[petsc-users] error in petsc-dev
Mohammad Mirzadeh
mirzadeh at gmail.com
Wed Apr 25 00:53:44 CDT 2012
When I do not explicitly set the type in petsc-dev I get errors:
[0]PETSC ERROR: --------------------- Error Message
------------------------------------
[0]PETSC ERROR: Object is in wrong state!
[0]PETSC ERROR: Mat object's type is not set: Argument # 1!
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Development HG revision:
5c943f0d8cbf252873fd4abeffa38c8d3c15987e HG Date: Mon Apr 09 22:04:11 2012
-0500
[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: ./petsc on a arch-linu named mohammad-laptop by mohammad
Tue Apr 24 22:49:38 2012
[0]PETSC ERROR: Libraries linked from
/home/mohammad/soft/petsc-dev/arch-linux2-cxx-debug/lib
[0]PETSC ERROR: Configure run at Mon Apr 9 23:17:27 2012
[0]PETSC ERROR: Configure options --with-clanguage=cxx --with-cc=gcc
--with-cxx=g++ --with-fc=gfortran --download-mpich=1
--download-f-blas-lapack=1 --download-hypre=1 --download-superlu_dist=1
--download-metis=1 --download-parmetis=1
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: MatMPIAIJSetPreallocation() line 3883 in
/home/mohammad/soft/petsc-dev/src/mat/impls/aij/mpi/mpiaij.c
[0]PETSC ERROR: --------------------- Error Message
------------------------------------
[0]PETSC ERROR: Object is in wrong state!
[0]PETSC ERROR: Must call MatXXXSetPreallocation() or MatSetUp() on
argument 1 "mat" before MatGetOwnershipRange()!
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Development HG revision:
5c943f0d8cbf252873fd4abeffa38c8d3c15987e HG Date: Mon Apr 09 22:04:11 2012
-0500
[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: ./petsc on a arch-linu named mohammad-laptop by mohammad
Tue Apr 24 22:49:38 2012
[0]PETSC ERROR: Libraries linked from
/home/mohammad/soft/petsc-dev/arch-linux2-cxx-debug/lib
[0]PETSC ERROR: Configure run at Mon Apr 9 23:17:27 2012
[0]PETSC ERROR: Configure options --with-clanguage=cxx --with-cc=gcc
--with-cxx=g++ --with-fc=gfortran --download-mpich=1
--download-f-blas-lapack=1 --download-hypre=1 --download-superlu_dist=1
--download-metis=1 --download-parmetis=1
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: MatGetOwnershipRange() line 6106 in
/home/mohammad/soft/petsc-dev/src/mat/interface/matrix.c
[0]PETSC ERROR: --------------------- Error Message
------------------------------------
[0]PETSC ERROR: Object is in wrong state!
[0]PETSC ERROR: Must call MatXXXSetPreallocation() or MatSetUp() on
argument 1 "mat" before MatAssemblyBegin()!
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Development HG revision:
5c943f0d8cbf252873fd4abeffa38c8d3c15987e HG Date: Mon Apr 09 22:04:11 2012
-0500
[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: ./petsc on a arch-linu named mohammad-laptop by mohammad
Tue Apr 24 22:49:38 2012
[0]PETSC ERROR: Libraries linked from
/home/mohammad/soft/petsc-dev/arch-linux2-cxx-debug/lib
[0]PETSC ERROR: Configure run at Mon Apr 9 23:17:27 2012
[0]PETSC ERROR: Configure options --with-clanguage=cxx --with-cc=gcc
--with-cxx=g++ --with-fc=gfortran --download-mpich=1
--download-f-blas-lapack=1 --download-hypre=1 --download-superlu_dist=1
--download-metis=1 --download-parmetis=1
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: MatAssemblyBegin() line 4810 in
/home/mohammad/soft/petsc-dev/src/mat/interface/matrix.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/documentation/faq.html#valgrind[0]PETSC ERROR:
or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory
corruption errors
[0]PETSC ERROR: likely location of problem given in stack below
[0]PETSC ERROR: --------------------- Stack Frames
------------------------------------
[0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
[0]PETSC ERROR: INSTEAD the line number of the start of the function
[0]PETSC ERROR: is given.
[0]PETSC ERROR: [0] MatAssemblyEnd_SeqAIJ line 800
/home/mohammad/soft/petsc-dev/src/mat/impls/aij/seq/aij.c
[0]PETSC ERROR: [0] MatAssemblyEnd line 4984
/home/mohammad/soft/petsc-dev/src/mat/interface/matrix.c
[0]PETSC ERROR: [0] MatAssemblyBegin line 4807
/home/mohammad/soft/petsc-dev/src/mat/interface/matrix.c
[0]PETSC ERROR: [0] MatGetOwnershipRange line 6101
/home/mohammad/soft/petsc-dev/src/mat/interface/matrix.c
[0]PETSC ERROR: [0] MatMPIAIJSetPreallocation line 3881
/home/mohammad/soft/petsc-dev/src/mat/impls/aij/mpi/mpiaij.c
[0]PETSC ERROR: --------------------- Error Message
------------------------------------
[0]PETSC ERROR: Signal received!
