<div dir="ltr">I can run it now, thanks. Although if I run it with valgrind 3.5.0 (should I update to the last version?) I get some memory leaks related with the function DMPlexCreateBoxMesh.<div><br></div><div><div>[salaza11@maya tutorials]$ valgrind --leak-check=full ./ex12 -run_type test -refinement_limit 0.0 -bc_type dirichlet -interpolate 0 -petscspace_order 1 -show_initial -dm_plex_print_fem 1</div>
<div>==9625== Memcheck, a memory error detector</div><div>==9625== Copyright (C) 2002-2009, and GNU GPL'd, by Julian Seward et al.</div><div>==9625== Using Valgrind-3.5.0 and LibVEX; rerun with -h for copyright info</div>
<div>==9625== Command: ./ex12 -run_type test -refinement_limit 0.0 -bc_type dirichlet -interpolate 0 -petscspace_order 1 -show_initial -dm_plex_print_fem 1</div><div>==9625== </div><div>Local function:</div><div>Vec Object: 1 MPI processes</div>
<div> type: seq</div><div>0</div><div>0.25</div><div>1</div><div>0.25</div><div>0.5</div><div>1.25</div><div>1</div><div>1.25</div><div>2</div><div>Initial guess</div><div>Vec Object: 1 MPI processes</div><div> type: seq</div>
<div>0.5</div><div>L_2 Error: 0.111111</div><div>Residual:</div><div>Vec Object: 1 MPI processes</div><div> type: seq</div><div>0</div><div>0</div><div>0</div><div>0</div><div>0</div><div>0</div><div>0</div><div>0</div><div>
0</div><div>Initial Residual</div><div>Vec Object: 1 MPI processes</div><div> type: seq</div><div>0</div><div>L_2 Residual: 0</div><div>Jacobian:</div><div>Mat Object: 1 MPI processes</div><div> type: seqaij</div><div>row 0: (0, 4) </div>
<div>Residual:</div><div>Vec Object: 1 MPI processes</div><div> type: seq</div><div>0</div><div>0</div><div>0</div><div>0</div><div>-2</div><div>0</div><div>0</div><div>0</div><div>0</div><div>Au - b = Au + F(0)</div><div>
Vec Object: 1 MPI processes</div><div> type: seq</div><div>0</div><div>Linear L_2 Residual: 0</div><div>==9625== </div><div>==9625== HEAP SUMMARY:</div><div>==9625== in use at exit: 288 bytes in 3 blocks</div><div>==9625== total heap usage: 2,484 allocs, 2,481 frees, 1,009,287 bytes allocated</div>
<div>==9625== </div><div>==9625== 48 bytes in 1 blocks are definitely lost in loss record 1 of 3</div><div>==9625== at 0x4A05E46: malloc (vg_replace_malloc.c:195)</div><div>==9625== by 0x5D8D4E1: writepoly (triangle.c:12012)</div>
<div>==9625== by 0x5D8FAAC: triangulate (triangle.c:13167)</div><div>==9625== by 0x56B0884: DMPlexGenerate_Triangle (plex.c:3749)</div><div>==9625== by 0x56B5EE4: DMPlexGenerate (plex.c:4503)</div><div>==9625== by 0x567F414: DMPlexCreateBoxMesh (plexcreate.c:668)</div>
<div>==9625== by 0x4051FA: CreateMesh (ex12.c:341)</div><div>==9625== by 0x408D3D: main (ex12.c:651)</div><div>==9625== </div><div>==9625== 96 bytes in 1 blocks are definitely lost in loss record 2 of 3</div><div>==9625== at 0x4A05E46: malloc (vg_replace_malloc.c:195)</div>
<div>==9625== by 0x5D8D485: writepoly (triangle.c:12004)</div><div>==9625== by 0x5D8FAAC: triangulate (triangle.c:13167)</div><div>==9625== by 0x56B0884: DMPlexGenerate_Triangle (plex.c:3749)</div><div>==9625== by 0x56B5EE4: DMPlexGenerate (plex.c:4503)</div>
<div>==9625== by 0x567F414: DMPlexCreateBoxMesh (plexcreate.c:668)</div><div>==9625== by 0x4051FA: CreateMesh (ex12.c:341)</div><div>==9625== by 0x408D3D: main (ex12.c:651)</div><div>==9625== </div><div>==9625== 144 bytes in 1 blocks are definitely lost in loss record 3 of 3</div>
<div>==9625== at 0x4A05E46: malloc (vg_replace_malloc.c:195)</div><div>==9625== by 0x5D8CD20: writenodes (triangle.c:11718)</div><div>==9625== by 0x5D8F9DE: triangulate (triangle.c:13132)</div><div>==9625== by 0x56B0884: DMPlexGenerate_Triangle (plex.c:3749)</div>
<div>==9625== by 0x56B5EE4: DMPlexGenerate (plex.c:4503)</div><div>==9625== by 0x567F414: DMPlexCreateBoxMesh (plexcreate.c:668)</div><div>==9625== by 0x4051FA: CreateMesh (ex12.c:341)</div><div>==9625== by 0x408D3D: main (ex12.c:651)</div>
<div>==9625== </div><div>==9625== LEAK SUMMARY:</div><div>==9625== definitely lost: 288 bytes in 3 blocks</div><div>==9625== indirectly lost: 0 bytes in 0 blocks</div><div>==9625== possibly lost: 0 bytes in 0 blocks</div>
<div>==9625== still reachable: 0 bytes in 0 blocks</div><div>==9625== suppressed: 0 bytes in 0 blocks</div><div>==9625== </div><div>==9625== For counts of detected and suppressed errors, rerun with: -v</div><div>
==9625== ERROR SUMMARY: 3 errors from 3 contexts (suppressed: 6 from 6)</div><div><br></div></div><div><br></div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Mar 3, 2014 at 7:05 PM, Matthew Knepley <span dir="ltr"><<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><div class="">On Mon, Mar 3, 2014 at 4:59 PM, Miguel Angel Salazar de Troya <span dir="ltr"><<a href="mailto:salazardetroya@gmail.com" target="_blank">salazardetroya@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">You are welcome, thanks for your help.</div></blockquote><div><br></div></div><div>Okay, I have rebuilt completely clean, and ex12 runs for me. Can you try again after pulling?</div>
<div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div><div class="h5"><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div class="gmail_extra">
<div class="gmail_quote">On Mon, Mar 3, 2014 at 4:13 PM, Matthew Knepley <span dir="ltr"><<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><div>On Mon, Mar 3, 2014 at 1:44 PM, Miguel Angel Salazar de Troya <span dir="ltr"><<a href="mailto:salazardetroya@gmail.com" target="_blank">salazardetroya@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Thanks. This is what I get.</div></div></blockquote><div><br></div></div><div>Okay, this was broken by a new push to master/next in the last few days. I have pushed a fix,</div>
<div>however next is currently broken due to a failure to check in a file. This should be fixed shortly,</div><div>and then ex12 will work. I will mail you when its ready.</div><div><br></div><div> Thanks for finding this,</div>
<div><br></div><div> Matt</div><div><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><div>(gdb) cont</div><div>Continuing.</div><div><br></div><div>Program received signal SIGSEGV, Segmentation fault.</div><div>0x00007fd6811bea7b in DMPlexComputeJacobianFEM (dm=0x159a180, X=0x168b5b0, </div>
