Hi Daniel, I have actually set
DEAL_II_WITH_SUNDIALS:BOOL=OFF so I don't really understand why it is trying to compile with sundials. Sundials is actually not installed on my system, so deal.ii must be using the bundled version. I will try to compile sundials and see if that helps. Best, Alex On Monday, June 7, 2021 at 3:37:11 p.m. UTC+2 d.arnd...@gmail.com wrote: > Alex, > > it looks like Trilinos and SUNDIALS are using different MPI > implementations that are incompatible. There is not much we can do about > this within deal.II. > Can you try to reinstall SUNDIALS or Trilinos using the same MPI > implementation as the other one? > > Best, > Daniel > > Am Mo., 7. Juni 2021 um 09:26 Uhr schrieb Alex Cumberworth < > alexanderc...@gmail.com>: > >> Hi Bruno, >> >> I repeated the compilation with deal.ii 9.3 and had the same error. I >> looked at the documentation in deal.ii for the class EpetraWrappers, and >> apparently it requires MPI: >> >> *This class implements a wrapper to the Trilinos distributed vector class >> Epetra_FEVector. This class is derived from the >> LinearAlgebra::VectorSpaceVector >> <https://www.dealii.org/current/doxygen/deal.II/classLinearAlgebra_1_1VectorSpaceVector.html> >> >> class. Note however that Epetra only works with Number = double. This class >> requires Trilinos to be compiled with MPI support.* >> Since epetra is a required trilinos module, does this mean that if >> trilinos is included, it must be compiled with MPI (and then therefore also >> deal.ii, as cmake does not allow non-matching MPI configurations between >> them)? >> >> I recompiled trilinos with mpi on (openmpi 4.0.5), but when attempting to >> recompile deal.ii with MPI on, I ended up with new errors. There are too >> many errors to paste here, but it begins with >> >> In file included from >> /home/ipausers/cumberworth/include/Teuchos_Time.hpp:56, >> >> >> >> from >> /home/ipausers/cumberworth/include/Teuchos_TimeMonitor.hpp:70, >> >> >> >> from >> /home/ipausers/cumberworth/include/Teuchos_CommUtilities.hpp:45, >> >> >> >> from >> /home/ipausers/cumberworth/include/Teuchos_CommHelpers.hpp:46, >> >> >> >> from >> /home/ipausers/cumberworth/include/Kokkos_TeuchosCommAdapters.hpp:47, >> >> >> >> from >> /home/ipausers/cumberworth/include/Sacado_Fad_ScalarTraitsImp.hpp:627, >> >> >> >> from >> /home/ipausers/cumberworth/include/Sacado_Fad_DFadTraits.hpp:144, >> >> >> >> from >> /home/ipausers/cumberworth/include/Sacado.hpp:51, >> >> >> >> from >> /home/ipausers/cumberworth/src/dealii-9.2.0/include/deal.II/base/numbers.h:151, >> >> >> >> from >> /home/ipausers/cumberworth/src/dealii-9.2.0/build13/include/deal.II/base/config.h:449, >> >> >> >> from >> /home/ipausers/cumberworth/src/dealii-9.2.0/source/sundials/arkode.cc:17: >> >> >> >> /home/ipausers/cumberworth/include/mpi.h:30:13: error: conflicting >> declaration ‘typedef int >> MPI_Datatype’ >> >> >> 30 | typedef int >> MPI_Datatype; >> >> >> >> | >> ^~~~~~~~~~~~ >> >> >> >> I have included the rest as an attachment. >> >> Best, >> Alex >> On Monday, June 7, 2021 at 2:03:34 p.m. UTC+2 bruno.t...@gmail.com wrote: >> >>> Alex, >>> >>> This is really strange. I've never seen that error before. Can you try >>> to install deal.II 9.3 >>> https://github.com/dealii/dealii/releases/tag/v9.3.0 and see if you >>> get the same error? >>> >>> Best, >>> >>> Bruno >>> >>> Le lun. 7 juin 2021 à 05:54, Alex Cumberworth >>> <alexanderc...