[petsc-users] Fwd: PETSc installation on Intrepid
Richard Tran Mills
rtm at eecs.utk.edu
Mon Jul 29 14:45:35 CDT 2013
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
/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
>>>>>>
>>>>>
>>>
--
Richard Tran Mills, Ph.D.
Computational Earth Scientist | Joint Assistant Professor
Hydrogeochemical Dynamics Team | EECS and Earth & Planetary Sciences
Oak Ridge National Laboratory | University of Tennessee, Knoxville
E-mail: rmills at ornl.gov V: 865-241-3198 http://climate.ornl.gov/~rmills
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