To check that I installed 8.4.1 with Spack
(see https://github.com/dealii/dealii/wiki/deal.II-in-Spack ) on our Centos
7 cluster,
and step-32 links perfectly fine with 8.4.1 and Trilinos 12.10.1.
$ ldd step-32 | grep dealii
libdeal_II.g.so.8.4.1 =>
<BLABLA>/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/dealii-8.4.1-rcitxfsnmzirmrvdgyeau43zj5s33axb/lib/libdeal_II.g.so.8.4.1
(0x00007fd205805000)
$ ldd step-32 | grep trilinos
libtrilinoscouplings.so.12 =>
<BLABLA>/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/trilinos-12.10.1-wg6gih3cwtvbqrb7l54yr7zrsdwdimud/lib/libtrilinoscouplings.so.12
(0x00007f4316047000)
Something is wrong in how you build Trilinos, maybe try using available
package manager (Spack / Candi ).
Regards,
Denis.
On Monday, May 8, 2017 at 6:09:26 PM UTC+2, Tim Miley wrote:
>
> I deleted and recreated the build directory, then ran the cmake again, and
> then did make -j 20 and make install.
>
> No change. The step-32 still fails to compile due to those apparently
> missing trilinos wrappers. I did try an older version of Trilinos this
> time, 11.8.1, just in case there were issues with the newer version.
>
> I may try to download 8.5.0 and see if that works.
>
> On Monday, May 1, 2017 at 8:03:12 AM UTC-7, Tim Miley wrote:
>>
>> Hello.
>>
>>
>> I’m a system administrator trying to build Trilinos for inclusion into
>> the Deal II software. I asked this question on the Trilinos user group,
>> but they told me to ask here.
>>
>>
>> I have built Trilinos 12.10.1 with Deal II 8.4.1.
>>
>>
>>
>> I used these modules to build Trilinos and these cmake options:
>>
>> Modules used:
>>
>> 1) gnu/4.7.2 4) p4est/1.1 7) swig/3.0.12
>>
>> 2) openmpi/2.1.0 5) hdf5/1.8.18 8) cmake/3.4.1
>>
>> 3) superlu/5.1.2 6) parmetis/4.0.2
>>
>>
>>
>> cmake ../trilinos-12.10.1-Source \
>>
>> -DTrilinos_ENABLE_Sacado=ON \
>>
>> -DTrilinos_ENABLE_Stratimikos=ON \
>>
>> -DTrilinos_ENABLE_MueLu=ON \
>>
>> -DCMAKE_BUILD_TYPE=RELEASE \
>>
>> -DBLAS_LIBRARY_NAMES:STRING="blas" \
>>
>> -DLAPACK_LIBRARY_NAMES:STRING="lapack" \
>>
>> -DCMAKE_VERBOSE_MAKEFILE=FALSE \
>>
>> -DTrilinos_VERBOSE_CONFIGURE=FALSE \
>>
>> -DTPL_ENABLE_MPI=ON \
>>
>> -DBUILD_SHARED_LIBS=ON \
>>
>> -DCMAKE_INSTALL_PREFIX=/gpfs3/applications/trilinos/12.10.1/$MODULES_MPINAME/$MODULES_MPIVER/$MODULES_CVEN/$MODULES_CVER
>>
>> \
>>
>> -DTPL_ENABLE_MKL=OFF \
>>
>> -DTPL_ENABLE_BLAS=ON \
>>
>> -DTPL_ENABLE_LAPACK=ON \
>>
>> -DTPL_BLAS_LIBRARIES='blas' \
>>
>> -DTPL_LAPACK_LIBRARIES='lapack' \
>>
>> -DTPL_ENABLE_Matio=OFF \
>>
>> -DTrilinos_ENABLE_CXX11=ON \
>>
>> -DBUILD_SHARED_LIBS=OFF
>>
>>
>>
>> I saw no notable errors, and the software installed without issues. With
>> Deal II, I used this:
>>
>>
>>
>> Module used:
>>
>> 1) gnu/4.7.2 4) p4est/1.1 7) swig/3.0.12
>>
>> 2) openmpi/2.1.0 5) hdf5/1.8.18 8) cmake/3.4.1
>>
>> 3) superlu/5.1.2 6) parmetis/4.0.2 9) trilinos/12.10.1
>>
>>
>>
>> cmake
>> -DCMAKE_INSTALL_PREFIX=/gpfs3/applications/deal_II/8.4.1/$MODULES_MPINAME/$MODULES_MPIVER/$MODULES_CVEN/$MODULES_CVER
>>
>> \
>>
>> -DDEAL_II_WITH_THREADS=OFF \
>>
>> -DDEAL_II_WITH_MPI=ON \
>>
>> -DDEAL_II_WITH_PETSC=OFF \
>>
>> -DDEAL_II_WITH_NETCDF=OFF \
>>
>> -DP4EST_DIR=/gpfs3/applications/p4est/1.1/$MODULES_MPINAME/$MODULES_MPIVER/$MODULES_CVEN/$MODULES_CVER
>>
>> \
>>
>> -DHDF5_DIR=/gpfs3/applications/hdf5/1.8.18/$MODULES_MPINAME/$MODULES_MPIVER/$MODULES_CVEN/$MODULES_CVER
>>
>> \
>>
>> -DTRILINOS_DIR=/gpfs3/applications/trilinos/12.10.1/$MODULES_MPINAME/$MODULES_MPIVER/$MODULES_CVEN/$MODULES_CVER
>>
>> \
>>
>> -DDEAL_II_COMPONENT_PARAMETER_GUI=ON \
>>
>> -DDEAL_II_WITH_P4EST=ON \
>>
>> -DDEAL_II_WITH_TRILINOS=ON \
>>
>> -DTrilinos_INCLUDE_DIRS=/gpfs3/applications/trilinos/12.10.1/$MODULES_MPINAME/$MODULES_MPIVER/$MODULES_CVEN/$MODULES_CVER/include
>>
>> \
>>
>> -DDEAL_II_WITH_CXX11=ON \
>>
>> ../dealii-8.4.1
>>
>>
>>
>> However, I get this kind of error when trying to build one of the test
>> files. Specifically, Step-32.
