[petsc-users] Building PETSc with Intel mpi

[Qin Lu]

It turns out the machine's Linux/glibc versions are too old. The configure passed the error after I switched to a new machine.
 
Thanks a lot,
Qin
 

________________________________
 From: Barry Smith <bsmith at mcs.anl.gov>
To: Qin Lu <lu_qin_2000 at yahoo.com> 
Cc: petsc-users <petsc-users at mcs.anl.gov> 
Sent: Saturday, March 22, 2014 5:30 PM
Subject: Re: [petsc-users] Building PETSc with Intel mpi
  


   There is something wrong with your environment. It is compiling the trivial program

int main() {
;
  return 0;
}
                        Pushing language C
                        Popping language C
sh: mpiicc  -o /tmp/petsc-cd5uJs/config.setCompilers/conftest    /tmp/petsc-cd5uJs/config.setCompilers/conftest.o 
Executing: mpiicc  -o /tmp/petsc-cd5uJs/config.setCompilers/conftest    /tmp/petsc-cd5uJs/config.setCompilers/conftest.o 
sh: 
Executing: /tmp/petsc-cd5uJs/config.setCompilers/conftest
sh: /tmp/petsc-cd5uJs/config.setCompilers/conftest
Executing: /tmp/petsc-cd5uJs/config.setCompilers/conftest
sh: 
ERROR while running executable: Could not execute "/tmp/petsc-cd5uJs/config.setCompilers/conftest":
/tmp/petsc-cd5uJs/config.setCompilers/conftest: error while loading shared libraries: /apps/compilers/intel_2013/impi/4.1.0.024/intel64/lib/libmpi.so.4: requires glibc 2.5 or later dynamic linker


but the resulting program cannot be run. Can you compile and run a simple MPI program on this machine with mpiicc ? Do the following

printf “int main(){ return 0;} > simple.c

mpiicc -o simple simple.c 

./simplec 

does it work?





On Mar 22, 2014, at 2:24 PM, Qin Lu <lu_qin_2000 at yahoo.com> wrote:

> I tried what you suggested and got the following error (configure .log attached):
> **************
> sh: 
> ERROR while running executable: Could not execute "/tmp/petsc-cd5uJs/config.setCompilers/conftest":
> /tmp/petsc-cd5uJs/config.setCompilers/conftest: error while loading shared libraries: /apps/compilers/intel_2013/impi/4.1.0.024/intel64/lib/libmpi.so.4: requires glibc 2.5 or later dynamic linker
> ******************
>  
> What can I do about this?
>  
> Thanks,
> Qin
> 
> From: Barry Smith <bsmith at mcs.anl.gov>
> To: Qin Lu <lu_qin_2000 at yahoo.com> 
> Cc: petsc-users <petsc-users at mcs.anl.gov> 
> Sent: Saturday, March 22, 2014 11:46 AM
> Subject: Re: [petsc-users] Building PETSc with Intel mpi
> 
> 
> On Mar 22, 2014, at 10:15 AM, Qin Lu <lu_qin_2000 at yahoo.com> wrote:
> 
> > The Intel mpi's wrappers to Intel compilers are mpiicc and mpiifort (not mpicc and mpif90), can PETSc's configure automatically pick them? Or I have to specify them explicitly (--with-cc=mpiicc --with-fc=mpiifort --with-mpi-compilers=0)?
> 
>   List 
> 
>   --with-cc=mpiicc --with-fc=mpiifort  
> 
>   do not list --with-mpi-compilers=0 or —with-mpi-dir or —with-mpi-libs
> 
>   Barry
> 
> 
> 
> 
> > 
> > Thanks,
> > Qin
> > 
> > From: Satish Balay <balay at mcs.anl.gov>
> > To: Qin Lu <lu_qin_2000 at yahoo.com> 
> > Cc: Barry Smith <bsmith at mcs.anl.gov>; petsc-users <petsc-users at mcs.anl.gov> 
> > Sent: Saturday, March 22, 2014 12:09 AM
> > Subject: Re: [petsc-users] Building PETSc with Intel mpi
> > 
> > > --with-mpi-dir=/apps/compilers/intel_2013/impi/4.1.0.024/intel64 --with-mpi-compilers=0
> > 
> > Does this mpi not come with mpicc/mpif90 wrappers? If they do - its best to use them.
> > 
> > If not - its best to look at the docs for this compiler - and specify it with the appropriate
> > 
> > --with-mpi-include --with-mpi-lib options, [instead of the above]
> > 
> > Satish
> > 
> > On Fri, 21 Mar 2014, Qin Lu wrote:
> > 
> > > Sourcing the .csh files of the compiler fixed the problem. Thanks! However, later it got another error (see the attached configure.log for details):
> > >  
> > > *******************************************************************************
> > >          UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log for details):
> > > -------------------------------------------------------------------------------
> > > Fortran error! mpi_init() could not be located!
> > > *******************************************************************************
> > > 
> > > It seems the configure did not link the Intel MPI libs. I used --with-mpi-dir to specify the MPI directory, can configure get the correct Intel MPI lib names? If I have to specify the lib names (using --with-mpi-lib?), which libs should I specify? I saw a lot of libs under the directory, such as libmpi.a, libmpi_ipl64.a, libmpi_mt.a, etc. 
> > >  
> > > Thanks a lot,
> > > Qin
> > >  
> > > 
> > > ________________________________
> > >  From: Barry Smith <bsmith at mcs.anl.gov>
> > > To: Qin Lu <lu_qin_2000 at yahoo.com> 
> > > Cc: petsc-users <petsc-users at mcs.anl.gov> 
> > > Sent: Friday, March 21, 2014 10:11 AM
> > > Subject: Re: [petsc-users] Building PETSc with Intel mpi
> > >  
> > > 
> > > 
> > >  Did you follow the directions here: http://www.mcs.anl.gov/petsc/documentation/faq.html#libimf
> > > 
> > >  Did it make any difference?
> > > 
> > > 
> > > On Mar 21, 2014, at 9:45 AM, Qin Lu <lu_qin_2000 at yahoo.com> wrote:
> > > 
> > > > Hello,
> > > >  
> > > > I was trying to build PETSc-3.4.2 with Intel MPI using Intel-2013 compilers in Linux, but got the error below. The configure.log is attached.
> > > >  
> > > > *******************************************************************************
> > > >                    UNABLE to EXECUTE BINARIES for ./configure 
> > > > -------------------------------------------------------------------------------
> > > > Cannot run executables created with FC. If this machine uses a batch system 
> > > > to submit jobs you will need to configure using ./configure with the additional option  --with-batch.
> > > >  Otherwise there is problem with the compilers. Can you compile and run code with your C/C++ (and maybe Fortran) compilers?
> > > > See http://www.mcs.anl.gov/petsc/documentation/faq.html#libimf
> > > > *******************************************************************************
> > > >  
> > > > Thanks a lot for any suggestions abut the problem,
> > > >  
> > > > Regards,
> > > > Qin
> > > 
> > > >  
> > > > <configure.log>
> > > 
> > 
> > 
> 
> 
> <configure.log>
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