[petsc-users] Fwd: PETSc installation on Intrepid
Satish Balay
balay at mcs.anl.gov
Mon Jul 29 14:49:41 CDT 2013
On Mon, 29 Jul 2013, Richard Tran Mills wrote:
> Hi Jitu,
>
> I suspect that this problem doesn't have anything to do with a PETSc configure
> problem on the machine. Strangely, I am not seeing the same error when I
> attempt to build the same file:
>
> mpixlf2003_r -qnosave -qxlf2003=polymorphic -c -g -qarch=450d -qtune=450
> -qmaxmem=-1 -I/home/rmills/proj/petsc/include
> -I/home/rmills/proj/petsc/bgp-ibm_g/include
> -I/soft/apps/current/hdf5-1.8.9/include
> -I/bgsys/drivers/V1R4M2_200_2010-100508P/ppc/comm/default/include
> -I/bgsys/drivers/V1R4M2_200_2010-100508P/ppc/comm/sys/include -I. -o utility.o
> utility.F90
> ** utility_module === End of Compilation 1 ===
> 1501-510 Compilation successful for file utility.F90.
>
> I do note that you need to add the compiler option '-qxlf2003=polymorphic' so
> that Fortran 2003 classes will work. I did this in my PETSc configure file by
> specifying ''--with-fc=mpixlf2003_r -qnosave -qxlf2003=polymorphic'', though I
> believe that the proper way to do this is specify the Fortran flags separately
> using '--FFLAGS=<string>'. You can have a look at my PETSc configure file on
> Intrepid at
These extra compiler flags can be added in pflotran makefile or invoke make with these options..
make FFLAGS=-qxlf2003=polymorphic flow
etc..
>
> /home/rmills/proj/petsc/config/bgp-gnu_g.py
>
> I'm still seeing lots of compile errors with the IBM compilers, which I am
> working through. Also working on GCC, though the "official" version of the
> compilers on the machine is too old. (An ALCF staff member did point me to a
> more recent build to try.)
>
> We should probably take this discussion off the petsc-users list unless we
> determine that it really is a problem with the PETSc configure.
>
> Best regards,
> Richard
>
>
> On 7/29/13 3:25 PM, Satish Balay wrote:
> > mpixlf2003_r -qnosave -c -O3 -qarch=450d -qtune=450 -qmaxmem=-1
> > -I/gpfs/home/jkumar/lib/petsc-hg/include
> > -I/gpfs/home/jkumar/lib/petsc-hg/arch-bgp-ibm-opt/i\
> > nclude -I/soft/apps/current/hdf5-1.8.9/include
> > -I/bgsys/drivers/V1R4M2_200_2010-100508P/ppc/comm/default/include
> > -I/bgsys/drivers/V1R4M2_200_2010-100508P/ppc/c\
> > omm/sys/include -I. -DMUALEM_SPLINE -DICE -o utility.o utility.F90
> > bgxlf2003_r: 1501-214 (W) command option M reserved for future use - ignored
> > "utility.F90", line 61.14: 1516-036 (S) Entity M1 has undefined type.
> > "utility.F90", line 62.14: 1516-036 (S) Entity IA1 has undefined type.
> > "utility.F90", line 63.14: 1516-036 (S) Entity IC1 has undefined type.
> > "utility.F90", line 65.14: 1516-036 (S) Entity M2 has undefined type.
> > "utility.F90", line 66.14: 1516-036 (S) Entity IA2 has undefined type.
> > "utility.F90", line 67.14: 1516-036 (S) Entity IC2 has undefined type.
> > "utility.F90", line 69.14: 1516-036 (S) Entity M3 has undefined type.
> > "utility.F90", line 70.14: 1516-036 (S) Entity IA3 has undefined type.
> > "utility.F90", line 71.14: 1516-036 (S) Entity IC3 has undefined type.
> > "utility.F90", 1520-031 (W) Option DLINES is ignored within Fortran 90 free
> > form and IBM free form.
> > ** Utility_module === End of Compilation 1 ===
> > 1501-511 Compilation failed for file utility.F90.
> > <<<<<<
> >
> > On Mon, 29 Jul 2013, Jitendra Kumar wrote:
> >
> > > Satish,
> > > By building my own zlib library specifying it through LIBS flag to PETSc
> > > configure, I was able to compile PETSC-Dev with HDF5 support on Intrepid.
> > > However, I ran into errors while building my application and it looks like
> > > the XLF Fortran is using case sensitive settings and is failing due to
> > > mixed uppercase/lowercase variable names in the code.
> > Are you sure this is the problem? I can't reporduce it with a simple code..
> >
> >
> > Satish
> >
> > --------
> > [balay at vestalac1 junk]$ cat foo.F
> > program main
> > implicit none
> > integer i
> > I=5
> > write(*,*) I
> > end
> > [balay at vestalac1 junk]$ mpixlf2003_r foo.F
> > ** main === End of Compilation 1 ===
> > 1501-510 Compilation successful for file foo.F.
> > [balay at vestalac1 junk]$ ./a.out
> > 5
> >
> >
> > > I have followed the
> > > /soft/apps/libraries/petsc/3.3-p6/xl-opt/conf/reconfigure-arch-bgp-ibm-opt.py
> > > and am not sure if there's something included or missing in the
> > > configuration causing this. I believe default is for XLF to not to be case
> > > sensitive, but I am not sure what do I have that's making it otherwise.
> > >
> > > I would appreciate if you can point me to anything I may be missing in my
> > > configuration file. Attached are petsc configuration file and log of my
> > > application compilation errors.
> > >
> > > Thanks,
> > > Jitu
> > >
> > >
> > >
> > > On Tue, Jul 16, 2013 at 12:59 PM, Satish Balay <balay at mcs.anl.gov> 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
> > > > > > >
> > > > > >
> > > >
>
>
>
More information about the petsc-users
mailing list