[CIG-SHORT] mpi missing error when trying to install nemesis
Niz
niz.moussatat at gmail.com
Tue Oct 5 19:56:00 PDT 2010
Hi
I configured petsc with the proper --PETSC_ARCH=gcc-4.4.3. and
installed it.[test ok] Then went to Pylith build directory. The
Configure went fine, but got an error
during "make"
====================
/home/tora/pylith/src/petsc-dev/include/petscmesh_solvers.hh:82:
error: ‘PETSC_OWN_VALUES’ was not declared in this scope
make[3]: *** [Solver.lo] Error 1
make[3]: Leaving directory
`/home/tora/pylith/scratch/build/gcc-4.4.3/pylith-dev/libsrc'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory
`/home/tora/pylith/scratch/build/gcc-4.4.3/pylith-dev/libsrc'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory
`/home/tora/pylith/scratch/build/gcc-4.4.3/pylith-dev'
make: *** [all] Error 2
====================
Any idea on what is ‘PETSC_OWN_VALUES’?
Thanks
Niz
============================================
config for PETSC
config/configure.py --PETSC_ARCH=${TOOLS_FORMAT} --with-debugging=0
--with-clanguage=c++ --with-mpi-compilers=1 --with-shared=1
--with-dynamic=1 --with-large-file-io=1
--with-blas-lapack-lib="-L/usr/lib/atlas -llapack_atlas -llapack
-latlas -lblas" --with-lgrind=0 --with-chaco=1 --download-chaco=1
--with-parmetis=1 --download-parmetis=1 --with-sieve=1 --with-boost=1
--download-boost=1 --with-ml=1 --download-ml=1
config for Pyth
config/configure.py --PETSC_ARCH=${TOOLS_FORMAT} --with-debugging=0
--with-clanguage=c++ --with-mpi-compilers=1 --with-shared=1
--with-dynamic=1 --with-large-file-io=1
--with-blas-lapack-lib="-L/usr/lib/atlas -llapack_atlas -llapack
-latlas -lblas" --with-lgrind=0 --with-chaco=1 --download-chaco=1
--with-parmetis=1 --download-parmetis=1 --with-sieve=1 --with-boost=1
--download-boost=1 --with-ml=1 --download-ml=1
2010/10/6, Niz <niz.moussatat at gmail.com>:
> discard my previous mail. Indeed it was llinux_gcc-4.4.3
>
> Thanks
> Niz.
>
> 2010/10/6, Niz <niz.moussatat at gmail.com>:
>> yes
>>
>> before installing anything I entered:
>>
>> export TOOLS_FORMAT=gcc-4.4.3
>> export PETSC_ARCH=${TOOLS_FORMAT}
>>
>> 2010/10/6, Brad Aagaard <baagaard at usgs.gov>:
>>> Niz-
>>>
>>> What was PETSC_ARCH set to when you configured PETSc? The value used at
>>> that time must match the one used when configuring PyLith.
>>>
>>> When you configured PyLith PETSC_ARCH was set to "gcc-4.4.3".
>>>
>>> Brad
>>>
>>>
>>> On 10/05/2010 06:00 PM, Niz wrote:
>>>> Brad
>>>>
>>>> I adapted the instructions detailed in Linux_Ubuntu_64.
>>>> I reached the Last Step, to install the Pylithdev where I ran:
>>>> cd $HOME/pylith/scratch/build/$TOOLS_FORMAT/pylith-dev
>>>> ${HOME}/pylith/src/pylith-dev/configure --config-cache
>>>> --enable-swig --enable-testing --enable-cubit --prefix=${TOOLS_DIR}
>>>> CPPFLAGS="-I${TOOLS_DIR}/include " LDFLAGS="-L${TOOLS_DIR}/lib "
>>>> CC=mpicc CXX=mpiCC CFLAGS="-O2 -fPIC" CXXFLAGS="-O2 -fPIC"
>>>>
>>>> so he replies:
>>>> ...
>>>> checking /home/tora/pylith/tools/gcc-4.4.3/bin/nemesis sysconfig... ok
>>>> checking for PETSc dir... /home/tora/pylith/src/petsc-dev
>>>> checking for PETSc arch... gcc-4.4.3
>>>> checking for PETSc config... no
>>>> configure: error: PETSc config dir not found; check PETSC_ARCH
>>>>
>>>> What did I miss? [I joined the config.log]
>>>>
>>>> Thanks
>>>> Niz.