<div> Jac=0x7fffae6e8a88, JacP=0x7fffae6e8a88, str=0x7fffae6e7970, </div><div> user=0x7fd6811be509)</div><div> at /home/salaza11/petsc/src/dm/impls/plex/plexfem.c:882</div><div>882 ierr = PetscFEGetDimension(fe[f], &Nb);CHKERRQ(ierr);</div>
<div>(gdb) where</div><div>#0 0x00007fd6811bea7b in DMPlexComputeJacobianFEM (dm=0x159a180, X=0x168b5b0, </div><div> Jac=0x7fffae6e8a88, JacP=0x7fffae6e8a88, str=0x7fffae6e7970, </div><div> user=0x7fd6811be509)</div>
<div> at /home/salaza11/petsc/src/dm/impls/plex/plexfem.c:882</div><div>#1 0x00007fd6814a5bf6 in SNESComputeJacobian_DMLocal (snes=0x14e9450, </div><div> X=0x1622ad0, A=0x7fffae6e8a88, B=0x7fffae6e8a88, ctx=0x1652300)</div>
<div> at /home/salaza11/petsc/src/snes/utils/dmlocalsnes.c:102</div><div>#2 0x00007fd6814cc609 in SNESComputeJacobian (snes=0x14e9450, X=0x1622ad0, </div><div> A=0x7fffae6e8a88, B=0x7fffae6e8a88)</div><div> at /home/salaza11/petsc/src/snes/interface/snes.c:2245</div>
<div>#3 0x000000000040af72 in main (argc=15, argv=0x7fffae6e8bc8)</div><div> at /home/salaza11/petsc/src/snes/examples/tutorials/ex12.c:784</div></div><div><br></div><div><br></div></div><div><div>
<div class="gmail_extra"><br><br>
<div class="gmail_quote">On Mon, Mar 3, 2014 at 1:40 PM, Matthew Knepley <span dir="ltr"><<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><div>On Mon, Mar 3, 2014 at 1:39 PM, Miguel Angel Salazar de Troya <span dir="ltr"><<a href="mailto:salazardetroya@gmail.com" target="_blank">salazardetroya@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">This is what I get at gdb when I type 'where'.</div></blockquote><div><br></div></div><div>You have to type 'cont', and then when it fails you type 'where'.</div>
<div><br></div><div> Matt</div><div><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><div>#0 0x000000310e0aa860 in __nanosleep_nocancel () from /lib64/libc.so.6</div>
<div>#1 0x000000310e0aa70f in sleep () from /lib64/libc.so.6</div>
<div>#2 0x00007fd83a00a8be in PetscSleep (s=10)</div><div> at /home/salaza11/petsc/src/sys/utils/psleep.c:52</div><div>#3 0x00007fd83a06f331 in PetscAttachDebugger ()</div><div> at /home/salaza11/petsc/src/sys/error/adebug.c:397</div>
<div>#4 0x00007fd83a0af1d2 in PetscOptionsCheckInitial_Private ()</div><div> at /home/salaza11/petsc/src/sys/objects/init.c:444</div><div>#5 0x00007fd83a0b6448 in PetscInitialize (argc=0x7fff5cd8df2c, </div><div> args=0x7fff5cd8df20, file=0x0, </div>
<div> help=0x60ce40 "Poisson Problem in 2d and 3d with simplicial finite elements.\nWe solve the Poisson problem in a rectangular\ndomain, using a parallel unstructured mesh (DMPLEX) to discretize it.\n\n\n")</div>
<div> at /home/salaza11/petsc/src/sys/objects/pinit.c:876</div><div>#6 0x0000000000408f2c in main (argc=15, argv=0x7fff5cd8f1f8)</div><div> at /home/salaza11/petsc/src/snes/examples/tutorials/ex12.c:663</div></div>
<div><br></div><div>The rest of the gdb output is attached. I am a bit ignorant with gdb, I apologize for that.</div><div><br></div></div><div><div><div class="gmail_extra"><br><br><div class="gmail_quote">
On Mon, Mar 3, 2014 at 12:48 PM, Matthew Knepley <span dir="ltr"><<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><div><div>On Mon, Mar 3, 2014 at 12:39 PM, Miguel Angel Salazar de Troya <span dir="ltr"><<a href="mailto:salazardetroya@gmail.com" target="_blank">salazardetroya@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Thanks for your response. Sorry I did not have the "next" version, but the "master" version. I still have an error though. I followed the steps given here (<a href="https://bitbucket.org/petsc/petsc/wiki/Home" target="_blank">https://bitbucket.org/petsc/petsc/wiki/Home</a>) to obtain the next version, I configured petsc as above and ran ex12 as above as well, getting this error:<div>
<br></div><div><div>[salaza11@maya tutorials]$ ./ex12 -run_type test -refinement_limit 0.0 -bc_type dirichlet -interpolate 0 -petscspace_order 1 -show_initial -dm_plex_print_fem 1</div><div><div>Local function:</div>
<div>Vec Object: 1 MPI processes</div>
<div> type: seq</div><div>0</div></div><div>0.25</div><div>1</div><div>0.25</div><div>0.5</div><div>1.25</div><div>1</div><div>1.25</div><div><div>2</div><div>Initial guess</div><div>Vec Object: 1 MPI processes</div>
<div> type: seq</div>
</div><div>0.5</div><div>L_2 Error: 0.111111</div><div><div><div>Residual:</div><div>Vec Object: 1 MPI processes</div><div> type: seq</div><div>0</div><div>0</div><div>0</div><div>0</div><div>0</div><div>0</div>
<div>0</div><div>0</div><div>
0</div><div>Initial Residual</div><div>Vec Object: 1 MPI processes</div><div> type: seq</div><div>0</div><div>L_2 Residual: 0</div></div></div></div></div></blockquote><div><br></div></div></div><div>Okay, now run with -start_in_debugger, and give me a stack trace using 'where'.</div>
<div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div><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><div><div>
<div>[0]PETSC ERROR: ------------------------------------------------------------------------</div>
<div>[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range</div><div>[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger</div><div>[0]PETSC ERROR: or see <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSC" target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSC</a> 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</div>
<div>[0]PETSC ERROR: likely location of problem given in stack below</div><div>[0]PETSC ERROR: --------------------- Stack Frames ------------------------------------</div><div>[0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,</div>
<div>[0]PETSC ERROR: INSTEAD the line number of the start of the function</div><div>[0]PETSC ERROR: is given.</div></div></div><div>[0]PETSC ERROR: [0] DMPlexComputeJacobianFEM line 871 /home/salaza11/petsc/src/dm/impls/plex/plexfem.c</div>
<div>
<div>[0]PETSC ERROR: [0] SNESComputeJacobian_DMLocal line 94 /home/salaza11/petsc/src/snes/utils/dmlocalsnes.c</div><div>[0]PETSC ERROR: [0] SNES user Jacobian function line 2244 /home/salaza11/petsc/src/snes/interface/snes.c</div>
