[Trilinos-Users] [11.2.1] undefined symbols w Amesos_CSparse

Denis Davydov davydden at gmail.com
Fri Jan 9 15:58:31 MST 2015


Dear all, 

The following could have been already discussed (if so please excuse me),
but i think it’s better to repeat it rather than miss the issue. 
CSparse is provided within SuiteSparse 4.2.1.

p.s. it’s good to know that mail archives will be available to public soon, so that one could check for such errors before posting to the user list. 

Regards,
Denis

=== linking error ===

Linking CXX shared library libamesos.dylib
cd /tmp/trilinos-gRxVEy/trilinos-11.12.1-Source/build/packages/amesos/src && /usr/local/Cellar/cmake/3.1.0/bin/cmake -E cmake_link_script CMakeFiles/amesos.dir/link.txt --verbose=1
/usr/local/bin/mpicxx  -O3 -DNDEBUG -dynamiclib -Wl,-headerpad_max_install_names -compatibility_version 11.0.0 -current_version 11.12.1 -o libamesos.11.12.1.dylib -install_name /tmp/trilinos-gRxVEy/trilinos-11.12.1-Source/build/packages/amesos/src/libamesos.11.dylib CMakeFiles/amesos.dir/Amesos_Status.cpp.o CMakeFiles/amesos.dir/Amesos_Control.cpp.o CMakeFiles/amesos.dir/Amesos_Support.cpp.o CMakeFiles/amesos.dir/Amesos_Umfpack.cpp.o CMakeFiles/amesos.dir/Amesos_Mumps.cpp.o CMakeFiles/amesos.dir/Amesos_CSparse.cpp.o CMakeFiles/amesos.dir/SuiteSparse/AMD/Source/amesos_amd_1.c.o CMakeFiles/amesos.dir/SuiteSparse/AMD/Source/amesos_amd_2.c.o CMakeFiles/amesos.dir/SuiteSparse/AMD/Source/amesos_amd_aat.c.o CMakeFiles/amesos.dir/SuiteSparse/AMD/Source/amesos_amd_control.c.o CMakeFiles/amesos.dir/SuiteSparse/AMD/Source/amesos_amd_defaults.c.o CMakeFiles/amesos.dir/SuiteSparse/AMD/Source/amesos_amd_dump.c.o CMakeFiles/amesos.dir/SuiteSparse/AMD/Source/amesos_amd_global.c.o CMakeFiles/amesos.dir/SuiteSparse/AMD/Source/amesos_amd_info.c.o CMakeFiles/amesos.dir/SuiteSparse/AMD/Source/amesos_amd_order.c.o CMakeFiles/amesos.dir/SuiteSparse/AMD/Source/amesos_amd_postorder.c.o CMakeFiles/amesos.dir/SuiteSparse/AMD/Source/amesos_amd_post_tree.c.o CMakeFiles/amesos.dir/SuiteSparse/AMD/Source/amesos_amd_preprocess.c.o CMakeFiles/amesos.dir/SuiteSparse/AMD/Source/amesos_amd_valid.c.o CMakeFiles/amesos.dir/SuiteSparse/AMD/Source/amesos_amd_l1.c.o CMakeFiles/amesos.dir/SuiteSparse/AMD/Source/amesos_amd_l2.c.o CMakeFiles/amesos.dir/SuiteSparse/AMD/Source/amesos_amd_l_aat.c.o CMakeFiles/amesos.dir/SuiteSparse/AMD/Source/amesos_amd_l_order.c.o CMakeFiles/amesos.dir/SuiteSparse/AMD/Source/amesos_amd_l_postorder.c.o CMakeFiles/amesos.dir/SuiteSparse/AMD/Source/amesos_amd_l_post_tree.c.o CMakeFiles/amesos.dir/SuiteSparse/AMD/Source/amesos_amd_l_preprocess.c.o CMakeFiles/amesos.dir/SuiteSparse/AMD/Source/amesos_amd_l_valid.c.o CMakeFiles/amesos.dir/SuiteSparse/COLAMD/Source/amesos_colamd.c.o CMakeFiles/amesos.dir/SuiteSparse/COLAMD/Source/amesos_colamd_l.c.o CMakeFiles/amesos.dir/SuiteSparse/COLAMD/Source/amesos_colamd_global.c.o CMakeFiles/amesos.dir/SuiteSparse/CHOLMOD/Core/amesos_cholmod_common.c.o CMakeFiles/amesos.dir/SuiteSparse/CHOLMOD/Core/amesos_cholmod_complex.c.o CMakeFiles/amesos.dir/SuiteSparse/CHOLMOD/Core/amesos_cholmod_error.c.o CMakeFiles/amesos.dir/SuiteSparse/CHOLMOD/Core/amesos_cholmod_memory.c.o CMakeFiles/amesos.dir/SuiteSparse/CHOLMOD/Core/amesos_cholmod_sparse.c.o CMakeFiles/amesos.dir/SuiteSparse/CHOLMOD/Core/amesos_cholmod_transpose.c.o CMakeFiles/amesos.dir/SuiteSparse/CAMD/Source/amesos_camd_2.c.o