>>>> -----------------------------------------
>>>> make check PETSc was fine:
>>>> tora at dragon:~/pylith/src/petsc-dev$ make
>>>> PETSC_DIR=/home/tora/pylith/src/petsc-dev PETSC_ARCH=linux_gcc-4.4.3
>>>> test
>>>> Running test examples to verify correct installation
>>>> .C/C++ example src/snes/examples/tutorials/ex19 run successfully with
>>>> 1 MPI process
>>>> C/C++ example src/snes/examples/tutorials/ex19 run successfully with 2
>>>> MPI processes
>>>> Fortran example src/snes/examples/tutorials/ex5f run successfully with
>>>> 1 MPI process
>>>> Completed test examples
>>>>
>>>> PS:I compiled spatial-data with mpicc/mpiCC, Python import
>>>> spatialdata/FIAT/pyre was ok. Nemesis import mpi was ok too. FIAT is
>>>> the 0.3.5 (I uninstalled the 0.9), and uninstalled all mpich I could
>>>> find. And changed PYTHON_VERSION to 2.6 (instead of 2.6.5) as you
>>>> just suggested to Birendra.
>>>> ----------------------------
>>>> 2010/10/5, Brad Aagaard<baagaard at usgs.gov>:
>>>>> Birendra-
>>>>>
>>>>> You should not rename the lib/python2.6 folder. You should change
>>>>> PYTHONPATH instead. The python2.6 folder was created automatically by
>>>>> "make install".
>>>>>
>>>>> Brad
>>>>>
>>>>>
>>>>> On 10/05/2010 11:52 AM, Birendra jha wrote:
>>>>>> Brad,
>>>>>>
>>>>>> I think I found the error. It is "python2.6" in site-packages folder
>>>>>> vs
>>>>>> "python2.6.5" in the PYTHONPATH. My python version is 2.6.5 which is
>>>>>> what
>>>>>> I have in PYTHONPATH but the folder name in $TOOLS_DIR/lib is
>>>>>> python2.6.
>>>>>>
>>>>>> When I rename this folder to python2.6.5 (should I rename PYTHONPATH
>>>>>> instead??), I can import spatialdata from within python and run make
>>>>>> for
>>>>>> pylith.
>>>>>>
>>>>>> I will keep you posted if I finish the make install and make check
>>>>>> successfully.
>>>>>>
>>>>>> Thanks
>>>>>> Birendra
>>>>>>
>>>>>>
>>>>>>
>>>>>> --- On Tue, 10/5/10, Brad Aagaard<baagaard at usgs.gov> wrote:
>>>>>>
>>>>>>> From: Brad Aagaard<baagaard at usgs.gov>
>>>>>>> Subject: Re: [CIG-SHORT] mpi missing error when trying to install
>>>>>>> nemesis
>>>>>>> To: "Birendra jha"<bjha7333 at yahoo.com>
>>>>>>> Date: Tuesday, October 5, 2010, 11:03 PM
>>>>>>> Birendra-
>>>>>>>
>>>>>>> The config.log shows that the spatialdata Python files are
>>>>>>> not found. This means either the PYTHONPATH is wrong or the
>>>>>>> files are not being installed into the install directory.
>>>>>>>
>>>>>>> What is the output of
>>>>>>>
>>>>>>> python
>>>>>>> import spatialdata
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> CIG-SHORT mailing list
>>>>>> CIG-SHORT at geodynamics.org
>>>>>> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> CIG-SHORT mailing list
>>>>> CIG-SHORT at geodynamics.org
>>>>> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>> --
>> ==========================================
>> Nizar MOUSSATAT
>> LGIT - Grenoble
>> tel: 06.43.59.39.44
>> ==========================================
>>
>
>
> --
> ==========================================
> Nizar MOUSSATAT
> LGIT - Grenoble
> tel: 06.43.59.39.44
> ==========================================
>
--
==========================================
Nizar MOUSSATAT
LGIT - Grenoble
tel: 06.43.59.39.44
==========================================
-------------- next part --------------
A non-text attachment was scrubbed...
Name: config.log
Type: text/x-log
Size: 43080 bytes
Desc: not available
Url : http://geodynamics.org/pipermail/cig-short/attachments/20101006/308e7ec7/attachment-0001.bin
More information about the CIG-SHORT
mailing list