[petsc-users] seg fault with VecGetArray

[Matthew Knepley]

On Sun, May 13, 2012 at 7:33 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.
>

You SEGV before it can evidently.


> 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"?
>

PetscValidHeaderSpecific(v,VEC_CLASSID,1);


>  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!:
>

None of this output about lost memory matters. Send the entire output to
petsc-maint

   Matt


> ==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
>>
>
>


-- 
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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