Dear deal.II developers,
I am glad about the release of deal.II 7.1. Thank you for the endless
contributions!
Today I am trying to build svn trunk deal.II (r*24610*, 7.2.pre) with system
*umfpack*, *petsc* and *trilinos*,
It went okay when I linked deal.II with umfpack (default is with amd not
metis) and petsc by
./configure --with-umfpack-include=/usr/include/suitesparse
--with-umfpack-libs=/usr/lib --with-petsc=/usr/lib/petscdir/3.1
--with-petsc-arch=linux-gnu-c-opt --enable-mpi --disable-threads
When I tried to link with extra trilinos by
./configure --with-umfpack-include=/usr/include/suitesparse
--with-umfpack-libs=/usr/lib --with-petsc=/usr/lib/petscdir/3.1
--with-petsc-arch=linux-gnu-c-opt --enable-mpi --disable-threads
--with-trilinos-include=/usr/include/trilinos
--with-trilinos-libs=/usr/lib #CC='mpicc
-std=c99' CXX='mpicxx -std=c++0x'
it failed with error
"checking for amd_info in -lamd... no
configure: error: installation of AMD could not be determined"
I have modified the Sacado_cmath.hpp according to FAQ by
sudo vim /usr/include/trilinos/Sacado_cmath.hpp
#ifndef _GLIBCXX_USE_C99_MATH
namespace std {
...
}#endif
Attached is the configure log with the error.
This error should not exist since the compile with umfpack (with amd)
has been okay with dealii.
Or do I have to build trilinos lower version myself (v9 or v10.0 for instance)?
I appreciate if you can help to clarify.
Sincerely,
Jichao
*Jichao Yin*
jyin1@sid-laptop:~/svn/deal.II$ ./configure --with-umfpack-include=/usr/include/suitesparse --with-umfpack-libs=/usr/lib --with-petsc=/usr/lib/petscdir/3.1 --with-petsc-arch=linux-gnu-c-opt --enable-mpi --disable-threads --with-trilinos-include=/usr/include/trilinos --with-trilinos-libs=/usr/lib #CC='mpicc -std=c99' CXX='mpicxx -std=c++0x'
Configuring deal.II version 7.2.pre
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
---------------- configuring C/C++ compilers ----------------
checking whether to explicitly use MPI... yes
checking for MPI C++ compiler... mpiCC
checking for MPI C compiler... mpicc
checking for gcc... mpicc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether mpicc accepts -g... yes
checking for mpicc option to accept ISO C89... none needed
checking for mpicc... /usr/local/bin/mpicc
checking whether we are using the GNU C++ compiler... yes
checking whether mpiCC accepts -g... yes
checking for mpiCC... /usr/local/bin/mpiCC
C++ compiler is gcc4.6 (subversion gcc4.6.1)
checking if the compiler is built for MPI... yes
checking whether compiler has a flag to support C++1x... yes
checking for std::array... yes
checking for std::condition_variable... yes
checking for std::function and std::bind... yes
checking for std::bind works with rvalues... yes
checking for std::shared_ptr... yes
checking for std::thread... yes
checking whether std::thread actually works... yes
checking for std::mutex... yes
checking for std::tuple... yes
checking whether C++1x support is complete enough... yes
checking for auto typed variables... yes
checking for range-based for... no
checking whether qualifiers in return types lead to a warning... no
checking whether the assembler understands -Wa,--compress-debug-sections... yes
checking for std::advance warning... no
checking whether MPI headers have unused parameters... no
checking whether -ggdb works... yes
C compiler is gcc4.6
checking whether AssertThrow works with debug flags... yes
checking whether AssertThrow works with optimized flags... yes
checking for local computed template typedef bug... no
checking for partially specialized template access control bug... no
checking for template member operator instantiation bug... no
checking for explicit destructor call bug... no
checking for 1st template friend in namespace bug... no
checking for 2nd template friend in namespace bug... no
checking for template specialization friend bug... no
checking for bug with implementing pure functions... yes. using workaround
checking for template template typedef bug... no
checking for address of template template function bug... no
checking for nested classes are implicit friends bug... no
checking for nested template class friends bug... yes. using workaround
checking for member variable specialization bug... no
checking for member array specialization bug... no
checking for template member function specialization bug... no
checking for long double optimization bug... no
