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

[(Rebecca) Xuefei YUAN]

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?

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>
>>
>>
>
>
> --
> 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