memory check of /snes/example/tutorials/ex29.c

Matthew Knepley knepley at gmail.com
Mon Jul 27 16:42:10 CDT 2009 

On Mon, Jul 27, 2009 at 4:34 PM, (Rebecca) Xuefei YUAN
<xy2102 at columbia.edu>wrote:

> Those unfreed bytes cause "out of memory" when it runs at bigger grid
> sizes. So I have to find out those unfreed memory and free them... Any
> suggestions?


Not from what you mailed in. On that DA line, I see PetscHeaderCreate(). Is
that what you see?

  Matt


>
> Thanks,
>
> R
>
>
> Quoting Matthew Knepley <knepley at gmail.com>:
>
>  On Mon, Jul 27, 2009 at 3:51 PM, (Rebecca) Xuefei YUAN
>> <xy2102 at columbia.edu>wrote:
>>
>>  Hi,
>>>
>>> My own code has some left bytes still reachable according to valgrind,
>>> then
>>> I use two different version petsc (2.3.3-p15 and 3.0.0-p1) to compile and
>>> make the files, it gives me different number of bytes left still
>>> reachable.
>>> Moreover, I picked up the /snes/example/tutorials/ex29.c as another
>>> example,
>>> and found that some bytes are still reachable, what is the cause of it?
>>> It
>>> shows that it is from DACreate2D() and the I use -malloc_dump to get
>>> those
>>> unfreed informations.
>>>
>>> I understand that for those 5 loss record, the 2nd, 3rd and 4th are true
>>> for all examples, but where do 1st and 5th ones come from? Also, the
>>> -malloc_dump information shows that there are
>>> "[0]Total space allocated 37780 bytes",
>>> but valgrind gives the information as
>>> "==26628==    still reachable: 132,828 bytes in 323 blocks"
>>>
>>> Why there is a big difference?
>>>
>>
>>
>> 1 is fine. It is from PMPI setup, which has some bytes not freed from
>> setting up the MPI
>> processes. The last one looks like an unfreed header for a DA, which is
>> strange.
>>
>>  Matt
>>
>>
>>
>>> Thanks very much!
>>>
>>> Rebecca
>>>
>>> Here is the message from valgrind of running ex29:
>>> ==26628== 32 bytes in 2 blocks are still reachable in loss record 1 of 5
>>> ==26628==    at 0x4022AB8: malloc (vg_replace_malloc.c:207)
>>> ==26628==    by 0x86F9A78: MPID_VCRT_Create (mpid_vc.c:62)
>>> ==26628==    by 0x86F743A: MPID_Init (mpid_init.c:116)
>>> ==26628==    by 0x86D040B: MPIR_Init_thread (initthread.c:288)
>>> ==26628==    by 0x86CFF2D: PMPI_Init (init.c:106)
>>> ==26628==    by 0x8613D69: PetscInitialize (pinit.c:503)
>>> ==26628==    by 0x804B796: main (ex29.c:139)
>>> ==26628==
>>> ==26628==
>>> ==26628== 156 (36 direct, 120 indirect) bytes in 1 blocks are definitely
>>> lost in loss record 2 of 5
>>> ==26628==    at 0x4022AB8: malloc (vg_replace_malloc.c:207)
>>> ==26628==    by 0x429B3E2: (within /lib/tls/i686/cmov/libc-2.7.so)
>>> ==26628==    by 0x429BC2D: __nss_database_lookup (in /lib/tls/i686/cmov/
>>> libc-2.7.so)
>>> ==26628==    by 0x4732FDB: ???
>>> ==26628==    by 0x473413C: ???
>>> ==26628==    by 0x4247D15: getpwuid_r (in /lib/tls/i686/cmov/libc-2.7.so
>>> )
>>> ==26628==    by 0x424765D: getpwuid (in /lib/tls/i686/cmov/libc-2.7.so)
>>> ==26628==    by 0x8623509: PetscGetUserName (fuser.c:68)
>>> ==26628==    by 0x85E0CF0: PetscErrorPrintfInitialize (errtrace.c:68)
