[petsc-users] configure cannot find a c preprocessor

Matthew Knepley knepley at gmail.com
Thu Dec 21 07:30:35 CST 2017 

On Thu, Dec 21, 2017 at 3:28 AM, Santiago Andres Triana <repepo at gmail.com>
wrote:

> There is no mpich install on this cluster... I will talk to the sysadmins
> to see if this is feasible...
>
> On other news, configure was successful by turning off C++, however make
> failed: (attached logs)
>
> ...
> ------------------------------------------
> Using mpiexec: /opt/sgi/mpt/mpt-2.12/bin/mpirun
> ==========================================
> Building PETSc using GNU Make with 32 build threads
> ==========================================
> gmake[2]: Entering directory `/space/hpc-home/trianas/petsc-3.8.3'
> Use "/usr/bin/gmake V=1" to see verbose compile lines, "/usr/bin/gmake
> V=0" to suppress.
>      CLINKER /space/hpc-home/trianas/petsc-3.8.3/arch-linux2-c-debug/lib/
> libpetsc.so.3.8.3
> /sw/sdev/binutils/x86_64/2.22/bin/ld: cannot find -lcpuset.so
> /sw/sdev/binutils/x86_64/2.22/bin/ld: cannot find -lbitmask.so
> collect2: error: ld returned 1 exit status
> gmake[2]: *** [/space/hpc-home/trianas/petsc-3.8.3/arch-linux2-c-debug/lib/libpetsc.so.3.8.3]
> Error 1
> gmake[2]: Leaving directory `/space/hpc-home/trianas/petsc-3.8.3'
> gmake[1]: *** [gnumake] Error 2
> gmake[1]: Leaving directory `/space/hpc-home/trianas/petsc-3.8.3'
> **************************ERROR*************************************
>   Error during compile, check arch-linux2-c-debug/lib/petsc/conf/make.log
>   Send it and arch-linux2-c-debug/lib/petsc/conf/configure.log to
> petsc-maint at mcs.anl.gov
> ********************************************************************
>
> there seems to be a problem with the libcpuset.so and libbitmask.so
> libraries. Make wants lcpuset.so and lbitmask.so, which do not exist in
> this system.
>

You can see by looking a few lines above in make.log that we preserve your
input:

  ...
 /sw/sdev/intel/parallel_studio_xe_2015_update_3-pguyan/composer_xe_2015.3.187/mkl/lib/mic
-L/sw/sdev/intel/parallel_studio_xe_2015_update_3-pguyan/composer_xe_2015.3.187/mkl/lib/mic
-Wl,-rpath,/space/hpc-apps/sw/sdev/gcc/x86_64/4.9.2/lib
-L/space/hpc-apps/sw/sdev/gcc/x86_64/4.9.2/lib -ldl -lgcc_s -ldl
/usr/lib64/libcpuset.so.1 /usr/lib64/libbitmask.so.1

So its the linker complaining. Why are these libraries necessary? Also,
maybe you could properly install them, meaning
make a link

  ln -d /usr/lib64/libcpuset.so.1 /usr/lib64/libcpuset.so

  Thanks,

     Matt


> On Thu, Dec 21, 2017 at 5:10 AM, Smith, Barry F. <bsmith at mcs.anl.gov>
> wrote:
>
>>
>>
>> > 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/Bui
>> ldSystem/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/
>>
>>
>


-- 
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/>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20171221/37185ce0/attachment.html>

More information about the petsc-users mailing list