Plugin not found: "SofaCaribou" using Python3

[Ziemnono]

Hi again, it is me :)
I tried to run the manufactured_solution.py and encounter 2 principal errors:

Checking SOFA_ROOT and SOFAPYTHON3_ROOT
Using environment variable SOFA_ROOT: /home/arnaud/dev/sofa_src/build/install
Using environment variable SOFAPYTHON3_ROOT: /home/arnaud/dev/sofa/plugins/SofaPython3
---------------------------------------
[ERROR]   [PluginManager] Plugin loading failed (/home/arnaud/dev/sofa_src/build/install/lib/libSofaBaseMechanics.so): /home/arnaud/dev/sofa_src/build/install/lib/libSofaBaseMechanics.so: undefined symbol: _ZN4sofa4core8topology12TopologyDataIjNS_4type6vectorIjNS3_16CPUMemoryManagerIjEEEEE21createTopologyHandlerEPNS1_16BaseMeshTopologyEPNS1_19TopologyDataHandlerIjS7_EE
[INFO]    [PluginManager] Loaded plugin: /home/arnaud/dev/sofa_src/build/install/lib/libSofaBoundaryCondition.so
[ERROR]   [RequiredPlugin(RequiredPlugin)] Plugin loading failed (/home/arnaud/dev/sofa_src/build/install/lib/libSofaBaseMechanics.so): /home/arnaud/dev/sofa_src/build/install/lib/libSofaBaseMechanics.so: undefined symbol: _ZN4sofa4core8topology12TopologyDataIjNS_4type6vectorIjNS3_16CPUMemoryManagerIjEEEEE21createTopologyHandlerEPNS1_16BaseMeshTopologyEPNS1_19TopologyDataHandlerIjS7_EE
  
Failed to load: ["SofaBaseMechanics"]
[ERROR]   [RequiredPlugin(SofaCaribou)] Plugin not found: "SofaCaribou"
  
Failed to load: ["SofaCaribou"]
[ERROR]   [SofaRuntime] ValueError: Object type LDLTSolver<SofaCaribou::solver::EigenSolver<Eigen::SparseMatrix<double, 0, int> >> was not created  
The object is in the factory but cannot be created.  
Requested template : None  
Used template      : SofaCaribou::solver::EigenSolver<Eigen::SparseMatrix<double, 0, int> > (default)  
Reason(s)          : The requested backend 'Pardiso' isn't compatible with the following template parameters: 'SofaCaribou::solver::EigenSolver<Eigen::SparseMatrix<double, 0, int> >'.

1. One comes from the line root.addObject('RequiredPlugin', pluginName='SofaBaseMechanics SofaBoundaryCondition') which looks to have difficulty in loading the SofaBaseMechanics plugin (related to the SofaPython3 plugin ?)
2. The other one directly concerns root.addObject('RequiredPlugin', name='SofaCaribou') where the plugin failed to be loaded..

I am quite surprised as the line import Sofa, SofaRuntime, SofaCaribou was successfully run.
Thank you for your help again !

[jnbrunet]

Hey @Ziemnono , almost there !

First error

Not sure why you got this link error for SofaBaseMechanics. @fredroy and @hugtalbot it looks like SofaBaseMechanics.so is missing a symbol from topology data, do you guys recently worked on this part? The missing method is:

sofa::core::topology::TopologyData<unsigned int, sofa::type::vector<unsigned int, sofa::type::CPUMemoryManager<unsigned int> > >::createTopologyHandler(sofa::core::topology::BaseMeshTopology*, sofa::core::topology::TopologyDataHandler<unsigned int, sofa::type::vector<unsigned int, sofa::type::CPUMemoryManager<unsigned int> > >*)

@Ziemnono , you could try to compile the latest SOFA release (git checkout v21.06) instead of the master branch which can be very unstable.

Second error

Next, for this error:

[ERROR]   [RequiredPlugin(SofaCaribou)] Plugin not found: "SofaCaribou"

It simply means that SOFA isn't able to find the plugin file libSofaCaribou.so. You can simply give it the path to SofaCaribou built directory (or one of its parent directory, the search will be recursive) using either:

1. The SOFA_PLUGIN_PATH environment variable. For example,

$ export SOFA_PLUGIN_PATH="/home/arnaud/dev/sofa/plugins/caribou/build"

2. Or, the AddPluginRepository component. Simply add it in your scene before loading the Caribou plugin. For example

import Sofa
def createScene(root):
    root.addObject('RequiredPlugin', name='SofaBaseUtils')
    root.addObject('AddPluginRepository ',  path='/home/arnaud/dev/sofa/plugins/caribou/build')
    root.addObject('RequiredPlugin', name='SofaCaribou')
   # (...)

