[petsc-users] error in petsc-dev

Hong Zhang hzhang at mcs.anl.gov
Wed Apr 25 09:47:56 CDT 2012 

Mohammad :

> When I do not explicitly set the type in petsc-dev I get errors:
>

Did you follow same procedural call as petsc examples, e.g.,
petsc-dev/src/ksp/ksp/examples/tutorials/ex2.c:
   ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
  ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,m*n,m*n);CHKERRQ(ierr);
  ierr = MatSetFromOptions(A);CHKERRQ(ierr);
  ierr =
MatMPIAIJSetPreallocation(A,5,PETSC_NULL,5,PETSC_NULL);CHKERRQ(ierr);
  ierr = MatSeqAIJSetPreallocation(A,5,PETSC_NULL);CHKERRQ(ierr);
...
Hong

>
> [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]PETSCERROR: 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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