[aspect-devel] aspect/deal.ii issue

[Cedric Thieulot]

hi, 

sorry for the stupid mistake. 
Compilation is ok now, but linking fails :
It seems that it has something to do with Trilinos, but my call to ./configure looks as follows:
 ./configure --enable-mpi --with-trilinos=/home/sepfem/source/trilinos-10.4.2-Source/build --with-p4est=/home/sepfem/source/p4est
(these Trilinos and P4est have been installed and used by Thomas for months)




=====aspect=======================MT== Linking lib/aspect
lib/obj/simulator_checkpoint_restart.g.o: In function `aspect::Simulator<2>::create_snapshot()':
checkpoint_restart.cc:(.text._ZN6aspect9SimulatorILi2EE15create_snapshotEv[aspect::Simulator<2>::create_snapshot()]+0x487): undefined reference to `dealii::parallel::distributed::SolutionTransfer<2, dealii::TrilinosWrappers::MPI::BlockVector, dealii::DoFHandler<2, 2> >::SolutionTransfer(dealii::DoFHandler<2, 2> const&)'
checkpoint_restart.cc:(.text._ZN6aspect9SimulatorILi2EE15create_snapshotEv[aspect::Simulator<2>::create_snapshot()]+0x4a0): undefined reference to `dealii::parallel::distributed::SolutionTransfer<2, dealii::TrilinosWrappers::MPI::BlockVector, dealii::DoFHandler<2, 2> >::prepare_serialization(std::vector<dealii::TrilinosWrappers::MPI::BlockVector const*, std::allocator<dealii::TrilinosWrappers::MPI::BlockVector const*> > const&)'
checkpoint_restart.cc:(.text._ZN6aspect9SimulatorILi2EE15create_snapshotEv[aspect::Simulator<2>::create_snapshot()]+0x4ec): undefined reference to `dealii::parallel::distributed::Triangulation<2, 2>::save(char const*) const'
checkpoint_restart.cc:(.text._ZN6aspect9SimulatorILi2EE15create_snapshotEv[aspect::Simulator<2>::create_snapshot()]+0x52f): undefined reference to `dealii::parallel::distributed::SolutionTransfer<2, dealii::TrilinosWrappers::MPI::BlockVector, dealii::DoFHandler<2, 2> >::~SolutionTransfer()'
checkpoint_restart.cc:(.text._ZN6aspect9SimulatorILi2EE15create_snapshotEv[aspect::Simulator<2>::create_snapshot()]+0x546): undefined reference to `dealii::parallel::distributed::SolutionTransfer<2, dealii::TrilinosWrappers::MPI::BlockVector, dealii::DoFHandler<2, 2> >::~SolutionTransfer()'
lib/obj/simulator_checkpoint_restart.g.o: In function `aspect::Simulator<2>::resume_from_snapshot()':
checkpoint_restart.cc:(.text._ZN6aspect9SimulatorILi2EE20resume_from_snapshotEv[aspect::Simulator<2>::resume_from_snapshot()]+0x5f): undefined reference to `dealii::parallel::distributed::Triangulation<2, 2>::load(char const*)'
checkpoint_restart.cc:(.text._ZN6aspect9SimulatorILi2EE20resume_from_snapshotEv[aspect::Simulator<2>::resume_from_snapshot()]+0x21c): undefined reference to `dealii::parallel::distributed::SolutionTransfer<2, dealii::TrilinosWrappers::MPI::BlockVector, dealii::DoFHandler<2, 2> >::SolutionTransfer(dealii::DoFHandler<2, 2> const&)'
checkpoint_restart.cc:(.text._ZN6aspect9SimulatorILi2EE20resume_from_snapshotEv[aspect::Simulator<2>::resume_from_snapshot()]+0x235): undefined reference to `dealii::parallel::distributed::SolutionTransfer<2, dealii::TrilinosWrappers::MPI::BlockVector, dealii::DoFHandler<2, 2> >::deserialize(std::vector<dealii::TrilinosWrappers::MPI::BlockVector*, std::allocator<dealii::TrilinosWrappers::MPI::BlockVector*> >&)'
