<div dir="ltr"><div dir="ltr">On Wed, Mar 13, 2019 at 12:04 PM Manuel Colera Rico <<a href="mailto:m.colera@upm.es">m.colera@upm.es</a>> wrote:<br></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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<p>After adding that line the problem gets fixed.</p>
<p></p></div></blockquote><div>Junchao, I submitted a PR against maint for this as you.</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div bgcolor="#FFFFFF"><p>Regards,</p>
<p>Manuel</p>
<p>---<br>
</p>
<div class="gmail-m_-5289257232827223512moz-cite-prefix">On 3/13/19 3:13 PM, Zhang, Junchao
wrote:<br>
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<div dir="ltr">Manuel, </div>
<div dir="ltr"> Could you try to add this line<br>
sbaij->free_imax_ilen = PETSC_TRUE;<br>
after line 2431 in
/opt/PETSc_library/petsc-3.10.4/src/mat/impls/sbaij/seq/sbaij.c<br>
<br>
</div>
<div dir="ltr"> PS: Matt, this bug looks unrelated to my
VecRestoreArrayRead_Nest fix.
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<div dir="ltr" class="gmail-m_-5289257232827223512gmail_signature">
<div dir="ltr">--Junchao Zhang</div>
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<div dir="ltr" class="gmail_attr">On Wed, Mar 13, 2019 at 9:05
AM Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>> wrote:<br>
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<div dir="ltr">On Wed, Mar 13, 2019 at 9:44 AM Manuel
Colera Rico via petsc-users <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>>
wrote:<br>
</div>
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<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Yes:<br>
<br>
[ 0]8416 bytes MatCreateSeqSBAIJWithArrays() line 2431
in <br>
/opt/PETSc_library/petsc-3.10.4/src/mat/impls/sbaij/seq/sbaij.c<br>
[ 0]8416 bytes MatCreateSeqSBAIJWithArrays() line 2431
in <br>
/opt/PETSc_library/petsc-3.10.4/src/mat/impls/sbaij/seq/sbaij.c<br>
[ 0]4544 bytes MatCreateSeqSBAIJWithArrays() line 2431
in <br>
/opt/PETSc_library/petsc-3.10.4/src/mat/impls/sbaij/seq/sbaij.c<br>
[ 0]4544 bytes MatCreateSeqSBAIJWithArrays() line 2431
in <br>
/opt/PETSc_library/petsc-3.10.4/src/mat/impls/sbaij/seq/sbaij.c<br>
</blockquote>
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<div>Junchao, do imax and ilen get missed in the Destroy
with the user provides arrays?</div>
<div><br>
</div>
<div> <a href="https://bitbucket.org/petsc/petsc/src/06a3e802b3873ffbfd04b71a0821522327dd9b04/src/mat/impls/sbaij/seq/sbaij.c#lines-2431" target="_blank">https://bitbucket.org/petsc/petsc/src/06a3e802b3873ffbfd04b71a0821522327dd9b04/src/mat/impls/sbaij/seq/sbaij.c#lines-2431</a></div>
<div><br>
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<div> Matt</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
I have checked that I have destroyed all the MatNest
matrices and all <br>
the submatrices individually.<br>
<br>
Manuel<br>
<br>
---<br>
<br>
On 3/13/19 2:28 PM, Jed Brown wrote:<br>
> Is there any output if you run with -malloc_dump?<br>
><br>
> Manuel Colera Rico via petsc-users <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>>
writes:<br>
><br>
>> Hi, Junchao,<br>
>><br>
>> I have installed the newest version of PETSc
and it works fine. I just<br>
>> get the following memory leak warning:<br>
>><br>
>> Direct leak of 28608 byte(s) in 12 object(s)
allocated from:<br>
>> #0 0x7f1ddd5caa38 in
__interceptor_memalign<br>
>>
../../../../gcc-8.1.0/libsanitizer/asan/asan_malloc_linux.cc:111<br>
>> #1 0x7f1ddbef1213 in PetscMallocAlign<br>
>>
(/opt/PETSc_library/petsc-3.10.4/mcr_20190313/lib/libpetsc.so.3.10+0x150213)<br>
>><br>
>> Thank you,<br>
>><br>
>> Manuel<br>
>><br>
