[Trilinos-Users] Error with --enable-epetraext-hdf5

ryuta suzu0037 at aem.umn.edu
Fri Aug 3 16:16:02 MDT 2007


../trilinos-${VERSION}/configure \
    --prefix=${HOME}/Development \
    --includedir=${HOME}/Development/include/trilinos \
    --enable-threads \
    --enable-mpi \
    --enable-tests \
    --enable-examples \
    --disable-python \
    --with-mpi-compilers=/usr/local/bin \
    --with-trilinos3pldir=${HOME}/Development \
    --with-ldflags="-L${HOME}/Development/lib" \
    --with-incdirs="-I${HOME}/Development/include" \
    --with-libs="-lmetis -lumfpack -lamd -lhdf5" \
    --with-zoltan \
    --disable-default-packages \
    --enable-performance \
    --enable-valgrind \
    --enable-coverage \
    --enable-latex \
    --enable-amesos \
    --enable-amesos-galeri \
    --enable-amesos-umfpack \
    --enable-anasazi \
    --enable-aztecoo \
    --enable-aztecoo-teuchos \
    --enable-aztecoo-ifpack \
    --enable-aztecoo-epetraext \
    --enable-epetra \
    --enable-epetraext \
    --enable-epetraext-btf \
    --enable-epetraext-experimental \
    --enable-epetraext-hdf5 \
    --enable-epetraext-triutils \
    --enable-epetraext-zoltan \
    --enable-didasko-epetra \
    --enable-didasko-epetraext \
    --enable-didasko-ifpack \
    --enable-didasko-teuchos \
    --enable-didasko-triutils \
    --enable-didasko-aztecoo \
    --enable-didasko-examples \
    --enable-didasko-tests \
    --enable-galeri \
    --enable-ifpack \
    --enable-ifpack-galeri \
    --enable-ifpack-teuchos \
    --enable-ifpack-amesos \
    --enable-ifpack-epetraext \
    --enable-ifpack-metis \
    --enable-isorropia \
    --enable-isorropia-epetra \
    --enable-isorropia-zoltan \
    --enable-isorropia-epetraext \
    --enable-isorropia-examples \
    --enable-isorropia-tests \
    --enable-kokkos \
    --enable-triutils \
    --enable-teuchos

Michael A Heroux wrote:
> Ryuta,
>
> Please send your configure invocation command.  In other words, what 
> arguments did you pass to configure?
>
> Mike
>
>
> On 8/3/07 12:30 PM, "ryuta" <suzu0037 at aem.umn.edu> wrote:
>
>     Hi,
>
>     I've been able to build most trilinos packages without problem
>     until I added HDF5 support for EpetraExt.
>
>     The problem occurs when building an example for HDF5-IO,
>     specifically at link stage.
>
>     My guess is that libepetraext is not built correctly and the
>     linker gets confused to resolve the symbols.
>     gcc-4.2.1 is used and I suspect the compiler is a culprit.
>
>
>     The following is the error message from linker:
>
>     /usr/local/bin/mpicxx  -g -O2 -L/home/ryuta/Development/lib  -o
>     HDF5_IO.exe  HDF5_IO-HDF5_IO.o -L/home/ryuta/Development/lib
>     -L/home/ryuta/Development/src/trilinos-7.0.9-build/packages/epetraext/src
>     -lepetraext -L/home/ryuta/Development/lib
>     -L/home/ryuta/Development/src/trilinos-7.0.9-build/packages/epetra/src
>     -lepetra -llapack -lblas -lmetis -lumfpack -lamd -lhdf5
>      -L/home/ryuta/Development/lib -L/usr/local/lib -L.
>     -L/usr/lib/gcc/i686-pc-linux-gnu/4.2.1
>     -L/usr/lib/gcc/i686-pc-linux-gnu/4.2.1/../../.. -lmetis -lumfpack
>     -lamd -lhdf5 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -lnsl
>     -lutil -lgfortranbegin -lgfortran -lm -lgcc_s -lpthread
>     -L/home/ryuta/Development/lib
>     -L/home/ryuta/Development/src/trilinos-7.0.9-build/packages/triutils/src
>     -ltriutils -L/home/ryuta/Development/lib
>     -L/home/ryuta/Development/src/trilinos-7.0.9-build/packages/epetra/src
>     -lepetra -llapack -lblas -lmetis -lumfpack -lamd -lhdf5
>      -L/home/ryuta/Development/lib -L/usr/local/lib -L.