checkpoint_restart.cc:(.text._ZN6aspect9SimulatorILi2EE20resume_from_snapshotEv[aspect::Simulator<2>::resume_from_snapshot()]+0x6d6): undefined reference to `dealii::parallel::distributed::SolutionTransfer<2, dealii::TrilinosWrappers::MPI::BlockVector, dealii::DoFHandler<2, 2> >::~SolutionTransfer()'
checkpoint_restart.cc:(.text._ZN6aspect9SimulatorILi2EE20resume_from_snapshotEv[aspect::Simulator<2>::resume_from_snapshot()]+0x6ed): undefined reference to `dealii::parallel::distributed::SolutionTransfer<2, dealii::TrilinosWrappers::MPI::BlockVector, dealii::DoFHandler<2, 2> >::~SolutionTransfer()'
lib/obj/simulator_checkpoint_restart.g.o: In function `aspect::Simulator<3>::create_snapshot()':
checkpoint_restart.cc:(.text._ZN6aspect9SimulatorILi3EE15create_snapshotEv[aspect::Simulator<3>::create_snapshot()]+0x487): undefined reference to `dealii::parallel::distributed::SolutionTransfer<3, dealii::TrilinosWrappers::MPI::BlockVector, dealii::DoFHandler<3, 3> >::SolutionTransfer(dealii::DoFHandler<3, 3> const&)'
checkpoint_restart.cc:(.text._ZN6aspect9SimulatorILi3EE15create_snapshotEv[aspect::Simulator<3>::create_snapshot()]+0x4a0): undefined reference to `dealii::parallel::distributed::SolutionTransfer<3, dealii::TrilinosWrappers::MPI::BlockVector, dealii::DoFHandler<3, 3> >::prepare_serialization(std::vector<dealii::TrilinosWrappers::MPI::BlockVector const*, std::allocator<dealii::TrilinosWrappers::MPI::BlockVector const*> > const&)'
checkpoint_restart.cc:(.text._ZN6aspect9SimulatorILi3EE15create_snapshotEv[aspect::Simulator<3>::create_snapshot()]+0x4ec): undefined reference to `dealii::parallel::distributed::Triangulation<3, 3>::save(char const*) const'
checkpoint_restart.cc:(.text._ZN6aspect9SimulatorILi3EE15create_snapshotEv[aspect::Simulator<3>::create_snapshot()]+0x52f): undefined reference to `dealii::parallel::distributed::SolutionTransfer<3, dealii::TrilinosWrappers::MPI::BlockVector, dealii::DoFHandler<3, 3> >::~SolutionTransfer()'
checkpoint_restart.cc:(.text._ZN6aspect9SimulatorILi3EE15create_snapshotEv[aspect::Simulator<3>::create_snapshot()]+0x546): undefined reference to `dealii::parallel::distributed::SolutionTransfer<3, dealii::TrilinosWrappers::MPI::BlockVector, dealii::DoFHandler<3, 3> >::~SolutionTransfer()'
lib/obj/simulator_checkpoint_restart.g.o: In function `aspect::Simulator<3>::resume_from_snapshot()':
checkpoint_restart.cc:(.text._ZN6aspect9SimulatorILi3EE20resume_from_snapshotEv[aspect::Simulator<3>::resume_from_snapshot()]+0x5f): undefined reference to `dealii::parallel::distributed::Triangulation<3, 3>::load(char const*)'
checkpoint_restart.cc:(.text._ZN6aspect9SimulatorILi3EE20resume_from_snapshotEv[aspect::Simulator<3>::resume_from_snapshot()]+0x21c): undefined reference to `dealii::parallel::distributed::SolutionTransfer<3, dealii::TrilinosWrappers::MPI::BlockVector, dealii::DoFHandler<3, 3> >::SolutionTransfer(dealii::DoFHandler<3, 3> const&)'
checkpoint_restart.cc:(.text._ZN6aspect9SimulatorILi3EE20resume_from_snapshotEv[aspect::Simulator<3>::resume_from_snapshot()]+0x235): undefined reference to `dealii::parallel::distributed::SolutionTransfer<3, dealii::TrilinosWrappers::MPI::BlockVector, dealii::DoFHandler<3, 3> >::deserialize(std::vector<dealii::TrilinosWrappers::MPI::BlockVector*, std::allocator<dealii::TrilinosWrappers::MPI::BlockVector*> >&)'
