<div dir="ltr"><div dir="ltr">On Fri, Apr 1, 2022 at 6:50 AM Roland Richter <<a href="mailto:roland.richter@ntnu.no">roland.richter@ntnu.no</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">
<div>
<p>I re-run my code with a debug version of PETSc, resulting in <br>
</p>
<p><span style="font-family:monospace"><span style="font-weight:bold;color:rgb(255,84,84);background-color:rgb(255,255,255)">[0]PETSC
ERROR: --------------------- Error Message
--------------------------------------------------------------</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">
</span><br>
[0]PETSC ERROR: Corrupt argument:
<a href="https://petsc.org/release/faq/#valgrind" target="_blank">https://petsc.org/release/faq/#valgrind</a>
<br>
[0]PETSC ERROR: Object already free: Parameter # 1
<br>
[0]PETSC ERROR: See <a href="https://petsc.org/release/faq/" target="_blank">https://petsc.org/release/faq/</a> for trouble
shooting.
<br>
[0]PETSC ERROR: Petsc Development GIT revision:
v3.17.0-8-gf6d6129e50 GIT Date: 2022-03-31 18:10:33 +0000
<br>
[0]PETSC ERROR: #1 VecGetSize() at
/home/roland/Downloads/git-files/petsc/src/vec/vec/interface/vector.c:670<br>
0 64
<br>
[0]PETSC ERROR: #2 VecDestroy() at
/home/roland/Downloads/git-files/petsc/src/vec/vec/interface/vector.c:375<br>
0 64
<br>
[0]PETSC ERROR: #3 VecGetArray() at
/home/roland/Downloads/git-files/petsc/src/vec/vec/interface/rvector.c:1780<br>
<br>
</span></p>
<p>I do not understand why it tries to access the vector, even
though it has been set to PETSC_NULL in the previous free-call.</p>
<p></p></div></blockquote><div>What code is setting that pointer to NULL?</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><p>Regards,</p>
<p>Roland<br>
</p>
<div>Am 31.03.22 um 15:50 schrieb Matthew
Knepley:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">On Thu, Mar 31, 2022 at 9:47 AM Roland Richter
<<a href="mailto:roland.richter@ntnu.no" target="_blank">roland.richter@ntnu.no</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">
<div>
<p>The backtrace is</p>
<p><span style="font-family:monospace"><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">#0
</span><span style="color:rgb(24,24,178);background-color:rgb(255,255,255)">0x00007fffeec4ba97</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> in </span><span style="color:rgb(178,104,24);background-color:rgb(255,255,255)">VecGetSize_Seq</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> () from </span><span style="color:rgb(24,178,24);background-color:rgb(255,255,255)">/opt/petsc/lib/libpetsc.so.3.016</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> </span><br>
#1 <span style="color:rgb(24,24,178);background-color:rgb(255,255,255)">0x00007fffeec78f5a</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> in </span><span style="color:rgb(178,104,24);background-color:rgb(255,255,255)">VecGetSize</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> () from </span><span style="color:rgb(24,178,24);background-color:rgb(255,255,255)">/opt/petsc/lib/libpetsc.so.3.016</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> </span><br>
#2 <span style="color:rgb(24,24,178);background-color:rgb(255,255,255)">0x0000000000410b73</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> in </span><span style="color:rgb(178,104,24);background-color:rgb(255,255,255)">test_ts_arma_with_pure_petsc_preconfigured_clean(unsigned
long, unsigned long,
arma::Col<std::complex<doubl</span><br>
e> > const&,
arma::Col<std::complex<double> >&,
double, double, double) [clone .constprop.0]<span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">
() </span><br>
#3 <span style="color:rgb(24,24,178);background-color:rgb(255,255,255)">0x0000000000414384</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> in </span><span style="color:rgb(178,104,24);background-color:rgb(255,255,255)">test_RK4_solvers_clean(unsigned
long, unsigned long, unsigned long, bool) [clone
.constprop.0]</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">
() </span><br>
#4 <span style="color:rgb(24,24,178);background-color:rgb(255,255,255)">0x0000000000405c6c</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> in </span><span style="color:rgb(178,104,24);background-color:rgb(255,255,255)">main</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> ()</span></span></p>
</div>
</blockquote>
<div>It looks like you are passing an invalid vector. If you
compiled in debug mode, it would tell you. I would run</div>
<div>in debug until my code was running like I expect, then
switch to optimized. You can do that by using two</div>
<div>different PETSC_ARCH configures, and switch at runtime
with that variable.</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>
<p>Regards,</p>
