Trilinos issueshttps://gitlab.osti.gov/jmwille/Trilinos/-/issues2016-11-14T15:57:36Zhttps://gitlab.osti.gov/jmwille/Trilinos/-/issues/774Xpetra::IO and short names may produce conflicts in third party applications2016-11-14T15:57:36ZJames WillenbringXpetra::IO and short names may produce conflicts in third party applications*Created by: tawiesn*
If a code has its own namespace/class "IO" there might be conflicts with Xpetra::IO and short name definitions ("Xpetra_UseShortNamesScalar.hpp").*Created by: tawiesn*
If a code has its own namespace/class "IO" there might be conflicts with Xpetra::IO and short name definitions ("Xpetra_UseShortNamesScalar.hpp").https://gitlab.osti.gov/jmwille/Trilinos/-/issues/737ROL build failures in continuous testing2016-11-01T14:49:40ZJames WillenbringROL build failures in continuous testing*Created by: bmpersc*
@trilinos/rol there are 6 build errors in ROL that can be seen at:
https://testing.sandia.gov/cdash/viewBuildError.php?buildid=2598859
*Created by: bmpersc*
@trilinos/rol there are 6 build errors in ROL that can be seen at:
https://testing.sandia.gov/cdash/viewBuildError.php?buildid=2598859
https://gitlab.osti.gov/jmwille/Trilinos/-/issues/525Panzer: compiler error: stk_mesh/base/CoordinateSystems.hpp: no such file2016-08-31T18:50:59ZJames WillenbringPanzer: compiler error: stk_mesh/base/CoordinateSystems.hpp: no such file*Created by: tawiesn*
@trilinos/panzer @trilinos/stk
After updating Trilinos to the most recent develop version (f1d9dfc6f055d8) i get the following errors:
> In file included from /home/tawiesn/software/trilinos/Trilinos/packages/pan...*Created by: tawiesn*
@trilinos/panzer @trilinos/stk
After updating Trilinos to the most recent develop version (f1d9dfc6f055d8) i get the following errors:
> In file included from /home/tawiesn/software/trilinos/Trilinos/packages/panzer/adapters-stk/src/Panzer_STK_Utilities.hpp:46:0,
> from /home/tawiesn/software/trilinos/Trilinos/packages/panzer/adapters-stk/src/Panzer_STK_Utilities.cpp:45:
> /home/tawiesn/software/trilinos/Trilinos/packages/panzer/adapters-stk/src/stk_interface/Panzer_STK_Interface.hpp:55:47: fatal error: stk_mesh/base/CoordinateSystems.hpp: No such file or directory
> #include <stk_mesh/base/CoordinateSystems.hpp>
> ^
> compilation terminated.
> In file included from /home/tawiesn/software/trilinos/Trilinos/packages/panzer/adapters-stk/src/Panzer_STK_SetupUtilities.hpp:46:0,
> from /home/tawiesn/software/trilinos/Trilinos/packages/panzer/adapters-stk/src/Panzer_STK_SetupUtilities.cpp:43:
> /home/tawiesn/software/trilinos/Trilinos/packages/panzer/adapters-stk/src/stk_interface/Panzer_STK_Interface.hpp:55:47: fatal error: stk_mesh/base/CoordinateSystems.hpp: No such file or directory
> #include <stk_mesh/base/CoordinateSystems.hpp>
> ^
> compilation terminated.
> In file included from /home/tawiesn/software/trilinos/Trilinos/packages/panzer/adapters-stk/src/Panzer_STKConnManager.hpp:57:0,
> from /home/tawiesn/software/trilinos/Trilinos/packages/panzer/adapters-stk/src/Panzer_STKConnManager.cpp:45:
> /home/tawiesn/software/trilinos/Trilinos/packages/panzer/adapters-stk/src/stk_interface/Panzer_STK_Interface.hpp:55:47: fatal error: stk_mesh/base/CoordinateSystems.hpp: No such file or directory
> #include <stk_mesh/base/CoordinateSystems.hpp>
> ^
> compilation terminated.