>     -L/usr/lib/gcc/i686-pc-linux-gnu/4.2.1
>     -L/usr/lib/gcc/i686-pc-linux-gnu/4.2.1/../../.. -lmetis -lumfpack
>     -lamd -lhdf5 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -lnsl
>     -lutil -lgfortranbegin -lgfortran -lm -lgcc_s -lpthread  -lblas
>     -lmetis -lumfpack -lamd -lhdf5   -L/home/ryuta/Development/lib
>     -L/usr/local/lib -L. -L/usr/lib/gcc/i686-pc-linux-gnu/4.2.1
>     -L/usr/lib/gcc/i686-pc-linux-gnu/4.2.1/../../.. -lmetis -lumfpack
>     -lamd -lhdf5 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -lnsl
>     -lutil -lgfortranbegin -lgfortran -lm -lgcc_s -lpthread
>     -L/home/ryuta/Development/lib
>     -L/home/ryuta/Development/src/trilinos-7.0.9-build/packages/teuchos/src
>     -lteuchos -lmetis -lumfpack -lamd -lhdf5  -llapack -lblas
>     -L/home/ryuta/Development/lib -L/usr/local/lib -L.
>     -L/usr/lib/gcc/i686-pc-linux-gnu/4.2.1
>     -L/usr/lib/gcc/i686-pc-linux-gnu/4.2.1/../../.. -lmetis -lumfpack
>     -lamd -lhdf5 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -lnsl
>     -lutil -lgfortranbegin -lgfortran -lm -lgcc_s -lpthread -lzoltan
>     -lparmetis -lmetis -lmetis -lumfpack -lamd -lhdf5  -llapack -lblas
>     -L/home/ryuta/Development/lib -L/usr/local/lib -L.
>     -L/usr/lib/gcc/i686-pc-linux-gnu/4.2.1
>     -L/usr/lib/gcc/i686-pc-linux-gnu/4.2.1/../../.. -lmetis -lumfpack
>     -lamd -lhdf5 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -lnsl
>     -lutil -lgfortranbegin -lgfortran -lm -lgcc_s -lpthread -lzoltan
>     -lparmetis -lmetis -lmetis -lumfpack -lamd -lhdf5
>     HDF5_IO-HDF5_IO.o: In function `main':
>     ../../../../../trilinos-7.0.9/packages/epetraext/example/inout/HDF5_IO.cpp:57:
>     undefined reference to `EpetraExt::HDF5::HDF5(Epetra_Comm const&)'
>     ../../../../../trilinos-7.0.9/packages/epetraext/example/inout/HDF5_IO.cpp:60:
>     undefined reference to
>     `EpetraExt::HDF5::Create(std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> >)'
>     ../../../../../trilinos-7.0.9/packages/epetraext/example/inout/HDF5_IO.cpp:70:
>     undefined reference to
>     `EpetraExt::HDF5::Write(std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> > const&, Epetra_Map
>     const&)'
>     ../../../../../trilinos-7.0.9/packages/epetraext/example/inout/HDF5_IO.cpp:72:
>     undefined reference to
>     `EpetraExt::HDF5::Write(std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> > const&,
>     Epetra_RowMatrix const&)'
>     ../../../../../trilinos-7.0.9/packages/epetraext/example/inout/HDF5_IO.cpp:74:
>     undefined reference to
>     `EpetraExt::HDF5::Write(std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> > const&,
>     Epetra_MultiVector const&)'
>     ../../../../../trilinos-7.0.9/packages/epetraext/example/inout/HDF5_IO.cpp:75:
>     undefined reference to
>     `EpetraExt::HDF5::Write(std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> > const&,
>     Epetra_MultiVector const&)'
>     ../../../../../trilinos-7.0.9/packages/epetraext/example/inout/HDF5_IO.cpp:77:
>     undefined reference to
>     `EpetraExt::HDF5::Write(std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> > const&,
>     std::basic_string<char, std::char_traits<char>,
>     std::allocator<char> > const&, int)'
>     ../../../../../trilinos-7.0.9/packages/epetraext/example/inout/HDF5_IO.cpp:78:
>     undefined reference to
>     `EpetraExt::HDF5::Write(std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> > const&,
>     std::basic_string<char, std::char_traits<char>,
>     std::allocator<char> > const&, double)'
>     ../../../../../trilinos-7.0.9/packages/epetraext/example/inout/HDF5_IO.cpp:79:
>     undefined reference to
