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

[Author]

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