[petsc-users] Petsc creates a random vector

Dmitry Karpeyev dkarpeev at gmail.com
Mon Aug 17 11:49:56 CDT 2015 

Use a dbg build with a debugger and/or valgrind.

Dmitry.

On Mon, Aug 17, 2015 at 11:31 AM Xujun Zhao <xzhao99 at gmail.com> wrote:

> This is run with PETSc opt mode, so the error message looks not very
> useful, see below:
> Probably I should use dbg version to see the details.
>
> [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: configure using --with-debugging=yes, recompile, link, and
> run
>
> [0]PETSC ERROR: to get more information on the crash.
>
> [1]PETSC ERROR:
> ------------------------------------------------------------------------
>
> [1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
>
> [1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>
> [1]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
>
> [1]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS
> X to find memory corruption errors
>
> [1]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
> run
>
> [2]PETSC ERROR:
> ------------------------------------------------------------------------
>
> [2]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
>
> [2]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>
> [2]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
>
> [2]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS
> X to find memory corruption errors
>
> [2]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
> run
>
> [2]PETSC ERROR: [1]PETSC ERROR: to get more information on the crash.
>
> to get more information on the crash.
>
> [3]PETSC ERROR:
> ------------------------------------------------------------------------
>
> [3]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
>
> [3]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>
> [3]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
>
> [3]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS
> X to find memory corruption errors
>
> [3]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
> run
>
> [3]PETSC ERROR: to get more information on the crash.
>
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
>
> [0]PETSC ERROR: Signal received
>
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
>
> [0]PETSC ERROR: Petsc Release Version 3.5.4, May, 23, 2015
>
> [0]PETSC ERROR: ./example-opt on a arch-darwin-c-opt named
> mcswl164.mcs.anl.gov by xzhao Mon Aug 17 11:20:33 2015
>
> [0]PETSC ERROR: Configure options --with-cc=gcc-4.9 --with-cxx=g++-4.9
> --with-fc=gfortran-4.9 --with-cxx-dialect=C++11 --download-mpich
> --download-fblaslapack --download-scalapack --download-mumps
> --download-superlu_dist --download-hypre --download-ml --download-parmetis
> --download-metis --download-triangle --download-chaco --download-elemental
> --with-debugging=0
>
> [0]PETSC ERROR: #1 User provided function() line 0 in  unknown file
>
> [1]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
>
> [1]PETSC ERROR: Signal received
>
> [1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
>
> [1]PETSC ERROR: Petsc Release Version 3.5.4, May, 23, 2015
>
> [1]PETSC ERROR: ./example-opt on a arch-darwin-c-opt named
> mcswl164.mcs.anl.gov by xzhao Mon Aug 17 11:20:33 2015
>
> [1]PETSC ERROR: Configure options --with-cc=gcc-4.9 --with-cxx=g++-4.9
> --with-fc=gfortran-4.9 --with-cxx-dialect=C++11 --download-mpich
> --download-fblaslapack --download-scalapack --download-mumps
> --download-superlu_dist --download-hypre --download-ml --download-parmetis
> --download-metis --download-triangle --download-chaco --download-elemental
> --with-debugging=0
>
> [1]PETSC ERROR: #1 User provided function() line 0 in  unknown file
>
> [2]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
>
> [2]PETSC ERROR: Signal received
>
> [2]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
>
> [2]PETSC ERROR: Petsc Release Version 3.5.4, May, 23, 2015
>
> [2]PETSC ERROR: ./example-opt on a arch-darwin-c-opt named
> mcswl164.mcs.anl.gov by xzhao Mon Aug 17 11:20:33 2015
>
> [2]PETSC ERROR: Configure options --with-cc=gcc-4.9 --with-cxx=g++-4.9
> --with-fc=gfortran-4.9 --with-cxx-dialect=C++11 --download-mpich
> --download-fblaslapack --download-scalapack --download-mumps
> --download-superlu_dist --download-hypre --download-ml --download-parmetis
> --download-metis --download-triangle --download-chaco --download-elemental
> --with-debugging=0
>
> [2]PETSC ERROR: #1 User provided function() line 0 in  unknown file
>