>>> ==26628==    by 0x8613E23: PetscInitialize (pinit.c:518)
>>> ==26628==    by 0x804B796: main (ex29.c:139)
>>> ==26628==
>>> ==26628==
>>> ==26628== 40 bytes in 5 blocks are indirectly lost in loss record 3 of 5
>>> ==26628==    at 0x4022AB8: malloc (vg_replace_malloc.c:207)
>>> ==26628==    by 0x429AFBB: __nss_lookup_function (in /lib/tls/i686/cmov/
>>> libc-2.7.so)
>>> ==26628==    by 0x4732FFB: ???
>>> ==26628==    by 0x473413C: ???
>>> ==26628==    by 0x4247D15: getpwuid_r (in /lib/tls/i686/cmov/libc-2.7.so
>>> )
>>> ==26628==    by 0x424765D: getpwuid (in /lib/tls/i686/cmov/libc-2.7.so)
>>> ==26628==    by 0x8623509: PetscGetUserName (fuser.c:68)
>>> ==26628==    by 0x85E0CF0: PetscErrorPrintfInitialize (errtrace.c:68)
>>> ==26628==    by 0x8613E23: PetscInitialize (pinit.c:518)
>>> ==26628==    by 0x804B796: main (ex29.c:139)
>>> ==26628==
>>> ==26628==
>>> ==26628== 80 bytes in 5 blocks are indirectly lost in loss record 4 of 5
>>> ==26628==    at 0x4022AB8: malloc (vg_replace_malloc.c:207)
>>> ==26628==    by 0x428839B: tsearch (in /lib/tls/i686/cmov/libc-2.7.so)
>>> ==26628==    by 0x429AF7D: __nss_lookup_function (in /lib/tls/i686/cmov/
>>> libc-2.7.so)
>>> ==26628==    by 0x4732FFB: ???
>>> ==26628==    by 0x473413C: ???
>>> ==26628==    by 0x4247D15: getpwuid_r (in /lib/tls/i686/cmov/libc-2.7.so
>>> )
>>> ==26628==    by 0x424765D: getpwuid (in /lib/tls/i686/cmov/libc-2.7.so)
>>> ==26628==    by 0x8623509: PetscGetUserName (fuser.c:68)
>>> ==26628==    by 0x85E0CF0: PetscErrorPrintfInitialize (errtrace.c:68)
>>> ==26628==    by 0x8613E23: PetscInitialize (pinit.c:518)
>>> ==26628==    by 0x804B796: main (ex29.c:139)
>>> ==26628==
>>> ==26628==
>>> ==26628== 132,796 bytes in 321 blocks are still reachable in loss record
>>> 5
>>> of 5
>>> ==26628==    at 0x4022AB8: malloc (vg_replace_malloc.c:207)
>>> ==26628==    by 0x85EF3AC: PetscMallocAlign (mal.c:40)
>>> ==26628==    by 0x85F049B: PetscTrMallocDefault (mtr.c:194)
>>> ==26628==    by 0x81BCD3F: DACreate2d (da2.c:364)
>>> ==26628==    by 0x804BAFB: main (ex29.c:153)
>>> ==26628==
>>> ==26628== LEAK SUMMARY:
>>> ==26628==    definitely lost: 36 bytes in 1 blocks.
>>> ==26628==    indirectly lost: 120 bytes in 10 blocks.
>>> ==26628==      possibly lost: 0 bytes in 0 blocks.
>>> ==26628==    still reachable: 132,828 bytes in 323 blocks.
>>> ==26628==         suppressed: 0 bytes in 0 blocks.
>>>
>>>
>>> --
>>> (Rebecca) Xuefei YUAN
>>> Department of Applied Physics and Applied Mathematics
>>> Columbia University
>>> Tel:917-399-8032
>>> www.columbia.edu/~xy2102 <http://www.columbia.edu/%7Exy2102> <
>>> http://www.columbia.edu/%7Exy2102>
>>>
>>>
>>>
>>
>> --
>> 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
>>
>>
>
>
> --
> (Rebecca) Xuefei YUAN
> Department of Applied Physics and Applied Mathematics
> Columbia University
> Tel:917-399-8032
> www.columbia.edu/~xy2102 <http://www.columbia.edu/%7Exy2102>
>
>


-- 
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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