<div>[0]PETSC ERROR: [0] SNESComputeJacobian line 2203 /home/salaza11/petsc/src/snes/interface/snes.c</div></div><div>[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------</div>
<div>[0]PETSC ERROR: Signal received</div><div>[0]PETSC ERROR: See http://<a href="http://www.mcs.anl.gov/petsc/documentation/faq.html" target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html</a> for trouble shooting.</div>
<div>
[0]PETSC ERROR: Petsc Development GIT revision: v3.4.3-4705-gfb6b3bc GIT Date: 2014-03-03 08:23:43 -0600</div><div>[0]PETSC ERROR: ./ex12 on a linux-gnu-c-debug named maya by salaza11 Mon Mar 3 11:49:15 2014</div><div>
<div>[0]PETSC ERROR: Configure options --download-mpich --download-scientificpython --download-triangle --download-ctetgen --download-chaco --with-c2html=0</div>
</div><div>[0]PETSC ERROR: #1 User provided function() line 0 in unknown file</div><div><div>application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0</div><div>[unset]: aborting job:</div><div>application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0</div>
</div></div><div><br></div></div><div><div><div class="gmail_extra"><br><br><div class="gmail_quote">On Sun, Mar 2, 2014 at 7:11 PM, Matthew Knepley <span dir="ltr"><<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><div>On Sun, Mar 2, 2014 at 6:54 PM, Miguel Angel Salazar de Troya <span dir="ltr"><<a href="mailto:salazardetroya@gmail.com" target="_blank">salazardetroya@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi everybody<div><br></div><div>I am trying to run example ex12.c without much success. I specifically run it with the command options:</div>
</div></blockquote><div><br></div></div><div>We need to start narrowing down differences, because it runs for me and our nightly tests. So, first can</div><div>you confirm that you are using the latest 'next' branch?</div>
<div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div><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><span style="font-family:arial,sans-serif;font-size:13px">./</span><span style="font-family:arial,sans-serif;font-size:13px">ex12</span><span style="font-family:arial,sans-serif;font-size:13px"> -run_type test -refinement_limit 0.0 -bc_type dirichlet -interpolate 0 -petscspace_order 1 -show_initial -dm_plex_print_fem 1</span><br>
</div><div><span style="font-family:arial,sans-serif;font-size:13px"><br></span></div><div><span style="font-family:arial,sans-serif;font-size:13px">And I get this output</span></div><div><span style="font-family:arial,sans-serif;font-size:13px"><br>
</span></div><div><div><font face="arial, sans-serif">Local function:</font></div><div><font face="arial, sans-serif">Vec Object: 1 MPI processes</font></div><div><font face="arial, sans-serif"> type: seq</font></div>
<div><font face="arial, sans-serif">0</font></div><div><font face="arial, sans-serif">1</font></div><div><font face="arial, sans-serif">1</font></div><div><font face="arial, sans-serif">2</font></div><div><font face="arial, sans-serif">1</font></div>
<div><font face="arial, sans-serif">2</font></div><div><font face="arial, sans-serif">2</font></div><div><font face="arial, sans-serif">3</font></div><div><font face="arial, sans-serif">Initial guess</font></div><div><font face="arial, sans-serif">Vec Object: 1 MPI processes</font></div>
<div><font face="arial, sans-serif"> type: seq</font></div><div><font face="arial, sans-serif">L_2 Error: 0.625</font></div><div><font face="arial, sans-serif">Residual:</font></div><div><font face="arial, sans-serif">Vec Object: 1 MPI processes</font></div>
<div><font face="arial, sans-serif"> type: seq</font></div><div><font face="arial, sans-serif">0</font></div><div><font face="arial, sans-serif">0</font></div><div><font face="arial, sans-serif">0</font></div><div><font face="arial, sans-serif">0</font></div>
<div><font face="arial, sans-serif">0</font></div><div><font face="arial, sans-serif">0</font></div><div><font face="arial, sans-serif">0</font></div><div><font face="arial, sans-serif">0</font></div><div><font face="arial, sans-serif">Initial Residual</font></div>
<div><font face="arial, sans-serif">Vec Object: 1 MPI processes</font></div><div><font face="arial, sans-serif"> type: seq</font></div><div><font face="arial, sans-serif">L_2 Residual: 0</font></div><div><font face="arial, sans-serif">[0]PETSC ERROR: ------------------------------------------------------------------------</font></div>
<div><font face="arial, sans-serif">[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range</font></div><div><font face="arial, sans-serif">[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger</font></div>
<div><font face="arial, sans-serif">[0]PETSC ERROR: or see <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSC" target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSC</a> 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</font></div>
<div><font face="arial, sans-serif">[0]PETSC ERROR: likely location of problem given in stack below</font></div><div><font face="arial, sans-serif">[0]PETSC ERROR: --------------------- Stack Frames ------------------------------------</font></div>
<div><font face="arial, sans-serif">[0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,</font></div><div><font face="arial, sans-serif">[0]PETSC ERROR: INSTEAD the line number of the start of the function</font></div>
<div><font face="arial, sans-serif">[0]PETSC ERROR: is given.</font></div><div><font face="arial, sans-serif">[0]PETSC ERROR: [0] DMPlexComputeJacobianFEM line 867 /home/salaza11/petsc/src/dm/impls/plex/plexfem.c</font></div>
<div><font face="arial, sans-serif">[0]PETSC ERROR: [0] SNESComputeJacobian_DMLocal line 94 /home/salaza11/petsc/src/snes/utils/dmlocalsnes.c</font></div><div><font face="arial, sans-serif">[0]PETSC ERROR: [0] SNES user Jacobian function line 2244 /home/salaza11/petsc/src/snes/interface/snes.c</font></div>
<div><font face="arial, sans-serif">[0]PETSC ERROR: [0] SNESComputeJacobian line 2203 /home/salaza11/petsc/src/snes/interface/snes.c</font></div><div><font face="arial, sans-serif">[0]PETSC ERROR: --------------------- Error Message ------------------------------------</font></div>