checkpoint_restart.cc:(.text._ZN6aspect9SimulatorILi3EE20resume_from_snapshotEv[aspect::Simulator<3>::resume_from_snapshot()]+0x6d6): undefined reference to `dealii::parallel::distributed::SolutionTransfer<3, dealii::TrilinosWrappers::MPI::BlockVector, dealii::DoFHandler<3, 3> >::~SolutionTransfer()'
checkpoint_restart.cc:(.text._ZN6aspect9SimulatorILi3EE20resume_from_snapshotEv[aspect::Simulator<3>::resume_from_snapshot()]+0x6ed): undefined reference to `dealii::parallel::distributed::SolutionTransfer<3, dealii::TrilinosWrappers::MPI::BlockVector, dealii::DoFHandler<3, 3> >::~SolutionTransfer()'
lib/obj/simulator_core.g.o: In function `aspect::Simulator<2>::Simulator(ompi_communicator_t*, dealii::ParameterHandler&)':
core.cc:(.text._ZN6aspect9SimulatorILi2EEC2EP19ompi_communicator_tRN6dealii16ParameterHandlerE[aspect::Simulator<2>::Simulator(ompi_communicator_t*, dealii::ParameterHandler&)]+0x2c9): undefined reference to `dealii::parallel::distributed::Triangulation<2, 2>::Triangulation(ompi_communicator_t*, dealii::Triangulation<2, 2>::MeshSmoothing, dealii::parallel::distributed::Triangulation<2, 2>::Settings)'
lib/obj/simulator_core.g.o: In function `aspect::Simulator<2>::Simulator(ompi_communicator_t*, dealii::ParameterHandler&)':
core.cc:(.text._ZN6aspect9SimulatorILi2EEC1EP19ompi_communicator_tRN6dealii16ParameterHandlerE[aspect::Simulator<2>::Simulator(ompi_communicator_t*, dealii::ParameterHandler&)]+0x2c9): undefined reference to `dealii::parallel::distributed::Triangulation<2, 2>::Triangulation(ompi_communicator_t*, dealii::Triangulation<2, 2>::MeshSmoothing, dealii::parallel::distributed::Triangulation<2, 2>::Settings)'
lib/obj/simulator_core.g.o: In function `aspect::Simulator<2>::setup_dofs()':
core.cc:(.text._ZN6aspect9SimulatorILi2EE10setup_dofsEv[aspect::Simulator<2>::setup_dofs()]+0x47b): undefined reference to `dealii::parallel::distributed::Triangulation<2, 2>::n_global_active_cells() const'
lib/obj/simulator_core.g.o: In function `aspect::Simulator<2>::start_timestep()':
core.cc:(.text._ZN6aspect9SimulatorILi2EE14start_timestepEv[aspect::Simulator<2>::start_timestep()]+0x3d2): undefined reference to `dealii::parallel::distributed::Triangulation<2, 2>::n_global_active_cells() const'
lib/obj/simulator_core.g.o: In function `aspect::Simulator<2>::refine_mesh(unsigned int)':
core.cc:(.text._ZN6aspect9SimulatorILi2EE11refine_meshEj[aspect::Simulator<2>::refine_mesh(unsigned int)]+0x12a): undefined reference to `void dealii::parallel::distributed::GridRefinement::refine_and_coarsen_fixed_fraction<2, dealii::Vector<float>, 2>(dealii::parallel::distributed::Triangulation<2, 2>&, dealii::Vector<float> const&, double, double)'
core.cc:(.text._ZN6aspect9SimulatorILi2EE11refine_meshEj[aspect::Simulator<2>::refine_mesh(unsigned int)]+0x299): undefined reference to `dealii::parallel::distributed::SolutionTransfer<2, dealii::TrilinosWrappers::MPI::BlockVector, dealii::DoFHandler<2, 2> >::SolutionTransfer(dealii::DoFHandler<2, 2> const&)'
core.cc:(.text._ZN6aspect9SimulatorILi2EE11refine_meshEj[aspect::Simulator<2>::refine_mesh(unsigned int)]+0x2c7): undefined reference to `dealii::parallel::distributed::SolutionTransfer<2, dealii::TrilinosWrappers::MPI::BlockVector, dealii::DoFHandler<2, 2> >::prepare_for_coarsening_and_refinement(std::vector<dealii::TrilinosWrappers::MPI::BlockVector const*, std::allocator<dealii::TrilinosWrappers::MPI::BlockVector const*> > const&)'
