[petsc-users] error running parallel on cluster

[Matthew Knepley]

On Mon, Apr 16, 2018 at 9:20 PM, Sepideh Kavousi <skavou1 at lsu.edu> wrote:

> Hello,
> I am solving a PDE where I have the spacial derivtive of the time
> derivative of a variable.  In the DMDATSSetIFunctionLocal function I
> defined d(dY/dt)/dx   as:
> (aYdot[j][i+1].p-aYdot[j][i-1].p)/(2.0*user->hx)
>

I do not think that you get ghosted Ydot in that function.

   Matt


> on my workstation, it is working but on the cluster it gives an error. I
> can not run with debugger on the cluster but I have checked and the error
> is related to this part and I do not have any problem on cluster when
> running in series. Can you please help me about it.
>
> the error is:
> 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/
> 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: likely location of problem given in stack below
> [0]PETSC ERROR: ---------------------  Stack Frames
> ------------------------------------
> [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not
> available,
> [0]PETSC ERROR:       INSTEAD the line number of the start of the function
> [0]PETSC ERROR:       is given.
> [0]PETSC ERROR: [0] TSComputeIFunction_DMDA line 63
> /ddnB/work/skavou1/petsc/src/ts/utils/dmdats.c
> [0]PETSC ERROR: [0] TS user implicit function line 829
> /ddnB/work/skavou1/petsc/src/ts/interface/ts.c
> [0]PETSC ERROR: [0] TSComputeIFunction line 815
> /ddnB/work/skavou1/petsc/src/ts/interface/ts.c
> [0]PETSC ERROR: [0] SNESTSFormFunction_Theta line 640
> /ddnB/work/skavou1/petsc/src/ts/impls/implicit/theta/theta.c
> [0]PETSC ERROR: [0] SNESTSFormFunction line 4564
> /ddnB/work/skavou1/petsc/src/ts/interface/ts.c
> [0]PETSC ERROR: [0] SNES user function line 2202
> /ddnB/work/skavou1/petsc/src/snes/interface/snes.c
> [0]PETSC ERROR: [0] SNESComputeFunction line 2187
> /ddnB/work/skavou1/petsc/src/snes/interface/snes.c
> [0]PETSC ERROR: [0] SNESSolve_NEWTONTR line 90
> /ddnB/work/skavou1/petsc/src/snes/impls/tr/tr.c
> [0]PETSC ERROR: [0] SNESSolve line 4203 /ddnB/work/skavou1/petsc/src/
> snes/interface/snes.c
> [0]PETSC ERROR: [0] TSTheta_SNESSolve line 175
> /ddnB/work/skavou1/petsc/src/ts/impls/implicit/theta/theta.c
> [0]PETSC ERROR: [0] TSStep_Theta line 191 /ddnB/work/skavou1/petsc/src/
> ts/impls/implicit/theta/theta.c
> [0]PETSC ERROR: [0] TSStep line 3526 /ddnB/work/skavou1/petsc/src/
> ts/interface/ts.c
> [0]PETSC ERROR: [0] TSSolve line 3668 /ddnB/work/skavou1/petsc/src/
> ts/interface/ts.c
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: Signal received
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> [0]PETSC ERROR: Petsc Release Version 3.9.0, unknown
> [0]PETSC ERROR: ./one.out on a debug named mike1 by skavou1 Mon Apr 16
> 20:11:44 2018
> [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++
> --with-fc=gfortran --download-mpich --download-fblaslapack
> [0]PETSC ERROR: #1 User provided function() line 0 in  unknown file
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
> ==29057==
> ==29057== HEAP SUMMARY:
> ==29057==     in use at exit: 560,151 bytes in 383 blocks
> ==29057==   total heap usage: 8,734 allocs, 8,351 frees, 4,449,350 bytes
> allocated
> ==29057==
> ==29057== LEAK SUMMARY:
> ==29057==    definitely lost: 0 bytes in 0 blocks
> ==29057==    indirectly lost: 0 bytes in 0 blocks
> ==29057==      possibly lost: 0 bytes in 0 blocks
> ==29057==    still reachable: 560,151 bytes in 383 blocks
> ==29057==         suppressed: 0 bytes in 0 blocks
> ==29057== Rerun with --leak-check=full to see details of leaked memory
> ==29057==
> ==29057== For counts of detected and suppressed errors, rerun with: -v
> ==29057== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 8 from 6)
>
>
>
>
> Thanks,
> Sepideh
>



-- 
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

https://www.cse.buffalo.edu/~knepley/ <http://www.caam.rice.edu/~mk51/>
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