<div><font face="arial, sans-serif">[0]PETSC ERROR: Signal received!</font></div><div><font face="arial, sans-serif">[0]PETSC ERROR: ------------------------------------------------------------------------</font></div><div>
<font face="arial, sans-serif">[0]PETSC ERROR: Petsc Development GIT revision: v3.4.3-3453-g0a94005 GIT Date: 2014-03-02 13:12:04 -0600</font></div><div><font face="arial, sans-serif">[0]PETSC ERROR: See docs/changes/index.html for recent updates.</font></div>
<div><font face="arial, sans-serif">[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.</font></div><div><font face="arial, sans-serif">[0]PETSC ERROR: See docs/index.html for manual pages.</font></div><div>
<font face="arial, sans-serif">[0]PETSC ERROR: ------------------------------------------------------------------------</font></div><div><font face="arial, sans-serif">[0]PETSC ERROR: ./ex12 on a linux-gnu-c-debug named maya by salaza11 Sun Mar 2 17:00:09 2014</font></div>
<div><font face="arial, sans-serif">[0]PETSC ERROR: Libraries linked from /home/salaza11/petsc/linux-gnu-c-debug/lib</font></div><div><font face="arial, sans-serif">[0]PETSC ERROR: Configure run at Sun Mar 2 16:46:51 2014</font></div>
<div><font face="arial, sans-serif">[0]PETSC ERROR: Configure options --download-mpich --download-scientificpython --download-triangle --download-ctetgen --download-chaco --with-c2html=0</font></div><div><font face="arial, sans-serif">[0]PETSC ERROR: ------------------------------------------------------------------------</font></div>
<div><font face="arial, sans-serif">[0]PETSC ERROR: User provided function() line 0 in unknown file</font></div><div><font face="arial, sans-serif">application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0</font></div>
<div><font face="arial, sans-serif">[unset]: aborting job:</font></div><div><font face="arial, sans-serif">application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0</font></div><div style="font-family:arial,sans-serif;font-size:13px">
<br></div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">Probably my problems could be on my configuration. I attach the configure.log. I ran ./configure like this</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br></div><div><div><font face="arial, sans-serif">./configure --download-mpich --download-scientificpython --download-triangle --download-ctetgen --download-chaco --with-c2html=0</font></div>
<div style="font-family:arial,sans-serif;font-size:13px"><br></div></div><div style="font-family:arial,sans-serif;font-size:13px">Thanks a lot in advance.</div></div><div><span style="font-family:arial,sans-serif;font-size:13px"><br>
</span></div><div><br></div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Jan 28, 2014 at 10:37 AM, Matthew Knepley <span dir="ltr"><<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><div>On Tue, Jan 28, 2014 at 10:31 AM, Yaakoub El Khamra <span dir="ltr"><<a href="mailto:yelkhamra@gmail.com" target="_blank">yelkhamra@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><br><div>If</div><div> <span style="font-family:Tahoma;font-size:13.63636302947998px">./</span><span style="font-family:Tahoma;font-size:13.63636302947998px">ex12</span><span style="font-family:Tahoma;font-size:13.63636302947998px"> -run_type test -dim 3 -refinement_limit 0.0125 -variable_coefficient field -interpolate 1 -petscspace_order 2 -show_initial -dm_plex_print_fem</span></div>
<div><span style="font-family:Tahoma;font-size:13.63636302947998px"><br></span></div><div><span style="font-family:Tahoma;font-size:13.63636302947998px">is for serial, any chance we can get the options to run in parallel?</span></div>
</div></blockquote><div><br></div></div><div>Just use mpiexec -n <procs></div><div><br></div><div> Matt</div><div><div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="gmail_extra"><div>
<br>Regards<br>Yaakoub El Khamra<br></div>
<br><br><div class="gmail_quote">On Fri, Jan 17, 2014 at 11:29 AM, Matthew Knepley <span dir="ltr"><<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><div>On Fri, Jan 17, 2014 at 11:06 AM, Jones,Martin Alexander <span dir="ltr"><<a href="mailto:MAJones2@mdanderson.org" target="_blank">MAJones2@mdanderson.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div>
<div style="direction:ltr;font-size:10pt;font-family:Tahoma"><br>
<div style="font-size:16px;font-family:'Times New Roman'">
<hr>
<div style="direction:ltr"><font color="#000000" face="Tahoma"><b>From:</b> Matthew Knepley [<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>]<br>
<b>Sent:</b> Friday, January 17, 2014 11:04 AM<br>
<b>To:</b> Jones,Martin Alexander<br>
<b>Cc:</b> <a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a><br>
<b>Subject:</b> Re: [petsc-users] Problems running ex12.c<br>
</font><br>
</div>
<div></div>
<div>
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">On Fri, Jan 17, 2014 at 11:00 AM, Jones,Martin Alexander
<span dir="ltr"><<a href="mailto:MAJones2@mdanderson.org" target="_blank">MAJones2@mdanderson.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div>
<div style="direction:ltr;font-size:10pt;font-family:Tahoma">These examples all seem to run excepting the following command,<br>
<br>
<span dir="ltr">ex12 -run_type test -dim 3 -refinement_limit 0.0125 -variable_coefficient field -interpolate 1 -petscspace_order 2 -show_initial -dm_plex_print_fem
<br>
<br>
I get the following ouput:<br>
<br>
./ex12 -run_type test -dim 3 -refinement_limit 0.0125 -variable_coefficient field -interpolate 1 -petscspace_order 2 -show_initial -dm_plex_print_fem<br>
Local function:<br>
./ex12: symbol lookup error: /opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_intel_thread.so: undefined symbol: omp_get_num_procs<br>
</span></div>
</div>
</blockquote>
<div><br>
</div>
<div>This is a build problem, but it should affect all the runs. Is this reproducible? Can you send configure.log? MKL is the worst. If this</div>
