[petsc-users] seg fault with VecGetArray

[Mohammad Mirzadeh]

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
>
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