<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">On Mon, Apr 16, 2018 at 9:20 PM, Sepideh Kavousi <span dir="ltr"><<a href="mailto:skavou1@lsu.edu" target="_blank">skavou1@lsu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div>Hello,</div>
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I am solving a PDE where I have the spacial derivtive of the time derivative of a variable. In the
<span>DMDATSSetIFunctionLocal</span> function I defined d(dY/dt)/dx as:</div>
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<span>(aYdot[j][i+1].p-aYdot[j][i-1]<wbr>.p)/(2.0*user->hx)</span></div></div></div></blockquote><div><br></div><div>I do not think that you get ghosted Ydot in that function.</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div id="m_734736110172724093divtagdefaultwrapper" dir="ltr" style="font-size:12pt;color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,"EmojiFont","Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols">
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<span>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. <br>
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<span>the error is:</span></div>
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<div>0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range<br>
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger<br>
[0]PETSC ERROR: or see <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind" target="_blank">http://www.mcs.anl.gov/petsc/<wbr>documentation/faq.html#<wbr>valgrind</a><br>
[0]PETSC ERROR: or try <a href="http://valgrind.org" target="_blank">http://valgrind.org</a> on GNU/linux and Apple Mac OS X to find memory corruption errors<br>
[0]PETSC ERROR: likely location of problem given in stack below<br>
[0]PETSC ERROR: --------------------- Stack Frames ------------------------------<wbr>------<br>
[0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,<br>
[0]PETSC ERROR: INSTEAD the line number of the start of the function<br>
[0]PETSC ERROR: is given.<br>
[0]PETSC ERROR: [0] TSComputeIFunction_DMDA line 63 /ddnB/work/skavou1/petsc/src/<wbr>ts/utils/dmdats.c<br>
[0]PETSC ERROR: [0] TS user implicit function line 829 /ddnB/work/skavou1/petsc/src/<wbr>ts/interface/ts.c<br>
[0]PETSC ERROR: [0] TSComputeIFunction line 815 /ddnB/work/skavou1/petsc/src/<wbr>ts/interface/ts.c<br>
[0]PETSC ERROR: [0] SNESTSFormFunction_Theta line 640 /ddnB/work/skavou1/petsc/src/<wbr>ts/impls/implicit/theta/theta.<wbr>c<br>
[0]PETSC ERROR: [0] SNESTSFormFunction line 4564 /ddnB/work/skavou1/petsc/src/<wbr>ts/interface/ts.c<br>
[0]PETSC ERROR: [0] SNES user function line 2202 /ddnB/work/skavou1/petsc/src/<wbr>snes/interface/snes.c<br>
[0]PETSC ERROR: [0] SNESComputeFunction line 2187 /ddnB/work/skavou1/petsc/src/<wbr>snes/interface/snes.c<br>
[0]PETSC ERROR: [0] SNESSolve_NEWTONTR line 90 /ddnB/work/skavou1/petsc/src/<wbr>snes/impls/tr/tr.c<br>
[0]PETSC ERROR: [0] SNESSolve line 4203 /ddnB/work/skavou1/petsc/src/<wbr>snes/interface/snes.c<br>
[0]PETSC ERROR: [0] TSTheta_SNESSolve line 175 /ddnB/work/skavou1/petsc/src/<wbr>ts/impls/implicit/theta/theta.<wbr>c<br>
[0]PETSC ERROR: [0] TSStep_Theta line 191 /ddnB/work/skavou1/petsc/src/<wbr>ts/impls/implicit/theta/theta.<wbr>c<br>
[0]PETSC ERROR: [0] TSStep line 3526 /ddnB/work/skavou1/petsc/src/<wbr>ts/interface/ts.c<br>
[0]PETSC ERROR: [0] TSSolve line 3668 /ddnB/work/skavou1/petsc/src/<wbr>ts/interface/ts.c<br>
[0]PETSC ERROR: --------------------- Error Message ------------------------------<wbr>------------------------------<wbr>--<br>
[0]PETSC ERROR: Signal received<br>
[0]PETSC ERROR: See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html" target="_blank">http://www.mcs.anl.gov/petsc/<wbr>documentation/faq.html</a> for trouble shooting.<br>
[0]PETSC ERROR: Petsc Release Version 3.9.0, unknown <br>
[0]PETSC ERROR: ./one.out on a debug named mike1 by skavou1 Mon Apr 16 20:11:44 2018<br>
[0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-mpich --download-fblaslapack<br>
[0]PETSC ERROR: #1 User provided function() line 0 in unknown file<br>
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0<br>
==29057== <br>
==29057== HEAP SUMMARY:<br>
==29057== in use at exit: 560,151 bytes in 383 blocks<br>
==29057== total heap usage: 8,734 allocs, 8,351 frees, 4,449,350 bytes allocated<br>
==29057== <br>
==29057== LEAK SUMMARY:<br>
==29057== definitely lost: 0 bytes in 0 blocks<br>
==29057== indirectly lost: 0 bytes in 0 blocks<br>
==29057== possibly lost: 0 bytes in 0 blocks<br>
==29057== still reachable: 560,151 bytes in 383 blocks<br>
==29057== suppressed: 0 bytes in 0 blocks<br>
==29057== Rerun with --leak-check=full to see details of leaked memory<br>
==29057== <br>
==29057== For counts of detected and suppressed errors, rerun with: -v<br>
==29057== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 8 from 6)<br>
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<span>Thanks,</span></div>
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<span>Sepideh<br>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div><div><br></div><div><a href="http://www.caam.rice.edu/~mk51/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div>
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