On Mon, Apr 16, 2018 at 9:20 PM, Sepideh Kavousi <skav...@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/>
