[petsc-users] dmplex with block size error
Rongliang Chen
rongliang.chan at gmail.com
Fri Aug 26 06:53:00 CDT 2016
Thanks. I am using a very old version, the petsc-3.6.1. I will try to
update my code to the latest version.
Best,
Rongliang
On 08/26/2016 07:47 PM, Matthew Knepley wrote:
> On Fri, Aug 26, 2016 at 5:52 AM, Rongliang Chen
> <rongliang.chan at gmail.com <mailto:rongliang.chan at gmail.com>> wrote:
>
> Hi Matt,
>
> I think there is a typo in the following code (line 633 and 636 in
> plexpreallocate.c).
>
>
> Those are fixed in the current 'master'. Which branch are you using?
>
> Thanks,
>
> Matt
>
> ==================
> } else {
> /* Only loop over blocks of rows */
> for (r = rStart/bs; r < rEnd/bs; ++r) {
> const PetscInt row = r*bs;
> PetscInt numCols, cStart, c;
>
> ierr = PetscSectionGetDof(sectionAdj, row,
> &numCols);CHKERRQ(ierr);
> ierr = PetscSectionGetOffset(sectionAdj, row,
> &cStart);CHKERRQ(ierr);
> for (c = cStart; c < cStart+numCols; ++c) {
> if ((cols[c] >= rStart*bs) && (cols[c] < rEnd*bs)) {
> ++dnz[r-rStart];
> if (cols[c] >= row) ++dnzu[r-rStart]; // I think
> "dnzu[r-rStart]" should be "dnzu[r-rStart/bs]", right?
> } else {
> ++onz[r-rStart];
> if (cols[c] >= row) ++onzu[r-rStart]; // I think
> "onzu[r-rStart]" should be "onzu[r-rStart/bs]" , right?
> }
> }
> }
> for (r = 0; r < (rEnd - rStart)/bs; ++r) {
> dnz[r] /= bs;
> onz[r] /= bs;
> dnzu[r] /= bs;
> onzu[r] /= bs;
> }
> }
> ==================
>
> Best,
> Rongliang
>
> On 08/18/2016 06:08 PM, Matthew Knepley wrote:
>> On Thu, Aug 18, 2016 at 5:05 AM, Rongliang Chen
>> <rongliang.chan at gmail.com <mailto:rongliang.chan at gmail.com>> wrote:
>>
>> Hi Matt,
>>
>> The log of the valgrind is attached. When I run with
>> valgrind, the following error message comes up.
>>
>>
>> The valgrind log says your code is writing over memory. Fix that
>> first.
>>
>> Matt
>>
>> -------------------------
>> [1]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> [1]PETSC ERROR: Arguments are incompatible
>> [1]PETSC ERROR: Cannot change block size 3670016 to 7
>> [1]PETSC ERROR: See
>> http://www.mcs.anl.gov/petsc/documentation/faq.html
>> <http://www.mcs.anl.gov/petsc/documentation/faq.html> for
>> trouble shooting.
>> [1]PETSC ERROR: Petsc Release Version 3.6.3, Dec, 03, 2015
>> [1]PETSC ERROR: ./fsi on a 64bit-debug named rlchen by rlchen
>> Thu Aug 18 17:59:43 2016
>> [1]PETSC ERROR: Configure options --download-blacs
>> --download-scalapack --download-metis --download-parmetis
>> --download-exodusii --download-netcdf --download-hdf5
>> --with-mpi-dir=/home/rlchen/soft/Program/mpich2-shared
>> --with-debugging=1 --download-fblaslapack --with-64-bit-indices
>> [1]PETSC ERROR: #1 PetscLayoutSetBlockSize() line 424 in
>> /home/rlchen/soft/petsc-3.6.3/src/vec/is/utils/pmap.c
>> [1]PETSC ERROR: #2 MatSetBlockSize() line 6920 in
>> /home/rlchen/soft/petsc-3.6.3/src/mat/interface/matrix.c
>> [1]PETSC ERROR: #3 MatXAIJSetPreallocation() line 282 in
>> /home/rlchen/soft/3D_fluid/FSI/Spmcs-v1.5/Fluid-petsc-3.6/src/application/Fluid/gcreate.c
>> ----------------------
>>
>> Best regards,
>> Rongliang
>>
>> On 08/18/2016 05:52 PM, Matthew Knepley wrote:
>>> Run with valgrind and send the log.
>>>
>>> Thanks,
>>>
>>> Matt
>>>
>>> On Thu, Aug 18, 2016 at 3:59 AM, Rongliang Chen
>>> <rongliang.chan at gmail.com <mailto:rongliang.chan at gmail.com>>
>>> wrote:
>>>
>>> Dear All,
>>>
>>> I try to use the block matrix (BAIJ) for the dmplex data
>>> structure with the option "-dm_mat_type baij" (the block
>>> size is 7). The code works fine when np = 1 but the
>>> following error comes up when np>1. And the code also
>>> works fine for np>1 if I set the block size to be 1. Any
>>> suggestions are highly appreciated.
>>>
>>> ----------------------------------------------------
>>> [1]PETSC ERROR: PetscMallocValidate: error detected at
>>> VecAXPY_Seq() line 89 in
>>> /home/rlchen/soft/petsc-3.6.3/src/vec/vec/impls/seq/bvec1.c
>>> [1]PETSC ERROR: Memory at address 0x1332571 is corrupted
>>> [1]PETSC ERROR: Probably write past beginning or end of
>>> array
>>> [1]PETSC ERROR: Last intact block allocated in
>>> PetscStrallocpy() line 188 in
>>> /home/rlchen/soft/petsc-3.6.3/src/sys/utils/str.c
>>> [1]PETSC ERROR: --------------------- Error Message
>>> --------------------------------------------------------------
>>> [1]PETSC ERROR: Memory corruption:
>>> http://www.mcs.anl.gov/petsc/documentation/installation.html#valgrind
>>> <http://www.mcs.anl.gov/petsc/documentation/installation.html#valgrind>
>>> [1]PETSC ERROR:
>>> [1]PETSC ERROR: See
>>> http://www.mcs.anl.gov/petsc/documentation/faq.html
>>> <http://www.mcs.anl.gov/petsc/documentation/faq.html>
>>> for trouble shooting.
>>> [1]PETSC ERROR: Petsc Release Version 3.6.3, Dec, 03, 2015
>>> [1]PETSC ERROR: ./fsi on a 64bit-debug named rlchen by
>>> rlchen Thu Aug 18 16:42:34 2016
>>> [1]PETSC ERROR: Configure options --download-blacs
>>> --download-scalapack --download-metis
>>> --download-parmetis --download-exodusii
>>> --download-netcdf --download-hdf5
>>> --with-mpi-dir=/home/rlchen/soft/Program/mpich2-shared
>>> --with-debugging=1 --download-fblaslapack
>>> --with-64-bit-indices
>>> [1]PETSC ERROR: #1 PetscMallocValidate() line 136 in
>>> /home/rlchen/soft/petsc-3.6.3/src/sys/memory/mtr.c
>>> [1]PETSC ERROR: #2 VecAXPY_Seq() line 89 in
>>> /home/rlchen/soft/petsc-3.6.3/src/vec/vec/impls/seq/bvec1.c
>>> [1]PETSC ERROR: #3 VecAXPY() line 640 in
>>> /home/rlchen/soft/petsc-3.6.3/src/vec/vec/interface/rvector.c
>>> ---------------------------------------------------
>>>
>>> Best regards,
>>> Rongliang
>>>
>>>
>>>
>>>
>>> --
>>> 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
>
>
>
>
> --
> 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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