Build problem for Pardisio solver plugin

[amazier]

Dear all,

I am currently trying to update an old plugin with my collaborator Igor Peterlik. To do so, we need several plugins: including CUDA and Pardisio Solver.

I first tried to compile with GCC 9 but faced incompatibilities with CUDA that only support GCC 8 (correct me if I am wrong).
To overcome this issue, I recompiled SOFA and plugins with GCC 8 but I face a last error with the Pardisio solver plugin that I did not encounter with GCC 9:

[23/24] Linking CXX shared library lib/libSofaPardisoSolver.so.0.1
FAILED: lib/libSofaPardisoSolver.so.0.1 
: && /lib/ccache/g++-8 -fPIC -Wall -W -Wno-padded -O3 -DNDEBUG -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2  -Wl,--no-undefined -lc -shared -Wl,-soname,libSofaPardisoSolver.so.0.1 -o lib/libSofaPardisoSolver.so.0.1 applications/plugins/SofaPardisoSolver/CMakeFiles/SofaPardisoSolver.dir/SparsePARDISOSolver.cpp.o applications/plugins/SofaPardisoSolver/CMakeFiles/SofaPardisoSolver.dir/initPardisoSolver.cpp.o -L/home/arnaud/dev/sofa/v20.06/src/applications/plugins/SofaPardisoSolver/extlibs -Wl,-rpath,/home/arnaud/dev/sofa/v20.06/src/applications/plugins/SofaPardisoSolver/extlibs:/home/arnaud/dev/sofa/v20.06/build/lib:  lib/libSofaBase.so.20.06.99  lib/libSofaGeneral.so.20.06.99  -lgfortran  -lblas  -llapack  -lgomp  lib/libSofaGeneralDeformable.so.20.06.99  lib/libSofaGeneralExplicitOdeSolver.so.20.06.99  lib/libSofaGeneralImplicitOdeSolver.so.20.06.99  lib/libSofaGeneralLinearSolver.so.20.06.99  lib/libSofaGeneralLoader.so.20.06.99  /usr/lib/x86_64-linux-gnu/libz.so  lib/libSofaGeneralObjectInteraction.so.20.06.99  lib/libSofaGeneralSimpleFem.so.20.06.99  lib/libSofaConstraint.so.20.06.99  lib/libSofaSimpleFem.so.20.06.99  lib/libSofaImplicitOdeSolver.so.20.06.99  lib/libSofaGeneralEngine.so.20.06.99  lib/libSofaUserInteraction.so.20.06.99  lib/libSofaGeneralRigid.so.20.06.99  lib/libSofaTopologyMapping.so.20.06.99  lib/libSofaGeneralTopology.so.20.06.99  lib/libSofaBoundaryCondition.so.20.06.99  lib/libSofaGeneralMeshCollision.so.20.06.99  lib/libSofaMeshCollision.so.20.06.99  lib/libSofaBaseCollision.so.20.06.99  lib/libSofaObjectInteraction.so.20.06.99  lib/libSofaDeformable.so.20.06.99  lib/libSofaRigid.so.20.06.99  lib/libSofaBaseMechanics.so.20.06.99  lib/libSofaEigen2Solver.so.20.06.99  lib/libSofaGeneralVisual.so.20.06.99  lib/libSofaBaseVisual.so.20.06.99  lib/libSofaBaseTopology.so.20.06.99  lib/libSofaGraphComponent.so.20.06.99  lib/libSofaSimulationTree.so.20.06.99  lib/libSofaBaseUtils.so.20.06.99  lib/libSofaGeneralAnimationLoop.so.20.06.99  lib/libSofaBaseLinearSolver.so.20.06.99  lib/libSofaSimulationCommon.so.20.06.99  lib/libSofaSimulationCore.so.20.06.99  lib/libSofaCore.so.20.06.99  lib/libSofaDefaultType.so.20.06.99  lib/libSofaHelper.so.20.06.99  /usr/lib/x86_64-linux-gnu/libGLU.so  /usr/lib/x86_64-linux-gnu/libGLX.so  /usr/lib/x86_64-linux-gnu/libOpenGL.so  /usr/lib/x86_64-linux-gnu/libGLEW.so  /usr/lib/x86_64-linux-gnu/libboost_system.so  /usr/lib/x86_64-linux-gnu/libboost_filesystem.so  /usr/lib/x86_64-linux-gnu/libboost_program_options.so  /usr/lib/x86_64-linux-gnu/libboost_thread.so  /usr/lib/x86_64-linux-gnu/libboost_chrono.so  /usr/lib/x86_64-linux-gnu/libboost_date_time.so  /usr/lib/x86_64-linux-gnu/libboost_atomic.so  lib/libgtest.so.2.6.2  -pthread  -Wl,-rpath-link,/home/arnaud/dev/sofa/v20.06/build/lib && :
/usr/bin/ld: applications/plugins/SofaPardisoSolver/CMakeFiles/SofaPardisoSolver.dir/SparsePARDISOSolver.cpp.o: in function
sofa::component::linearsolver::SparsePARDISOSolver<sofa::component::linearsolver::CompressedRowSparseMatrix<double, sofa::helper::vector<double, sofa::helper::CPUMemoryManager<double> >, sofa::helper::vector<int, sofa::helper::CPUMemoryManager<int> > >, sofa::component::linearsolver::FullVector<double> >::callPardiso(sofa::component::linearsolver::SparsePARDISOSolver<sofa::component::linearsolver::CompressedRowSparseMatrix<double, sofa::helper::vector<double, sofa::helper::CPUMemoryManager<double> >, sofa::helper::vector<int, sofa::helper::CPUMemoryManager<int> > >, sofa::component::linearsolver::FullVector<double> >::SparsePARDISOSolverInvertData*, int, sofa::component::linearsolver::FullVector<double>*, sofa::component::linearsolver::FullVector<double>*)':
SparsePARDISOSolver.cpp:(.text._ZN4sofa9component12linearsolver19SparsePARDISOSolverINS1_25CompressedRowSparseMatrixIdNS_6helper6vectorIdNS4_16CPUMemoryManagerIdEEEENS5_IiNS6_IiEEEEEENS1_10FullVectorIdEEE11callPardisoEPNSE_29SparsePARDISOSolverInvertDataEiPSD_SH_[_ZN4sofa9component12linearsolver19SparsePARDISOSolverINS1_25CompressedRowSparseMatrixIdNS_6helper6vectorIdNS4_16CPUMemoryManagerIdEEEENS5_IiNS6_IiEEEEEENS1_10FullVectorIdEEE11callPardisoEPNSE_29SparsePARDISOSolverInvertDataEiPSD_SH_]+0x1b7): undefined reference to pardiso_
/usr/bin/ld: applications/plugins/SofaPardisoSolver/CMakeFiles/SofaPardisoSolver.dir/SparsePARDISOSolver.cpp.o: in function sofa::component::linearsolver::SparsePARDISOSolver<sofa::component::linearsolver::CompressedRowSparseMatrix<double, sofa::helper::vector<double, sofa::helper::CPUMemoryManager<double> >, sofa::helper::vector<int, sofa::helper::CPUMemoryManager<int> > >, sofa::component::linearsolver::FullVector<double> >::SparsePARDISOSolverInvertData::SparsePARDISOSolverInvertData(int, std::ostream&, std::ostream&)':
SparsePARDISOSolver.cpp:(.text._ZN4sofa9component12linearsolver19SparsePARDISOSolverINS1_25CompressedRowSparseMatrixIdNS_6helper6vectorIdNS4_16CPUMemoryManagerIdEEEENS5_IiNS6_IiEEEEEENS1_10FullVectorIdEEE29SparsePARDISOSolverInvertDataC2EiRSoSG_[_ZN4sofa9component12linearsolver19SparsePARDISOSolverINS1_25CompressedRowSparseMatrixIdNS_6helper6vectorIdNS4_16CPUMemoryManagerIdEEEENS5_IiNS6_IiEEEEEENS1_10FullVectorIdEEE29SparsePARDISOSolverInvertDataC5EiRSoSG_]+0x277): undefined reference to pardisoinit_
