[petsc-users] Problems running ex12.c
Miguel Angel Salazar de Troya
salazardetroya at gmail.com
Sun Mar 30 13:57:47 CDT 2014
Hello everybody
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.
petsc-dev:
#undef __FUNCT__
#define __FUNCT__ "SetupSection"
PetscErrorCode SetupSection(DM dm, AppCtx *user)
{
DM cdm = dm;
const PetscInt id = 1;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = PetscObjectSetName((PetscObject) user->fe[0],
"potential");CHKERRQ(ierr);
while (cdm) {
ierr = DMSetNumFields(cdm, 1);CHKERRQ(ierr);
ierr = DMSetField(cdm, 0, (PetscObject) user->fe[0]);CHKERRQ(ierr);
ierr = DMPlexAddBoundary(cdm, user->bcType == DIRICHLET, user->bcType
== NEUMANN ? "boundary" : "marker", 0, user->exactFuncs[0], 1, &id,
user);CHKERRQ(ierr);
ierr = DMPlexGetCoarseDM(cdm, &cdm);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
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.
Thanks in advance
Miguel
On Sat, Mar 15, 2014 at 4:16 PM, Miguel Angel Salazar de Troya <
salazardetroya at gmail.com> wrote:
> Thanks a lot.
>
>
> On Sat, Mar 15, 2014 at 3:36 PM, Matthew Knepley <knepley at gmail.com>wrote:
>
>> On Sat, Mar 15, 2014 at 3:31 PM, Miguel Angel Salazar de Troya <
>> salazardetroya at gmail.com> wrote:
>>
>>> Hello everybody
>>>
>>> I keep trying to understand this example. I don't have any problems with
>>> this example when I run it like this:
>>>
>>> [salaza11 at maya PETSC]$ ./ex12 -bc_type dirichlet -interpolate
>>> -petscspace_order 1 -variable_coefficient nonlinear -dim 2 -run_type full
>>> -show_solution
>>> Number of SNES iterations = 5
>>> L_2 Error: 0.107289
>>> Solution
>>> Vec Object: 1 MPI processes
>>> type: seq
>>> 0.484618
>>>
>>> However, when I change the boundary conditions to Neumann, I get this
>>> error.
>>>
>>> [salaza11 at maya PETSC]$ ./ex12 -bc_type neumann -interpolate 1
>>> -petscspace_order 2 -variable_coefficient nonlinear -dim 2 -run_type full
>>> -show_solution
>>>
>>
>> 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
>> order to become more familiar, take a look at the tests that I run here:
>>
>>
>> https://bitbucket.org/petsc/petsc/src/64715f0f033346c10c77b73cf58216d111db8789/config/builder.py?at=master#cl-216
>>
>> Matt
>>
>> [0]PETSC ERROR: --------------------- Error Message
>>> --------------------------------------------------------------
>>> [0]PETSC ERROR: Petsc has generated inconsistent data
>>> [0]PETSC ERROR: Number of dual basis vectors 0 not equal to dimension 1
>>> [0]PETSC ERROR: See http://
>>> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble
>>> shooting.
>>> [0]PETSC ERROR: Petsc Development GIT revision: v3.4.3-4776-gb18359b
>>> GIT Date: 2014-03-04 10:53:30 -0600
>>> [0]PETSC ERROR: ./ex12 on a linux-gnu-c-debug named maya by salaza11 Sat
>>> Mar 15 14:28:05 2014
>>> [0]PETSC ERROR: Configure options --download-mpich
>>> --download-scientificpython --download-triangle --download-ctetgen
>>> --download-chaco --with-c2html=0
>>> [0]PETSC ERROR: #1 PetscDualSpaceSetUp_Lagrange() line 1763 in
>>> /home/salaza11/petsc/src/dm/dt/interface/dtfe.c
>>> [0]PETSC ERROR: #2 PetscDualSpaceSetUp() line 1277 in
>>> /home/salaza11/petsc/src/dm/dt/interface/dtfe.c
>>> [0]PETSC ERROR: #3 SetupElementCommon() line 474 in
>>> /home/salaza11/workspace/PETSC/ex12.c
>>> [0]PETSC ERROR: #4 SetupBdElement() line 559 in
>>> /home/salaza11/workspace/PETSC/ex12.c
>>> [0]PETSC ERROR: #5 main() line 755 in
>>> /home/salaza11/workspace/PETSC/ex12.c
>>> [0]PETSC ERROR: ----------------End of Error Message -------send entire
>>> error message to petsc-maint at mcs.anl.gov----------
>>> application called MPI_Abort(MPI_COMM_WORLD, 77) - process 0
>>> [unset]: aborting job:
>>> application called MPI_Abort(MPI_COMM_WORLD, 77) - process 0
>>>
>>> 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.
