[petsc-users] dmplex with block size error
Rongliang Chen
rongliang.chan at gmail.com
Fri Aug 26 05:52:27 CDT 2016
Hi Matt,
I think there is a typo in the following code (line 633 and 636 in
plexpreallocate.c).
==================
} 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
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