/usr/bin/ld: applications/plugins/SofaPardisoSolver/CMakeFiles/SofaPardisoSolver.dir/SparsePARDISOSolver.cpp.o: in function sofa::component::linearsolver::SparsePARDISOSolver<sofa::component::linearsolver::CompressedRowSparseMatrix<sofa::defaulttype::Mat<3u, 3u, double>, sofa::helper::vector<sofa::defaulttype::Mat<3u, 3u, double>, sofa::helper::CPUMemoryManager<sofa::defaulttype::Mat<3u, 3u, double> > >, sofa::helper::vector<int, sofa::helper::CPUMemoryManager<int> > >, sofa::component::linearsolver::FullVector<double> >::callPardiso(sofa::component::linearsolver::SparsePARDISOSolver<sofa::component::linearsolver::CompressedRowSparseMatrix<sofa::defaulttype::Mat<3u, 3u, double>, sofa::helper::vector<sofa::defaulttype::Mat<3u, 3u, double>, sofa::helper::CPUMemoryManager<sofa::defaulttype::Mat<3u, 3u, double> > >, sofa::helper::vector<int, sofa::helper::CPUMemoryManager<int> > >, sofa::component::linearsolver::FullVector<double> >::SparsePARDISOSolverInvertData*, int, sofa::component::linearsolver::FullVector<double>*, sofa::component::linearsolver::FullVector<double>*)':
SparsePARDISOSolver.cpp:(.text._ZN4sofa9component12linearsolver19SparsePARDISOSolverINS1_25CompressedRowSparseMatrixINS_11defaulttype3MatILj3ELj3EdEENS_6helper6vectorIS6_NS7_16CPUMemoryManagerIS6_EEEENS8_IiNS9_IiEEEEEENS1_10FullVectorIdEEE11callPardisoEPNSH_29SparsePARDISOSolverInvertDataEiPSG_SK_[_ZN4sofa9component12linearsolver19SparsePARDISOSolverINS1_25CompressedRowSparseMatrixINS_11defaulttype3MatILj3ELj3EdEENS_6helper6vectorIS6_NS7_16CPUMemoryManagerIS6_EEEENS8_IiNS9_IiEEEEEENS1_10FullVectorIdEEE11callPardisoEPNSH_29SparsePARDISOSolverInvertDataEiPSG_SK_]+0x1b7): undefined reference to pardiso_
/usr/bin/ld: applications/plugins/SofaPardisoSolver/CMakeFiles/SofaPardisoSolver.dir/SparsePARDISOSolver.cpp.o: in function sofa::component::linearsolver::SparsePARDISOSolver<sofa::component::linearsolver::CompressedRowSparseMatrix<sofa::defaulttype::Mat<3u, 3u, double>, sofa::helper::vector<sofa::defaulttype::Mat<3u, 3u, double>, sofa::helper::CPUMemoryManager<sofa::defaulttype::Mat<3u, 3u, double> > >, sofa::helper::vector<int, sofa::helper::CPUMemoryManager<int> > >, sofa::component::linearsolver::FullVector<double> >::SparsePARDISOSolverInvertData::SparsePARDISOSolverInvertData(int, std::ostream&, std::ostream&)':
SparsePARDISOSolver.cpp:(.text._ZN4sofa9component12linearsolver19SparsePARDISOSolverINS1_25CompressedRowSparseMatrixINS_11defaulttype3MatILj3ELj3EdEENS_6helper6vectorIS6_NS7_16CPUMemoryManagerIS6_EEEENS8_IiNS9_IiEEEEEENS1_10FullVectorIdEEE29SparsePARDISOSolverInvertDataC2EiRSoSJ_[_ZN4sofa9component12linearsolver19SparsePARDISOSolverINS1_25CompressedRowSparseMatrixINS_11defaulttype3MatILj3ELj3EdEENS_6helper6vectorIS6_NS7_16CPUMemoryManagerIS6_EEEENS8_IiNS9_IiEEEEEENS1_10FullVectorIdEEE29SparsePARDISOSolverInvertDataC5EiRSoSJ_]+0x277): undefined reference to pardisoinit_
collect2: error: ld returned 1 exit status
ninja: build stopped: subcommand failed.

