[petsc-users] configure cannot find a c preprocessor

[Matthew Knepley]

On Wed, Dec 20, 2017 at 6:31 PM, Santiago Andres Triana <repepo at gmail.com>
wrote:

> I got a different error now... hope it's a good sign!
>
> hpca-login:~/petsc-3.8.3> ./configure --with-cc=gcc --with-fc=gfortran
> --with-cxx=g++ --with-mpi-include=/opt/sgi/mpt/mpt-2.12/include
> --with-mpi-lib="-L/opt/sgi/mpt/mpt-2.12/lib -lmpi -lpthread"
> LIBS="/usr/lib64/libcpuset.so.1 /usr/lib64/libbitmask.so.1"
> ============================================================
> ===================
>              Configuring PETSc to compile on your system
>
> ============================================================
> ===================
> TESTING: CxxMPICheck from config.packages.MPI(config/
> BuildSystem/config/packages/MPI.py:351)
> ************************************************************
> *******************
>          UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log for
> details):
> ------------------------------------------------------------
> -------------------
> C++ error! MPI_Finalize() could not be located!
> ************************************************************
> *******************
>

It looks like there is crazy C++ stuff in SGI MPT. I can see two chioces:

  a) Turn off C++: --with-cxx=0

  b) Find out what crazy C++ library MPT has and stick it in --with-mpi-lib

No amount of MPI optimization is worth this pain. Does your machine have an
MPICH install?

