on a somewhat related topic, I recently found I have the CHKERRXX option which throws exceptions. This seems to be a better option for me since in some some functions with return values I cannot use CHKERRQ/V. If I use this, do I need to catch the exception in myself or is it caught by petsc?
On Sun, May 13, 2012 at 4:33 PM, Mohammad Mirzadeh <mirzadeh at gmail.com>wrote: > > > 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/20120513/0667b8ad/attachment.htm>