[petsc-users] Fwd: PETSc installation on Intrepid

Satish Balay balay at mcs.anl.gov
Wed Jul 17 15:29:44 CDT 2013 

You can try using the configure option:

LIBS=/soft/apps/zlib-1.2.3/lib/libz.a

Satish

On Wed, 17 Jul 2013, Richard Tran Mills wrote:

> Hi Satish,
> 
> I think something for handling the libz problem must be missing. I just tried
> configuring on Intrepid with the configure script appended to this email and I
> get the same problem:
> 
> Compression library [libz.a or equivalent] not found
> 
> I believe that the library that I need is present on the system:
> 
> rmills at login1.intrepid:~/proj/petsc> ls -l /soft/apps/zlib-1.2.3/lib/
> total 128
> -rwxrwxr-x 1 rloy software 108724 2010-04-21 01:35 libz.a
> 
> Any ideas on what I need to do to get configure.py to find and use this?
> 
> Thanks,
> Richard
> 
> #!/usr/bin/python
> if __name__ == '__main__':
>   import sys
>   import os
>   sys.path.insert(0, os.path.abspath('config'))
>   import configure
>   configure_options = [
>     '--with-hdf5-dir=/soft/apps/current/hdf5-1.8.9',
>     '--download-cmake=1',
>     '--download-metis=1',
>     '--download-parmetis=1',
>     '--known-bits-per-byte=8',
>     '--known-level1-dcache-assoc=0',
>     '--known-level1-dcache-linesize=32',
>     '--known-level1-dcache-size=32768',
>     '--known-memcmp-ok=1',
>     '--known-mpi-long-double=1',
>     '--known-mpi-shared-libraries=0',
>     '--known-sizeof-MPI_Comm=4',
>     '--known-sizeof-MPI_Fint=4',
>     '--known-sizeof-char=1',
>     '--known-sizeof-double=8',
>     '--known-sizeof-float=4',
>     '--known-sizeof-int=4',
>     '--known-sizeof-long-long=8',
>     '--known-sizeof-long=4',
>     '--known-sizeof-short=2',
>     '--known-sizeof-size_t=4',
>     '--known-sizeof-void-p=4',
>     '--prefix=/soft/apps/libraries/petsc/3.3-p2/xl-opt',
>     '--with-batch=1',
> #'--with-blacs-include=/soft/apps/libraries/alcf/current/xl/SCALAPACK/',
> #'--with-blacs-lib=/soft/apps/libraries/alcf/current/xl/SCALAPACK/lib/libscalapack.a',
> '--with-blas-lapack-lib=-L/soft/apps/libraries/alcf/current/xl/LAPACK/lib
> -llapack -L/soft/apps/libraries/alcf/current/xl/BLAS/lib -lblas',
>     '--with-cc=mpixlc_r',
>     '--with-cxx=mpixlcxx_r',
>     '--with-debugging=0',
>     '--with-fc=mpixlf77_r -qnosave',
>     '--with-fortran-kernels=1',
>     '--with-is-color-value-type=short',
> '--with-scalapack-include=/soft/apps/libraries/alcf/current/xl/SCALAPACK/',
> '--with-scalapack-lib=/soft/apps/libraries/alcf/current/xl/SCALAPACK/lib/libscalapack.a',
>     '--with-shared-libraries=0',
>     '--with-x=0',
>     '--with-debugging=1',
>     '-COPTFLAGS=-g',
>     '-CXXOPTFLAGS=-g',
>     '-FOPTFLAGS=-g',
>   ]
>   configure.petsc_configure(configure_options)
> 
> On 7/16/13 12:59 PM, Satish Balay wrote:
> > --download-package might not work on all machines. --download-hdf5=1 does
> > not work on bg/p
> > 
> > However there is hdf5 installed on it. You can try using
> > --with-hdf5-include/--with-hdf5-lib options.
> > 
> > There could still be an issue with "Compression library [libz.a or
> > equivalent] not found" but I think the workarround is already in
> > petsc-dev.
> > 
> > Satish
> > 
> > 
> > 
> > On Tue, 16 Jul 2013, Jitendra Kumar wrote:
> > 
> > > Thanks Satish. I tried using the configuration you pointed me to with the
> > > addition of --download-hdf5=1 and got error "Compression library [libz.a
> > > or