<div>Roland Richter</div>
<div><br>
</div>
<div>Am 31.03.22 um 15:35 schrieb Matthew Knepley:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">On Thu, Mar 31, 2022 at 9:01 AM Roland
Richter <<a href="mailto:roland.richter@ntnu.no" target="_blank">roland.richter@ntnu.no</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">
<div>
<p>Hei,</p>
<p>Thanks for the idea! I added a simple
std::cout for both constructor and destructor,
and found out that my destructor is called
multiple times, while the constructor is
called only once. This could explain the error
(double free), but I do not know why segfault
is thrown even though I explicitly check if
the vector has been used. Are there
explanations for that?</p>
</div>
</blockquote>
<div>Run with -start_in_debugger and get the stack
trace when it faults. Right now, I have no idea
where it is faulting.</div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
<div> <br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<p>Regards,</p>
<p>Roland Richter<br>
</p>
<div>Am 31.03.22 um 12:14 schrieb Matthew
Knepley:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">On Thu, Mar 31, 2022 at 5:58
AM Roland Richter <<a href="mailto:roland.richter@ntnu.no" target="_blank">roland.richter@ntnu.no</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">
<div>
<p>Hei,</p>
<p>For a project I wanted to combine
boost::odeint for timestepping and
PETSc-based vectors and matrices for
calculating the right hand side. As
comparison for both timing and
correctness I set up an
armadillo-based right hand side
(with the main-function being in <b>main.cpp</b>,
and the test code in <b>test_timestepping_clean.cpp</b>)<br>
</p>
<p>In theory, the code works fine, but
I have some issues with cleaning up
afterwards in my struct <i>Petsc_RHS_state_clean</i>.
My initial intention was to set up
all involved matrices and vectors
within the constructor, and free the
memory in the destructor. To avoid
freeing vectors I have not used I
initially set them to <i>PETSC_NULL</i>,
and check if this value has been
changed before calling <i>VecDestroy().</i></p>
</div>
</blockquote>
<div>You do not need to check. Destroy()
functions already check for NULL.</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<p> However, when doing that I get the
following error:</p>
<p><span style="font-family:monospace"><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">[0]PETSC
ERROR:
------------------------------------------------------------------------
</span><br>
[0]PETSC ERROR: Caught signal
number 11 SEGV: Segmentation
Violation, probably memory access
out of range <br>
[0]PETSC ERROR: Try option
-start_in_debugger or
-on_error_attach_debugger <br>
[0]PETSC ERROR: or see <a href="https://petsc.org/release/faq/#valgrind" target="_blank">https://petsc.org/release/faq/#valgrind</a>
<br>
[0]PETSC ERROR: or try <a href="http://valgrind.org" target="_blank">http://valgrind.org</a>
on GNU/linux and Apple Mac OS X to
find memory corruption errors <br>
[0]PETSC ERROR: configure using
--with-debugging=yes, recompile,
link, and run <br>
[0]PETSC ERROR: to get more
information on the crash. <br>
<span style="font-weight:bold;color:rgb(255,84,84);background-color:rgb(255,255,255)">[0]PETSC
ERROR: ---------------------
Error Message
--------------------------------------------------------------</span></span></p>
<p>If I comment out that code in
~Petsc_RHS_state_clean(), the
program runs, but will use ~17 GByte
of RAM during runtime. As the memory
is not used immediately in full, but
rather increases during running, I
assume a memory leak somewhere.
Where does it come from, and how can
I avoid it?</p>
</div>
</blockquote>
<div>It must be that your constructor is
called multiple times without calling
your destructor. I cannot understand
this code in order</div>
<div>to see where that happens, but you
should just be able to run in the
debugger and put a break point at the
creation and<br>
</div>
<div>destruction calls.</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>
<p>Thanks!</p>
<p>Regards,</p>
<p>Roland Richter<br>
</p>
<p><span style="font-family:monospace"></span></p>
</div>
</blockquote>
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-- <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>
<div><br>
</div>
<div><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br>
</div>
</div>
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-- <br>
<div dir="ltr">
<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>
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-- <br>
<div dir="ltr">
<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>
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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>