> In file included from /home/tawiesn/software/trilinos/Trilinos/packages/panzer/adapters-stk/src/Panzer_STK_SurfaceNodeNormals.cpp:45:0:
> /home/tawiesn/software/trilinos/Trilinos/packages/panzer/adapters-stk/src/stk_interface/Panzer_STK_Interface.hpp:55:47: fatal error: stk_mesh/base/CoordinateSystems.hpp: No such file or directory
> #include <stk_mesh/base/CoordinateSystems.hpp>
> ^
> compilation terminated.
> In file included from /home/tawiesn/software/trilinos/Trilinos/packages/panzer/adapters-stk/src/Panzer_STK_IOClosureModel_Factory_decl.hpp:50:0,
> from /home/tawiesn/software/trilinos/build/do-configure-drekar/packages/panzer/adapters-stk/src/Panzer_STK_IOClosureModel_Factory.hpp:1,
> from /home/tawiesn/software/trilinos/Trilinos/packages/panzer/adapters-stk/src/Panzer_STK_IOClosureModel_Factory.cpp:45:
> /home/tawiesn/software/trilinos/Trilinos/packages/panzer/adapters-stk/src/stk_interface/Panzer_STK_Interface.hpp:55:47: fatal error: stk_mesh/base/CoordinateSystems.hpp: No such file or directory
> #include <stk_mesh/base/CoordinateSystems.hpp>
> ^
> compilation terminated.
> In file included from /home/tawiesn/software/trilinos/Trilinos/packages/panzer/adapters-stk/src/Panzer_STK_WorksetFactory.hpp:50:0,
> from /home/tawiesn/software/trilinos/Trilinos/packages/panzer/adapters-stk/src/Panzer_STK_WorksetFactory.cpp:43:
> /home/tawiesn/software/trilinos/Trilinos/packages/panzer/adapters-stk/src/stk_interface/Panzer_STK_Interface.hpp:55:47: fatal error: stk_mesh/base/CoordinateSystems.hpp: No such file or directory
> #include <stk_mesh/base/CoordinateSystems.hpp>
> ^
> compilation terminated.
https://gitlab.osti.gov/jmwille/Trilinos/-/issues/524Various problems in building trilinos2016-07-26T19:49:56ZJames WillenbringVarious problems in building trilinos*Created by: leonavery*
I'm trying to build Trilinos on an old centos 6 system, on which I have installed, I believe, all prerequisites. I've run into some unexpected behaviors that I don't understand. I configured and generated Makefil...*Created by: leonavery*
I'm trying to build Trilinos on an old centos 6 system, on which I have installed, I believe, all prerequisites. I've run into some unexpected behaviors that I don't understand. I configured and generated Makefiles with cmake-gui, then used "make -k VERBOSE=1 all" for the build, so I could see which exact commands failed.
The first occurred while building Mesquite. I got a mort of errors about undefined references to MPi functions. g++ was used in the build, and when I manually issued the command, replacing g++ with mpic++, it worked. I have MPI_USE_COMPILER_WRAPPERS=ON, and I even manually set the paths to the wrappers in MPI_{C,CXX,Fortran}_COMPILER. So why aren't the wrappers being used? (This one I was able to get around by setting Trilinos_EXTRA_LINK_FLAGS:STRING="-lmpi".)