<div>persists, I would just switch to --download-f-blas-lapack.</div></div></div></div></div></div></div></div></blockquote><div><br></div></div><div>Thanks. I have some advice on options</div><div><br></div><div> --with-precision=single # I would not use this unless you are doing something special, like CUDA</div>
<div> --with-clanguage=C++ # I would recommend switching to C, the build is much faster</div><div> --with-mpi-dir=/usr --with-mpi4py=0</div><div> --with-shared-libraries --CFLAGS=-O0 --CXXFLAGS=-O0 --with-fc=0</div><div>
--with-etags=1 # This is unnecessary</div><div> --with-blas-lapack-lib="[/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_rt.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_intel_thread.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_core.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libiomp5.so]" # Here is the problem, see below</div>
<div> --download-metis</div><div> --download-fiat=yes --download-generator --download-scientificpython # Get rid of these, they are obsolete</div><div><br></div><div>Your MKL needs another library for the OpenMP symbols. I would recommend switching to --download-f2cblaslapack,</div>
<div>or you can try and find that library.</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div><div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div><div style="direction:ltr;font-size:10pt;font-family:Tahoma"><div style="font-size:16px;font-family:'Times New Roman'"><div><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div>
<div style="direction:ltr;font-size:10pt;font-family:Tahoma"><span dir="ltr"></span>
<div style="font-size:16px;font-family:'Times New Roman'">
<hr>
<div style="direction:ltr"><font color="#000000" face="Tahoma"><b>From:</b> Matthew Knepley [<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>]<br>
<b>Sent:</b> Thursday, January 16, 2014 6:35 PM<br>
<b>To:</b> Jones,Martin Alexander<br>
<b>Cc:</b> <a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a><br>
<b>Subject:</b> Re: [petsc-users] Problems running ex12.c<br>
</font><br>
</div>
<div></div>
<div>
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">On Thu, Jan 16, 2014 at 5:43 PM, Jones,Martin Alexander <span dir="ltr">
<<a href="mailto:MAJones2@mdanderson.org" target="_blank">MAJones2@mdanderson.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div>
<div style="direction:ltr;font-size:10pt;font-family:Tahoma">Hi, This is the next error message after configuring and building with the triangle package when trying to run ex12</div>
</div>
</blockquote>
<div><br>
</div>
<div>This is my fault for bad defaults. I will fix. Try running</div>
<div><br>
</div>
<div> ./ex12 -run_type test -refinement_limit 0.0 -bc_type dirichlet -interpolate 0 -petscspace_order 1 -show_initial -dm_plex_print_fem 1</div>
<div><br>
</div>
<div>for a representative run. Then you could try 3D</div>
<div><br>
</div>
<div> ex12 -run_type test -dim 3 -refinement_limit 0.0125 -variable_coefficient field -interpolate 1 -petscspace_order 2 -show_initial -dm_plex_print_fem </div>
<div><br>
</div>
<div>or a full run</div>
<div><br>
</div>
<div> ex12 -refinement_limit 0.01 -bc_type dirichlet -interpolate -petscspace_order 1</div>
<div><br>
</div>
<div> ex12 -refinement_limit 0.01 -bc_type dirichlet -interpolate -petscspace_order 2</div>
<div><br>
</div>
<div>Let me know if those work.</div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div>
<div style="direction:ltr;font-size:10pt;font-family:Tahoma">
<div>
<div>./ex12</div>
<div>[0]PETSC ERROR: ------------------------------------------------------------------------</div>
<div>[0]PETSC ERROR: Caught signal number 8 FPE: Floating Point Exception,probably divide by zero</div>
<div>[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger</div>
<div>[0]PETSC ERROR: or see <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSC" target="_blank">
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSC</a> 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</div>
<div>[0]PETSC ERROR: likely location of problem given in stack below</div>
<div>[0]PETSC ERROR: --------------------- Stack Frames ------------------------------------</div>
<div>[0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,</div>
<div>[0]PETSC ERROR: INSTEAD the line number of the start of the function</div>
<div>[0]PETSC ERROR: is given.</div>
<div>[0]PETSC ERROR: [0] DMPlexComputeResidualFEM line 531 /home/mjonesa/PETSc/petsc/src/dm/impls/plex/plexfem.c</div>
<div>[0]PETSC ERROR: [0] SNESComputeFunction_DMLocal line 63 /home/mjonesa/PETSc/petsc/src/snes/utils/dmlocalsnes.c</div>
<div>[0]PETSC ERROR: [0] SNES user function line 2088 /home/mjonesa/PETSc/petsc/src/snes/interface/snes.c</div>
<div>[0]PETSC ERROR: [0] SNESComputeFunction line 2076 /home/mjonesa/PETSc/petsc/src/snes/interface/snes.c</div>
<div>[0]PETSC ERROR: [0] SNESSolve_NEWTONLS line 144 /home/mjonesa/PETSc/petsc/src/snes/impls/ls/ls.c</div>
<div>[0]PETSC ERROR: [0] SNESSolve line 3765 /home/mjonesa/PETSc/petsc/src/snes/interface/snes.c</div>
<div>[0]PETSC ERROR: --------------------- Error Message ------------------------------------</div>
<div>[0]PETSC ERROR: Signal received!</div>
<div>[0]PETSC ERROR: ------------------------------------------------------------------------</div>
<div>[0]PETSC ERROR: Petsc Development GIT revision: v3.4.3-2317-gcd0e7f7 GIT Date: 2014-01-15 20:33:42 -0600</div>
<div>[0]PETSC ERROR: See docs/changes/index.html for recent updates.</div>
<div>[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.</div>
<div>[0]PETSC ERROR: See docs/index.html for manual pages.</div>
<div>[0]PETSC ERROR: ------------------------------------------------------------------------</div>
<div>[0]PETSC ERROR: ./ex12 on a arch-linux2-cxx-debug named maeda by mjonesa Thu Jan 16 17:41:23 2014</div>
<div>[0]PETSC ERROR: Libraries linked from /home/mjonesa/local/lib</div>
<div>[0]PETSC ERROR: Configure run at Thu Jan 16 17:38:33 2014</div>
<div>[0]PETSC ERROR: Configure options --prefix=/home/mjonesa/local --with-blas-lapack-lib="[/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_rt.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_intel_thread.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_core.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libiomp5.so]"
