[petsc-users] Petsc creates a random vector
Xujun Zhao
xzhao99 at gmail.com
Mon Aug 17 11:31:42 CDT 2015
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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