The second problem is with PyTrilinos, specifcally with the NOX-PETSc interface. During configuration, there are errors from SWIG about several header files not being found. These headers are present in the source distribution at trilinos-12.6.3-Source/packages/nox/src-petsc, but apparently swig is not told to look for headers there. The same problem occurs during compilation. Compilation of several c++ files fails, because they are unable to find the same headers that swig failed to find. g++ is passed a long list of -I flags for this compilation, but there is no -I<path>/trilinos-12.6.3-Source/packages/nox/src-petsc in the list. I don't know enough about cmake to figure out how it produces the list of include directories, but apparently this one is being left out for PyTrilinos. (I'm now trying to work around it with CMAKE_CXX_FLAGS.)
https://gitlab.osti.gov/jmwille/Trilinos/-/issues/44MueLu: Epetra examples won't build unless Tpetra_INST_SERIAL=ON2016-05-18T19:44:36ZJames WillenbringMueLu: Epetra examples won't build unless Tpetra_INST_SERIAL=ON*Created by: mhoemmen*
@trilinos/muelu
When I enable TpetraCore and all forward dependencies (including secondary stable packages), and turn on OpenMP, the build fails in MueLu with link errors, due to "missing" Tpetra Serial instanti...*Created by: mhoemmen*
@trilinos/muelu
When I enable TpetraCore and all forward dependencies (including secondary stable packages), and turn on OpenMP, the build fails in MueLu with link errors, due to "missing" Tpetra Serial instantiations.
https://gitlab.osti.gov/jmwille/Trilinos/-/issues/329Missing ETI for Amesos2Wrapper breaks linking of Ifpack2 and all downstream p...2016-05-02T21:11:11ZJames WillenbringMissing ETI for Amesos2Wrapper breaks linking of Ifpack2 and all downstream packages*Created by: tawiesn*
> This issue appears to be this commit:
>
> https://github.com/trilinos/Trilinos/commit/4312d673edacb4b4aa82d0b0fa47b9738bfd980f#diff-4c11d37d5b774d63c2acd88a73299d88
>
> which introduced BlockRelaxation< row_mat...*Created by: tawiesn*
> This issue appears to be this commit:
>
> https://github.com/trilinos/Trilinos/commit/4312d673edacb4b4aa82d0b0fa47b9738bfd980f#diff-4c11d37d5b774d63c2acd88a73299d88
>
> which introduced BlockRelaxation< row_matrix , SparseContainer < row_matrix , Amesos2Wrapper<row_matrix> > > without ETI of BlockRelaxation on that set of template parameters.
>
> -Eric
https://gitlab.osti.gov/jmwille/Trilinos/-/issues/284Panzer: build and test parallel netcdf 4.4.0 for Drekar stack2016-04-22T02:28:59ZJames WillenbringPanzer: build and test parallel netcdf 4.4.0 for Drekar stack*Created by: rppawlo*
@trilinos/panzer Need to test out new version of netcdf. Notes from @gsjaardema and @bartlettroscoe are below:
Sorry for all the responses, but just for completeness here are the SEACAS responses to the question:...*Created by: rppawlo*
@trilinos/panzer Need to test out new version of netcdf. Notes from @gsjaardema and @bartlettroscoe are below:
Sorry for all the responses, but just for completeness here are the SEACAS responses to the question:
@bartlettroscoe wrote:
3) What TPLs should be enabled? (The SEMS Dev Env assumes blas and lapack are already on the system and provides boost, hdf5, netcdf, parmetis, scotch, qd, superlu, and zlib)
4) Of the TPLs that are enabled, what versions of TPLs should considered standard?
SEACAS uses:
NetCDF -- as new as possible. Recommend 4.4.0 however, 4.3.3.1 or later is possible. Built with --enable-netcdf4, parallel enabled, and recommend --enable-pnetcdf.
HDF5 -- needed if NetCDF has --enable-netcdf4. Recommend 1.8.15 or 1.8.16; The most recent 1.10.X series is not yet supported.
Parallel-NetCDF (PNetCDF) if NetCDF is built with --enable-pnetcdf. Note that this is a different library than NetCDF. Recommend 1.7.0, but 1.6.1 is ok.
MatIO for reading/writing MatLab files. From https://github.com/tbeu/matio.git which is the current active development fork. Version 1.5.3 or later built with support for hdf5-based files.
CGNS -- version 3.3.0 preferred. Built with ENABLE_SCOPIING and ENABLE_HDF5.