--with-c2html=0 --with-clanguage=c++ PETSC_ARCH=arch-linux2-cxx-debug --download-triangle</div>
<div>[0]PETSC ERROR: ------------------------------------------------------------------------</div>
<div>[0]PETSC ERROR: User provided function() line 0 in unknown file</div>
<div>application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0</div>
<div style="font-size:16px;font-family:'Times New Roman'">
<hr>
<div style="direction:ltr"><font color="#000000" face="Tahoma"><b>From:</b> Matthew Knepley [<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>]<br>
<b>Sent:</b> Thursday, January 16, 2014 4:37 PM<br>
<b>To:</b> Jones,Martin Alexander<br>
<b>Cc:</b> <a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a><br>
<b>Subject:</b> Re: [petsc-users] Problems running ex12.c<br>
</font><br>
</div>
<div></div>
<div>
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">On Thu, Jan 16, 2014 at 4:33 PM, Jones,Martin Alexander <span dir="ltr">
<<a href="mailto:MAJones2@mdanderson.org" target="_blank">MAJones2@mdanderson.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div>
<div style="direction:ltr;font-size:10pt;font-family:Tahoma">Hi, I have downloaded and built the dev version you suggested. I think I need the triangle package to run this particular case. Is there any thing else that appears wrong in what I have done from
the error messages below:<br>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>Great! Its running. You can reconfigure like this:</div>
<div><br>
</div>
<div> $PETSC_DIR/$PETSC_ARCH/conf/reconfigure-$PETSC_ARCH.py --download-triangle</div>
<div><br>
</div>
<div>and then rebuild</div>
<div><br>
</div>
<div> make</div>
<div><br>
</div>
<div>and then rerun. You can load meshes, but its much easier to have triangle create them.</div>
<div><br>
</div>
<div> Thanks for being patient,</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div>
<div style="direction:ltr;font-size:10pt;font-family:Tahoma">[0]PETSC ERROR: --------------------- Error Message ------------------------------------<br>
[0]PETSC ERROR: No support for this operation for this object type!<br>
[0]PETSC ERROR: Mesh generation needs external package support.<br>
Please reconfigure with --download-triangle.!<br>
[0]PETSC ERROR: ------------------------------------------------------------------------<br>
[0]PETSC ERROR: Petsc Development GIT revision: v3.4.3-2317-gcd0e7f7 GIT Date: 2014-01-15 20:33:42 -0600<br>
[0]PETSC ERROR: See docs/changes/index.html for recent updates.<br>
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.<br>
[0]PETSC ERROR: See docs/index.html for manual pages.<br>
[0]PETSC ERROR: ------------------------------------------------------------------------<br>
[0]PETSC ERROR: ./ex12 on a arch-linux2-cxx-debug named maeda by mjonesa Thu Jan 16 16:28:20 2014<br>
[0]PETSC ERROR: Libraries linked from /home/mjonesa/local/lib<br>
[0]PETSC ERROR: Configure run at Thu Jan 16 16:25:53 2014<br>
[0]PETSC ERROR: Configure options --prefix=/home/mjonesa/local --with-clanguage=c++ --with-c2html=0 --with-blas-lapack-lib="[/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_rt.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_intel_thread.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_core.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libiomp5.so]"<br>
[0]PETSC ERROR: ------------------------------------------------------------------------<br>
[0]PETSC ERROR: DMPlexGenerate() line 4332 in /home/mjonesa/PETSc/petsc/src/dm/impls/plex/plex.c<br>
[0]PETSC ERROR: DMPlexCreateBoxMesh() line 600 in /home/mjonesa/PETSc/petsc/src/dm/impls/plex/plexcreate.c<br>
[0]PETSC ERROR: CreateMesh() line 295 in /home/mjonesa/PETSc/petsc/src/snes/examples/tutorials/ex12.c<br>
[0]PETSC ERROR: main() line 659 in /home/mjonesa/PETSc/petsc/src/snes/examples/tutorials/ex12.c<br>
application called MPI_Abort(MPI_COMM_WORLD, 56) - process 0<br>
<div style="font-size:16px;font-family:'Times New Roman'">
<hr>
<div style="direction:ltr"><font color="#000000" face="Tahoma"><b>From:</b> Matthew Knepley [<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>]<br>
<b>Sent:</b> Thursday, January 16, 2014 4:06 PM<br>
<b>To:</b> Jones,Martin Alexander<br>
<b>Cc:</b> <a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a><br>
<b>Subject:</b> Re: [petsc-users] Problems running ex12.c<br>
</font><br>
</div>
<div></div>
<div>
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">On Thu, Jan 16, 2014 at 4:05 PM, Jones,Martin Alexander <span dir="ltr">
<<a href="mailto:MAJones2@mdanderson.org" target="_blank">MAJones2@mdanderson.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div>
<div style="direction:ltr;font-size:10pt;font-family:Tahoma">Hi. I changed the ENV variable to the correct entry. when I type make ex12 I get this:<br>
<br>
mjonesa@maeda:~/PETSc/petsc-3.4.3/src/snes/examples/tutorials$ make ex12<br>
g++ -o ex12.o -c -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g -fPIC -I/home/mjonesa/PETSc/petsc-3.4.3/include -I/home/mjonesa/PETSc/petsc-3.4.3/arch-linux2-cxx-debug/include -I/home/mjonesa/PETSc/petsc-3.4.3/include/mpiuni -D__INSDIR__=src/snes/examples/tutorials/
ex12.c<br>
ex12.c:14:18: fatal error: ex12.h: No such file or directory<br>
compilation terminated.<br>
make: *** [ex12.o] Error 1<br>
<br>
Any help of yours is very much appreciated.<br>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>Yes, this relates to my 3). This is not going to work for you with the release. Please see the link I sent.</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div>
<div style="direction:ltr;font-size:10pt;font-family:Tahoma">
<div style="font-size:16px;font-family:'Times New Roman'">
<hr>
<div style="direction:ltr"><font color="#000000" face="Tahoma"><b>From:</b> Matthew Knepley [<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>]<br>
<b>Sent:</b> Thursday, January 16, 2014 3:58 PM<br>
<b>To:</b> Jones,Martin Alexander<br>
<b>Cc:</b> <a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a><br>
<b>Subject:</b> Re: [petsc-users] Problems running ex12.c<br>
</font><br>
</div>
<div></div>
<div>
