<div dir="ltr">Thanks for your response. Now I am trying to modify this example to include Dirichlet and Neumann conditions at the same time.<div><br></div><div>I can see that inside of DMPlexCreateSquareBoundary there is an option ("-dm_plex_separate_marker") to just mark the top boundary with 1. I understand that only this side would have Dirichlet conditions that are described by the function bcFuncs in user.fem (the exact function in this example). However, when we run the Neumann condition, we fix all the boundary as Neumann condition with the function DMPlexAddBoundary, is this right?</div>
<div><br></div><div>Could there be a way to just fix a certain boundary with the Neumann condition in this example? Would it be easier with an external library as Exodus II?</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">
On Sun, Mar 30, 2014 at 7:51 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 Sun, Mar 30, 2014 at 7:07 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. Your help is really useful to me. <div><br></div><div>The difference between the analytic and the field options are that for the field options the function is projected onto the function space defined for feAux right? What is the advantage of doing this? </div>
</div></blockquote><div><br></div></div><div>If it is not purely a function of the coordinates, or you do not know that function, there is no option left.</div><div class=""><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><div>Also, for this field case I see that the function always has to be a vector. What if we wanted to implement a heterogeneous material in linear elasticity? Would we implement the constitutive tensor as a vector? It would not be very difficult I think, I just want to make sure it would be this way.</div>
</div></blockquote><div><br></div></div><div>Its not a vector, which indicates a particular behavior under coordinate transformations, but an array</div><div>which can hold any data you want.</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 dir="ltr"><div><div>Thanks in advance</div><span><font color="#888888"><div>Miguel</div>
</font></span></div></div><div><div><div class="gmail_extra"><br><br><div class="gmail_quote">On Sun, Mar 30, 2014 at 2:01 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 30, 2014 at 1:57 PM, Miguel Angel Salazar de Troya <span dir="ltr"><<a href="mailto:salazardetroya@gmail.com" target="_blank">salazardetroya@gmail.com</a>></span> wrote:<br>
</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hello everybody<div><br></div><div><div>I had a question about this example. In the petsc-dev next version, why don't we create a PetscSection in the function SetupSection, but we do it in the function SetupMaterialSection and in the function SetupSection of the petsc-current version.</div>
</div></div></blockquote><div><br></div><div>1) I wanted to try and make things more automatic for the user</div><div><br></div><div>2) I needed a way to automatically layout data for coarser/finer grids in unstructured MG</div>
<div><br></div><div>Thus, now when you set for PetscFE into the DM using DMSetField(), it will automatically create</div><div>the section on the first call to DMGetDefaultSection().</div><div><br></div><div>I do not have a similar provision now for materials, so you create your own section. I think this is</div>
<div>alright until we have some idea of a nicer interface.</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>petsc-dev:</div><div><br></div><div><div>#undef __FUNCT__</div><div>#define __FUNCT__ "SetupSection"</div><div>PetscErrorCode SetupSection(DM dm, AppCtx *user)</div><div>
{</div><div> DM cdm = dm;</div><div> const PetscInt id = 1;</div><div> PetscErrorCode ierr;</div><div><br></div><div> PetscFunctionBeginUser;</div><div> ierr = PetscObjectSetName((PetscObject) user->fe[0], "potential");CHKERRQ(ierr);</div>
<div> while (cdm) {</div><div> ierr = DMSetNumFields(cdm, 1);CHKERRQ(ierr);</div><div> ierr = DMSetField(cdm, 0, (PetscObject) user->fe[0]);CHKERRQ(ierr);</div><div> ierr = DMPlexAddBoundary(cdm, user->bcType == DIRICHLET, user->bcType == NEUMANN ? "boundary" : "marker", 0, user->exactFuncs[0], 1, &id, user);CHKERRQ(ierr);</div>
<div> ierr = DMPlexGetCoarseDM(cdm, &cdm);CHKERRQ(ierr);</div><div> }</div><div> PetscFunctionReturn(0);</div><div>}</div><div><br></div><div><br></div><div>It seems that it adds the number of fields directly to the DM, and takes the number of components that were specified in SetupElementCommon, but what about the number of degrees of freedom? Why we added it for the MaterialSection but not for the regular Section.</div>
<div><br></div><div>Thanks in advance</div><span><font color="#888888"><div>Miguel</div></font></span></div></div><div><div><div class="gmail_extra"><br><br><div class="gmail_quote">
On Sat, Mar 15, 2014 at 4:16 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 a lot.</div><div><div><div class="gmail_extra"><br><br><div class="gmail_quote">
On Sat, Mar 15, 2014 at 3:36 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 Sat, Mar 15, 2014 at 3:31 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:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">Hello everybody<div><br></div><div>I keep trying to understand this example. I don't have any problems with this example when I run it like this:</div>
<div><br></div><div><div>[salaza11@maya PETSC]$ ./ex12 -bc_type dirichlet -interpolate -petscspace_order 1 -variable_coefficient nonlinear -dim 2 -run_type full -show_solution</div>
<div>Number of SNES iterations = 5</div><div>L_2 Error: 0.107289</div><div>Solution</div><div>Vec Object: 1 MPI processes</div><div> type: seq</div><div>0.484618</div></div><div><br></div><div>However, when I change the boundary conditions to Neumann, I get this error.</div>