>     `EpetraExt::HDF5::Write(std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> > const&,
>     std::basic_string<char, std::char_traits<char>,
>     std::allocator<char> > const&, std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> > const&)'
>     ../../../../../trilinos-7.0.9/packages/epetraext/example/inout/HDF5_IO.cpp:80:
>     undefined reference to
>     `EpetraExt::HDF5::Write(std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> > const&,
>     std::basic_string<char, std::char_traits<char>,
>     std::allocator<char> > const&, std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> > const&)'
>     ../../../../../trilinos-7.0.9/packages/epetraext/example/inout/HDF5_IO.cpp:81:
>     undefined reference to
>     `EpetraExt::HDF5::Write(std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> > const&,
>     std::basic_string<char, std::char_traits<char>,
>     std::allocator<char> > const&, std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> > const&)'
>     ../../../../../trilinos-7.0.9/packages/epetraext/example/inout/HDF5_IO.cpp:83:
>     undefined reference to
>     `EpetraExt::HDF5::Write(std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> > const&,
>     std::basic_string<char, std::char_traits<char>,
>     std::allocator<char> > const&, int)'
>     ../../../../../trilinos-7.0.9/packages/epetraext/example/inout/HDF5_IO.cpp:84:
>     undefined reference to
>     `EpetraExt::HDF5::Write(std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> > const&,
>     std::basic_string<char, std::char_traits<char>,
>     std::allocator<char> > const&, int)'
>     ../../../../../trilinos-7.0.9/packages/epetraext/example/inout/HDF5_IO.cpp:87:
>     undefined reference to
>     `EpetraExt::HDF5::Write(std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> > const&,
>     Teuchos::ParameterList const&)'
>     ../../../../../trilinos-7.0.9/packages/epetraext/example/inout/HDF5_IO.cpp:92:
>     undefined reference to
>     `EpetraExt::HDF5::Write(std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> > const&,
>     std::basic_string<char, std::char_traits<char>,
>     std::allocator<char> > const&, int, int, void*)'
>     ../../../../../trilinos-7.0.9/packages/epetraext/example/inout/HDF5_IO.cpp:96:
>     undefined reference to
>     `EpetraExt::HDF5::Write(std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> > const&,
>     std::basic_string<char, std::char_traits<char>,
>     std::allocator<char> > const&, int, int, void*)'
>     ../../../../../trilinos-7.0.9/packages/epetraext/example/inout/HDF5_IO.cpp:114:
>     undefined reference to
>     `EpetraExt::HDF5::IsContained(std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> >)'
>     ../../../../../trilinos-7.0.9/packages/epetraext/example/inout/HDF5_IO.cpp:116:
>     undefined reference to
>     `EpetraExt::HDF5::Read(std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> > const&, Epetra_Map*&)'
>     ../../../../../trilinos-7.0.9/packages/epetraext/example/inout/HDF5_IO.cpp:117:
>     undefined reference to
>     `EpetraExt::HDF5::Read(std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> > const&, Epetra_Map
>     const&, Epetra_Map const&, Epetra_CrsMatrix*&)'
>     ../../../../../trilinos-7.0.9/packages/epetraext/example/inout/HDF5_IO.cpp:130:
>     undefined reference to
>     `EpetraExt::HDF5::Read(std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> > const&,
>     std::basic_string<char, std::char_traits<char>,
>     std::allocator<char> > const&, int&)'
>     ../../../../../trilinos-7.0.9/packages/epetraext/example/inout/HDF5_IO.cpp:135:
>     undefined reference to
