On Sat, May 12, 2012 at 3:16 AM, Matthew Knepley <knepley at gmail.com> wrote:
> On Sat, May 12, 2012 at 4:33 AM, Mohammad Mirzadeh <mirzadeh at > gmail.com>wrote: > >> Hi guys, >> >> I'm having a really weird issue here! My code seg faults for certain >> problem size and after using gdb I have been able to pinpoint the problem >> to a VecGetArray call. Here's a series of things I have tried so far >> >> 1) -on_error_attach_debugger -----> unsuccessful; does not launch >> debugger >> 2) -start_in_debugger -------> unsuccessful; does not start debugger >> > > Run with -log_summary. It will tell you what options the program got. > Also, are there errors relating to X? Send > all output to petsc-maint at mcs.anl.gov > > Matt, -log_summary also does not generate any output! I was eventually able to start_in_debugger using xterm. Previously I was trying to start in kdbg. Even with xterm, -on_error_attach_debugger does not start the debugger. In either case, starting the debugger in xterm using -start_in_debugger or attaching the debugger myself manually, I get a segfault at VecGetArray and then the program terminates without any further output. > 3) attaching debugger myself -----> code runs in debugger and seg faults >> when calling VecGetArray >> > > Is this a debug build? What dereference is causing the SEGV? Is the Vec a > valid object? It sounds like > it has been corrupted. > > Yes; with the -g option. How can I check if Vec is "valid"? 4) using ierr=VecGetArray;CHKERRQ(ierr) ------> PETSc does not produce >> error messages; the code simply seg faults and terminates >> 5) checking the values of ierr inside the debugger ---------> They are >> all 0 up untill the code terminates; I think this means petsc does not >> generate error? >> 6) checking for memory leak with valgrind -----------> All I get are >> leaks from OpenMPI and PetscInitialize and PetscFinalize; I think these are >> just routine and safe? >> > > Should I attach the whole valgrind output here or send it to petsc-maint? I just repeast these two a couple of times!: ==4508== 320 (288 direct, 32 indirect) bytes in 1 blocks are definitely lost in loss record 2,644 of 2,665 ==4508== at 0x4C2815C: malloc (vg_replace_malloc.c:236) ==4508== by 0x86417ED: ??? ==4508== by 0x5D4D099: orte_rml_base_comm_start (in /usr/lib/openmpi/lib/libopen-rte.so.0.0.0) ==4508== by 0x8640AD1: ??? ==4508== by 0x5D3AFE6: orte_ess_base_app_setup (in /usr/lib/openmpi/lib/libopen-rte.so.0.0.0) ==4508== by 0x8846E41: ??? ==4508== by 0x5D23A52: orte_init (in /usr/lib/openmpi/lib/libopen-rte.so.0.0.0) ==4508== by 0x5A9E806: ??? (in /usr/lib/openmpi/lib/libmpi.so.0.0.1) ==4508== by 0x5ABFD7F: PMPI_Init (in /usr/lib/openmpi/lib/libmpi.so.0.0.1) ==4508== by 0x530A90: PetscInitialize(int*, char***, char const*, char const*) (pinit.c:668) ==4508== by 0x4A4955: PetscSession::PetscSession(int*, char***, char const*, char const*) (utilities.h:17) ==4508== by 0x4A1DA5: main (main_Test2.cpp:49) ==4508== 74 bytes in 1 blocks are definitely lost in loss record 2,411 of 2,665 ==4508== at 0x4C2815C: malloc (vg_replace_malloc.c:236) ==4508== by 0x6F2DDA1: strdup (strdup.c:43) ==4508== by 0x5F85117: ??? (in /usr/lib/openmpi/lib/libopen-pal.so.0.0.0) ==4508== by 0x5F85359: mca_base_param_lookup_string (in /usr/lib/openmpi/lib/libopen-pal.so.0.0.0) ==4508== by 0xB301869: ??? ==4508== by 0xB2F5126: ??? ==4508== by 0x5F82E17: mca_base_components_open (in /usr/lib/openmpi/lib/libopen-pal.so.0.0.0) ==4508== by 0x5ADA6BA: mca_btl_base_open (in /usr/lib/openmpi/lib/libmpi.so.0.0.1) ==4508== by 0xA6A9B93: ??? ==4508== by 0x5F82E17: mca_base_components_open (in /usr/lib/openmpi/lib/libopen-pal.so.0.0.0) ==4508== by 0x5AE3C88: mca_pml_base_open (in /usr/lib/openmpi/lib/libmpi.so.0.0.1) ==4508== by 0x5A9E9E0: ??? (in /usr/lib/openmpi/lib/libmpi.so.0.0.1) but eventually I get: ==4508== LEAK SUMMARY: ==4508== definitely lost: 5,949 bytes in 55 blocks ==4508== indirectly lost: 3,562 bytes in 32 blocks ==4508== possibly lost: 0 bytes in 0 blocks ==4508== still reachable: 181,516 bytes in 2,660 blocks ==4508== suppressed: 0 bytes in 0 blocks ==4508== Reachable blocks (those to which a pointer was found) are not shown. ==4508== To see them, rerun with: --leak-check=full --show-reachable=y which seems considerable! > How can we say anything without the valgrind output? > > Matt > > >> >> What else can I try to find the problem? Any recommendation is really >> appreciated! >> >> Thanks, >> Mohammad >> > > > > -- > 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20120513/afd9e11a/attachment.htm>