>>>
>>> [salaza11 at maya PETSC]$ ./ex12 -bc_type neumann -interpolate 1
>>> -petscspace_order 2 -variable_coefficient nonlinear -dim 2 -run_type full
>>> -show_solution -petscdualspace_order 1
>>> [0]PETSC ERROR: PetscTrFreeDefault() called from PetscFESetUp_Basic()
>>> line 2492 in /home/salaza11/petsc/src/dm/dt/interface/dtfe.c
>>> [0]PETSC ERROR: Block [id=0(32)] at address 0x1cc32f0 is corrupted
>>> (probably write past end of array)
>>> [0]PETSC ERROR: Block allocated in PetscFESetUp_Basic() line 2483 in
>>> /home/salaza11/petsc/src/dm/dt/interface/dtfe.c
>>> [0]PETSC ERROR: --------------------- Error Message
>>> --------------------------------------------------------------
>>> [0]PETSC ERROR: Memory corruption:
>>> http://www.mcs.anl.gov/petsc/documentation/installation.html#valgrind
>>> [0]PETSC ERROR: Corrupted memory
>>> [0]PETSC ERROR: See http://
>>> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble
>>> shooting.
>>> [0]PETSC ERROR: Petsc Development GIT revision: v3.4.3-4776-gb18359b
>>> GIT Date: 2014-03-04 10:53:30 -0600
>>> [0]PETSC ERROR: ./ex12 on a linux-gnu-c-debug named maya by salaza11 Sat
>>> Mar 15 14:37:34 2014
>>> [0]PETSC ERROR: Configure options --download-mpich
>>> --download-scientificpython --download-triangle --download-ctetgen
>>> --download-chaco --with-c2html=0
>>> [0]PETSC ERROR: #1 PetscTrFreeDefault() line 289 in
>>> /home/salaza11/petsc/src/sys/memory/mtr.c
>>> [0]PETSC ERROR: #2 PetscFESetUp_Basic() line 2492 in
>>> /home/salaza11/petsc/src/dm/dt/interface/dtfe.c
>>> [0]PETSC ERROR: #3 PetscFESetUp() line 2126 in
>>> /home/salaza11/petsc/src/dm/dt/interface/dtfe.c
>>> [0]PETSC ERROR: #4 SetupElementCommon() line 482 in
>>> /home/salaza11/workspace/PETSC/ex12.c
>>> [0]PETSC ERROR: #5 SetupElement() line 506 in
>>> /home/salaza11/workspace/PETSC/ex12.c
>>> [0]PETSC ERROR: #6 main() line 754 in
>>> /home/salaza11/workspace/PETSC/ex12.c
>>> [0]PETSC ERROR: ----------------End of Error Message -------send entire
>>> error message to petsc-maint at mcs.anl.gov----------
>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>>> [unset]: aborting job:
>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>>> [salaza11 at maya PETSC]$
>>>
>>>
>>> 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:
>>>
>>> - Where could I find more resources in order to understand the PETSc
>>> implementation of dual spaces for FE?
>>> - Why does it run with Dirichlet but not with Neumann?
>>>
>>> Thanks in advance.
>>> Miguel.
>>>
>>>
>>> On Tue, Mar 4, 2014 at 11:28 PM, Matthew Knepley <knepley at gmail.com>wrote:
>>>
>>>> On Tue, Mar 4, 2014 at 12:01 PM, Matthew Knepley <knepley at gmail.com>wrote:
>>>>
>>>>> On Tue, Mar 4, 2014 at 11:51 AM, Miguel Angel Salazar de Troya <
>>>>> salazardetroya at gmail.com> wrote:
>>>>>
>>>>>> 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.
>>>>>>
>>>>>
>>>>> I will check it out.
>>>>>
>>>>
>>>> This is now fixed.
>>>>
>>>> Thanks for finding it
>>>>
>>>> Matt
>>>>
>>>>
>>>>> Thanks,
>>>>>
>>>>> Matt
>>>>>
>>>>>
>>>>>> [salaza11 at 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
>>>>>> ==9625== Memcheck, a memory error detector
>>>>>> ==9625== Copyright (C) 2002-2009, and GNU GPL'd, by Julian Seward et
>>>>>> al.
