<div dir="ltr"><div dir="ltr">On Thu, Mar 31, 2022 at 9:47 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>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>
<p></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>
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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>
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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>