[petsc-users] configure cannot find a c preprocessor

Wed Dec 20 22:10:09 CST 2017

> On Dec 20, 2017, at 5:52 PM, Matthew Knepley <knepley at gmail.com> wrote:
> 
> 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

   3) filter the error message as previously discussed (this time for C++), then one does not have "find out what crazy..."  since the mpicxx knows it.

   Barry

> 
> 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/