>>>>>> ==9625== Using Valgrind-3.5.0 and LibVEX; rerun with -h for copyright
>>>>>> info
>>>>>> ==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
>>>>>> ==9625==
>>>>>> Local function:
>>>>>> Vec Object: 1 MPI processes
>>>>>> type: seq
>>>>>> 0
>>>>>> 0.25
>>>>>> 1
>>>>>> 0.25
>>>>>> 0.5
>>>>>> 1.25
>>>>>> 1
>>>>>> 1.25
>>>>>> 2
>>>>>> Initial guess
>>>>>> Vec Object: 1 MPI processes
>>>>>> type: seq
>>>>>> 0.5
>>>>>> L_2 Error: 0.111111
>>>>>> Residual:
>>>>>> Vec Object: 1 MPI processes
>>>>>> type: seq
>>>>>> 0
>>>>>> 0
>>>>>> 0
>>>>>> 0
>>>>>> 0
>>>>>> 0
>>>>>> 0
>>>>>> 0
>>>>>> 0
>>>>>> Initial Residual
>>>>>> Vec Object: 1 MPI processes
>>>>>> type: seq
>>>>>> 0
>>>>>> L_2 Residual: 0
>>>>>> Jacobian:
>>>>>> Mat Object: 1 MPI processes
>>>>>> type: seqaij
>>>>>> row 0: (0, 4)
>>>>>> Residual:
>>>>>> Vec Object: 1 MPI processes
>>>>>> type: seq
>>>>>> 0
>>>>>> 0
>>>>>> 0
>>>>>> 0
>>>>>> -2
>>>>>> 0
>>>>>> 0
>>>>>> 0
>>>>>> 0
>>>>>> Au - b = Au + F(0)
>>>>>> Vec Object: 1 MPI processes
>>>>>> type: seq
>>>>>> 0
>>>>>> Linear L_2 Residual: 0
>>>>>> ==9625==
>>>>>> ==9625== HEAP SUMMARY:
>>>>>> ==9625== in use at exit: 288 bytes in 3 blocks
>>>>>> ==9625== total heap usage: 2,484 allocs, 2,481 frees, 1,009,287
>>>>>> bytes allocated
>>>>>> ==9625==
>>>>>> ==9625== 48 bytes in 1 blocks are definitely lost in loss record 1 of
>>>>>> 3
>>>>>> ==9625== at 0x4A05E46: malloc (vg_replace_malloc.c:195)
>>>>>> ==9625== by 0x5D8D4E1: writepoly (triangle.c:12012)
>>>>>> ==9625== by 0x5D8FAAC: triangulate (triangle.c:13167)
>>>>>> ==9625== by 0x56B0884: DMPlexGenerate_Triangle (plex.c:3749)
>>>>>> ==9625== by 0x56B5EE4: DMPlexGenerate (plex.c:4503)
>>>>>> ==9625== by 0x567F414: DMPlexCreateBoxMesh (plexcreate.c:668)
>>>>>> ==9625== by 0x4051FA: CreateMesh (ex12.c:341)
>>>>>> ==9625== by 0x408D3D: main (ex12.c:651)
>>>>>> ==9625==
>>>>>> ==9625== 96 bytes in 1 blocks are definitely lost in loss record 2 of
>>>>>> 3
>>>>>> ==9625== at 0x4A05E46: malloc (vg_replace_malloc.c:195)
>>>>>> ==9625== by 0x5D8D485: writepoly (triangle.c:12004)
>>>>>> ==9625== by 0x5D8FAAC: triangulate (triangle.c:13167)
>>>>>> ==9625== by 0x56B0884: DMPlexGenerate_Triangle (plex.c:3749)
>>>>>> ==9625== by 0x56B5EE4: DMPlexGenerate (plex.c:4503)
>>>>>> ==9625== by 0x567F414: DMPlexCreateBoxMesh (plexcreate.c:668)
>>>>>> ==9625== by 0x4051FA: CreateMesh (ex12.c:341)
>>>>>> ==9625== by 0x408D3D: main (ex12.c:651)
>>>>>> ==9625==
>>>>>> ==9625== 144 bytes in 1 blocks are definitely lost in loss record 3
>>>>>> of 3
>>>>>> ==9625== at 0x4A05E46: malloc (vg_replace_malloc.c:195)
>>>>>> ==9625== by 0x5D8CD20: writenodes (triangle.c:11718)
>>>>>> ==9625== by 0x5D8F9DE: triangulate (triangle.c:13132)
>>>>>> ==9625== by 0x56B0884: DMPlexGenerate_Triangle (plex.c:3749)
>>>>>> ==9625== by 0x56B5EE4: DMPlexGenerate (plex.c:4503)
>>>>>> ==9625== by 0x567F414: DMPlexCreateBoxMesh (plexcreate.c:668)
>>>>>> ==9625== by 0x4051FA: CreateMesh (ex12.c:341)
>>>>>> ==9625== by 0x408D3D: main (ex12.c:651)
>>>>>> ==9625==
>>>>>> ==9625== LEAK SUMMARY:
>>>>>> ==9625== definitely lost: 288 bytes in 3 blocks
>>>>>> ==9625== indirectly lost: 0 bytes in 0 blocks
>>>>>> ==9625== possibly lost: 0 bytes in 0 blocks