ParMetis -- used by IOSS library in a parallel build. Recommend index type set to 64-bit.
At an absolute minimum with no parallel-IO support, can use just the NetCDF library.
https://gitlab.osti.gov/jmwille/Trilinos/-/issues/259ninja and nvcc_wrapper2016-04-01T15:53:10ZJames Willenbringninja and nvcc_wrapper*Created by: bathmatt*
This was emailed about but making a formal bug report.
@bartlettroscoe @crtrott
If one configures trilinos to use ninja and build with cuda/nvcc_wrapper the compile fails with building dependencies.
Not sure wh...*Created by: bathmatt*
This was emailed about but making a formal bug report.
@bartlettroscoe @crtrott
If one configures trilinos to use ninja and build with cuda/nvcc_wrapper the compile fails with building dependencies.
Not sure where the issue is,
/projects/install/rhel6-x86_64/sems/compiler/gcc/4.9.2/openmpi/1.10.1/bin/mpicxx -I. -Ipackages/kokkos/core/src -I/home/mbetten/Trilinos/Trilinos/packages/kokkos/core/src -I/usr/local/cuda/include -std=c++11 -g -O0 -MMD -MT packages/kokkos/core/src/CMakeFiles/kokkoscore.dir/impl/Kokkos_Core.cpp.o -MF packages/kokkos/core/src/CMakeFiles/kokkoscore.dir/impl/Kokkos_Core.cpp.o.d -o packages/kokkos/core/src/CMakeFiles/kokkoscore.dir/impl/Kokkos_Core.cpp.o -c /home/mbetten/Trilinos/Trilinos/packages/kokkos/core/src/impl/Kokkos_Core.cpp
g++: error: packages/kokkos/core/src/CMakeFiles/kokkoscore.dir/impl/Kokkos_Core.cpp.o.d: No such file or directory
[66/4434] Building C object packages/zoltan/src/CMakeFiles/zoltan.dir/coloring/coloring.c.o
https://gitlab.osti.gov/jmwille/Trilinos/-/issues/220Duplicate lib refs if one uses cmake Trilinos_ENABLE_INSTALL_CMAKE_CONFIG_FIL...2016-03-17T14:58:23ZJames WillenbringDuplicate lib refs if one uses cmake Trilinos_ENABLE_INSTALL_CMAKE_CONFIG_FILES:BOOL=ON*Created by: bathmatt*
First this is a low priority ticket, but when I do an install of trilinos and export the cmake stuff, and use it in my application I get a lot of duplicate lib paths, roughly 30 per lib. I've attached the link li...*Created by: bathmatt*
First this is a low priority ticket, but when I do an install of trilinos and export the cmake stuff, and use it in my application I get a lot of duplicate lib paths, roughly 30 per lib. I've attached the link line in the file. If there could be some consolidation that would be great, it is hard to see the tree from the forest.
[link.txt](https://github.com/trilinos/Trilinos/files/176948/link.txt)
https://gitlab.osti.gov/jmwille/Trilinos/-/issues/216Unable to Specify --map-by numa:PE=4 in Trilinos Configuration for MPI Tests2016-03-16T20:06:58ZJames WillenbringUnable to Specify --map-by numa:PE=4 in Trilinos Configuration for MPI Tests*Created by: nmhamster*
@bartlettroscoe I have been specifying `-D MPI_EXEC_POST_NUMPROCS_FLAGS:STRING="--map-by numa:PE=4"` in my Trilinos configuration but it appears that this is being passed to `mpirun` or `mpiexec` as a single argu...*Created by: nmhamster*
@bartlettroscoe I have been specifying `-D MPI_EXEC_POST_NUMPROCS_FLAGS:STRING="--map-by numa:PE=4"` in my Trilinos configuration but it appears that this is being passed to `mpirun` or `mpiexec` as a single argument (i.e. not two arguments).
I'd like to be able to run the Trilinos test in a sensible binding mode for OpenMP on `hansen`, `shiller` and `shepard`.