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">On Thu, Jan 16, 2014 at 3:55 PM, Jones,Martin Alexander <span dir="ltr">
<<a href="mailto:MAJones2@mdanderson.org" target="_blank">MAJones2@mdanderson.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div>
<div style="direction:ltr;font-size:10pt;font-family:Tahoma">Thanks!<br>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>You built with PETSC_ARCH=arch-linux2-cxx-debug</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
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<div style="direction:ltr"><font color="#000000" face="Tahoma"><b>From:</b> Matthew Knepley [<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>]<br>
<b>Sent:</b> Thursday, January 16, 2014 3:31 PM<br>
<b>To:</b> Jones,Martin Alexander<br>
<b>Cc:</b> <a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a><br>
<b>Subject:</b> Re: [petsc-users] Problems running ex12.c<br>
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<div class="gmail_extra">
<div class="gmail_quote">On Thu, Jan 16, 2014 at 3:11 PM, Jones,Martin Alexander <span dir="ltr">
<<a href="mailto:MAJones2@mdanderson.org" target="_blank">MAJones2@mdanderson.org</a>></span> wrote:<br>
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<p class="MsoNormal"><span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Now I went to the directory where ex12.c sits and just did a ‘make ex12.c’ with the following error if this helps? :<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">mjonesa@maeda:~/PETSc/petsc-3.4.3/src/snes/examples/tutorials$ make ex12.c<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">/home/mjonesa/PETSc/petsc-3.4.3/conf/variables:108: /home/mjonesa/PETSc/petsc-3.4.3/linux-gnu-cxx-debug/conf/petscvariables: No such file or directory<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">/home/mjonesa/PETSc/petsc-3.4.3/conf/rules:962: /home/mjonesa/PETSc/petsc-3.4.3/linux-gnu-cxx-debug/conf/petscrules: No such file or directory<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">make: *** No rule to make target `/home/mjonesa/PETSc/petsc-3.4.3/linux-gnu-cxx-debug/conf/petscrules'. Stop.</span></p>
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<div>1) You would type 'make ex12'</div>
<div><br>
</div>
<div>2) Either you PETSC_DIR (<span style="color:rgb(31,73,125);font-family:Calibri,sans-serif;font-size:14.44444465637207px">/home/mjonesa/PETSc/petsc-3.</span><span style="color:rgb(31,73,125);font-family:Calibri,sans-serif;font-size:14.44444465637207px">4.3</span>)
or PETSC_ARCH (<span style="color:rgb(31,73,125);font-family:Calibri,sans-serif;font-size:14.44444465637207px">linux-gnu-cxx-debug</span>) environment variables</div>
<div> do not match what you built. Please send configure.log and make.log</div>
<div><br>
</div>
<div>3) Since it was only recently added, if you want to use the FEM functionality, you must use the development version:</div>
<div><br>
</div>
<div> <a href="http://www.mcs.anl.gov/petsc/developers/index.html" target="_blank">http://www.mcs.anl.gov/petsc/developers/index.html</a></div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
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<p class="MsoNormal"><span style="color:rgb(31,73,125);font-family:Calibri,sans-serif;font-size:11pt"> </span></p>
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<p class="MsoNormal"><b><span style="font-size:10pt;font-family:Tahoma,sans-serif">From:</span></b><span style="font-size:10pt;font-family:Tahoma,sans-serif"> Matthew Knepley [mailto:<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>]
<br>
<b>Sent:</b> Thursday, January 16, 2014 2:48 PM<br>
<b>To:</b> Jones,Martin Alexander<br>
<b>Cc:</b> <a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a><br>
<b>Subject:</b> Re: [petsc-users] Problems running ex12.c<u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">On Thu, Jan 16, 2014 at 2:35 PM, Jones,Martin Alexander <<a href="mailto:MAJones2@mdanderson.org" target="_blank">MAJones2@mdanderson.org</a>> wrote:<u></u><u></u></p>
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<p class="MsoNormal">Hello To Whom it Concerns,<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">I am trying to run the tutorial ex12.c by running <span style="color:rgb(178,34,34)">
'bin/pythonscripts/PetscGenerateFEMQuadrature.py dim order dim 1 laplacian dim order dim 1 boundary src/snes/examples/tutorials/ex12.h'</span><br>
but getting the following error:<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">$ bin/pythonscripts/PetscGenerateFEMQuadrature.py dim order dim 1 laplacian dim order dim 1 boundary src/snes/examples/tutorials/ex12.h<br>
Traceback (most recent call last):<br>
File "bin/pythonscripts/PetscGenerateFEMQuadrature.py", line 15, in <module><br>
from FIAT.reference_element import default_simplex<br>
ImportError: No module named FIAT.reference_element<u></u><u></u></p>
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<p class="MsoNormal"><br>
I have removed the requirement of generating the header file (its now all handled in C). I thought<u></u><u></u></p>
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<p class="MsoNormal">I changed the documentation everywhere (including the latest tutorial slides). Can you try running<u></u><u></u></p>
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<p class="MsoNormal">with 'master' (or 'next'), and point me toward the old docs?<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal"> Thanks,<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal"> Matt<br clear="all">
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<p class="MsoNormal"><u></u> <span><font color="#888888"><u></u></font></span></p>
<span><font color="#888888"></font></span></div>
<span><font color="#888888">
<p class="MsoNormal">-- <br>
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 <u></u><u></u></p>
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<span><font color="#888888"><br>
<br clear="all">
<span><font color="#888888">
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-- <br>
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 </font></span></font></span></div>
<span><font color="#888888"></font></span></div>