>>>>>> ==9625== still reachable: 0 bytes in 0 blocks
>>>>>> ==9625== suppressed: 0 bytes in 0 blocks
>>>>>> ==9625==
>>>>>> ==9625== For counts of detected and suppressed errors, rerun with: -v
>>>>>> ==9625== ERROR SUMMARY: 3 errors from 3 contexts (suppressed: 6 from
>>>>>> 6)
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Mon, Mar 3, 2014 at 7:05 PM, Matthew Knepley <knepley at gmail.com>wrote:
>>>>>>
>>>>>>> On Mon, Mar 3, 2014 at 4:59 PM, Miguel Angel Salazar de Troya <
>>>>>>> salazardetroya at gmail.com> wrote:
>>>>>>>
>>>>>>>> You are welcome, thanks for your help.
>>>>>>>>
>>>>>>>
>>>>>>> Okay, I have rebuilt completely clean, and ex12 runs for me. Can you
>>>>>>> try again after pulling?
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> Matt
>>>>>>>
>>>>>>>
>>>>>>>> On Mon, Mar 3, 2014 at 4:13 PM, Matthew Knepley <knepley at gmail.com
>>>>>>>> > wrote:
>>>>>>>>
>>>>>>>>> On Mon, Mar 3, 2014 at 1:44 PM, Miguel Angel Salazar de Troya <
>>>>>>>>> salazardetroya at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> Thanks. This is what I get.
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Okay, this was broken by a new push to master/next in the last few
>>>>>>>>> days. I have pushed a fix,
>>>>>>>>> however next is currently broken due to a failure to check in a
>>>>>>>>> file. This should be fixed shortly,
>>>>>>>>> and then ex12 will work. I will mail you when its ready.
>>>>>>>>>
>>>>>>>>> Thanks for finding this,
>>>>>>>>>
>>>>>>>>> Matt
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> (gdb) cont
>>>>>>>>>> Continuing.
>>>>>>>>>>
>>>>>>>>>> Program received signal SIGSEGV, Segmentation fault.
>>>>>>>>>> 0x00007fd6811bea7b in DMPlexComputeJacobianFEM (dm=0x159a180,
>>>>>>>>>> X=0x168b5b0,
>>>>>>>>>> Jac=0x7fffae6e8a88, JacP=0x7fffae6e8a88, str=0x7fffae6e7970,
>>>>>>>>>> user=0x7fd6811be509)
>>>>>>>>>> at /home/salaza11/petsc/src/dm/impls/plex/plexfem.c:882
>>>>>>>>>> 882 ierr = PetscFEGetDimension(fe[f], &Nb);CHKERRQ(ierr);
>>>>>>>>>> (gdb) where
>>>>>>>>>> #0 0x00007fd6811bea7b in DMPlexComputeJacobianFEM (dm=0x159a180,
>>>>>>>>>> X=0x168b5b0,
>>>>>>>>>> Jac=0x7fffae6e8a88, JacP=0x7fffae6e8a88, str=0x7fffae6e7970,
>>>>>>>>>> user=0x7fd6811be509)
>>>>>>>>>> at /home/salaza11/petsc/src/dm/impls/plex/plexfem.c:882
>>>>>>>>>> #1 0x00007fd6814a5bf6 in SNESComputeJacobian_DMLocal
>>>>>>>>>> (snes=0x14e9450,
>>>>>>>>>> X=0x1622ad0, A=0x7fffae6e8a88, B=0x7fffae6e8a88,
>>>>>>>>>> ctx=0x1652300)
>>>>>>>>>> at /home/salaza11/petsc/src/snes/utils/dmlocalsnes.c:102
>>>>>>>>>> #2 0x00007fd6814cc609 in SNESComputeJacobian (snes=0x14e9450,
>>>>>>>>>> X=0x1622ad0,
>>>>>>>>>> A=0x7fffae6e8a88, B=0x7fffae6e8a88)
>>>>>>>>>> at /home/salaza11/petsc/src/snes/interface/snes.c:2245
>>>>>>>>>> #3 0x000000000040af72 in main (argc=15, argv=0x7fffae6e8bc8)
>>>>>>>>>> at /home/salaza11/petsc/src/snes/examples/tutorials/ex12.c:784
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Mon, Mar 3, 2014 at 1:40 PM, Matthew Knepley <
>>>>>>>>>> knepley at gmail.com> wrote:
>>>>>>>>>>
>>>>>>>>>>> On Mon, Mar 3, 2014 at 1:39 PM, Miguel Angel Salazar de Troya <
>>>>>>>>>>> salazardetroya at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> This is what I get at gdb when I type 'where'.
