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<div class="moz-cite-prefix">Thanks. I am using a very old version,
the petsc-3.6.1. I will try to update my code to the latest
version.<br>
<br>
Best,<br>
Rongliang <br>
<br>
On 08/26/2016 07:47 PM, Matthew Knepley wrote:<br>
</div>
<blockquote
cite="mid:CAMYG4Gm2-yBoe8Qq_knULUT3PVg05vyMcPFKpWtsMirqvSbfcQ@mail.gmail.com"
type="cite">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">On Fri, Aug 26, 2016 at 5:52 AM,
Rongliang Chen <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:rongliang.chan@gmail.com" target="_blank">rongliang.chan@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>Hi Matt,<br>
<br>
I think there is a typo in the following code (line
633 and 636 in plexpreallocate.c).<br>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>Those are fixed in the current 'master'. Which branch
are you using?</div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div> ==================<br>
} else {<br>
/* Only loop over blocks of rows */<br>
for (r = rStart/bs; r < rEnd/bs; ++r) {<br>
const PetscInt row = r*bs;<br>
PetscInt numCols, cStart, c;<br>
<br>
ierr = PetscSectionGetDof(sectionAdj, row,
&numCols);CHKERRQ(ierr);<br>
ierr = PetscSectionGetOffset(<wbr>sectionAdj,
row, &cStart);CHKERRQ(ierr);<br>
for (c = cStart; c < cStart+numCols; ++c) {<br>
if ((cols[c] >= rStart*bs) &&
(cols[c] < rEnd*bs)) {<br>
++dnz[r-rStart];<br>
if (cols[c] >= row) ++dnzu[r-rStart]; //
I think "dnzu[r-rStart]" should be
"dnzu[r-rStart/bs]", right?<br>
} else {<br>
++onz[r-rStart];<br>
if (cols[c] >= row) ++onzu[r-rStart]; //
I think "onzu[r-rStart]" should be "onzu[r-rStart/bs]"
, right?<br>
}<br>
}<br>
}<br>
for (r = 0; r < (rEnd - rStart)/bs; ++r) {<br>
dnz[r] /= bs;<br>
onz[r] /= bs;<br>
dnzu[r] /= bs;<br>
onzu[r] /= bs;<br>
}<br>
}<br>
==================<br>
<br>
Best,<br>
Rongliang<br>
<br>
On 08/18/2016 06:08 PM, Matthew Knepley wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">On Thu, Aug 18, 2016 at
5:05 AM, Rongliang Chen <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:rongliang.chan@gmail.com"
target="_blank">rongliang.chan@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0
0 0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>Hi Matt,<br>
<br>
The log of the valgrind is attached. When
I run with valgrind, the following error
message comes up.<br>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>The valgrind log says your code is writing
over memory. Fix that first.</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0
0 0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div> -------------------------<br>
[1]PETSC ERROR: ---------------------
Error Message
------------------------------<wbr>------------------------------<wbr>--<br>
[1]PETSC ERROR: Arguments are incompatible<br>
[1]PETSC ERROR: Cannot change block size
3670016 to 7<br>
[1]PETSC ERROR: See <a
moz-do-not-send="true"
href="http://www.mcs.anl.gov/petsc/documentation/faq.html"
target="_blank">http://www.mcs.anl.gov/petsc/d<wbr>ocumentation/faq.html</a>
for trouble shooting.<br>
[1]PETSC ERROR: Petsc Release Version
3.6.3, Dec, 03, 2015 <br>
[1]PETSC ERROR: ./fsi on a 64bit-debug
named rlchen by rlchen Thu Aug 18 17:59:43
2016<br>
[1]PETSC ERROR: Configure options
--download-blacs --download-scalapack
--download-metis --download-parmetis
--download-exodusii --download-netcdf
--download-hdf5
--with-mpi-dir=/home/rlchen/so<wbr>ft/Program/mpich2-shared
--with-debugging=1 --download-fblaslapack
--with-64-bit-indices<br>
[1]PETSC ERROR: #1
PetscLayoutSetBlockSize() line 424 in
/home/rlchen/soft/petsc-3.6.3/<wbr>src/vec/is/utils/pmap.c<br>
[1]PETSC ERROR: #2 MatSetBlockSize() line
6920 in /home/rlchen/soft/petsc-3.6.3/<wbr>src/mat/interface/matrix.c<br>
[1]PETSC ERROR: #3
MatXAIJSetPreallocation() line 282 in
/home/rlchen/soft/3D_fluid/FSI<wbr>/Spmcs-v1.5/Fluid-petsc-3.6/<wbr>src/application/Fluid/gcreate.<wbr>c<br>
----------------------<br>
<br>
Best regards,<br>
Rongliang<br>
<br>
On 08/18/2016 05:52 PM, Matthew Knepley
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Run with valgrind and send
the log.