checking for anonymous namespace and name mangling bug... no
checking for anonymous namespace and weak linkage bug... no
checking for bogus warning with anonymous namespaces... no
checking for SFINAE bug... no
checking for template operator disambiguation bug... no
checking for array assignment in conditional bug... no
checking for array argument bug... no
checking for explicit template constructor bug... no
checking for const member deduction bug... no
checking for warning bug with type qualifiers... no
checking for problem with -Wsynth and std::complex... no
checking for problem with -Wctor-dtor-privacy... no
checking whether vector iterators are plain pointers... no
checking for __PRETTY_FUNCTION__... yes
checking for std::iterator class... yes
checking for std::i/ostringstream classes... yes
checking for std::numeric_limits classes... yes
checking for <ostream> header... yes
checking for <iosfwd> header... yes
checking for __builtin_expect... yes
checking for __verbose_terminate_handler... yes
checking for glibc-like stacktrace information... yes
checking whether compiler accepts -rdynamic... yes
checking for libstdc++ demangler... yes
checking for minimal std::vector<T> capacity... 1
checking for minimal std::vector<bool> capacity... 64
checking for exception specifications on abort()... none
checking whether getrusage is properly declared... yes
checking whether isnan is declared with debug flags... yes
checking whether isnan is declared with optimized flags... yes
checking for std::isfinite... yes
checking for rand_r... no
checking for quad vs. quad_t define... no
checking for definitions of error codes in errno.h... yes
checking for gethostname... yes
checking for getpid... yes
checking how to run the C++ preprocessor... /usr/local/bin/mpiCC -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for sys/syscall.h... yes
checking for sys/times.h... yes
checking for times... yes
checking for bad socket functions/FPU interaction... no
---------------- configuring F77 compilers ------------------
checking for gfortran... /usr/bin/gfortran
F77 compiler is gcc4.6
checking for e_wsfe in -lg2c... no
checking for _gfortran_allocate in -lgfortran... no
checking for _gfortran_st_write_done in -lgfortran... yes
---------------- configuring shared/static libs -------------
checking whether compiler understands option -Wl,-soname... yes
checking whether compiler understands option -Wl,-dynamic,-install_name... no
checking whether compiler understands option -Wl,-rpath... yes
checking for ar... ar
checking for ar... /usr/bin/ar
checking for ranlib... ranlib
checking for ranlib... /usr/bin/ranlib
---------------- configuring optional features --------------
---------------- configuring additional libs ----------------
checking boost/shared_ptr.hpp usability... yes
checking boost/shared_ptr.hpp presence... yes
checking for boost/shared_ptr.hpp... yes
checking boost/type_traits.hpp usability... yes
checking boost/type_traits.hpp presence... yes
checking for boost/type_traits.hpp... yes
checking boost/tuple/tuple.hpp usability... yes
checking boost/tuple/tuple.hpp presence... yes
checking for boost/tuple/tuple.hpp... yes
checking for boost::shared_ptr assignment operator= template buglet... no
checking for boost::bind compiler internal error... no
checking for boost::graph compiler internal error... no
checking for PETSc library directory... /usr/lib/petscdir/3.1
checking for PETSc version... 3.1.0
checking for PETSc library architecture... linux-gnu-c-opt
checking for PETSc libmpiuni library... not found
checking for consistency of PETSc and deal.II MPI settings... yes
checking for PETSc scalar complex... no
checking for SLEPc include directory... not found
checking for Trilinos directory... not found
checking for Trilinos header directory... /usr/include/trilinos
checking for Trilinos library directory... /usr/lib
checking for Trilinos version... 10.4.0
checking Epetra_config.h presence... yes
checking for consistency of Trilinos and deal.II MPI settings... yes
checking whether Trilinos uses shared libraries... yes
checking whether Trilinos uses static libraries... no