>> ---<br>
>><br>
>> On 3/12/19 7:08 PM, Zhang, Junchao wrote:<br>
>>> Hi, Manuel,<br>
>>> I recently fixed a problem in
VecRestoreArrayRead. Basically, I<br>
>>> added VecRestoreArrayRead_Nest. Could you
try the master branch of<br>
>>> PETSc to see if it fixes your problem?<br>
>>> Thanks.<br>
>>><br>
>>> --Junchao Zhang<br>
>>><br>
>>><br>
>>> On Mon, Mar 11, 2019 at 6:56 AM Manuel
Colera Rico via petsc-users<br>
>>> <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>
<mailto:<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>>>
wrote:<br>
>>><br>
>>> Hello,<br>
>>><br>
>>> I need to solve a 2*2 block linear
system. The matrices A_00, A_01,<br>
>>> A_10, A_11 are constructed
separately via<br>
>>> MatCreateSeqAIJWithArrays and<br>
>>> MatCreateSeqSBAIJWithArrays. Then, I
construct the full system matrix<br>
>>> with MatCreateNest, and use
MatNestGetISs and PCFieldSplitSetIS to<br>
>>> set<br>
>>> up the PC, trying to follow the
procedure described here:<br>
>>> <a href="https://www.mcs.anl.gov/petsc/petsc-current/src/snes/examples/tutorials/ex70.c.html" rel="noreferrer" target="_blank">
https://www.mcs.anl.gov/petsc/petsc-current/src/snes/examples/tutorials/ex70.c.html</a>.<br>
>>><br>
>>> However, when I run the code with
Leak Sanitizer, I get the<br>
>>> following error:<br>
>>><br>
>>>
=================================================================<br>
>>> ==54927==ERROR: AddressSanitizer:
attempting free on address which<br>
>>> was<br>
>>> not malloc()-ed: 0x627000051ab8 in
thread T0<br>
>>> #0 0x7fbd95c08f30 in
__interceptor_free<br>
>>>
../../../../gcc-8.1.0/libsanitizer/asan/asan_malloc_linux.cc:66<br>
>>> #1 0x7fbd92b99dcd in
PetscFreeAlign<br>
>>>
(/opt/PETSc_library/petsc/manuel_OpenBLAS_petsc/lib/libpetsc.so.3.8+0x146dcd)<br>
>>> #2 0x7fbd92ce0178 in
VecRestoreArray_Nest<br>
>>>
(/opt/PETSc_library/petsc/manuel_OpenBLAS_petsc/lib/libpetsc.so.3.8+0x28d178)<br>
>>> #3 0x7fbd92cd627d in
VecRestoreArrayRead<br>
>>>
(/opt/PETSc_library/petsc/manuel_OpenBLAS_petsc/lib/libpetsc.so.3.8+0x28327d)<br>
>>> #4 0x7fbd92d1189e in
VecScatterBegin_SSToSS<br>
>>>
(/opt/PETSc_library/petsc/manuel_OpenBLAS_petsc/lib/libpetsc.so.3.8+0x2be89e)<br>
>>> #5 0x7fbd92d1a414 in
VecScatterBegin<br>
>>>
(/opt/PETSc_library/petsc/manuel_OpenBLAS_petsc/lib/libpetsc.so.3.8+0x2c7414)<br>
>>> #6 0x7fbd934a999c in
PCApply_FieldSplit<br>
>>>
(/opt/PETSc_library/petsc/manuel_OpenBLAS_petsc/lib/libpetsc.so.3.8+0xa5699c)<br>
>>> #7 0x7fbd93369071 in PCApply<br>
>>>
(/opt/PETSc_library/petsc/manuel_OpenBLAS_petsc/lib/libpetsc.so.3.8+0x916071)<br>
>>> #8 0x7fbd934efe77 in
KSPInitialResidual<br>
>>>
(/opt/PETSc_library/petsc/manuel_OpenBLAS_petsc/lib/libpetsc.so.3.8+0xa9ce77)<br>
>>> #9 0x7fbd9350272c in
KSPSolve_GMRES<br>
>>>
(/opt/PETSc_library/petsc/manuel_OpenBLAS_petsc/lib/libpetsc.so.3.8+0xaaf72c)<br>
>>> #10 0x7fbd934e3c01 in KSPSolve<br>
>>>
(/opt/PETSc_library/petsc/manuel_OpenBLAS_petsc/lib/libpetsc.so.3.8+0xa90c01)<br>
>>><br>
>>> Disabling Leak Sanitizer also
outputs an "invalid pointer" error.<br>
>>><br>
>>> Did I forget something when writing
the code?<br>
>>><br>
>>> Thank you,<br>
>>><br>
>>> Manuel<br>
>>><br>
>>> ---<br>
>>><br>
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<div>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>
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<div><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br>
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</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>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><br></div><div><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div></div>