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

[TAY wee-beng]

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 
> <mailto: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
>>     <mailto: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 <mailto: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?

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

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