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<span><font color="#888888">
<div><br>
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-- <br>
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 </font></span></font></span></div>
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<span><font color="#888888"><br>
<br clear="all">
<span><font color="#888888">
<div><br>
</div>
-- <br>
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 </font></span></font></span></div>
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<span><font color="#888888"><br>
<br clear="all">
<span><font color="#888888">
<div><br>
</div>
-- <br>
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 </font></span></font></span></div>
<span><font color="#888888"></font></span></div>
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<br clear="all"><span><font color="#888888">
<div><br>
</div>
-- <br>
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 </font></span></font></span></div><span><font color="#888888">
</font></span></div><span><font color="#888888">
</font></span></div><span><font color="#888888">
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<br clear="all"><span><font color="#888888">
<div><br>
</div>
-- <br>
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 </font></span></font></span></div><span><font color="#888888">
</font></span></div><span><font color="#888888">
</font></span></div><span><font color="#888888">
</font></span></div><span><font color="#888888">
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</font></span></blockquote></div></div></div><span><font color="#888888"><div><div><br><br clear="all"><div><br></div>-- <br>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></font></span></div></div>
</blockquote></div><br></div>
</blockquote></div></div></div><div><div><br><br clear="all"><span><font color="#888888"><div><br></div>-- <br>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
</font></span></div></div></div></div><span><font color="#888888">
</font></span></blockquote></div><span><font color="#888888"><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><font face="verdana, sans-serif"><b>Miguel Angel Salazar de Troya</b></font><span><font color="#888888"><br>
<font face="arial,helvetica,sans-serif">Graduate Research Assistant<br>
Department of Mechanical Science and Engineering<br></font>University of Illinois at Urbana-Champaign<br><a href="tel:%28217%29%20550-2360" value="+12175502360" target="_blank">(217) 550-2360</a><br>
<a href="mailto:salaza11@illinois.edu" target="_blank">salaza11@illinois.edu</a></font></span><div><br></div></div>
</font></span></div>
</blockquote></div></div></div><div><div><br><br clear="all"><div><br></div>-- <br>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></div></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><font face="verdana, sans-serif"><b>Miguel Angel Salazar de Troya</b></font><span><font color="#888888"><br><font face="arial,helvetica,sans-serif">Graduate Research Assistant<br>
Department of Mechanical Science and Engineering<br></font>University of Illinois at Urbana-Champaign<br><a href="tel:%28217%29%20550-2360" value="+12175502360" target="_blank">(217) 550-2360</a><br>
<a href="mailto:salaza11@illinois.edu" target="_blank">salaza11@illinois.edu</a></font></span><div><br></div></div>
</div>
</div></div></blockquote></div></div></div><div><div><br><br clear="all"><div><br></div>-- <br>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></div></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><font face="verdana, sans-serif"><b>Miguel Angel Salazar de Troya</b></font><span><font color="#888888"><br><font face="arial,helvetica,sans-serif">Graduate Research Assistant<br>
Department of Mechanical Science and Engineering<br></font>University of Illinois at Urbana-Champaign<br><a href="tel:%28217%29%20550-2360" value="+12175502360" target="_blank">(217) 550-2360</a><br>
<a href="mailto:salaza11@illinois.edu" target="_blank">salaza11@illinois.edu</a></font></span><div><br></div></div>
</div>
</div></div></blockquote></div></div></div><div><div><br><br clear="all"><div><br></div>-- <br>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></div></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><font face="verdana, sans-serif"><b>Miguel Angel Salazar de Troya</b></font><span><font color="#888888"><br><font face="arial,helvetica,sans-serif">Graduate Research Assistant<br>
Department of Mechanical Science and Engineering<br></font>University of Illinois at Urbana-Champaign<br><a href="tel:%28217%29%20550-2360" value="+12175502360" target="_blank">(217) 550-2360</a><br>
<a href="mailto:salaza11@illinois.edu" target="_blank">salaza11@illinois.edu</a></font></span><div><br></div></div>
</div>
</div></div></blockquote></div></div></div><div><div><br><br clear="all"><div><br></div>-- <br>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></div></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><font face="verdana, sans-serif"><b>Miguel Angel Salazar de Troya</b></font><span><font color="#888888"><br><font face="arial,helvetica,sans-serif">Graduate Research Assistant<br>
Department of Mechanical Science and Engineering<br></font>University of Illinois at Urbana-Champaign<br><a href="tel:%28217%29%20550-2360" value="+12175502360" target="_blank">(217) 550-2360</a><br>
<a href="mailto:salaza11@illinois.edu" target="_blank">salaza11@illinois.edu</a></font></span><div><br></div></div>
</div>
</div></div></blockquote></div></div></div><div><div class="h5"><br><br clear="all"><div><br></div>-- <br>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></div></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><font face="verdana, sans-serif"><b>Miguel Angel Salazar de Troya</b></font><span><font color="#888888"><br><font face="arial,helvetica,sans-serif">Graduate Research Assistant<br>
Department of Mechanical Science and Engineering<br></font>University of Illinois at Urbana-Champaign<br>(217) 550-2360<br>
<a href="mailto:salaza11@illinois.edu" target="_blank">salaza11@illinois.edu</a></font></span><div><br></div></div>
</div>