> > > equivalent] not found
> > > "
> > > 
> > > Do I need to load some package to get this?
> > > 
> > > Jitu
> > > 
> > > 
> > > On Tue, Jul 16, 2013 at 11:59 AM, Satish Balay <balay at mcs.anl.gov> wrote:
> > > 
> > > > As the message indicates you need '--with-batch' option on this machine
> > > > 
> > > > Check one of the default builds on intrepid for configure options to
> > > > use..
> > > > 
> > > > [perhaps
> > > > /soft/apps/libraries/petsc/3.3-p6/xl-opt/conf/reconfigure-arch-bgp-ibm-opt.py]
> > > > 
> > > > Satish
> > > > 
> > > > On Tue, 16 Jul 2013, Jitendra Kumar wrote:
> > > > 
> > > > > I ran into following errors while trying to build PETSc-dev on
> > > > > Intrepid
> > > > > @ALCF.  (configure.log attached)
> > > > > 
> > > > > 
> > > > *******************************************************************************
> > > > >           UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log
> > > > > for
> > > > > details):
> > > > > 
> > > > 
> > > > -------------------------------------------------------------------------------
> > > > > Cannot run executable to determine size of char. 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?
> > > > > 
> > > > *******************************************************************************
> > > > >    File "/gpfs/home/jkumar/lib/petsc/config/configure.py", line 293,
> > > > > in
> > > > > petsc_configure
> > > > >      framework.configure(out = sys.stdout)
> > > > >    File
> > > > > "/gpfs/home/jkumar/lib/petsc/config/BuildSystem/config/framework.py",
> > > > line
> > > > > 933, in configure
> > > > >      child.configure()
> > > > >    File
> > > > > "/gpfs/home/jkumar/lib/petsc/config/BuildSystem/config/types.py",
> > > > > line 386, in configure
> > > > >      map(lambda type: self.executeTest(self.checkSizeof, type),
> > > > > ['char','void *', 'short', 'int', 'long', 'long long', 'float',
> > > > > 'double',
> > > > > 'size_t'])
> > > > >    File
> > > > > "/gpfs/home/jkumar/lib/petsc/config/BuildSystem/config/types.py",
> > > > > line 386, in <lambda>
> > > > >      map(lambda type: self.executeTest(self.checkSizeof, type),
> > > > > ['char','void *', 'short', 'int', 'long', 'long long', 'float',
> > > > > 'double',
> > > > > 'size_t'])
> > > > >    File
> > > > > "/gpfs/home/jkumar/lib/petsc/config/BuildSystem/config/base.py",
> > > > > line 115, in executeTest
> > > > >      ret = apply(test, args,kargs)
> > > > >    File
> > > > > "/gpfs/home/jkumar/lib/petsc/config/BuildSystem/config/types.py",
> > > > > line 296, in checkSizeof
> > > > >      raise RuntimeError(msg)
> > > > > 
> > > > > This is what my configuration looks like (adapted from
> > > > > config/examples/arch-bgp-ibm-opt.py)
> > > > > configure_options = [
> > > > >    '--with-cc=mpixlc',
> > > > >    '--with-fc=mpixlf90',
> > > > >    '--with-cxx=mpixlcxx',
> > > > >    'COPTFLAGS=-O3',
> > > > >    'FOPTFLAGS=-O3',
> > > > >    '--with-debugging=0',
> > > > >    '--with-cmake=/soft/apps/fen/cmake-2.8.3/bin/cmake',
> > > > > #  '--with-hdf5=/soft/apps/hdf5-1.8.0',
> > > > >    '--download-parmetis=1',
> > > > >    '--download-metis=1',
> > > > >    '--download-plapack=1',
> > > > >    '--download-hdf5=1'
> > > > >    ]
> > > > > 
> > > > > I would appreciate any help building the llbrary there.
> > > > > 
> > > > > Thanks,
> > > > > Jitu
> > > > > 
> > > > 
> 
> 
>

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