>>
>>
>>
>> Currently Loaded Modulefiles:
>>
>> 1) gnu/4.7.2 4) deal-ii/8.4.1 7) parmetis/4.0.2
>>
>> 2) openmpi/2.1.0 5) p4est/1.1 8) swig/3.0.12
>>
>> 3) trilinos/12.10.1 6) superlu/5.1.2 9) hdf5/1.8.18
>>
>> [xxx step-32]$ cmake .
>>
>> -- Autopilot invoked
>>
>> ###
>>
>> #
>>
>> # Project step-32 set up with deal.II-8.4.1 found at
>>
>> # /gpfs3/applications/deal_II/8.4.1/openmpi/2.1.0/gnu/4.7.2
>>
>> #
>>
>> # CMAKE_BUILD_TYPE: Debug
>>
>> #
>>
>> # You can now run…
>>
>> -- Configuring done
>>
>> -- Generating done
>>
>> -- Build files have been written to: /home/xxx/step-32
>>
>>
>>
>> [xxx step-32]$ make
>>
>> Scanning dependencies of target step-32
>>
>> Linking CXX executable step-32
>>
>> CMakeFiles/step-32.dir/step-32.cc.o: In function
>> `Step32::BoussinesqFlowProblem<
>>
>> 2>::project_temperature_field()':
>>
>> /home/xxx/step-32/step-32.cc:1768: undefined reference to `void
>> dealii::ConstraintMatrix::distribute<dealii::TrilinosWrappers::MPI::Vector>(dealii::TrilinosWrappers::MPI::Vector&)
>>
>> const'
>>
>> CMakeFiles/step-32.dir/step-32.cc.o: In function
>> `dealii::Solver<dealii::TrilinosWrappers::MPI::BlockVector>::~Solver()':
>>
>> /gpfs3/applications/deal_II/8.4.1/openmpi/2.1.0/gnu/4.7.2/include/deal.II/lac/solver.h:325:
>>
>> undefined reference to
>> `dealii::GrowingVectorMemory<dealii::TrilinosWrappers::MPI::BlockVector>::~GrowingVectorMemory()'
>>
>> /gpfs3/applications/deal_II/8.4.1/openmpi/2.1.0/gnu/4.7.2/include/deal.II/lac/solver.h:325:
>>
>> undefined reference to
>> `dealii::GrowingVectorMemory<dealii::TrilinosWrappers::MPI::BlockVector>::~GrowingVectorMemory()'
>>
>> CMakeFiles/step-32.dir/step-32.cc.o: In function
>> `Step32::BoussinesqFlowProblem<2>::solve()':
>>
>> /home/xxx/step-32/step-32.cc:3034: undefined reference to `void
>> dealii::ConstraintMatrix::distribute<dealii::TrilinosWrappers::MPI::BlockVector>(dealii::TrilinosWrappers::MPI::BlockVector&)
>>
>> const'
>>
>> /home/xxx/step-32/step-32.cc:3100: undefined reference to `void
>> dealii::ConstraintMatrix::distribute<dealii::TrilinosWrappers::MPI::Vector>(dealii::TrilinosWrappers::MPI::Vector&)
>>
>> const'
>>
>>
>>
>> This is only an excerpt from a long list of errors that look similar.
>> So, it looks like Trilinos libraries are missing some sort of C++ symbols.
>>
>>
>>
>> The module looks like this:
>>
>> set name trilinos
>>
>> set ver 12.10.1
>>
>> set root /gpfs3/applications/trilinos
>>
>> set mpiroot
>> $root/$ver/$env(MODULES_MPINAME)/$env(MODULES_MPIVER)/$env(MODULES_CVEN)/$env(MODULES_CVER)
>>
>> prepend-path -d ":" LD_LIBRARY_PATH "${mpiroot}/lib"
>>
>> prepend-path -d ":" INCLUDE "${mpiroot}/include"
>>
>>
>>
>> setenv TRILINOS_DIR $mpiroot
>>
>>
>>
>> Has anyone seen this problem before? I have no idea how to fix the issue.
>>
>>
>>
>
--
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