Installation

[Panyasantisuk Jarunan]

Hi,

I have upgraded Petsc to 3.0.0. For the configuration(1) I got C++ 
error. Anyway I could do make but make test failed for Fortran 
example(2).

Do you have any idea? I would be appreciate for any advise. Thank you 
very much.

Regards,
Jarunan

- - - - (1) - - - -

./config/configure.py --with-cc=/usr/local/mpich-ifc-ssh/bin/mpicc 
--with-fc=/usr/local/mpich-ifc-ssh/bin/mpif90 
--download-f-blas-lapack=1 --download-hypre=1 --download-ml=1 
--with-cxx=icpc --with-mpi-dir=/usr/local/mpich-ifc-ssh --with-shared=0
=================================================================================
             Configuring PETSc to compile on your system
=================================================================================
=================================================================================                                                                Warning: [with-mpi-dir] option is used along with options: ['with-cc', 'with-fc', 'with-cxx']                                              This prevents configure from picking up MPI compilers from specified mpi-dir.                                                                                                                                                                                                         Sugest using *only* [with-mpi-dir] option - and no other compiler option.                                                                  This way - mpi compilers from /usr/local/mpich-ifc-ssh are used.                                                                     =================================================================================                                                          TESTING: CxxMPICheck from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:598)                                               
*********************************************************************************
         UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log 
for details):
---------------------------------------------------------------------------------------
C++ error! MPI_Finalize() could not be located!



- - - - (2) - - - -

make test

Running test examples to verify correct installation
C/C++ example src/snes/examples/tutorials/ex19 run successfully with 1 
MPI process
C/C++ example src/snes/examples/tutorials/ex19 run successfully with 2 
MPI processes
Graphics example src/snes/examples/tutorials/ex19 run successfully with 
1 MPI process
Error running Fortran example src/snes/examples/tutorials/ex5f with 1 
MPI process
See http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html
0 - <NO ERROR MESSAGE> : Could not convert index 1140850688 into a pointer
The index may be an incorrect argument.
Possible sources of this problem are a missing "include 'mpif.h'",
a misspelled MPI object (e.g., MPI_COM_WORLD instead of MPI_COMM_WORLD)
or a misspelled user variable for an MPI object (e.g.,
com instead of comm).
[0]  Aborting program !
[0] Aborting program!
p0_31302:  p4_error: : 9039
Completed test examples


-- 
Jarunan PANYASANTISUK
MSc. in Computational Mechanics
Erasmus Mundus Master Program
Ecole Centrale de Nantes
1, rue de la noë, 44321 NANTES, FRANCE



Matthew Knepley <knepley at gmail.com> a écrit :

> On Thu, Jan 15, 2009 at 9:42 AM, Panyasantisuk Jarunan <
> Jarunan.Panyasantisuk at eleves.ec-nantes.fr> wrote:
>
>> When I create a matrix with MatCreateMPIAIJWithSplitArrays, as it doesn't
>> copy the values so I have to use MatSetValues to set the internal value?
>
>
> 1) You should upgrade to 3.0.0
>
> 2) You should not have to call MatSetValues(). It will use the arrays you
> provide.
>
>  Matt
>
>
>>
>> --
>> Jarunan PANYASANTISUK
>> MSc. in Computational Mechanics
>> Erasmus Mundus Master Program
>> Ecole Centrale de Nantes
>> 1, rue de la noë, 44321 NANTES, FRANCE
>>
>>
>>
>> Barry Smith <bsmith at mcs.anl.gov> a Ã(c)crit :
>>
>>
>>>   You should be able to use MatCreateMPIAIJWithSplitArrays(),
>>>  MatCreateMPIAIJWithArrays() or MatMPIAIJSetPreallocationCSR()
>>> from Fortran. Are you using PETSc 3.0.0?
>>>
>>>   The arguments for MatCreateMPIAIJWithArrays() or
>>>  MatMPIAIJSetPreallocationCSR() have the same meaning
>>> (in fact MatCreateMPIAIJWithArrays() essentially calls
>>>  MatCreateMPIAIJWithArrays()).
>>>
>>>   Barry
>>>
>>> On Jan 14, 2009, at 7:38 AM, Panyasantisuk Jarunan wrote:
>>>
>>>  Oh, I could not use MatCreateMPIAIJWithArrays either but the  mechanism
>>>> below works.
>>>>
>>>>    call MatCreate(PETSC_COMM_WORLD,D,ierr)
>>>>    call MatSetSizes(D,N,N,PETSC_DETERMINE,PETSC_DETERMINE,
>>>>   $     ierr)
>>>>    call MatSetType(D,MATMPIAIJ,ierr) ! to set type a parallel matrix
>>>>    call MatSetFromOptions(D,ierr)
>>>>    call MatMPIAIJSetPreallocationCSR(D,pointer,Column,v,ierr)
>>>>
>>>> Where pointer is start-row indices a
>>>>    Column is local column indices
>>>>    v is value
>>>>
>>>> Is there the different beteween the start-row indices in
>>>>  MatMPIAIJSetPreallocationCSR and row indices in  
>>>> MatCreateMPIAIJWithArrays
>>>> ?
>>>>
>>>>
>>>>
>>>> Regards,
>>>> Jarunan
>>>>
>>>>
>>>>
>>>>
>>>> Hello,
>>>>
>>>> To define a matrix with arrays, I cannot use
>>>>  MatCreateMPIAIJWithSplitArrays in my program which is written in  
>>>> Fortran:
>>>>
>>>>    call MatCreateMPIAIJWithSplitArrays(PETSC_COMM_WORLD,N,N,
>>>>   $     PETSC_DETERMINE,PETSC_DETERMINE,pointer,column,v,opointer,
>>>>   $     oColumn,ov,D,ierr)
>>>>
>>>> The error is
>>>> F:246: undefined reference to `matcreatempiaijwithsplitarrays_'
>>>>
>>>> I could use MatCreateMPIAIJWithArrays but the off diagonal values  are
>>>> missing with this command.
>>>>
>>>> I would be appreciate for any advice. Thank you before hand.
>>>>
>>>> Regards,
>>>> Jarunan
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Jarunan PANYASANTISUK
>>>> MSc. in Computational Mechanics
>>>> Erasmus Mundus Master Program
>>>> Ecole Centrale de Nantes
>>>> 1, rue de la noë, 44321 NANTES, FRANCE
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>>
>
>
> --
> What most experimenters take for granted before they begin their experiments
> is infinitely more interesting than any results to which their experiments
> lead.
> -- Norbert Wiener
>