So far I have backed off to `--bind-to-socket` (a single argument) but it would be better to not have MPI ranks conflicting if we can avoid that (and use the true mapping option).
https://gitlab.osti.gov/jmwille/Trilinos/-/issues/137ShyLU Build Error on KNL with Intel 16.1 (missing -lcamd?)2016-03-08T19:53:32ZJames WillenbringShyLU Build Error on KNL with Intel 16.1 (missing -lcamd?)*Created by: nmhamster*
I am getting the following build error on a KNL build but I cannot see -lcamd in the link line. I don't specify it in the cmake configure but then the configure does successfully complete. Am I missing something ...*Created by: nmhamster*
I am getting the following build error on a KNL build but I cannot see -lcamd in the link line. I don't specify it in the cmake configure but then the configure does successfully complete. Am I missing something obvious or is the build system missing a needed library?
```
[ 95%] Linking CXX executable symbolic_factor_serial.exe
cd /home/sdhammo/git/trilinos-github-repo/build-bddc/packages/shylu/tacho/example && /home/projects/x86-64-haswell/cmake/3.3.2/bin/cmake -E cmake_link_script CMakeFiles/symbolic_factor_serial.dir/link.txt --verbose=1
/home/projects/x86-64-knl/openmpi/1.10.1/intel/16.1.150/bin/mpicxx -O3 -g -xMIC-AVX512 -fopenmp -std=c++11 -qopenmp -L/home/projects/x86-64-knl/numa/2.0.10-static/lib -lnuma CMakeFiles/symbolic_factor_serial.dir/example_symbolic_factor_serial.cpp.o -o symbolic_factor_serial.exe -rdynamic ../src/libshylutacho.a ../../../teuchos/kokkoscomm/src/libteuchoskokkoscomm.a ../../../teuchos/kokkoscompat/src/libteuchoskokkoscompat.a ../../../teuchos/remainder/src/libteuchosremainder.a ../../../teuchos/numerics/src/libteuchosnumerics.a ../../../teuchos/comm/src/libteuchoscomm.a ../../../teuchos/parameterlist/src/libteuchosparameterlist.a ../../../teuchos/core/src/libteuchoscore.a ../../../kokkos/algorithms/src/libkokkosalgorithms.a ../../../kokkos/containers/src/libkokkoscontainers.a ../../../kokkos/core/src/libkokkoscore.a -Wl,-Bstatic -lptscotch -lptscotcherr -lscotch -lscotcherr -Wl,-Bdynamic -mkl -mkl -lhwloc -Wl,-Bstatic -lcholmod -lamd -lcolamd -lsuitesparseconfig -lptscotch -lptscotcherr -lscotch -lscotcherr -Wl,-Bdynamic -lhwloc
CMakeFiles/symbolic_factor_serial.dir/example_symbolic_factor_serial.cpp.o: In function `int Tacho::exampleSymbolicFactor<double, int, int, Kokkos::Serial, void>(std::string, int, int, int, int, int, bool, bool, bool, bool)':
/home/sdhammo/git/trilinos-github-repo/packages/shylu/tacho/src/graph_helper_camd.hpp:85: undefined reference to `camd_defaults'
/home/sdhammo/git/trilinos-github-repo/packages/shylu/tacho/src/graph_helper_camd.hpp:86: undefined reference to `camd_control'
/home/sdhammo/git/trilinos-github-repo/packages/shylu/tacho/src/graph_helper_camd.hpp:93: undefined reference to `camd_order'
make[2]: *** [packages/shylu/tacho/example/symbolic_factor_serial.exe] Error 1
make[2]: Leaving directory `/home/sdhammo/git/trilinos-github-repo/build-bddc'
make[1]: *** [packages/shylu/tacho/example/CMakeFiles/symbolic_factor_serial.dir/all] Error 2
make[1]: Leaving directory `/home/sdhammo/git/trilinos-github-repo/build-bddc'
make: *** [all] Error 2
```