[Trilinos-Users] Error with --enable-epetraext-hdf5
James Willenbring
jmwille at sandia.gov
Wed Aug 8 09:44:03 MDT 2007
I have recently heard from others that the --enable-epetraext-hdf5 option
does not compile when mpi is enabled. Has anyone been able to compile with
the --enable-epetraext-hdf5 and --enable-mpi options?
Jim
_____
From: trilinos-users-bounces at software.sandia.gov
[mailto:trilinos-users-bounces at software.sandia.gov] On Behalf Of ryuta
Sent: Friday, August 03, 2007 5:16 PM
To: Michael A Heroux
Cc: trilinos-users at software.sandia.gov
Subject: Re: [Trilinos-Users] Error with --enable-epetraext-hdf5
../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" <mailto:suzu0037 at aem.umn.edu>
<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:5
7: undefined reference to `EpetraExt::HDF5::HDF5(Epetra_Comm const&)'
../../../../../trilinos-7.0.9/packages/epetraext/example/inout/HDF5_IO.cpp:6
0: 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:7
0: 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:7
2: 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:7
4: 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:7
5: 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:7
7: 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:7
8: 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:7
9: 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:8
0: 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:8
1: 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:8
3: 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:8
4: 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:8
7: 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:9
2: 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:9
6: 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:1
14: 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:1
16: 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:1
17: 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:1
30: 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:1
35: 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:1
36: 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:1
42: 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:1
43: 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:1
44: 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:1
45: 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:1
49: 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:1
52: 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:1
22: 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:1
24: 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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