[petsc-users] Debugger question

[Anton Popov]

I support 100% what Barry said. Just get the work done. Cray and IBM 
Linux systems do not support ALL the systems calls that PETSc uses. So 
it's always kind of problem to purge manually petscconf.h in between of 
"configure" and "make" on their machines. I wander how you could install 
any PETSc without modifying petscconf.h. If you just don't care, usually 
you get segfaults right at PetscInitialize() step. Literally it means, 
there is no way you can debug anything, they should reinstall PETSc, 
keeping in mind the exact list of system calls they support, and PETSc 
requirements.

By the way, the times when GNU compilers were "order of magnitude" 
slower than "vendor compilers" have passed long ago. Just give it a try, 
compile some simple computationally intensive code with gcc and 
something from "vendor" with aggressive optimization, and check 
execution time on a large data set. I'm sure you'll be surprised.

Cheers,
Anton

On 4/3/12 3:57 AM, Barry Smith wrote:
> On Apr 2, 2012, at 8:10 PM, Tabrez Ali wrote:
>
>> Hello
>>
>> I am trying to debug a program using the switch '-on_error_attach_debugger' but  the vendor/sysadmin built PETSc 3.2.00 is unable to start the debugger in xterm (see text below). But xterm is installed. What am I doing wrong?
>>
>> Btw the segfault happens during a call to MatMult but only with vendor/sysadmin supplied PETSc 3.2 with PGI and Intel compilers only and _not_ with CRAY or GNU compilers.
>     My advice, blow off "the vendor/sysadmin supplied PETSc 3.2" and just built it yourself so you can get real work done instead of trying to debug their mess.   I promise the vendor one is not like a billion times faster or anything.
>
>     Barry
>
>
>
>> I also dont get the segfault if I build PETSc 3.2-p7 myself with PGI/Intel compilers.
>>
>> Any ideas on how to diagnose the problem? Unfortunately I cannot seem to run valgrind on this particular machine.
>>
>> Thanks in advance.
>>
>> Tabrez
>>
>> ---
>>
>> stali at krakenpf1:~/meshes>  which xterm
>> /usr/bin/xterm
>> stali at krakenpf1:~/meshes>  aprun -n 1 ./defmod -f 2d_point_load_dyn_abc.inp -on_error_attach_debugger
>> ...
>> ...
>> ...
>> [0]PETSC ERROR: ------------------------------------------------------------------------
>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
>> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>> [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/faq.html#valgrind[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
>> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
>> [0]PETSC ERROR: to get more information on the crash.
>> [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
>> [0]PETSC ERROR: PETSC: Attaching gdb to ./defmod of pid 32384 on display localhost:20.0 on machine nid10649
>> Unable to start debugger in xterm: No such file or directory
>> aborting job:
>> application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0
>> _pmii_daemon(SIGCHLD): [NID 10649] [c23-3c0s6n1] [Mon Apr  2 13:06:48 2012] PE 0 exit signal Aborted
>> Application 133198 exit codes: 134
>> Application 133198 resources: utime ~1s, stime ~0s

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