<div><br></div><div><div>[salaza11@maya PETSC]$ ./ex12 -bc_type neumann -interpolate 1 -petscspace_order 2 -variable_coefficient nonlinear -dim 2 -run_type full -show_solution</div></div></div></blockquote><div><br></div>
</div><div>Here you set the order of the element used in bulk, but not on the boundary where you condition is, so it defaults to 0. In</div><div>order to become more familiar, take a look at the tests that I run here:</div>
<div>
<br></div><div> <a href="https://bitbucket.org/petsc/petsc/src/64715f0f033346c10c77b73cf58216d111db8789/config/builder.py?at=master#cl-216" target="_blank">https://bitbucket.org/petsc/petsc/src/64715f0f033346c10c77b73cf58216d111db8789/config/builder.py?at=master#cl-216</a></div>
<div><div>
<div><br></div><div> Matt</div><div><br></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 dir="ltr">
<div><div>[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------</div>
<div>[0]PETSC ERROR: Petsc has generated inconsistent data</div><div>[0]PETSC ERROR: Number of dual basis vectors 0 not equal to dimension 1</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: v3.4.3-4776-gb18359b GIT Date: 2014-03-04 10:53:30 -0600</div><div>[0]PETSC ERROR: ./ex12 on a linux-gnu-c-debug named maya by salaza11 Sat Mar 15 14:28:05 2014</div>
<div>
[0]PETSC ERROR: Configure options --download-mpich --download-scientificpython --download-triangle --download-ctetgen --download-chaco --with-c2html=0</div><div>[0]PETSC ERROR: #1 PetscDualSpaceSetUp_Lagrange() line 1763 in /home/salaza11/petsc/src/dm/dt/interface/dtfe.c</div>
<div>[0]PETSC ERROR: #2 PetscDualSpaceSetUp() line 1277 in /home/salaza11/petsc/src/dm/dt/interface/dtfe.c</div><div>[0]PETSC ERROR: #3 SetupElementCommon() line 474 in /home/salaza11/workspace/PETSC/ex12.c</div><div>[0]PETSC ERROR: #4 SetupBdElement() line 559 in /home/salaza11/workspace/PETSC/ex12.c</div>
<div>[0]PETSC ERROR: #5 main() line 755 in /home/salaza11/workspace/PETSC/ex12.c</div><div>[0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint@mcs.anl.gov----------</div><div>
application called MPI_Abort(MPI_COMM_WORLD, 77) - process 0</div><div>[unset]: aborting job:</div><div>application called MPI_Abort(MPI_COMM_WORLD, 77) - process 0</div><div><br></div><div>I honestly do not know much about using dual spaces in a finite element context. I have been trying to find some material that could help me without much success. I tried to modify the dual space order with the option -petscdualspace_order but I kept getting errors. In particular, I got this when I set it to 1.</div>
<div><br></div><div><div>[salaza11@maya PETSC]$ ./ex12 -bc_type neumann -interpolate 1 -petscspace_order 2 -variable_coefficient nonlinear -dim 2 -run_type full -show_solution -petscdualspace_order 1</div><div>
[0]PETSC ERROR: PetscTrFreeDefault() called from PetscFESetUp_Basic() line 2492 in /home/salaza11/petsc/src/dm/dt/interface/dtfe.c</div><div>[0]PETSC ERROR: Block [id=0(32)] at address 0x1cc32f0 is corrupted (probably write past end of array)</div>
<div>[0]PETSC ERROR: Block allocated in PetscFESetUp_Basic() line 2483 in /home/salaza11/petsc/src/dm/dt/interface/dtfe.c</div><div>[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------</div>
<div>[0]PETSC ERROR: Memory corruption: <a href="http://www.mcs.anl.gov/petsc/documentation/installation.html#valgrind" target="_blank">http://www.mcs.anl.gov/petsc/documentation/installation.html#valgrind</a></div><div>
[0]PETSC ERROR: Corrupted memory</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: v3.4.3-4776-gb18359b GIT Date: 2014-03-04 10:53:30 -0600</div>
<div>[0]PETSC ERROR: ./ex12 on a linux-gnu-c-debug named maya by salaza11 Sat Mar 15 14:37:34 2014</div><div>[0]PETSC ERROR: Configure options --download-mpich --download-scientificpython --download-triangle --download-ctetgen --download-chaco --with-c2html=0</div>
<div>[0]PETSC ERROR: #1 PetscTrFreeDefault() line 289 in /home/salaza11/petsc/src/sys/memory/mtr.c</div><div>[0]PETSC ERROR: #2 PetscFESetUp_Basic() line 2492 in /home/salaza11/petsc/src/dm/dt/interface/dtfe.c</div><div>
[0]PETSC ERROR: #3 PetscFESetUp() line 2126 in /home/salaza11/petsc/src/dm/dt/interface/dtfe.c</div>
<div>[0]PETSC ERROR: #4 SetupElementCommon() line 482 in /home/salaza11/workspace/PETSC/ex12.c</div><div>[0]PETSC ERROR: #5 SetupElement() line 506 in /home/salaza11/workspace/PETSC/ex12.c</div><div>[0]PETSC ERROR: #6 main() line 754 in /home/salaza11/workspace/PETSC/ex12.c</div>
<div>[0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint@mcs.anl.gov----------</div><div>application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0</div><div>[unset]: aborting job:</div>
<div>application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0</div><div>[salaza11@maya PETSC]$ </div><div><br></div><div><br></div><div>Then again, I do not know much what I am doing given my ignorance with respect to the dual spaces in FE. I apologize for that. My questions are:</div>
<div><br></div><div>- Where could I find more resources in order to understand the PETSc implementation of dual spaces for FE?</div><div>- Why does it run with Dirichlet but not with Neumann?</div><div>
<br></div><div>Thanks in advance.</div><div>Miguel.</div></div></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Mar 4, 2014 at 11:28 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:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">
<div>On Tue, Mar 4, 2014 at 12:01 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:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">
<div>On Tue, Mar 4, 2014 at 11:51 AM, 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:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><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>
