[petsc-users] extract data from vector in petsc into fortran array

[Bo Sun]

Hi Barry,
Thank you for your reply.  Sorry to confuse you. The strange data means
that when I run the case using only one cpu, after some steps, the case
blows up or give wrong data. I think that is because the local memory is
not enough. And some case gives the following error message "

[0]PETSC ERROR: --------------------- Error Message
------------------------------------
[0]PETSC ERROR: Out of memory. This could be due to allocating
[0]PETSC ERROR: too large an object or bleeding by not properly
[0]PETSC ERROR: destroying unneeded objects.
[0]PETSC ERROR: Memory allocated 0 Memory used by process 1882513408
[0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info.
[0]PETSC ERROR: Memory requested 2628072!
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 3.2.0, Patch 6, Wed Jan 11 09:28:45
CST 2012
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: ./main on a arch-linu named lightningsmp.its.iastate.edu by
sciam Thu May  3 15:58:24 2012
[0]PETSC ERROR: Libraries linked from
/work/doe_ar1/sciam/petsc-3.2-p6/arch-linux2-c-opt/lib
[0]PETSC ERROR: Configure run at Wed Apr  4 12:45:08 2012
[0]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif90
--with-debugging=0 FOPTFLAGS="-O3 -qarch=p4 -qtune=p4"
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: PetscMallocAlign() line 49 in src/sys/memory/mal.c
[0]PETSC ERROR: VecCreate_Seq() line 40 in src/vec/vec/impls/seq/bvec3.c
[0]PETSC ERROR: VecSetType() line 53 in src/vec/vec/interface/vecreg.c
[0]PETSC ERROR: VecDuplicate_Seq() line 800 in src/vec/vec/impls/seq/bvec2.c
[0]PETSC ERROR: VecDuplicate() line 541 in src/vec/vec/interface/vector.c
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/petsc-as/documentation/faq.html#valgrind[0]PETSCERROR:
or try
http://valgrind.org on GNU/linux and Apple Mac OS X to find memory
corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: --------------------- Error Message
------------------------------------
[0]PETSC ERROR: Signal received!
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 3.2.0, Patch 6, Wed Jan 11 09:28:45
CST 2012
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: ./main on a arch-linu named lightningsmp.its.iastate.edu by
sciam Thu May  3 15:58:24 2012
[0]PETSC ERROR: Libraries linked from
/work/doe_ar1/sciam/petsc-3.2-p6/arch-linux2-c-opt/lib
[0]PETSC ERROR: Configure run at Wed Apr  4 12:45:08 2012
[0]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif90
--with-debugging=0 FOPTFLAGS="-O3 -qarch=p4 -qtune=p4"
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: User provided function() line 0 in unknown directory
unknown file
------------------------------------------------------------------------------------------------------------------------------

The input from fortran array to petsc vector and output from petsc vector
to fortran array happens in each loop. I guess that I didn't do
appropriate  destroy to the vector in petsc.

Regards,
Bo

On Wed, May 2, 2012 at 11:01 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:

>
> On May 2, 2012, at 11:32 PM, Bo Sun wrote:
>
> > Hi there,
> > I am coding using Fortran 90 with petsc. I extract the results from
> vector in petsc as follows,
> >
> >    PetscScalar, pointer :: xx_v(:)
> >    Vec pet_u
> >
> >    ..............
> >    call VecGetArrayF90(pet_u,xx_v,ierr)
> >     data_for_fortran = xx_v
> >     call VecRestoreArrayF90(pet_u,xx_v,ierr)
> >    ...................
> >
> >
> > For small size of vector, there is no problem. But when the size of
> vector is above million, some strange data appear.
>
>    What do you mean strange data? Is this reproducable? Do two different
> Fortran compilers give the same problem? I you can send us a simple Fortran
> code that demonstrates the problem we can try to reproduce it. Please send
> such a bug report to petsc-maint at mcs.anl.gov
>
>   VecGetArrayF90() is generally the way to go, other things are more
> cumbersome.
> >
>
>
> > Could you recommend another way to output the data of vector in petsc
> into fortran array ?
> >
> >
> > Thanks,
> > Bo
>
>


-- 
--------------------------------------------------------------------
CFD
Mechanical Engineering
Iowa State University
50011
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