[petsc-users] Error - Out of memory. This could be due to allocating too large an object or bleeding by not properly ...

[Matthew Knepley]

On Wed, Feb 24, 2016 at 9:28 AM, TAY wee-beng <zonexo at gmail.com> wrote:

>
> On 24/2/2016 11:18 PM, Matthew Knepley wrote:
>
> On Wed, Feb 24, 2016 at 9:16 AM, TAY wee-beng <zonexo at gmail.com> wrote:
>
>>
>> On 24/2/2016 9:12 PM, Matthew Knepley wrote:
>>
>> On Wed, Feb 24, 2016 at 1:54 AM, TAY wee-beng < <zonexo at gmail.com>
>> zonexo at gmail.com> wrote:
>>
>>>
>>> On 24/2/2016 10:28 AM, Matthew Knepley wrote:
>>>
>>> On Tue, Feb 23, 2016 at 7:50 PM, TAY wee-beng < <zonexo at gmail.com>
>>> zonexo at gmail.com> wrote:
>>>
>>>> Hi,
>>>>
>>>> I got this error (also attached, full) when running my code. It happens
>>>> after a few thousand time steps.
>>>>
>>>> The strange thing is that for 2 different clusters, it stops at 2
>>>> different time steps.
>>>>
>>>> I wonder if it's related to DM since this happens after I added DM into
>>>> my code.
>>>>
>>>> In this case, how can I find out the error? I'm thinking valgrind may
>>>> take very long and gives too many false errors.
>>>
>>>
>>> It is very easy to find leaks. You just run a few steps with
>>> -malloc_dump and see what is left over.
>>>
>>>    Matt
>>>
>>> Hi Matt,
>>>
>>> Do you mean running my a.out with the -malloc_dump and stop after a few
>>> time steps?
>>>
>>> What and how should I "see" then?
>>>
>>
>> -malloc_dump outputs all unfreed memory to the screen after
>> PetscFinalize(), so you should see the leak.
>> I guess it might be possible to keep creating things that you freed all
>> at once at the end, but that is less likely.
>>
>>    Matt
>>
>>
>> Hi,
>>
>> 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?
>>
>
> Its really hard to tell by looking at it. What I do is remove things until
> there is no leak, then progressively
> put thing back in until I have the culprit. Then you can think about what
> is not destroyed.
>
>   Matt
>
> Ok so let me get this clear. When it shows:
>
> [21]Total space allocated 1728961264 bytes
> [21]1861664 bytes MatCheckCompressedRow() line 60 in
> /home/wtay/Codes/petsc-3.6.3/src/mat/utils/compressedrow.c
> [21]16 bytes PetscStrallocpy() line 188 in
> /home/wtay/Codes/petsc-3.6.3/src/sys/utils/str.c
> [21]624 bytes ISLocalToGlobalMappingCreate() line 270 in /home/wtay/Codes
>
> ....
>
> Does it mean that it's simply allocating space ie normal? Or does it show
> that there's memory leak ie error?
>

I gave the wrong option. That dumps everything. Lets just look at the leaks
with -malloc_test.

 Sorry about that,

    Matt


> If it's error, should I zoom in and debug around this time at this region?
>
> Thanks
>
>
>
>> Thanks.
>>
>>
>>>
>>>
>>>> --
>>>> Thank you
>>>>
>>>> Yours sincerely,
>>>>
>>>> TAY wee-beng
>>>>
>>>>
>>>
>>>
>>> --
>>> What most experimenters take for granted before they begin their
>>> experiments is infinitely more interesting than any results to which their
>>> experiments lead.
>>> -- Norbert Wiener
>>>
>>>
>>>
>>
>>
>> --
>> What most experimenters take for granted before they begin their
>> experiments is infinitely more interesting than any results to which their
>> experiments lead.
>> -- Norbert Wiener
>>
>>
>>
>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
>
>


-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20160224/5c0b690a/attachment-0001.html>