3. Or, using the SofaRuntime python module. For example:

import Sofa
import SofaRuntime
SofaRuntime.PluginRepository.addFirstPath('/home/arnaud/dev/sofa/plugins/caribou/build')

def createScene(root):
    root.addObject('RequiredPlugin', name='SofaCaribou')
   # (...)

Note that since the search is recursive, you could add the path /home/arnaud/dev/sofa/plugins in one of these search paths and have SOFA find any plugins compiled under this "plugins" directory.

Third error

Now, for the last error:

[ERROR]   [SofaRuntime] ValueError: Object type LDLTSolver<SofaCaribou::solver::EigenSolver<Eigen::SparseMatrix<double, 0, int> >> was not created  
The object is in the factory but cannot be created.  
Requested template : None  
Used template      : SofaCaribou::solver::EigenSolver<Eigen::SparseMatrix<double, 0, int> > (default)  
Reason(s)          : The requested backend 'Pardiso' isn't compatible with the following template parameters: 'SofaCaribou::solver::EigenSolver<Eigen::SparseMatrix<double, 0, int> >'.

This is because you didn't compile Caribou with MKL support, hence Pardiso sparse solvers aren't available. You can have a look on the Caribou builder docker image to check how MKL is installed on ubuntu 20.04. To use Eigen sparse solvers (a bit slower but no dependency needed) instead of Pardiso, simply change in your scene

root.addObject('LDLTSolver', backend='Pardiso')

for

root.addObject('LDLTSolver', backend='Eigen')

Let me know how that goes!

[Ziemnono]

Salut @jnbrunet,
Thank you very much for all those indications, I switched to the stable SOFA version and used your commands to make the example work!
Hence the output of manufactured_soution.py is diverging:

Time step                : 5
Context                  : /
Max iterations           : 10
Residual tolerance (abs) : 1e-15
Residual tolerance (rel) : 1e-10
Correction tolerance     : 1e-05
Linear solver            : /LDLTSolver

Newton iteration #1      |R| = 3.070686e+82  |R|/|R0| = 1.000000e+00  |du| / |U| = 1.000000e+00  Time = 6 ms
Newton iteration #2      |R| = 9.098330e+81  |R|/|R0| = 2.962963e-01  |du| / |U| = 4.000000e-01  Time = 3 ms
Newton iteration #3      |R| = 2.695802e+81  |R|/|R0| = 8.779150e-02  |du| / |U| = 2.105263e-01  Time = 3 ms
Newton iteration #4      |R| = 7.987560e+80  |R|/|R0| = 2.601229e-02  |du| / |U| = 1.230769e-01  Time = 3 ms
Newton iteration #5      |R| = 2.366684e+80  |R|/|R0| = 7.707347e-03  |du| / |U| = 7.582938e-02  Time = 3 ms
Newton iteration #6      |R| = 7.012399e+79  |R|/|R0| = 2.283658e-03  |du| / |U| = 4.812030e-02  Time = 3 ms
Newton iteration #7      |R| = 2.077748e+79  |R|/|R0| = 6.766395e-04  |du| / |U| = 3.108305e-02  Time = 3 ms
Newton iteration #8      |R| = 6.156290e+78  |R|/|R0| = 2.004858e-04  |du| / |U| = 2.030135e-02  Time = 3 ms
Newton iteration #9      |R| = 1.824086e+78  |R|/|R0| = 5.940319e-05  |du| / |U| = 1.335350e-02  Time = 3 ms
Newton iteration #10     |R| = 5.404699e+77  |R|/|R0| = 1.760095e-05  |du| / |U| = 8.823783e-03  Time = 3 ms
[DIVERGED] The number of Newton iterations reached the maximum of 10 iterations.

relative L2 error at 100% load: 125780184395449.69

I will try to investigate it when I have the time. But thank you very much for your efforts the rest is working perfectly fine :)

[jnbrunet]

This should not happen! I created an issue #86 and will try to investigate also on my side. It is possible I committed a wrong version of the scripts, I'll look around in my files.

Are you at least able to run some of the scene files?

Edit:
The p1 mesh is off for some reason, you can swap to a quadratic one and it should converge. See my comment in #86 . Warning, using the p2 mesh is a bit slower to compute, assembling the manufactured solution in python is painfully slow. It is in my todo to swap it in c++!

[Ziemnono]

Yes I ran a few examples and they seem to work well but I cannot manage to have a GUI appearing, I will try to ping some people on Gitter because using import Soga.Gui is not working...
Thanks for the advice ;)