>     `EpetraExt::HDF5::Read(std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> > const&,
>     Epetra_MultiVector*&)'
>     ../../../../../trilinos-7.0.9/packages/epetraext/example/inout/HDF5_IO.cpp:136:
>     undefined reference to
>     `EpetraExt::HDF5::Read(std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> > const&,
>     Epetra_MultiVector*&)'
>     ../../../../../trilinos-7.0.9/packages/epetraext/example/inout/HDF5_IO.cpp:142:
>     undefined reference to
>     `EpetraExt::HDF5::Read(std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> > const&,
>     std::basic_string<char, std::char_traits<char>,
>     std::allocator<char> > const&, int&)'
>     ../../../../../trilinos-7.0.9/packages/epetraext/example/inout/HDF5_IO.cpp:143:
>     undefined reference to
>     `EpetraExt::HDF5::Read(std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> > const&,
>     std::basic_string<char, std::char_traits<char>,
>     std::allocator<char> > const&, int&)'
>     ../../../../../trilinos-7.0.9/packages/epetraext/example/inout/HDF5_IO.cpp:144:
>     undefined reference to
>     `EpetraExt::HDF5::Read(std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> > const&,
>     std::basic_string<char, std::char_traits<char>,
>     std::allocator<char> > const&, int, int, void*)'
>     ../../../../../trilinos-7.0.9/packages/epetraext/example/inout/HDF5_IO.cpp:145:
>     undefined reference to
>     `EpetraExt::HDF5::Read(std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> > const&,
>     std::basic_string<char, std::char_traits<char>,
>     std::allocator<char> > const&, int, int, void*)'
>     ../../../../../trilinos-7.0.9/packages/epetraext/example/inout/HDF5_IO.cpp:149:
>     undefined reference to
>     `EpetraExt::HDF5::Read(std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> > const&,
>     std::basic_string<char, std::char_traits<char>,
>     std::allocator<char> > const&, std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> >&)'
>     ../../../../../trilinos-7.0.9/packages/epetraext/example/inout/HDF5_IO.cpp:152:
>     undefined reference to
>     `EpetraExt::HDF5::Read(std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> > const&,
>     Teuchos::ParameterList&)'
>     ../../../../../trilinos-7.0.9/packages/epetraext/example/inout/HDF5_IO.cpp:122:
>     undefined reference to
>     `EpetraExt::HDF5::Read(std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> > const&,
>     std::basic_string<char, std::char_traits<char>,
>     std::allocator<char> > const&, int&)'
>     ../../../../../trilinos-7.0.9/packages/epetraext/example/inout/HDF5_IO.cpp:124:
>     undefined reference to
>     `EpetraExt::HDF5::Read(std::basic_string<char,
>     std::char_traits<char>, std::allocator<char> > const&, Epetra_Map
>     const&, Epetra_Map const&, Epetra_CrsMatrix*&)'
>     collect2: ld returned 1 exit status
>     make[2]: *** [HDF5_IO.exe] Error 1
>     make[2]: Leaving directory
>     `/home/ryuta/Development/src/trilinos-7.0.9-build/packages/epetraext/example/inout'
>     make[1]: *** [all-recursive] Error 1
>     make[1]: Leaving directory
>     `/home/ryuta/Development/src/trilinos-7.0.9-build/packages/epetraext/example'
>
>
>     FYI:
>
>     nm src/libepetraext.a | grep HDF5
>     EpetraExt_HDF5.o:
>     00000070 t _GLOBAL__I__ZN9EpetraExt4HDF5C2ERK11Epetra_Comm
>     00000fc0 T _ZN9EpetraExt4HDF511IsContainedESs
>     00016bd0 T _ZN9EpetraExt4HDF517ReadMapPropertiesERKSsRiS3_S3_
>     00017b10 T _ZN9EpetraExt4HDF522ReadBlockMapPropertiesERKSsRiS3_S3_S3_
>     00015700 T
>     _ZN9EpetraExt4HDF522ReadCrsGraphPropertiesERKSsRiS3_S3_S3_S3_
>     00013c00 T
