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.c...@gmail.com <mailto:rongliang.c...@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.c...@gmail.com <mailto:rongliang.c...@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.c...@gmail.com <mailto:rongliang.c...@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