Thank you for your help and have a nice day,
Best,

Arnaud

[Hugo]

Hi @amazier

Did you clean your build just before updating your GCC version?
Best

Hugo

[amazier]

Hi Hugo,

Thank you for your reply, I will try to erase the build and build from scratch and let you know 🙂
Best,

[amazier]

Hi all,
I still do obtain the same error even by recreating another build.

[Hugo]

Hey @amazier

Now SofaMJED works well.
Regarding Pardiso, have you solved your issue?
Otherwise I will compile it on my machine this week-end.

Best

Hugo

[amazier]

Hi Hugo,
Sorry for replying after the weekend…
Good news for the plugin! Let me know when I can access it!
Unfortunately, yes I still have the same issue…

Have a nice day,
Arnaud

[Hugo]

I got it to compile as you did and got the same runtime error (loading the plugin):

[ERROR]   [PluginManager] Plugin loading failed (/data/Softwares/sofa/build/build-master/lib/libSofaPardisoSolver.so): /data/Softwares/sofa/build/build-master/lib/libSofaPardisoSolver.so: undefined symbol: pardisoinit_

The symbol pardisoinit_ is missing, which means that in the newer versions of pardiso, the constructor of pardisoinit() (maybe the number of parameters) changed. Let’s try to investigate both on our side, the first to succeed let the other know and make a nice pull-request 😉

Best

Hugo

[Hugo]

Hi @amazier

Did you well compiled the plugin using GCC ?

Best

Hugo

[amazier]

Hi Hugo,
Thanks for replying. I tried with the master version and I obtain the following (quite long and funny) error:

[53/54] Linking CXX shared library lib/libSofaPardisoSolver.so.0.1
FAILED: lib/libSofaPardisoSolver.so.0.1 
: && /usr/lib/ccache/c++ -fPIC -O3 -DNDEBUG  -Wl,--no-undefined -lc -shared -Wl,-soname,libSofaPardisoSolver.so.0.1 -o lib/libSofaPardisoSolver.so.0.1 applications/plugins/SofaPardisoSolver/CMakeFiles/SofaPardisoSolver.dir/SparsePARDISOSolver.cpp.o applications/plugins/SofaPardisoSolver/CMakeFiles/SofaPardisoSolver.dir/initPardisoSolver.cpp.o -L/home/arnaud/dev/sofa/v20.06/src/applications/plugins/SofaPardisoSolver/extlibs -Wl,-rpath,/home/arnaud/dev/sofa/v20.06/src/applications/plugins/SofaPardisoSolver/extlibs:/home/arnaud/dev/sofa/v20.06/build/lib:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::  lib/libSofaBase.so.20.12.99  lib/libSofaGeneral.so.20.12.99  -lSofaSimulationTree  -lgfortran  -lblas  -llapack  -lgomp  lib/libSofaGeneralAnimationLoop.so.20.12.99  lib/libSofaSimulationCommon.so.20.12.99  lib/libSofaGeneralDeformable.so.20.12.99  lib/libSofaGeneralEngine.so.20.12.99  lib/libSofa.GL.so.20.12.99  /usr/lib/x86_64-linux-gnu/libGLU.so  /usr/lib/x86_64-linux-gnu/libGLX.so  /usr/lib/x86_64-linux-gnu/libOpenGL.so  /usr/lib/x86_64-linux-gnu/libGLEW.so  lib/libSofaGeneralExplicitOdeSolver.so.20.12.99  lib/libSofaGeneralImplicitOdeSolver.so.20.12.99  lib/libSofaGeneralLinearSolver.so.20.12.99  lib/libSofaGeneralRigid.so.20.12.99  lib/libSofaGeneralObjectInteraction.so.20.12.99  lib/libSofaConstraint.so.20.12.99  lib/libSofaUserInteraction.so.20.12.99  lib/libSofaBoundaryCondition.so.20.12.99  lib/libSofaGeneralMeshCollision.so.20.12.99  lib/libSofaMeshCollision.so.20.12.99  lib/libSofaBaseCollision.so.20.12.99  lib/libSofaObjectInteraction.so.20.12.99  lib/libSofaRigid.so.20.12.99  lib/libSofaGeneralVisual.so.20.12.99  lib/libSofaBaseVisual.so.20.12.99  lib/libSofaGraphComponent.so.20.12.99  lib/libSofaBaseUtils.so.20.12.99  lib/libSofaTopologyMapping.so.20.12.99  lib/libSofaGeneralSimpleFem.so.20.12.99  lib/libSofaBaseMechanics.so.20.12.99  lib/libSofaGeneralTopology.so.20.12.99  lib/libSofaDeformable.so.20.12.99  lib/libSofaEigen2Solver.so.20.12.99  lib/libSofaSimpleFem.so.20.12.99  lib/libSofaBaseLinearSolver.so.20.12.99  lib/libSofaBaseTopology.so.20.12.99  lib/libSofaImplicitOdeSolver.so.20.12.99  lib/libSofaGeneralLoader.so.20.12.99  lib/libSofaSimulationCore.so.20.12.99  lib/libSofaCore.so.20.12.99  lib/libSofaDefaultType.so.20.12.99  lib/libSofaHelper.so.20.12.99  lib/libSofa.Type.so.20.12.99  lib/libSofa.Config.so.20.12.99  /usr/lib/x86_64-linux-gnu/libboost_system.so  /usr/lib/x86_64-linux-gnu/libboost_filesystem.so  /usr/lib/x86_64-linux-gnu/libboost_program_options.so  /usr/lib/x86_64-linux-gnu/libboost_thread.so  /usr/lib/x86_64-linux-gnu/libboost_chrono.so  /usr/lib/x86_64-linux-gnu/libboost_date_time.so  /usr/lib/x86_64-linux-gnu/libboost_atomic.so  lib/libgtest.so.2.6.2  -pthread  /usr/lib/x86_64-linux-gnu/libz.so  -Wl,-rpath-link,/home/arnaud/dev/sofa/v20.06/build/lib && :
/usr/bin/ld: cannot find -lSofaSimulationTree

Unfortunately, I did not find the solution…
Best,
Arnaud

[Hugo]

Hi @amazier

It works on my side:

I just made a PR #1830 for updating the plugin and a README to guide you.
Let me know if it helps.

Best

Hugo

[amazier]

Hi Hugo,

Thanks for the fix. I checked out on your PR but unfortunately, it is still not compiling… I still have the same error.
When I check the cmake I see that PARDISO_LIB is empty.
I tried to build from scratch with ninja.
Sorry to bother you the PR is super clear.

Best
Arnaud

[jnbrunet]

Hey Arnaud,

Where is the library that you downloaded from the pardiso’s website? It should look like “libpardiso(…).so”.

Once you find it, you need to put this path into the cmake variable “PARDISO_LIB”. For example, on my PC, I do:

cmake -DPARDISO_LIB=/opt/libpardiso600-GNU800-X86-64.so ..

J-N

[amazier]

Hey J-N,

Thanks, I did not specify the path indeed!
Now everything is working fine, very efficient solver!

I close the issue, thanks to the consortium!
Have a nice day,
Arnaud

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