.cpp:108:
  Error detected by Simbody method Xml::readFromFile(): Failed to load the Xml file 'ikfile' with error 'Failed to open file (line=0, col=0)'.
  (Required condition 'loadOK' was not met.)

A problem occurred when trying to load file 'ikfile'.

were ikfile is the xml file that was generated by the script.
Any idea?

Emiliano

simtk.org

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