[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 11:33 PM, Matthew Knepley wrote:
> On Wed, Feb 24, 2016 at 9:28 AM, TAY wee-beng <zonexo at gmail.com 
> <mailto: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
>>     <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?
>
>
> I gave the wrong option. That dumps everything. Lets just look at the 
> leaks with -malloc_test.
>
>  Sorry about that,
>
>     Matt
Oh ic .. no prob. I'll try again then.
>
>     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

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