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Thu, Aug 18,
2016 at 3:59 AM, Rongliang Chen <span
dir="ltr"><<a
moz-do-not-send="true"
href="mailto:rongliang.chan@gmail.com"
target="_blank">rongliang.chan@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex">Dear All,<br>
<br>
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.<br>
<br>
------------------------------<wbr>----------------------<br>
[1]PETSC ERROR: PetscMallocValidate:
error detected at VecAXPY_Seq() line
89 in /home/rlchen/soft/petsc-3.6.3/<wbr>src/vec/vec/impls/seq/bvec1.c<br>
[1]PETSC ERROR: Memory at address
0x1332571 is corrupted<br>
[1]PETSC ERROR: Probably write past
beginning or end of array<br>
[1]PETSC ERROR: Last intact block
allocated in PetscStrallocpy() line
188 in
/home/rlchen/soft/petsc-3.6.3/<wbr>src/sys/utils/str.c<br>
[1]PETSC ERROR:
--------------------- Error Message
------------------------------<wbr>------------------------------<wbr>--<br>
[1]PETSC ERROR: Memory corruption: <a
moz-do-not-send="true"
href="http://www.mcs.anl.gov/petsc/documentation/installation.html#valgrind"
rel="noreferrer" target="_blank">http://www.mcs.anl.gov/petsc/d<wbr>ocumentation/installation.html<wbr>#valgrind</a><br>
[1]PETSC ERROR:<br>
[1]PETSC ERROR: See <a
moz-do-not-send="true"
href="http://www.mcs.anl.gov/petsc/documentation/faq.html"
rel="noreferrer" target="_blank">http://www.mcs.anl.gov/petsc/d<wbr>ocumentation/faq.html</a>
for trouble shooting.<br>
[1]PETSC ERROR: Petsc Release
Version 3.6.3, Dec, 03, 2015<br>
[1]PETSC ERROR: ./fsi on a
64bit-debug named rlchen by rlchen
Thu Aug 18 16:42:34 2016<br>
[1]PETSC ERROR: Configure options
--download-blacs
--download-scalapack
--download-metis --download-parmetis
--download-exodusii
--download-netcdf --download-hdf5
--with-mpi-dir=/home/rlchen/so<wbr>ft/Program/mpich2-shared
--with-debugging=1
--download-fblaslapack
--with-64-bit-indices<br>
[1]PETSC ERROR: #1
PetscMallocValidate() line 136 in
/home/rlchen/soft/petsc-3.6.3/<wbr>src/sys/memory/mtr.c<br>
[1]PETSC ERROR: #2 VecAXPY_Seq()
line 89 in
/home/rlchen/soft/petsc-3.6.3/<wbr>src/vec/vec/impls/seq/bvec1.c<br>
[1]PETSC ERROR: #3 VecAXPY() line
640 in
/home/rlchen/soft/petsc-3.6.3/<wbr>src/vec/vec/interface/rvector.<wbr>c<br>
------------------------------<wbr>---------------------<br>
<br>
Best regards,<br>
Rongliang<br>
</blockquote>
</div>
<br>
<br clear="all">
<span class="HOEnZb"><font
color="#888888"> <span><font
color="#888888">
<div><br>
</div>
-- <br>
<div
data-smartmail="gmail_signature">What
most experimenters take for
granted before they begin
their experiments is
infinitely more interesting
than any results to which
their experiments lead.<br>
-- Norbert Wiener</div>
</font></span></font></span></div>
<span class="HOEnZb"><font color="#888888">
</font></span></blockquote>
<span class="HOEnZb"><font color="#888888">
<br>
</font></span></div>
<span class="HOEnZb"><font color="#888888"> </font></span></blockquote>
<span class="HOEnZb"><font color="#888888"> </font></span></div>
<span class="HOEnZb"><font color="#888888"> <br>
<br clear="all">
<div><br>
</div>
-- <br>
<div data-smartmail="gmail_signature">What
most experimenters take for granted before
they begin their experiments is infinitely
more interesting than any results to which
their experiments lead.<br>
-- Norbert Wiener</div>
</font></span></div>
</div>
</blockquote>
<br>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div class="gmail_signature" data-smartmail="gmail_signature">What
most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results
to which their experiments lead.<br>
-- Norbert Wiener</div>
</div>
</div>
</blockquote>
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