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