CMakeFiles/amesos.dir/SuiteSparse/CAMD/Source/amesos_camd_postorder.c.o CMakeFiles/amesos.dir/Amesos_Klu.cpp.o CMakeFiles/amesos.dir/SuiteSparse/KLU/Source/amesos_klu_analyze.c.o CMakeFiles/amesos.dir/SuiteSparse/KLU/Source/amesos_klu_analyze_given.c.o CMakeFiles/amesos.dir/SuiteSparse/KLU/Source/amesos_klu_impl.c.o CMakeFiles/amesos.dir/SuiteSparse/KLU/Source/amesos_klu_defaults.c.o CMakeFiles/amesos.dir/SuiteSparse/KLU/Source/amesos_klu_diagnostics.c.o CMakeFiles/amesos.dir/SuiteSparse/KLU/Source/amesos_klu_dump.c.o CMakeFiles/amesos.dir/SuiteSparse/KLU/Source/amesos_klu_extract.c.o CMakeFiles/amesos.dir/SuiteSparse/KLU/Source/amesos_klu_factor.c.o CMakeFiles/amesos.dir/SuiteSparse/KLU/Source/amesos_klu_free_numeric.c.o CMakeFiles/amesos.dir/SuiteSparse/KLU/Source/amesos_klu_free_symbolic.c.o CMakeFiles/amesos.dir/SuiteSparse/KLU/Source/amesos_klu_kernel.c.o CMakeFiles/amesos.dir/SuiteSparse/KLU/Source/amesos_klu_memory.c.o CMakeFiles/amesos.dir/SuiteSparse/KLU/Source/amesos_klu_refactor.c.o CMakeFiles/amesos.dir/SuiteSparse/KLU/Source/amesos_klu_scale.c.o CMakeFiles/amesos.dir/SuiteSparse/KLU/Source/amesos_klu_solve.c.o CMakeFiles/amesos.dir/SuiteSparse/KLU/Source/amesos_klu_sort.c.o CMakeFiles/amesos.dir/SuiteSparse/KLU/Source/amesos_klu_tsolve.c.o CMakeFiles/amesos.dir/SuiteSparse/BTF/Source/amesos_btf_order.c.o CMakeFiles/amesos.dir/SuiteSparse/BTF/Source/amesos_btf_maxtrans.c.o CMakeFiles/amesos.dir/SuiteSparse/BTF/Source/amesos_btf_strongcomp.c.o CMakeFiles/amesos.dir/SuiteSparse/BTF/Source/amesos_btf_l_order.c.o CMakeFiles/amesos.dir/SuiteSparse/BTF/Source/amesos_btf_l_maxtrans.c.o CMakeFiles/amesos.dir/SuiteSparse/BTF/Source/amesos_btf_l_strongcomp.c.o CMakeFiles/amesos.dir/Amesos_Scalapack.cpp.o CMakeFiles/amesos.dir/Amesos.cpp.o CMakeFiles/amesos.dir/Amesos_Superlu.cpp.o CMakeFiles/amesos.dir/CrsMatrixTranspose.cpp.o CMakeFiles/amesos.dir/Amesos_Lapack.cpp.o ../../epetraext/src/libepetraext.11.12.1.dylib /usr/local/lib/libdmumps.dylib /usr/local/lib/libpord.dylib /usr/local/lib/libscalapack.dylib /usr/local/lib/libcxsparse.a /usr/local/lib/libamd.a /usr/local/lib/libcolamd.a /usr/local/lib/libsuitesparseconfig.a /usr/local/lib/libumfpack.a /usr/local/lib/libamd.a /usr/local/lib/libcolamd.a /usr/local/lib/libcholmod.a /usr/local/lib/libsuitesparseconfig.a /usr/local/lib/libsuperlu.a /usr/local/lib/libparmetis.a /usr/local/lib/libmetis.dylib ../../triutils/src/libtriutils.11.12.1.dylib ../../epetra/src/libepetra.11.12.1.dylib ../../teuchos/remainder/src/libteuchosremainder.11.12.1.dylib ../../teuchos/numerics/src/libteuchosnumerics.11.12.1.dylib ../../teuchos/comm/src/libteuchoscomm.11.12.1.dylib ../../teuchos/parameterlist/src/libteuchosparameterlist.11.12.1.dylib ../../teuchos/core/src/libteuchoscore.11.12.1.dylib /usr/lib/liblapack.dylib /usr/lib/libblas.dylib /usr/local/lib/libHYPRE.a /usr/local/lib/libhdf5.dylib /usr/lib/libz.dylib /usr/local/lib/libamd.a /usr/local/lib/libumfpack.a /usr/local/lib/libamd.a /usr/local/lib/libumfpack.a /usr/local/lib/libcolamd.a /usr/local/lib/libcholmod.a /usr/local/lib/libsuitesparseconfig.a 
Undefined symbols for architecture x86_64:
  "Amesos_CSparse::Amesos_CSparse(Epetra_LinearProblem const&)", referenced from:
      Amesos::Create(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, Epetra_LinearProblem const&) in Amesos.cpp.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)

