[petsc-users] error running parallel on cluster

[Sepideh Kavousi]

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)

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
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