[petsc-users] WHY "C++ error! MPI_Finalize() could not be located!"? Thanks.
Matthew Knepley
knepley at gmail.com
Sun Jan 18 04:32:55 CST 2015
On Sun, Jan 18, 2015 at 3:28 AM, Jerry <orzgodlo at gmail.com> wrote:
> Thanks, Matthew.
>
> I thought "--with-cc" "--with-cxx " "--with-fc" are all needed, according
> to the following webpage
> http://www.mcs.anl.gov/petsc/documentation/installation.html
>
Only if you want to turn on those features. I'll see if we can clarify that.
Glad it works.
Thanks,
Matt
>
> Now, I configured as follows, and then compile. It seems ok.
>
> ./configure --prefix=/usr/local --with-cc=gcc --with-cxx=0 --with-fc=0
> --with-mpi-include=/usr/include/mpi --with-mpi-lib=/usr/lib/libmpi.so
>
>
> 2015-01-17 11:29 GMT-08:00 Matthew Knepley <knepley at gmail.com>:
>
>> On Sat, Jan 17, 2015 at 1:18 PM, Jerry <orzgodlo at gmail.com> wrote:
>>
>>> Hi, Matthew.
>>>
>>> Please find attached the configure log. Thanks.
>>>
>>
>> There are problems with C++ and this MPI install:
>>
>> Executing: g++ -o /tmp/petsc-FhcRYT/config.libraries/conftest -Wall
>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g -O0
>> /tmp/petsc-FhcRYT/config.libraries/conftest.o -Wl,-rpath,/usr/lib
>> -L/usr/lib -lmpi -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.8
>> -L/usr/lib/gcc/x86_64-linux-gnu/4.8 -Wl,-rpath,/usr/lib/x86_64-linux-gnu
>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu
>> -L/lib/x86_64-linux-gnu -Wl,-rpath,/usr/lib/x86_64-linux-gnu
>> -L/usr/lib/x86_64-linux-gnu -ldl -lgcc_s -ldl
>> Possible ERROR while running linker: exit code 256
>> stderr:
>> /tmp/petsc-FhcRYT/config.libraries/conftest.o: In function
>> `MPI::Intracomm::Intracomm()':
>> /usr/include/mpi/openmpi/ompi/mpi/cxx/intracomm.h:25: undefined reference
>> to `MPI::Comm::Comm()'
>> /tmp/petsc-FhcRYT/config.libraries/conftest.o: In function
>> `MPI::Intracomm::Intracomm(ompi_communicator_t*)':
>> /usr/include/mpi/openmpi/ompi/mpi/cxx/intracomm_inln.h:23: undefined
>> reference to `MPI::Comm::Comm()'
>> /tmp/petsc-FhcRYT/config.libraries/conftest.o: In function
>> `MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&),
>> bool)':
>> /usr/include/mpi/openmpi/ompi/mpi/cxx/op_inln.h:122: undefined reference
>> to `ompi_mpi_cxx_op_intercept'
>> /tmp/petsc-FhcRYT/config.libraries/conftest.o:(.data.rel.ro._ZTVN3MPI3WinE[_ZTVN3MPI3WinE]+0x48):
>> undefined reference to `MPI::Win::Free()'
>> /tmp/petsc-FhcRYT/config.libraries/conftest.o:(.data.rel.ro._ZTVN3MPI8DatatypeE[_ZTVN3MPI8DatatypeE]+0x78):
>> undefined reference to `MPI::Datatype::Free()'
>> collect2: error: ld returned 1 exit status
>>
>> If you are using your own installation of MPI, it is best to use its
>> compiler wrappers:
>>
>> --with-cc=/usr/bin/mpicc --with-cxx=/usr/bin/mpicxx
>>
>> instead of the MPI flags (since it looks like you missed a library).
>> Also, do you really
>> need to build PETSc with C++? If not, leave it out using
>>
>> --with-cxx=0
>>
>> Thanks,
>>
>> Matt
>>
>>
>>> -Jerry
>>>
>>> 2015-01-17 4:52 GMT-08:00 Matthew Knepley <knepley at gmail.com>:
>>>
>>>> Send the whole configure.log
>>>>
>>>> Thanks,
>>>>
>>>> Matt
>>>>
>>>> On Sat, Jan 17, 2015 at 4:07 AM, Jerry <orzgodlo at gmail.com> wrote:
>>>>
>>>>> Hi, all.
>>>>>
>>>>> I am trying to configure&compile petsc. However, during configuring, I
>>>>> got the following error (C++ error! MPI_Finalize() could not be located!).
>>>>> I am also copying the last few lines in configure.log.
>>>>>
>>>>> But I am sure mpi.h is under the folder I specified
>>>>> (--with-mpi-include=/usr/include/mpi )
>>>>>
>>>>> Any idea about the problem? Thanks.
>>>>>
>>>>>
>>>>> $$ ./configure --prefix=~/local --with-cc=gcc --with-cxx=g++
>>>>> --with-fc=gfortran --with-mpi-include=/usr/include/mpi
>>>>> --with-mpi-lib=/usr/lib/libmpi.so
>>>>>
>>>>>
>>>>> ===============================================================================
>>>>> Configuring PETSc to compile on your
>>>>> system
>>>>>
>>>>> ===============================================================================
>>>>> TESTING: CxxMPICheck from
>>>>> config.packages.MPI(config/BuildSystem/config/packages*******************************************************************************
>>>>> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log
>>>>> for details):
>>>>>
>>>>> -------------------------------------------------------------------------------
>>>>> C++ error! MPI_Finalize() could not be located!
>>>>>
>>>>> *******************************************************************************
>>>>>
>>>>>
>>>>>
>>>>> =========== Last few lines from configure.log ================
>>>>>
>>>>>
>>>>>
>>>>> *******************************************************************************
>>>>> File "./config/configure.py", line 272, in petsc_configure
>>>>> framework.configure(out = sys.stdout)
>>>>> File
>>>>> "/home/delia/workspace/programs/petsc/config/BuildSystem/config/framework.py",
>>>>> line 941, in configure
>>>>> child.configure()
>>>>> File
>>>>> "/home/delia/workspace/programs/petsc/config/BuildSystem/config/package.py",
>>>>> line 606, in configure
>>>>> self.executeTest(self.configureLibrary)
>>>>> File
>>>>> "/home/delia/workspace/programs/petsc/config/BuildSystem/config/base.py",
>>>>> line 126, in executeTest
>>>>> ret = test(*args,**kargs)
>>>>> File
>>>>> "/home/delia/workspace/programs/petsc/config/BuildSystem/config/packages/MPI.py",
>>>>> line 660, in CxxMPICheck
>>>>> raise RuntimeError('C++ error! MPI_Finalize() could not be
>>>>> located!')
>>>>>
>>>>> ================================================================================
>>>>> Finishing Configure Run at Sat Jan 17 01:34:31 2015
>>>>>
>>>>> ================================================================================
>>>>>
>>>>>
>>>>> Jerry
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> What most experimenters take for granted before they begin their
>>>> experiments is infinitely more interesting than any results to which their
>>>> experiments lead.
>>>> -- Norbert Wiener
>>>>
>>>
>>>
>>
>>
>> --
>> What most experimenters take for granted before they begin their
>> experiments is infinitely more interesting than any results to which their
>> experiments lead.
>> -- Norbert Wiener
>>
>
>
--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
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