Creating an isolated environment for working with Sofa

[daserk]

Hello. Let me start by saying I am quite new to SOFA and Docker, so detailed answers or descriptions of trivial stuff would be very helpful. Thanks. 🙂

My host computer is running the latest release of PopOS (21.04), and I am trying to run version 21.06 of SOFA.

My goal is creating an isolated environment to work with Sofa. My goal is not to develop Sofa but use it with my desired plugins to run soft body and soft robot simulations.

I want an isolated environment so that:

1. Whatever happens in my local machine doesn’t conflict with SOFA.
2. I get consistent results on all of my machines.
3. My colleges can replicate the results I get.

Since I am working with other people some isolated environment like Docker seems like a good option. So I compiled Sofa with the per-configured docker image and followed the build steps to successfully compile SOFA.

I ran the docker container with the wrapper provided here to be able to use GUI applications (for example, I was able to use cmake-gui when compiling SOFA).

However, when finished compiling and trying to start runSofa I get the following output.

So my first problem is I am not able to start the runSofa GUI.

My second goal after this is creating the complete workflow environment with the SoftRobots plugin and SofaPython so that I can write SOFA scenes in the python syntax and run the simulations.

I also would like to run SOFA directly from my Python IDE as described in the SofaPython documentation, but wasn’t able to get that to work either.

Any help is highly appreciated.

[Hugo]

Hi @daserk

For such a docker topic, let me poke @younesssss for a bit of support.
Could you give a look please @younesssss ?

Best

Hugo

[younesssss]

Hi @daserk,

I am sorry, I can’t get access to your output file.
Can you just paste it here directly ?

Thanks.

[younesssss]

Hi @daserk,

I am sorry, I can’t get access to your output file.
Can you just paste it here directly ?
Thanks.

[daserk]

Hey @younesssss

I added a link to Pastebin in the main thread, but here’s the output.

root@577a9dff15ce:/builds/sofa/build/bin# ./runSofa
[INFO]    [runSofa] PluginRepository paths = /builds/sofa/build/plugins:/builds/sofa/build/lib
[INFO]    [runSofa] DataRepository paths = /builds/sofa/src/share:/builds/sofa/src/examples:/builds/sofa/build:/builds/sofa/build
[INFO]    [runSofa] GuiDataRepository paths = /builds/sofa/src/applications/projects/runSofa/resources:/builds/sofa/src/modules/SofaGuiQt/src/sofa/gui/qt/resources:/builds/sofa/build
[INFO]    [runSofa] Loading automatically plugin list in /builds/sofa/build/lib/plugin_list.conf.default
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaSimpleFem.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaRigid.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaDeformable.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaObjectInteraction.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaMeshCollision.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaEngine.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaExplicitOdeSolver.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaImplicitOdeSolver.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaLoader.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaGeneralVisual.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaGraphComponent.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaGeneralMeshCollision.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaBoundaryCondition.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaGeneralAnimationLoop.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaGeneralDeformable.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaGeneralEngine.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaGeneralExplicitOdeSolver.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaGeneralImplicitOdeSolver.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaGeneralLinearSolver.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaGeneralRigid.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaGeneralObjectInteraction.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaGeneralSimpleFem.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaGeneralTopology.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaTopologyMapping.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaUserInteraction.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaConstraint.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaGeneralLoader.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaExporter.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaSparseSolver.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaPreconditioner.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaHaptics.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaValidation.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaDenseSolver.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaNonUniformFem.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaOpenglVisual.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaMiscTopology.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaMiscExtra.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaMiscForceField.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaMiscEngine.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaMiscSolver.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaMiscFem.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaMiscMapping.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libSofaMiscCollision.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libCImgPlugin.so
[INFO]    [PluginManager] Loaded plugin: /builds/sofa/build/lib/libLMConstraint.so
[INFO]    [GUIManager] lastUsedGUI.ini not found; using default GUI.
QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-root'
libGL error: MESA-LOADER: failed to retrieve device information
libGL error: image driver extension not found
libGL error: failed to load driver: radeon
libGL error: failed to open /dev/dri/card0: No such file or directory
libGL error: failed to load driver: radeonsi
Warning: Setting a new default format with a different version or profile after the global shared context is created may cause issues with context sharing.
The constructor with a QGLFormat is deprecated, use the regular contructor instead.
[25:25:0707/232951.402424:ERROR:zygote_host_impl_linux.cc(89)] Running as root without --no-sandbox is not supported. See https://crbug.com/638180.
[WARNING] [SofaSimulationGraph] the library has not been cleaned up (sofa::simulation::graph::cleanup() has never been called, see sofa/helper/init.h)
[WARNING] [SofaSimulationCommon] the library has not been cleaned up (sofa::simulation::common::cleanup() has never been called, see sofa/helper/init.h)
[WARNING] [SofaSimulationCore] the library has not been cleaned up (sofa::simulation::core::cleanup() has never been called, see sofa/helper/init.h)
[WARNING] [SofaCore] the library has not been cleaned up (sofa::core::cleanup() has never been called, see sofa/helper/init.h)
[WARNING] [SofaDefaultType] the library has not been cleaned up (sofa::defaulttype::cleanup() has never been called, see sofa/helper/init.h)
[WARNING] [SofaHelper] the library has not been cleaned up (sofa::helper::cleanup() has never been called, see sofa/helper/init.h)
root@577a9dff15ce:/builds/sofa/build/bin# 

[younesssss]

Hi @daserk,

Sorry for my late response.
I have some questions.
When I read the output I see your problem is related to libGL. Did you install it?

What is the output of these commands.
1. docker run $extra_run_args $image runSofa
2. docker run $extra_run_args $image runSofa -g batch -l SofaPython -n 100

In Sofa, you also have the headless option (See https://github.com/sofa-framework/sofa/tree/a1ad067766b804b2985db227ac41bb504098a6d6/modules/SofaHeadlessRecorder for more).

Then you can generate the output videos of your simulation the only downside is that your simulation is not interactive

[Author]

Posts