  Thanks,

     Matt


> On Thu, Dec 21, 2017 at 12:21 AM, Satish Balay <balay at mcs.anl.gov> wrote:
>
>> Hm configure is misbehaving with /usr/lib64/libcpuset.so.1 notation. Try:
>>
>> ./configure --with-cc=gcc --with-fc=gfortran --with-cxx=g++
>> --with-mpi-include=/opt/sgi/mpt/mpt-2.12/include
>> --with-mpi-lib="-L/opt/sgi/mpt/mpt-2.12/lib -lmpi -lpthread"
>> LIBS="/usr/lib64/libcpuset.so.1 /usr/lib64/libbitmask.so.1"
>>
>> Satish
>>
>>
>> On Wed, 20 Dec 2017, Santiago Andres Triana wrote:
>>
>> > thanks Satish,
>> >
>> > did not work unfortunately, configure.log attached. Here's the output:
>> >
>> > hpca-login:~/petsc-3.8.3> ./configure --with-cc=gcc --with-fc=gfortran
>> > --with-cxx=g++ --with-mpi-include=/opt/sgi/mpt/mpt-2.12/include
>> > --with-mpi-lib="-L/opt/sgi/mpt/mpt-2.12/lib -lmpi -lpthread
>> > /usr/lib64/libcpuset.so.1 /usr/lib64/libbitmask.so.1"
>> > ============================================================
>> ===================
>> >              Configuring PETSc to compile on your system
>> >
>> > ============================================================
>> ===================
>> > TESTING: check from
>> > config.libraries(config/BuildSystem/config/libraries.py:158)
>> >
>> > ************************************************************
>> *******************
>> >          UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log
>> for
>> > details):
>> > ------------------------------------------------------------
>> -------------------
>> > --with-mpi-lib=['-L/opt/sgi/mpt/mpt-2.12/lib', '-lmpi', '-lpthread',
>> > '/usr/lib64/libcpuset.so.1', '/usr/lib64/libbitmask.so.1'] and
>> > --with-mpi-include=['/opt/sgi/mpt/mpt-2.12/include'] did not work
>> > ************************************************************
>> *******************
>> >
>> > On Thu, Dec 21, 2017 at 12:07 AM, Satish Balay <balay at mcs.anl.gov>
>> wrote:
>> >
>> > > Its strange compiler.
>> > >
>> > > You can try:
>> > >
>> > > ./configure --with-cc=gcc --with-fc=gfortran --with-cxx=g++
>> > > --with-mpi-include=/opt/sgi/mpt/mpt-2.12/include
>> > > --with-mpi-lib="-L/opt/sgi/mpt/mpt-2.12/lib -lmpi -lpthread
>> > > /usr/lib64/libcpuset.so.1 /usr/lib64/libbitmask.so.1"
>> > >
>> > > Satish
>> > >
>> > > On Wed, 20 Dec 2017, Santiago Andres Triana wrote:
>> > >
>> > > > This is what I get:
>> > > >
>> > > > hpca-login:~> mpicc -show
>> > > > gcc -I/opt/sgi/mpt/mpt-2.12/include -L/opt/sgi/mpt/mpt-2.12/lib
>> -lmpi
>> > > > -lpthread /usr/lib64/libcpuset.so.1 /usr/lib64/libbitmask.so.1
>> > > >
>> > > > On Wed, Dec 20, 2017 at 11:59 PM, Satish Balay <balay at mcs.anl.gov>
>> > > wrote:
>> > > >
>> > > > > >>>
>> > > > > Executing: mpicc -E  -I/dev/shm/pbs.3111462.hpc-
>> > > pbs/petsc-fdYfuH/config.setCompilers
>> > > > > /dev/shm/pbs.3111462.hpc-pbs/petsc-fdYfuH/config.
>> > > setCompilers/conftest.c
>> > > > > stderr:
>> > > > > gcc: warning: /usr/lib64/libcpuset.so.1: linker input file unused
>> > > because
>> > > > > linking not done
>> > > > > gcc: warning: /usr/lib64/libbitmask.so.1: linker input file unused
>> > > because
>> > > > > linking not done
>> > > > > <<<<
>> > > > >
>> > > > > Looks like your mpicc is printing this verbose thing on stdout
>> [why is
>> > > > > it doing a link check during preprocesing?] - thus confusing PETSc
>> > > > > configure.
>> > > > >
>> > > > > Workarround is to fix this compiler not to print such messages.
>> Or use
>> > > > > different compilers..
>> > > > >
>> > > > > What do you have for:
>> > > > >
>> > > > > mpicc -show
>> > > > >
>> > > > >
>> > > > > Satish
>> > > > >
>> > > > > On Wed, 20 Dec 2017, Santiago Andres Triana wrote:
>> > > > >
>> > > > > > Dear petsc-users,
>> > > > > >
>> > > > > > I'm trying to install petsc in a cluster using SGI's MPT. The
>> mpicc
>> > > > > > compiler is in the search path. The configure command is:
>> > > > > >
>> > > > > > ./configure --with-scalar-type=complex --with-mumps=1
>> > > --download-mumps
>> > > > > > --download-parmetis --download-metis --download-scalapack
>> > > > > >
>> > > > > > However, this leads to an error (configure.log attached):
>> > > > > >
>> > > > > > ============================================================
>> > > > > ===================
>> > > > > >              Configuring PETSc to compile on your system
>> > > > > >
>> > > > > > ============================================================
>> > > > > ===================
>> > > > > > TESTING: checkCPreprocessor from
>> > > > > > config.setCompilers(config/BuildSystem/config/setCompilers.
>> py:599)
>> > > > > >
>> > > > > > ************************************************************
>> > > > > *******************
>> > > > > >          UNABLE to CONFIGURE with GIVEN OPTIONS    (see
>> > > configure.log for
>> > > > > > details):
>> > > > > > ------------------------------------------------------------
>> > > > > -------------------
>> > > > > > Cannot find a C preprocessor
>> > > > > > ************************************************************
>> > > > > *******************
>> > > > > >
>> > > > > > The configure.log says something about cpp32, here's the
>> excerpt:
>> > > > > >
>> > > > > > Possible ERROR while running preprocessor: exit code 256
>> > > > > > stderr:
>> > > > > > gcc: error: cpp32: No such file or directory
>> > > > > >
>> > > > > >
>> > > > > > Any ideas of what is going wrong? any help or comments are
>> highly
>> > > > > > appreciated. Thanks in advance!
>> > > > > >
>> > > > > > Andres
>> > > > > >
>> > > > >
>> > > > >
>> > > >
>> > >
>> > >
>> >
>>
>>
>


-- 
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

https://www.cse.buffalo.edu/~knepley/ <http://www.caam.rice.edu/~mk51/>
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