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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi, This is the next error message after configuring and building with the triangle package when trying to run ex12
<div><br>
</div>
<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 http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors</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-family: Times New Roman; color: #000000; font-size: 16px">
<hr tabindex="-1">
<div id="divRpF569002" style="direction: ltr; "><font face="Tahoma" size="2" color="#000000"><b>From:</b> Matthew Knepley [knepley@gmail.com]<br>
<b>Sent:</b> Thursday, January 16, 2014 4:37 PM<br>
<b>To:</b> Jones,Martin Alexander<br>
<b>Cc:</b> petsc-users@mcs.anl.gov<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:0 0 0 .8ex; border-left:1px #ccc 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:0 0 0 .8ex; border-left:1px #ccc 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:0 0 0 .8ex; border-left:1px #ccc 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:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
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<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>
</div>
</div>
</div>
<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>
</div>
<div>
<p class="MsoNormal">I changed the documentation everywhere (including the latest tutorial slides). Can you try running<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">with 'master' (or 'next'), and point me toward the old docs?<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal"> Thanks,<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal"> Matt<br clear="all">
<u></u><u></u></p>
<div>
<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>
</font></span></div>
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<span><font color="#888888"><br>
<br clear="all">
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<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 class="HOEnZb"><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 class="HOEnZb"><font color="#888888"></font></span></div>
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<span class="HOEnZb"><font color="#888888"></font></span></div>
<span class="HOEnZb"><font color="#888888"><br>
<br clear="all">
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</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>
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</div>
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</blockquote>
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<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>
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