core.cc:(.text._ZN6aspect9SimulatorILi2EE11refine_meshEj[aspect::Simulator<2>::refine_mesh(unsigned int)]+0x2dc): undefined reference to `dealii::parallel::distributed::Triangulation<2, 2>::execute_coarsening_and_refinement()'
core.cc:(.text._ZN6aspect9SimulatorILi2EE11refine_meshEj[aspect::Simulator<2>::refine_mesh(unsigned int)]+0x4f3): undefined reference to `dealii::parallel::distributed::SolutionTransfer<2, dealii::TrilinosWrappers::MPI::BlockVector, dealii::DoFHandler<2, 2> >::interpolate(std::vector<dealii::TrilinosWrappers::MPI::BlockVector*, std::allocator<dealii::TrilinosWrappers::MPI::BlockVector*> >&)'
core.cc:(.text._ZN6aspect9SimulatorILi2EE11refine_meshEj[aspect::Simulator<2>::refine_mesh(unsigned int)]+0x620): undefined reference to `dealii::parallel::distributed::SolutionTransfer<2, dealii::TrilinosWrappers::MPI::BlockVector, dealii::DoFHandler<2, 2> >::~SolutionTransfer()'
core.cc:(.text._ZN6aspect9SimulatorILi2EE11refine_meshEj[aspect::Simulator<2>::refine_mesh(unsigned int)]+0x637): undefined reference to `dealii::parallel::distributed::SolutionTransfer<2, dealii::TrilinosWrappers::MPI::BlockVector, dealii::DoFHandler<2, 2> >::~SolutionTransfer()'
lib/obj/simulator_core.g.o: In function `aspect::Simulator<3>::Simulator(ompi_communicator_t*, dealii::ParameterHandler&)':
core.cc:(.text._ZN6aspect9SimulatorILi3EEC2EP19ompi_communicator_tRN6dealii16ParameterHandlerE[aspect::Simulator<3>::Simulator(ompi_communicator_t*, dealii::ParameterHandler&)]+0x2c9): undefined reference to `dealii::parallel::distributed::Triangulation<3, 3>::Triangulation(ompi_communicator_t*, dealii::Triangulation<3, 3>::MeshSmoothing, dealii::parallel::distributed::Triangulation<3, 3>::Settings)'
lib/obj/simulator_core.g.o: In function `aspect::Simulator<3>::Simulator(ompi_communicator_t*, dealii::ParameterHandler&)':
core.cc:(.text._ZN6aspect9SimulatorILi3EEC1EP19ompi_communicator_tRN6dealii16ParameterHandlerE[aspect::Simulator<3>::Simulator(ompi_communicator_t*, dealii::ParameterHandler&)]+0x2c9): undefined reference to `dealii::parallel::distributed::Triangulation<3, 3>::Triangulation(ompi_communicator_t*, dealii::Triangulation<3, 3>::MeshSmoothing, dealii::parallel::distributed::Triangulation<3, 3>::Settings)'
lib/obj/simulator_core.g.o: In function `aspect::Simulator<3>::setup_dofs()':
core.cc:(.text._ZN6aspect9SimulatorILi3EE10setup_dofsEv[aspect::Simulator<3>::setup_dofs()]+0x47b): undefined reference to `dealii::parallel::distributed::Triangulation<3, 3>::n_global_active_cells() const'
lib/obj/simulator_core.g.o: In function `aspect::Simulator<3>::start_timestep()':
core.cc:(.text._ZN6aspect9SimulatorILi3EE14start_timestepEv[aspect::Simulator<3>::start_timestep()]+0x3d2): undefined reference to `dealii::parallel::distributed::Triangulation<3, 3>::n_global_active_cells() const'
lib/obj/simulator_core.g.o: In function `aspect::Simulator<3>::refine_mesh(unsigned int)':
core.cc:(.text._ZN6aspect9SimulatorILi3EE11refine_meshEj[aspect::Simulator<3>::refine_mesh(unsigned int)]+0x12a): undefined reference to `void dealii::parallel::distributed::GridRefinement::refine_and_coarsen_fixed_fraction<3, dealii::Vector<float>, 3>(dealii::parallel::distributed::Triangulation<3, 3>&, dealii::Vector<float> const&, double, double)'