@gmail.com> a écrit : >>> > >>> > Hello, >>> > >>> > I recompiled trilinos without tpetra to sidestep this error, but ended >>> up with another error involving epetra, and apparently epetra is minimal >>> module required for trilinos with deal.ii, so I cannot do the same >>> thing.The error: >>> > >>> > [ 31%] Building CXX object >>> source/numerics/CMakeFiles/obj_numerics_debug.dir/data_out_dof_data.cc.o >>> > In file included from >>> /home/ipausers/cumberworth/src/dealii-9.2.0/source/numerics/data_out_dof_data.cc:28: >>> >>> >>> > >>> /home/ipausers/cumberworth/src/dealii-9.2.0/include/deal.II/numerics/data_out_dof_data.templates.h:429:33: >>> >>> error: ‘EpetraWrappers’ is not a member of ‘dealii::LinearAlgebra’ >>> > 429 | VectorHelper<LinearAlgebra::EpetraWrappers::Vector>::extract( >>> > | ^~~~~~~~~~~~~~ >>> > >>> /home/ipausers/cumberworth/src/dealii-9.2.0/include/deal.II/numerics/data_out_dof_data.templates.h:429:55: >>> >>> error: template argument 1 is invalid >>> > 429 | VectorHelper<LinearAlgebra::EpetraWrappers::Vector>::extract( >>> > | ^ >>> > >>> /home/ipausers/cumberworth/src/dealii-9.2.0/include/deal.II/numerics/data_out_dof_data.templates.h:430:28: >>> >>> error: ‘EpetraWrappers’ in namespace ‘dealii::LinearAlgebra’ does not name >>> a type >>> > 430 | const LinearAlgebra::EpetraWrappers::Vector & /*vector*/, >>> > | ^~~~~~~~~~~~~~ >>> > >>> /home/ipausers/cumberworth/src/dealii-9.2.0/include/deal.II/numerics/data_out_dof_data.templates.h:430:51: >>> >>> error: expected unqualified-id before ‘&’ token >>> > 430 | const LinearAlgebra::EpetraWrappers::Vector & /*vector*/, >>> > | ^ >>> > >>> /home/ipausers/cumberworth/src/dealii-9.2.0/include/deal.II/numerics/data_out_dof_data.templates.h:430:50: >>> >>> error: expected ‘)’ before ‘&’ token >>> > 430 | const LinearAlgebra::EpetraWrappers::Vector & /*vector*/, >>> > | ^~ >>> > | ) >>> > >>> /home/ipausers/cumberworth/src/dealii-9.2.0/include/deal.II/numerics/data_out_dof_data.templates.h:429:65: >>> >>> note: to match this ‘(’ >>> > 429 | VectorHelper<LinearAlgebra::EpetraWrappers::Vector>::extract( >>> > | ^ >>> > >>> /home/ipausers/cumberworth/src/dealii-9.2.0/include/deal.II/numerics/data_out_dof_data.templates.h:430:51: >>> >>> error: non-member function ‘void >>> dealii::internal::DataOutImplementation::extract(...)’ cannot have >>> ref-qualifier >>> > 430 | const LinearAlgebra::EpetraWrappers::Vector & /*vector*/, >>> > | ^ >>> > >>> /home/ipausers/cumberworth/src/dealii-9.2.0/include/deal.II/numerics/data_out_dof_data.templates.h:430:51: >>> >>> error: ‘extract’ is not a template function >>> > make[2]: *** >>> [source/numerics/CMakeFiles/obj_numerics_debug.dir/build.make:303: >>> source/numerics/CMakeFiles/obj_numerics_debug.dir/data_out_dof_data.cc.o] >>> Error 1 >>> > make[1]: *** [CMakeFiles/Makefile2:3317: >>> source/numerics/CMakeFiles/obj_numerics_debug.dir/all] Error 2 >>> > make: *** [Makefile:149: all] Error 2 >>> > >>> > Best, >>> > Alex >>> > On Friday, June 4, 2021 at 5:24:03 p.m. UTC+2 Alex Cumberworth wrote: >>> >> >>> >> Hi Vachan, >>> >> >>> >> Thanks for your response. This actually works. However, I still end >>> up with an incompatibility of the MPI configuration between the Trilinos >>> library and deal.ii. I ended up compiling Trilinos from source (12-4-1), >>> but during compilation of deal.ii, I have a new error: >>> >> >>> >> In file included from >>> /home/ipausers/cumberworth/src/dealii-9.2.0/include/deal.II/dofs/dof_accessor.templates.h:35, >>> >>> >>> >> from >>> /home/ipausers/cumberworth/src/dealii-9.2.0/include/deal.II/dofs/dof_accessor.h:2069, >>> >>> >>> >> from >>> /home/ipausers/cumberworth/src/dealii-9.2.0/source/numerics/data_out.cc:18: >>> >> >>> /home/ipausers/cumberworth/src/dealii-9.2.0/include/deal.II/lac/read_write_vector.h:624:21: >>> >>> error: ‘Vector’ in namespace ‘Tpetra’ does not name a template type >>> >> 624 | const Tpetra::Vector<Number, int, types::global_dof_index> >>> &tpetra_vector, >>> >> | ^~~~~~ >>> >> >>> /home/ipausers/cumberworth/src/dealii-9.2.0/include/deal.II/lac/read_write_vector.h:624:27: >>> >>> error: expected ‘,’ or ‘...’ before ‘<’ token >>> >> 624 | const Tpetra::Vector<Number, int, types::global_dof_index> >>> &tpetra_vector, >>> >> | ^ >>> >> make[2]: *** >>> [source/numerics/CMakeFiles/obj_numerics_debug.dir/build.make:82: >>> source/numerics/CMakeFiles/obj_numerics_debug.dir/data_out.cc.o] Error 1 >>> >> make[1]: *** [CMakeFiles/Makefile2:3317: >>> source/numerics/CMakeFiles/obj_numerics_debug.dir/all] Error 2 >>> >> make: *** [Makefile:149: all] Error 2 >>> >> >>> >> The same error occurs when I use version 13 of Trilinos. >>> >> >>> >> Best, >>> >> Alex >>> >> >>> >> On Thursday, June 3, 2021 at 1:30:49 p.m. UTC+2 vachanpo...@gmail.com >>> wrote: >>> >>> >>> >>> Hi Alex, >>> >>> >>> >>> I previously ran into a lot of issues when I tried to install dealii >>> on our institute's cluster. The OS was different though and I had problems >>> with PETSc. >>> >>> >>> >>> I don't know if this helps but this is the relevant section in >>> dealii-9.2.0/cmake/modules/FindTRILINOS.cmake file which searches for >>> epetra. >>> >>> >>> >>> # Look for Epetra_config.h - we'll query it to determine MPI and >>> 64bit >>> >>> # indices support: >>> >>> # >>> >>> DEAL_II_FIND_FILE(EPETRA_CONFIG_H Epetra_config.h >>> >>> HINTS ${Trilinos_INCLUDE_DIRS} >>> >>> >>> >>> NO_DEFAULT_PATH NO_CMAKE_ENVIRONMENT_PATH NO_CMAKE_PATH >>> >>> NO_SYSTEM_ENVIRONMENT_PATH NO_CMAKE_SYSTEM_PATH >>> NO_CMAKE_FIND_ROOT_PATH >>> >>> ) >>> >>> >>> >>> Notice the hint: it is Trilinos_INCLUDE_DIRS and not >>> TRILINOS_INCLUDE_DIRS. If your dealii version also has Trilinos in >>> smallcase, then maybe making this change will do the job. You may even try >>> manually adding the full path in the cmake module file as a hint. >>> >>> >>> >>> Hope this helps >>> >>> Vachan >>> >>> >>> >>> On Thu, 3 Jun 2021 at 15:07, Alex Cumberworth < >>> alexanderc...@gmail.com> wrote: >>> >>>> >>> >>>> Hello, >>> >>>> >>> >>>> The file does exist and is readable. If I set a manual include flag >>> it is able to find it: >>> >>>> >>> >>>> CMAKE_CXX_FLAGS_DEBUGRELEASE >>> -I/opt/ohpc/pub/libs/gnu9/openmpi4/trilinos/13.0.0/include >>> >>>> >>> >>>> then it is able to get past this point. From the output in my >>> previous message, it seems that cmake is not looking in the right place for >>> these header files, and I have no idea how to set this properly: >>> >>>> >>> >>>> -- TRILINOS_INCLUDE_DIRS: >>> /include;/opt/ohpc/pub/libs/gnu9/openmpi4/hdf5/1.10.6/include;/usr/include;/opt/ohpc/pub/libs/gnu9/openmpi4/boost/1.73.0/include >>> >>> >>> >>>> -- TRILINOS_USER_INCLUDE_DIRS: >>> /include;/opt/ohpc/pub/libs/gnu9/openmpi4/hdf5/1.10.6/include;/usr/include;/opt/ohpc/pub/libs/gnu9/openmpi4/boost/1.73.0/include >>> >>> >>> >>>> >>> >>>> There are further issues past this point, but perhaps if I >>> understand the problem here that will help with the later issues. >>> >>>> >>> >>>> Best, >>> >>>> Alex >>> >>>> >>> >>>> On Tuesday, June 1, 2021 at 9:02:12 p.m. UTC+2 Wolfgang Bangerth >>> wrote: >>> >>>>> >>> >>>>> >>> >>>>> Alex, >>> >>>>> >>> >>>>> > I have also tried >>> >>>>> > >>> >>>>> > cmake >>> -DTRILINOS_DIR=/opt/ohpc/pub/libs/gnu9/openmpi4/trilinos/13.0.0 .. >>> >>>>> > >>> >>>>> > It is also unable to find the epetra header file. >>> >>>>> >>> >>>>> I can not tell why that would be so (but you should be able to >>> find out by >>> >>>>> searching for the place in CMakeFiles/CMakeErrors.log where it >>> shows you the >>> >>>>> command that was executed to find that file). It may be that the >>> file just >>> >>>>> doesn't exist. It may be that it's not readable. It may be that >>> the compiler >>> >>>>> finds an error in it. >>> >>>>> >>> >>>>> If you can't figure out how to use that installation, why not >>> install Trilinos >>> >>>>> yourself in your home directory and take it from there? >>> >>>>> >>> >>>>> Best >>> >>>>> W. >>> >>>>> >>> >>>>> >>> >>>>> -- >>> >>>>> >>> ------------------------------------------------------------------------ >>> >>>>> Wolfgang Bangerth email: bang...@colostate.edu >>> >>>>> www: http://www.math.colostate.edu/~bangerth/ >>> >>>>> >>> >>>> -- >>> >>>> The deal.II project is located at http://www.dealii.org/ >>> >>>> For mailing list/forum options, see >>> https://groups.google.com/d/forum/dealii?hl=en >>> >>>> --- >>> >>>> >>> >>>> You received this message because you are subscribed to the Google >>> Groups "deal.II User Group" group. >>> >>>> To unsubscribe from this group and stop receiving emails from it, >>> send an email to dealii+un...@googlegroups.com. >>> >>>> To view this discussion on the web visit >>> https://groups.google.com/d/msgid/dealii/1f525829-638b-42f4-badd-01d70d5de9efn%40googlegroups.com. >>> >>> >>> > >>> > -- >>> > The deal.II project is located at http://www.dealii.org/ >>> > For mailing list/forum options, see >>> https://groups.google.com/d/forum/dealii?hl=en >>> > --- >>> > You received this message because you are subscribed to a topic in the >>> Google Groups "deal.II User Group" group. >>> > To unsubscribe from this topic, visit >>> https://groups.google.com/d/topic/dealii/3_Tr8HLd7UM/unsubscribe. >>> > To unsubscribe from this group and all its topics, send an email to >>> dealii+un...@googlegroups.com. >>> > To view this discussion on the web visit >>> https://groups.google.com/d/msgid/dealii/10a02d5f-98e2-472b-a21e-edf146acad9bn%40googlegroups.com. >>> >>> >>> >> -- >> The deal.II project is located at http://www.dealii.org/ >> For mailing list/forum options, see >> https://groups.google.com/d/forum/dealii?hl=en >> --- >> You received this message because you are subscribed to the Google Groups >> "deal.II User Group" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to dealii+un...@googlegroups.com. >> > To view this discussion on the web visit >> https://groups.google.com/d/msgid/dealii/227af8d3-726e-4675-a54b-79f8626c9d8dn%40googlegroups.com >> >> <https://groups.google.com/d/msgid/dealii/227af8d3-726e-4675-a54b-79f8626c9d8dn%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> > -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. 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