>     _ZN9EpetraExt4HDF523ReadCrsMatrixPropertiesERKSsRiS3_S3_S3_S3_RdS4_
>     00016090 T _ZN9EpetraExt4HDF523ReadIntVectorPropertiesERKSsRi
>     000208c0 T _ZN9EpetraExt4HDF525ReadMultiVectorPropertiesERKSsRiS3_
>     0001e420 T _ZN9EpetraExt4HDF526ReadIntDistArrayPropertiesERKSsRiS3_
>     0001bf80 T _ZN9EpetraExt4HDF529ReadDoubleDistArrayPropertiesERKSsRiS3_
>     00005250 T _ZN9EpetraExt4HDF54OpenESsi
>     000167f0 T
>     _ZN9EpetraExt4HDF54ReadERKSsRK10Epetra_MapRP16Epetra_IntVector
>     000250b0 T
>     _ZN9EpetraExt4HDF54ReadERKSsRK10Epetra_MapRP18Epetra_MultiVector
>     0001d720 T
>     _ZN9EpetraExt4HDF54ReadERKSsRK10Epetra_MapRPNS_9DistArrayIdEE
>     0001fbc0 T
>     _ZN9EpetraExt4HDF54ReadERKSsRK10Epetra_MapRPNS_9DistArrayIiEE
>     00014b30 T
>     _ZN9EpetraExt4HDF54ReadERKSsRK10Epetra_MapS5_RP15Epetra_CrsGraph
>     00014540 T
>     _ZN9EpetraExt4HDF54ReadERKSsRK10Epetra_MapS5_RP16Epetra_CrsMatrix
>     00026d00 T _ZN9EpetraExt4HDF54ReadERKSsRN7Teuchos13ParameterListE
>     00017400 T _ZN9EpetraExt4HDF54ReadERKSsRP10Epetra_Map
>     00018340 T _ZN9EpetraExt4HDF54ReadERKSsRP15Epetra_BlockMap
>     00015fb0 T _ZN9EpetraExt4HDF54ReadERKSsRP15Epetra_CrsGraph
>     00014a50 T _ZN9EpetraExt4HDF54ReadERKSsRP16Epetra_CrsMatrix
>     00016aa0 T _ZN9EpetraExt4HDF54ReadERKSsRP16Epetra_IntVector
>     00021e90 T _ZN9EpetraExt4HDF54ReadERKSsRP18Epetra_MultiVector
>     0001d550 T _ZN9EpetraExt4HDF54ReadERKSsRPNS_9DistArrayIdEE
>     0001f9f0 T _ZN9EpetraExt4HDF54ReadERKSsRPNS_9DistArrayIiEE
>     00003860 T _ZN9EpetraExt4HDF54ReadERKSsS2_RSs
>     00011a80 T _ZN9EpetraExt4HDF54ReadERKSsS2_Rd
>     00012b40 T _ZN9EpetraExt4HDF54ReadERKSsS2_Ri
>     00001e60 T _ZN9EpetraExt4HDF54ReadERKSsS2_iiPv
>     000000e0 T _ZN9EpetraExt4HDF54ReadERKSsS2_iiiPv
>     0001b6b0 T _ZN9EpetraExt4HDF55WriteERKSsRK10Epetra_Map
>     0001ba30 T _ZN9EpetraExt4HDF55WriteERKSsRK15Epetra_BlockMap
>     0001ab20 T _ZN9EpetraExt4HDF55WriteERKSsRK15Epetra_CrsGraph
>     0001b310 T _ZN9EpetraExt4HDF55WriteERKSsRK16Epetra_IntVector
>     00019f30 T _ZN9EpetraExt4HDF55WriteERKSsRK16Epetra_RowMatrix
>     00025190 T _ZN9EpetraExt4HDF55WriteERKSsRK18Epetra_MultiVector
>     000296c0 T _ZN9EpetraExt4HDF55WriteERKSsRKN7Teuchos13ParameterListE
>     0001dbc0 T _ZN9EpetraExt4HDF55WriteERKSsRKNS_9DistArrayIdEE
>     00020060 T _ZN9EpetraExt4HDF55WriteERKSsRKNS_9DistArrayIiEE
>     0000f280 T _ZN9EpetraExt4HDF55WriteERKSsS2_S2_
>     00018d40 T _ZN9EpetraExt4HDF55WriteERKSsS2_d
>     00019640 T _ZN9EpetraExt4HDF55WriteERKSsS2_i
>     00002f60 T _ZN9EpetraExt4HDF55WriteERKSsS2_iiPv
>     00001470 T _ZN9EpetraExt4HDF55WriteERKSsS2_iiiPKv
>     00005980 T _ZN9EpetraExt4HDF56CreateESs
>     000000c0 T _ZN9EpetraExt4HDF5C1ERK11Epetra_Comm
>     00000000 T _ZN9EpetraExt4HDF5C2ERK11Epetra_Comm
>     EpetraExt_HDF5_DistObject.o:
>     00000050 t _GLOBAL__I__ZN9EpetraExt4HDF55WriteERKSsRKNS_6HandleE
>              U _ZN9EpetraExt4HDF511IsContainedESs
>     00000070 T _ZN9EpetraExt4HDF520ReadHandlePropertiesERKSsRSsRi
>     00000ec0 T _ZN9EpetraExt4HDF54ReadERKSsRNS_6HandleE
>              U _ZN9EpetraExt4HDF54ReadERKSsS2_RSs
>              U _ZN9EpetraExt4HDF54ReadERKSsS2_Rd
>              U _ZN9EpetraExt4HDF54ReadERKSsS2_Ri
>              U _ZN9EpetraExt4HDF54ReadERKSsS2_iiiPv
>     00001d30 T _ZN9EpetraExt4HDF55WriteERKSsRKNS_6HandleE
>              U _ZN9EpetraExt4HDF55WriteERKSsS2_S2_
>              U _ZN9EpetraExt4HDF55WriteERKSsS2_d
>              U _ZN9EpetraExt4HDF55WriteERKSsS2_i
>              U _ZN9EpetraExt4HDF55WriteERKSsS2_iiiPKv
>
>
>
>     ------------------------------------------------------------------------
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