core.cc:(.text._ZN6aspect9SimulatorILi3EE11refine_meshEj[aspect::Simulator<3>::refine_mesh(unsigned int)]+0x299): undefined reference to `dealii::parallel::distributed::SolutionTransfer<3, dealii::TrilinosWrappers::MPI::BlockVector, dealii::DoFHandler<3, 3> >::SolutionTransfer(dealii::DoFHandler<3, 3> const&)'
core.cc:(.text._ZN6aspect9SimulatorILi3EE11refine_meshEj[aspect::Simulator<3>::refine_mesh(unsigned int)]+0x2c7): undefined reference to `dealii::parallel::distributed::SolutionTransfer<3, dealii::TrilinosWrappers::MPI::BlockVector, dealii::DoFHandler<3, 3> >::prepare_for_coarsening_and_refinement(std::vector<dealii::TrilinosWrappers::MPI::BlockVector const*, std::allocator<dealii::TrilinosWrappers::MPI::BlockVector const*> > const&)'
core.cc:(.text._ZN6aspect9SimulatorILi3EE11refine_meshEj[aspect::Simulator<3>::refine_mesh(unsigned int)]+0x2dc): undefined reference to `dealii::parallel::distributed::Triangulation<3, 3>::execute_coarsening_and_refinement()'
core.cc:(.text._ZN6aspect9SimulatorILi3EE11refine_meshEj[aspect::Simulator<3>::refine_mesh(unsigned int)]+0x4f3): undefined reference to `dealii::parallel::distributed::SolutionTransfer<3, dealii::TrilinosWrappers::MPI::BlockVector, dealii::DoFHandler<3, 3> >::interpolate(std::vector<dealii::TrilinosWrappers::MPI::BlockVector*, std::allocator<dealii::TrilinosWrappers::MPI::BlockVector*> >&)'
core.cc:(.text._ZN6aspect9SimulatorILi3EE11refine_meshEj[aspect::Simulator<3>::refine_mesh(unsigned int)]+0x620): undefined reference to `dealii::parallel::distributed::SolutionTransfer<3, dealii::TrilinosWrappers::MPI::BlockVector, dealii::DoFHandler<3, 3> >::~SolutionTransfer()'
core.cc:(.text._ZN6aspect9SimulatorILi3EE11refine_meshEj[aspect::Simulator<3>::refine_mesh(unsigned int)]+0x637): undefined reference to `dealii::parallel::distributed::SolutionTransfer<3, dealii::TrilinosWrappers::MPI::BlockVector, dealii::DoFHandler<3, 3> >::~SolutionTransfer()'
lib/obj/simulator_helper_functions.g.o: In function `aspect::Simulator<2>::output_statistics()':
helper_functions.cc:(.text._ZN6aspect9SimulatorILi2EE17output_statisticsEv[aspect::Simulator<2>::output_statistics()]+0x330): undefined reference to `dealii::parallel::distributed::Triangulation<2, 2>::memory_consumption_p4est() const'
helper_functions.cc:(.text._ZN6aspect9SimulatorILi2EE17output_statisticsEv[aspect::Simulator<2>::output_statistics()]+0x377): undefined reference to `dealii::parallel::distributed::Triangulation<2, 2>::memory_consumption() const'
lib/obj/simulator_helper_functions.g.o: In function `aspect::Simulator<3>::output_statistics()':
helper_functions.cc:(.text._ZN6aspect9SimulatorILi3EE17output_statisticsEv[aspect::Simulator<3>::output_statistics()]+0x330): undefined reference to `dealii::parallel::distributed::Triangulation<3, 3>::memory_consumption_p4est() const'
helper_functions.cc:(.text._ZN6aspect9SimulatorILi3EE17output_statisticsEv[aspect::Simulator<3>::output_statistics()]+0x377): undefined reference to `dealii::parallel::distributed::Triangulation<3, 3>::memory_consumption() const'
collect2: ld returned 1 exit status
make: *** [lib/aspect] Error 1

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