checking for the set of Trilinos libraries... trilinos_msqutil trilinos_mesquite trilinos_pytrilinos trilinos_ctrilinos trilinos_moochothyra trilinos_moocho trilinos_rythmos trilinos_moertel trilinos_locathyra trilinos_locaepetra trilinos_loca trilinos_noxthyra trilinos_noxepetra trilinos_nox trilinos_intrepid trilinos_ModeLaplace trilinos_anasaziepetra trilinos_anasazi trilinos_fei_test_utils trilinos_fei_trilinos trilinos_fei_base trilinos_stratimikos trilinos_stratimikosbelos trilinos_stratimikosaztecoo trilinos_stratimikosamesos trilinos_stratimikosml trilinos_stratimikosifpack trilinos_tifpack trilinos_belostpetra trilinos_belosepetra trilinos_belos trilinos_ml trilinos_komplex trilinos_ifpack trilinos_pamgen_extras trilinos_pamgen trilinos_amesos trilinos_galeri trilinos_aztecoo trilinos_dpliris trilinos_isorropia trilinos_optipack trilinos_thyratpetra trilinos_thyraepetraext trilinos_thyraepetra trilinos_thyra trilinos_epetraext trilinos_tpetrainout trilinos_tpetra trilinos_triutils trilinos_globipack trilinos_shards trilinos_zoltan trilinos_epetra trilinos_kokkoslinalg trilinos_kokkosnodeapi trilinos_kokkos trilinos_rtop trilinos_sacado trilinos_tpi trilinos_teuchos
checking whether we can use -Wno-unused to suppress Trilinos warnings... yes
checking whether we can use -Wno-overloaded-virtual to suppress Trilinos warnings... yes
checking whether we can use -Wno-extra to suppress Trilinos warnings... yes
checking whether Sacado_cmath.hpp is C++11 compatible... yes
checking Amesos.h usability... yes
checking Amesos.h presence... yes
checking for Amesos.h... yes
checking Epetra_CrsGraph.h usability... yes
checking Epetra_CrsGraph.h presence... yes
checking for Epetra_CrsGraph.h... yes
checking Epetra_CrsMatrix.h usability... yes
checking Epetra_CrsMatrix.h presence... yes
checking for Epetra_CrsMatrix.h... yes
checking Epetra_Import.h usability... yes
checking Epetra_Import.h presence... yes
checking for Epetra_Import.h... yes
checking Epetra_LinearProblem.h usability... yes
checking Epetra_LinearProblem.h presence... yes
checking for Epetra_LinearProblem.h... yes
checking Epetra_Map.h usability... yes
checking Epetra_Map.h presence... yes
checking for Epetra_Map.h... yes
checking Epetra_MultiVector.h usability... yes
checking Epetra_MultiVector.h presence... yes
checking for Epetra_MultiVector.h... yes
checking Epetra_Operator.h usability... yes
checking Epetra_Operator.h presence... yes
checking for Epetra_Operator.h... yes
checking Epetra_SerialComm.h usability... yes
checking Epetra_SerialComm.h presence... yes
checking for Epetra_SerialComm.h... yes
checking Epetra_Vector.h usability... yes
checking Epetra_Vector.h presence... yes
checking for Epetra_Vector.h... yes
checking Ifpack.h usability... yes
checking Ifpack.h presence... yes
checking for Ifpack.h... yes
checking ml_MultiLevelPreconditioner.h usability... yes
checking ml_MultiLevelPreconditioner.h presence... yes
checking for ml_MultiLevelPreconditioner.h... yes
checking AztecOO.h usability... yes
checking AztecOO.h presence... yes
checking for AztecOO.h... yes
checking AztecOO_Operator.h usability... yes
checking AztecOO_Operator.h presence... yes
checking for AztecOO_Operator.h... yes
checking Sacado.hpp usability... yes
checking Sacado.hpp presence... yes
checking for Sacado.hpp... yes
checking Teuchos_ParameterList.hpp usability... yes
checking Teuchos_ParameterList.hpp presence... yes
checking for Teuchos_ParameterList.hpp... yes
checking Teuchos_RCP.hpp usability... yes
checking Teuchos_RCP.hpp presence... yes
checking for Teuchos_RCP.hpp... yes
checking Teuchos_RefCountPtr.hpp usability... yes
checking Teuchos_RefCountPtr.hpp presence... yes
checking for Teuchos_RefCountPtr.hpp... yes
checking for ARPACK library directory... no
checking for MUMPS library directory... no
checking whether p4est will be used... no
checking for HSL subroutines... none found
checking for crc32 in -lz... no
checking whether byte ordering is bigendian... no
checking for /opt/tecplot/360/lib/tecio.a... no
checking for /opt/tecplot/360/include/TECIO.h... no
checking netcdfcpp.h usability... yes
checking netcdfcpp.h presence... yes
checking for netcdfcpp.h... yes
checking for nc_open in -lnetcdf... no
checking umfpack.h usability... yes
checking umfpack.h presence... yes
checking for umfpack.h... yes
checking amd.h usability... yes
checking amd.h presence... yes
checking for amd.h... yes
checking UFconfig.h usability... yes
checking UFconfig.h presence... yes
checking for UFconfig.h... yes
checking for amd_info in -lamd... no
configure: error: installation of AMD could not be determined
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