== cmake command == 

cmake
..
-DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/trilinos/11.12.1
-DCMAKE_BUILD_TYPE=Release
-DBUILD_SHARED_LIBS=ON
-DTPL_ENABLE_BLAS=ON
-DTPL_ENABLE_LAPACK=ON
-DTPL_ENABLE_Zlib:BOOL=ON
-DTrilinos_ENABLE_ALL_PACKAGES=ON
-DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES=ON
-DTrilinos_ENABLE_TESTS:BOOL=ON
-DTrilinos_ENABLE_EXAMPLES:BOOL=ON
-DTrilinos_VERBOSE_CONFIGURE:BOOL=OFF
-DTrilinos_WARNINGS_AS_ERRORS_FLAGS=""
-DSacado_ENABLE_TESTS=OFF
-DEpetraExt_ENABLE_TESTS=OFF
-DTPL_ENABLE_MPI:BOOL=ON
-DTrilinos_ENABLE_OpenMP:BOOL=OFF
-DTrilinos_ENABLE_CXX11:BOOL=OFF
-DTrilinos_ENABLE_ShyLU:BOOL=OFF
-DTrilinos_ENABLE_Teko:BOOL=OFF
-DTPL_ENABLE_Boost:BOOL=ON
-DTPL_ENABLE_Scotch:BOOL=OFF
-DTPL_ENABLE_Netcdf:BOOL=ON
-DTPL_ENABLE_ADOLC:BOOL=OFF
-DTPL_ENABLE_AMD:BOOL=ON
-DTPL_ENABLE_CSparse:BOOL=ON
-DCSparse_LIBRARY_NAMES=cxsparse;amd;colamd;suitesparseconfig
-DTPL_ENABLE_Cholmod:BOOL=ON
-DTPL_ENABLE_UMFPACK:BOOL=ON
-DUMFPACK_LIBRARY_NAMES=umfpack;amd;colamd;cholmod;suitesparseconfig
-DTPL_ENABLE_CppUnit:BOOL=OFF
-DTPL_ENABLE_Eigen:BOOL=OFF
-DTPL_ENABLE_GLPK:BOOL=OFF
-DTPL_ENABLE_HDF5:BOOL=ON
-DTPL_ENABLE_HWLOC:BOOL=OFF
-DTPL_ENABLE_HYPRE:BOOL=ON
-DTPL_ENABLE_METIS:BOOL=ON
-DTPL_ENABLE_MUMPS:BOOL=ON
-DTPL_ENABLE_PETSC:BOOL=OFF
-DTPL_ENABLE_ParMETIS:BOOL=ON
-DTPL_ENABLE_SCALAPACK:BOOL=ON
-DTPL_ENABLE_SuperLU:BOOL=ON
-DSuperLU_INCLUDE_DIRS=/usr/local/Cellar/superlu/4.3_1/include/superlu
-DTPL_ENABLE_SuperLUDist:BOOL=OFF
-DTPL_ENABLE_TBB:BOOL=ON
-DTPL_ENABLE_X11:BOOL=OFF
-DTrilinos_ENABLE_Fortran=ON
-DTrilinos_ENABLE_PyTrilinos:BOOL=OFF


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