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<div class="moz-cite-prefix">On 24/2/2016 11:33 PM, Matthew Knepley
wrote:<br>
</div>
<blockquote
cite="mid:CAMYG4GmFzs68OsbR4LPNeoHmNjEkMnC2LFWsCuM3fmrZ=7XpGQ@mail.gmail.com"
type="cite">
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<div class="gmail_quote">On Wed, Feb 24, 2016 at 9:28 AM, TAY
wee-beng <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:zonexo@gmail.com" target="_blank">zonexo@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
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<div>On 24/2/2016 11:18 PM, Matthew Knepley wrote:<br>
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<div class="gmail_quote">On Wed, Feb 24, 2016 at
9:16 AM, TAY wee-beng <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:zonexo@gmail.com"
target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:zonexo@gmail.com">zonexo@gmail.com</a></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 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
moz-do-not-send="true"
href="mailto:zonexo@gmail.com"
target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:zonexo@gmail.com">zonexo@gmail.com</a></a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="margin:0 0 0
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solid;padding-left:1ex">
<div bgcolor="#FFFFFF"
text="#000000"> <br>
<div>On 24/2/2016 10:28 AM,
Matthew Knepley wrote:<br>
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<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
moz-do-not-send="true"
href="mailto:zonexo@gmail.com" target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:zonexo@gmail.com">zonexo@gmail.com</a></a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0 0 0
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#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>
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</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>
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<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>
</div>
</blockquote>
Oh ic .. no prob. I'll try again then.<br>
<blockquote
cite="mid:CAMYG4GmFzs68OsbR4LPNeoHmNjEkMnC2LFWsCuM3fmrZ=7XpGQ@mail.gmail.com"
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<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0
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<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>
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<div bgcolor="#FFFFFF" text="#000000"> Thanks.<br>
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style="margin:0 0 0
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color="#888888"><br>
<span><font
color="#888888">
-- <br>
Thank you<br>
<br>
Yours
sincerely,<br>
<br>
TAY wee-beng<br>
<br>
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-- <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>
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<span><font color="#888888"> <br>
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<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">
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<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>
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<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>
</blockquote>
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