> [3]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
>
> [3]PETSC ERROR: Signal received
>
> [3]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
>
> [3]PETSC ERROR: Petsc Release Version 3.5.4, May, 23, 2015
>
> [3]PETSC ERROR: ./example-opt on a arch-darwin-c-opt named
> mcswl164.mcs.anl.gov by xzhao Mon Aug 17 11:20:33 2015
>
> [3]PETSC ERROR: Configure options --with-cc=gcc-4.9 --with-cxx=g++-4.9
> --with-fc=gfortran-4.9 --with-cxx-dialect=C++11 --download-mpich
> --download-fblaslapack --download-scalapack --download-mumps
> --download-superlu_dist --download-hypre --download-ml --download-parmetis
> --download-metis --download-triangle --download-chaco --download-elemental
> --with-debugging=0
>
> [3]PETSC ERROR: #1 User provided function() line 0 in  unknown file
>
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1
>
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 2
>
> [cli_0]: aborting job:
>
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>
> [cli_1]: aborting job:
>
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1
>
> [cli_2]: aborting job:
>
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 2
>
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 3
>
> [cli_3]: aborting job:
>
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 3
>
> On Mon, Aug 17, 2015 at 11:16 AM, Dmitry Karpeyev <dkarpeev at gmail.com>
> wrote:
>
>> Xujun,
>> Regarding your original question: please send the complete error message.
>> Dmitry.
>>
>> On Mon, Aug 17, 2015 at 11:15 AM Xujun Zhao <xzhao99 at gmail.com> wrote:
>>
>>> Ahhhh, I should drink some coffee in the morning.
>>> Now it passed the test!
>>>
>>> On Mon, Aug 17, 2015 at 11:13 AM, Matthew Knepley <knepley at gmail.com>
>>> wrote:
>>>
>>>> On Mon, Aug 17, 2015 at 11:02 AM, Xujun Zhao <xzhao99 at gmail.com> wrote:
>>>>
>>>>> No. It gives the following error msg:
>>>>>
>>>>
>>>> Did you build the executable?
>>>>
>>>>   cd src/vec/vec/examples/tutorials
>>>>   make ex43
>>>>
>>>>     Matt
>>>>
>>>>
>>>>> mpirun -np 2 ex43
>>>>>
>>>>> [proxy:0:0 at mcswl164.mcs.anl.gov] [proxy:0:0 at mcswl164.mcs.anl.gov]
>>>>> HYDU_create_process (utils/launch/launch.c:75): HYDU_create_process
>>>>> (utils/launch/launch.c:75): execvp error on file ex43 (No such file or
>>>>> directory)
>>>>>
>>>>> execvp error on file ex43 (No such file or directory)
>>>>>
>>>>> On Mon, Aug 17, 2015 at 10:57 AM, Matthew Knepley <knepley at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> On Mon, Aug 17, 2015 at 10:49 AM, Xujun Zhao <xzhao99 at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi all,
>>>>>>>
>>>>>>> I want PETSc to generate random vector using VecSetRandom()
>>>>>>> following given examples, but failed and showed some "out of memory" error.
>>>>>>> The following is the code, which goes well until it reaches VecSetRandom().
>>>>>>> Can anyone help me figure out the reason? Thanks a lot.
>>>>>>>
>>>>>>
>>>>>> Does src/vec/vec/examples/tests/ex43.c run for you?
>>>>>>
>>>>>>  Thanks,
>>>>>>
>>>>>>     Matt
>>>>>>
>>>>>>
>>>>>>> XZ
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --------------------------------------------------------------------------------------------
>>>>>>>   Vec             u;
>>>>>>>   PetscRandom     rand_ctx;     /* random number generator context */
>>>>>>>   PetscMPIInt     size, rank;
>>>>>>>   PetscInt        n, dn;
>>>>>>>
>>>>>>>
>>>>>>>   MPI_Comm_rank(PETSC_COMM_WORLD,&rank);//CHKERRQ(ierr);
>>>>>>>   MPI_Comm_size(PETSC_COMM_WORLD,&size);//CHKERRQ(ierr);
>>>>>>>   n  = N/size + 1;
>>>>>>>   dn = n*size - N;
>>>>>>>   if ( dn>0 && rank<dn ) n -= 1;
>>>>>>>   printf("--->test in petsc_random_vector(): rank = %d, n =
>>>>>>> %d\n",rank,n);
>>>>>>>
>>>>>>>
>>>>>>>   VecCreate(PETSC_COMM_WORLD,&u);
>>>>>>>   VecSetSizes(u,n,N);
>>>>>>>   PetscRandomCreate(PETSC_COMM_WORLD, &rand_ctx);
>>>>>>> #if defined(PETSC_HAVE_DRAND48)
>>>>>>>   PetscRandomSetType(rand_ctx,PETSCRAND48);
>>>>>>> #elif defined(PETSC_HAVE_RAND)
>>>>>>>   PetscRandomSetType(rand_ctx,PETSCRAND);
>>>>>>> #endif
>>>>>>>   PetscRandomSetFromOptions(rand_ctx);
>>>>>>>
>>>>>>>
>>>>>>>   VecSetRandom(u,rand_ctx);
>>>>>>>   PetscRandomDestroy(&rand_ctx);
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> 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
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> 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
>>>>
>>>
>>>
>
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