</blockquote><div><br></div></div><div>I will check it out.</div></div></div></div></blockquote><div><br></div></div><div>This is now fixed.</div><div><br></div><div> Thanks for finding it</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 dir="ltr"><div class="gmail_extra"><div class="gmail_quote">
<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 dir="ltr"><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><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></div><div>Jacobian:</div><div>Mat Object: 1 MPI processes</div><div> type: seqaij</div>
<div>row 0: (0, 4) </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><div>-2</div><div>0</div><div>0</div><div>0</div><div>0</div><div>Au - b = Au + F(0)</div>
<div><div>
Vec Object: 1 MPI processes</div><div> type: seq</div><div>0</div></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><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:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">
<div>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:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style: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><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><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:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style: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:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style: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:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style: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:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style: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:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style: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:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style: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:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style: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:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style: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:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style: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:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style: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:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style: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:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style: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:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style: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:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style: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:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style: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:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style: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>
<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 3:31 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>
</font><br>
</div>
<div></div>
<div>
<div dir="ltr">
<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>
<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 lang="EN-US">
<div>
<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>
</div>
</div>
</blockquote>
<div><br>
</div>
<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>
<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 lang="EN-US">
<div>
<p class="MsoNormal"><span style="color:rgb(31,73,125);font-family:Calibri,sans-serif;font-size:11pt"> </span></p>
<div>
<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>
<div>
<div>
<div>
<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>
<div>
<div>
<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">
<u></u><u></u></p>
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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">
<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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<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>
<span><font color="#888888"></font></span></div>
<span><font color="#888888"></font></span></div>
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<span><font color="#888888"></font></span></blockquote>
<span><font color="#888888"></font></span></div>
<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>
<span><font color="#888888"></font></span></div>
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<span><font color="#888888"></font></span></div>
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<span><font color="#888888"></font></span></blockquote>
<span><font color="#888888"></font></span></div>
<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>
<span><font color="#888888"></font></span></div>
<span><font color="#888888"></font></span></div>
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<span><font color="#888888"></font></span></div>
<span><font color="#888888"></font></span></div>
<span><font color="#888888"></font></span></blockquote>
<span><font color="#888888"></font></span></div>
<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><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">
</font></span></div><span><font color="#888888">
</font></span></blockquote><span><font color="#888888">
</font></span></div><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><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">
</font></span></div><span><font color="#888888">
</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><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></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><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>