<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">On Wed, Feb 24, 2016 at 9:28 AM, TAY wee-beng <span dir="ltr"><<a href="mailto:zonexo@gmail.com" target="_blank">zonexo@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div>On 24/2/2016 11:18 PM, Matthew Knepley
wrote:<br>
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<blockquote type="cite">
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<div class="gmail_quote">On Wed, Feb 24, 2016 at 9:16 AM, TAY
wee-beng <span dir="ltr"><<a href="mailto:zonexo@gmail.com" target="_blank">zonexo@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div>On 24/2/2016 9:12 PM, Matthew Knepley wrote:<br>
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<blockquote type="cite">
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<div class="gmail_extra">
<div class="gmail_quote">On Wed, Feb 24, 2016 at
1:54 AM, TAY wee-beng <span dir="ltr"><<a href="mailto:zonexo@gmail.com" target="_blank"></a><a href="mailto:zonexo@gmail.com" target="_blank">zonexo@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"> <br>
<div>On 24/2/2016 10:28 AM, Matthew Knepley
wrote:<br>
</div>
<blockquote type="cite">
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<div class="gmail_extra">
<div class="gmail_quote">On Tue, Feb
23, 2016 at 7:50 PM, TAY wee-beng <span dir="ltr"><<a href="mailto:zonexo@gmail.com" target="_blank"></a><a href="mailto:zonexo@gmail.com" target="_blank">zonexo@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<br>
I got this error (also attached,
full) when running my code. It
happens after a few thousand time
steps.<br>
<br>
The strange thing is that for 2
different clusters, it stops at 2
different time steps.<br>
<br>
I wonder if it's related to DM
since this happens after I added
DM into my code.<br>
<br>
In this case, how can I find out
the error? I'm thinking valgrind
may take very long and gives too
many false errors.</blockquote>
<div><br>
</div>
<div>It is very easy to find leaks.
You just run a few steps with
-malloc_dump and see what is left
over.</div>
<div><br>
</div>
<div> Matt</div>
</div>
</div>
</div>
</blockquote>
Hi Matt, <br>
<br>
Do you mean running my a.out with the
-malloc_dump and stop after a few time
steps?<br>
<br>
What and how should I "see" then?</div>
</blockquote>
<div><br>
</div>
<div>-malloc_dump outputs all unfreed memory to
the screen after PetscFinalize(), so you
should see the leak.</div>
<div>I guess it might be possible to keep
creating things that you freed all at once at
the end, but that is less likely.</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
</div>
</div>
</div>
</blockquote>
Hi,<br>
<br>
I got the output. I have zipped it since it's rather
big. So it seems to be from DM routines but can you help
me where the error is from?<br>
</div>
</blockquote>
<div><br>
</div>
<div>Its really hard to tell by looking at it. What I do is
remove things until there is no leak, then progressively</div>
<div>put thing back in until I have the culprit. Then you
can think about what is not destroyed.</div>
<div><br>
</div>
<div> Matt</div>
</div>
</div>
</div>
</blockquote>
Ok so let me get this clear. When it shows:<br>
<br>
[21]Total space allocated 1728961264 bytes<br>
[21]1861664 bytes MatCheckCompressedRow() line 60 in
/home/wtay/Codes/petsc-3.6.3/src/mat/utils/compressedrow.c<br>
[21]16 bytes PetscStrallocpy() line 188 in
/home/wtay/Codes/petsc-3.6.3/src/sys/utils/str.c<br>
[21]624 bytes ISLocalToGlobalMappingCreate() line 270 in
/home/wtay/Codes<br>
<br>
....<br>
<br>
Does it mean that it's simply allocating space ie normal? Or does it
show that there's memory leak ie error? <br></div></blockquote><div><br></div><div>I gave the wrong option. That dumps everything. Lets just look at the leaks with -malloc_test.</div><div><br></div><div> Sorry about that,</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">
If it's error, should I zoom in and debug around this time at this
region?<br>
<br>
Thanks<br>
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<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"> Thanks.<br>
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<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span><font color="#888888"><br>
<span><font color="#888888">
-- <br>
Thank you<br>
<br>
Yours sincerely,<br>
<br>
TAY wee-beng<br>
<br>
</font></span></font></span></blockquote>
<span><font color="#888888"> </font></span></div>
<span><font color="#888888"> <br>
<br clear="all">
<span><font color="#888888">
<div><br>
</div>
-- <br>
<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>
</font></span></font></span></div>
<span><font color="#888888"> </font></span></div>
<span><font color="#888888">
</font></span></blockquote>
<span><font color="#888888">
<br>
</font></span></div>
<span><font color="#888888"> </font></span></blockquote>
<span><font color="#888888"> </font></span></div>
<span><font color="#888888"> <br>
<br clear="all"><span class="HOEnZb"><font color="#888888">
<div><br>
</div>
-- <br>
<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>
</font></span></font></span></div><span class="HOEnZb"><font color="#888888">
</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>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">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>