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Development HG revision:
5c943f0d8cbf252873fd4abeffa38c8d3c15987e HG Date: Mon Apr 09 22:04:11 2012
-0500
[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: ./petsc on a arch-linu named mohammad-laptop by mohammad
Tue Apr 24 22:49:38 2012
[0]PETSC ERROR: Libraries linked from
/home/mohammad/soft/petsc-dev/arch-linux2-cxx-debug/lib
[0]PETSC ERROR: Configure run at Mon Apr 9 23:17:27 2012
[0]PETSC ERROR: Configure options --with-clanguage=cxx --with-cc=gcc
--with-cxx=g++ --with-fc=gfortran --download-mpich=1
--download-f-blas-lapack=1 --download-hypre=1 --download-superlu_dist=1
--download-metis=1 --download-parmetis=1
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: User provided function() line 0 in unknown directory
unknown file
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
Even more than that, I get lots of errors apparently complaining that I
have not preallocated the matrix:
[0]PETSC ERROR: --------------------- Error Message
------------------------------------
[0]PETSC ERROR: Argument out of range!
[0]PETSC ERROR: New nonzero at (6,209) caused a malloc!
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Development HG revision:
5c943f0d8cbf252873fd4abeffa38c8d3c15987e HG Date: Mon Apr 09 22:04:11 2012
-0500
[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: ./petsc on a arch-linu named mohammad-laptop by mohammad
Tue Apr 24 22:44:09 2012
[0]PETSC ERROR: Libraries linked from
/home/mohammad/soft/petsc-dev/arch-linux2-cxx-debug/lib
[0]PETSC ERROR: Configure run at Mon Apr 9 23:17:27 2012
[0]PETSC ERROR: Configure options --with-clanguage=cxx --with-cc=gcc
--with-cxx=g++ --with-fc=gfortran --download-mpich=1
--download-f-blas-lapack=1 --download-hypre=1 --download-superlu_dist=1
--download-metis=1 --download-parmetis=1
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: MatSetValues_MPIAIJ() line 507 in
/home/mohammad/soft/petsc-dev/src/mat/impls/aij/mpi/mpiaij.c
[0]PETSC ERROR: MatSetValues() line 1148 in
/home/mohammad/soft/petsc-dev/src/mat/interface/matrix.c
I do not see these with 3.2-p6. Does 3.2-p6 has any mechanism for such
alerts?
On Tue, Apr 24, 2012 at 5:58 PM, Hong Zhang <hzhang at mcs.anl.gov> wrote:
> Mohammad :
>
>>
>> Is this also true with MatSetType()? petsc-dev seems to need it (3.2-p6
>> does not) but it's not listed in the changes link ...
>>
> There is no change on MatSetType(). The default type is aij.
> You can check petsc examples,
> e.g. petsc-dev/src/ksp/ksp/examples/tutorials/ex2.c
>
> Hong
>
>>
>>
>> On Tue, Apr 24, 2012 at 4:27 PM, Mohammad Mirzadeh <mirzadeh at gmail.com>wrote:
>>
>>> Thanks Hong.
>>>
>>>
>>> On Tue, Apr 24, 2012 at 4:25 PM, Hong Zhang <hzhang at mcs.anl.gov> wrote:
>>>
>>>> See
>>>> http://www.mcs.anl.gov/petsc/documentation/changes/dev.html:
>>>>
>>>> You MUST now call MatXXXSetPreallocation() or MatSetUp() on any matrix
>>>> you create directly (not using DMCreateMatrix()) before calling
>>>> MatSetValues(), MatSetValuesBlocked() etc.
>>>>
>>>>
>>>> On Tue, Apr 24, 2012 at 6:01 PM, Mohammad Mirzadeh <mirzadeh at gmail.com>wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> While trying to figure out a problem, I came across the following
>>>>> situation. Consider the following code:
>>>>>
>>>>> int main (int argc, char **argv){
>>>>>
>>>>> PetscInitialize(&argc, &argv, (char*)0, help);
>>>>>
>>>>>
>>>>> Mat m;
>>>>>
>>>>> MatCreate(PETSC_COMM_WORLD, &m);
>>>>>
>>>>> MatSetSizes(m, 10, 10, PETSC_DECIDE, PETSC_DECIDE);
>>>>>
>>>>> MatSetFromOptions(m);
>>>>>
>>>>> MatAssemblyBegin(m, MAT_FINAL_ASSEMBLY);
>>>>>
>>>>> MatAssemblyEnd(m, MAT_FINAL_ASSEMBLY);
>>>>>
>>>>> MatView(m, PETSC_VIEWER_STDOUT_WORLD);
>>>>>
>>>>> MatDestroy(&m);
>>>>>
>>>>>
>>>>> PetscFinalize();
>>>>>
>>>>> return 0;
>>>>>
>>>>> }
>>>>>
>>>>>
>>>>> This runs without any problem under 3.2-p6 but fails with petsc-dev:
>>>>>
>>>>> [0]PETSC ERROR: --------------------- Error Message
>>>>> ------------------------------------
>>>>> [0]PETSC ERROR: Object is in wrong state!
>>>>> [0]PETSC ERROR: Must call MatXXXSetPreallocation() or MatSetUp() on
>>>>> argument 1 "mat" before MatAssemblyBegin()!
>>>>> [0]PETSC ERROR:
>>>>> ------------------------------------------------------------------------
>>>>>
>>>>> Eventually I could fix this by adding MatSetUp(m) after setting the
>>>>> options. Why do I need this in petsc-dev? Does this somehow preallocate the
>>>>> matrix?
>>>>>
>>>> Yes.
>>>>
>>>> Hong
>>>>
>>>>>
>>>>> Thanks,
>>>>> Mohammad
>>>>>
>>>>
>>>>
>>>
>>
>
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