[petsc-users] Solving Poisson equation with multigrid

[Michele Rosso]

Thanks Satish, now the compilation goes smooth, despite a warning during 
the configuration step:

===============================================================================
               Warning: PETSC_ARCH from environment does not match 
command-line or name of script.
               Warning: Using from command-line or name of script: 
arch-test-cray, ignoring environment: interlagos
===============================================================================

I still have a problem though:  when I compile my code the following 
warning is issued:

/u/sciteam/mrosso/LIBS/petsc-3.4.0/arch-test-cray/lib/libpetsc.a(dlimpl.o): 
In function `PetscDLOpen':
/mnt/a/u/sciteam/mrosso/LIBS/petsc-3.4.0/src/sys/dll/dlimpl.c:109: 
warning: Using 'dlopen' in statically linked applications requires at 
runtime the shared libraries from the glibc version used for linking
/u/sciteam/mrosso/LIBS/petsc-3.4.0/arch-test-cray/lib/libpetsc.a(send.o): In 
function `PetscOpenSocket':
/mnt/a/u/sciteam/mrosso/LIBS/petsc-3.4.0/src/sys/classes/viewer/impls/socket/send.c:97: 
warning: Using 'gethostbyname' in statically linked applications 
requires at runtime the shared libraries from the glibc version used for 
linking

and the run stops because of the following error:

         libhugetlbfs:  ERROR: RTLD_NEXT used in code not dynamically loaded

Thanks again for your help.

Michele

> On Thu, 6 Jun 2013, Michele Rosso wrote:
>
>> Hi Satish,
>>
>> I tried what you suggested:
>>
>> #!/usr/bin/python
>> if __name__ == '__main__':
>>    import sys
>>    import os
>>    sys.path.insert(0, os.path.abspath('config'))
>>    import configure
>>    configure_options = [
>>      'PETSC_DIR=/u/sciteam/mrosso/LIBS/petsc-3.4.0',
>>      '--with-cc=cc',
>>      '--with-clib-autodetect=0',
>>      '--with-cxx=CC',
>>      '--with-cxxlib-autodetect=0',
>>      '--with-fc=ftn',
>>      '--with-fortranlib-autodetect=0',
>>      '--with-x=0',
>>      '--with-debgging=0',
>>      '--COPTFLAGS=-O3',
>>      '--FOPTFLAGS=-O3',
>>      'FFLAGS=-F -em',
>>      'LIBS=-L/opt/cray/cce/8.1.7/CC/x86-64/lib/x86-64/ -lcray-c++ -rts
>                                      you have an extra space here  ^  It should be -lcray-c++-rt
>
> Satish
>
>
>> -lcraystdc++ -lsupc++ -lgcc_eh',
>>      'PETSC_ARCH=arch-test-cray',
>>    ]
>>    configure.petsc_configure(configure_options)
>>
>> but now I receive another error:
>>
>> "C compiler you provided with -with-cc=cc does not work"
>>
>> I attached the log file. Thanks for your help.
>>
>> Michele
>>
>>
>> On 06/05/2013 02:15 PM, Satish Balay wrote:
>>> Sorry my configure cmd file was from an older test case for c++.
>>>
>>> Do you need c++ build of PETSc? If not - suggest removing
>>> --with-clanguage=C++ option.
>>>
>>> [Majority of use cases should not need --with-clanguage=C++ - even if
>>> user code is using PETSc from C++]
>>>
>>> If c++ is needed - you can try adding: CXXCPPFLAGS='-h gnu'
>>>
>>> Satish
>>>
>>> On Wed, 5 Jun 2013, Michele Rosso wrote:
>>>
>>>> Thank you Satish for your help.
>>>> I followed you instructions, but I am getting some errors during the
>>>> compilation.
>>>> I attached the python script I used to configure PETSc, and the logs for
>>>> both
>>>> configure and make.
>>>>
>>>>
>>>> Michele
>>>>
>>>> On 05/31/2013 05:08 PM, Satish Balay wrote:
>>>>> The following is my configure command to build PETSc on a cray with
>>>>> cray compilers:
>>>>>
>>>>> $ cat reconfigure-arch-test-cray.py
>>>>> #!/usr/bin/python
>>>>> if __name__ == '__main__':
>>>>>      import sys
>>>>>      import os
>>>>>      sys.path.insert(0, os.path.abspath('config'))
>>>>>      import configure
>>>>>      configure_options = [
>>>>>        '--with-cc=cc',
>>>>>        '--with-clanguage=C++',
>>>>>        '--with-clib-autodetect=0',
>>>>>        '--with-cxx=CC',
>>>>>        '--with-cxxlib-autodetect=0',
>>>>>        '--with-fc=ftn',
>>>>>        '--with-fortranlib-autodetect=0',
>>>>>        '--with-x=0',
>>>>>        'FFLAGS=-F -em',
>>>>>        'LIBS=-L/opt/cray/cce/8.1.4/CC/x86-64/lib/x86-64/ -lcray-c++-rts
>>>>> -lcraystdc++ -lsupc++ -lgcc_eh',
>>>>>        'PETSC_ARCH=arch-test-cray',
>>>>>      ]
>>>>>      configure.petsc_configure(configure_options)
>>>>> <<<<<<<<<
>>>>>
>>>>> And you might have to look for the recommended optimization flags - and
>>>>> use
>>>>> with:
>>>>> --with-debgging=0 COPTFLAGS= FOPTFLAGS= CXXOPTFLAGS= etc.
>>>>>
>>>>> And on BlueWaters - you would have to remove the following lines from
>>>>> PETSC_ARCH/include/petscconf.h [before runing 'make all' to build the
>>>>> libraries]
>>>>>
>>>>> #ifndef PETSC_HAVE_GETPWUID
>>>>> #define PETSC_HAVE_GETPWUID 1
>>>>> #endif
>>>>> <<<<<
>>>>>
>>>>> Satish
>>>>>
>>>>> On Fri, 31 May 2013, Michele Rosso wrote:
>>>>>
>>>>>> Thanks, but I'd rather use Cray since only a small part of my code
>>>>>> relies
>>>>>> on
>>>>>> PETSc and, as suggested by the BW staff,
>>>>>> Cray-compiled code performs generally better on Cray system.
>>>>>>
>>>>>> Michele
>>>>>>
>>>>>> On 05/31/2013 02:57 PM, Jed Brown wrote:
>>>>>>> Michele Rosso <mrosso at uci.edu> writes:
>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> I confirm that
>>>>>>>>
>>>>>>>>              -pc_type gamg  -pc_mg_cycle_type v
>>>>>>>> -pc_gamg_agg_nsmooths 1
>>>>>>>>
>>>>>>>> produces the correct shift in PETSc 3.4.
>>>>>>>> So my problem is solved.   I will upgrade to 3.4 in my productive
>>>>>>>> machine installation.
>>>>>>>> It is a Cray machine (Blue Waters). Assuming I want to use the
>>>>>>>> Cray
>>>>>>>> compiler, which options should I use for ./configure
>>>>>>>> for the installation.
>>>>>>> Or the Intel compiler or GCC.  PETSc should run at similar speed
>>>>>>> with
>>>>>>> any.  IIRC, Cray recommends the Intel compiler on their machines
>>>>>>> with
>>>>>>> Intel CPUs.  There are examples in config/examples/.
>>>>>>>
>>

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