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> You have to type 'cont', and then when it fails you type 'where'.
>>>>>>>>>>>
>>>>>>>>>>> Matt
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> #0 0x000000310e0aa860 in __nanosleep_nocancel () from
>>>>>>>>>>>> /lib64/libc.so.6
>>>>>>>>>>>> #1 0x000000310e0aa70f in sleep () from /lib64/libc.so.6
>>>>>>>>>>>> #2 0x00007fd83a00a8be in PetscSleep (s=10)
>>>>>>>>>>>> at /home/salaza11/petsc/src/sys/utils/psleep.c:52
>>>>>>>>>>>> #3 0x00007fd83a06f331 in PetscAttachDebugger ()
>>>>>>>>>>>> at /home/salaza11/petsc/src/sys/error/adebug.c:397
>>>>>>>>>>>> #4 0x00007fd83a0af1d2 in PetscOptionsCheckInitial_Private ()
>>>>>>>>>>>> at /home/salaza11/petsc/src/sys/objects/init.c:444
>>>>>>>>>>>> #5 0x00007fd83a0b6448 in PetscInitialize (argc=0x7fff5cd8df2c,
>>>>>>>>>>>> args=0x7fff5cd8df20, file=0x0,
>>>>>>>>>>>> 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")
>>>>>>>>>>>> at /home/salaza11/petsc/src/sys/objects/pinit.c:876
>>>>>>>>>>>> #6 0x0000000000408f2c in main (argc=15, argv=0x7fff5cd8f1f8)
>>>>>>>>>>>> at
>>>>>>>>>>>> /home/salaza11/petsc/src/snes/examples/tutorials/ex12.c:663
>>>>>>>>>>>>
>>>>>>>>>>>> The rest of the gdb output is attached. I am a bit ignorant
>>>>>>>>>>>> with gdb, I apologize for that.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On Mon, Mar 3, 2014 at 12:48 PM, Matthew Knepley <
>>>>>>>>>>>> knepley at gmail.com> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> On Mon, Mar 3, 2014 at 12:39 PM, Miguel Angel Salazar de Troya
>>>>>>>>>>>>> <salazardetroya at gmail.com> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> 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 (
>>>>>>>>>>>>>> https://bitbucket.org/petsc/petsc/wiki/Home) to obtain the
>>>>>>>>>>>>>> next version, I configured petsc as above and ran ex12 as above as well,
>>>>>>>>>>>>>> getting this error:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> [salaza11 at 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
>>>>>>>>>>>>>> Local function:
>>>>>>>>>>>>>> Vec Object: 1 MPI processes
>>>>>>>>>>>>>> type: seq
>>>>>>>>>>>>>> 0
>>>>>>>>>>>>>> 0.25
>>>>>>>>>>>>>> 1
>>>>>>>>>>>>>> 0.25
>>>>>>>>>>>>>> 0.5
>>>>>>>>>>>>>> 1.25
>>>>>>>>>>>>>> 1
>>>>>>>>>>>>>> 1.25
>>>>>>>>>>>>>> 2
>>>>>>>>>>>>>> Initial guess
>>>>>>>>>>>>>> Vec Object: 1 MPI processes
>>>>>>>>>>>>>> type: seq
>>>>>>>>>>>>>> 0.5
>>>>>>>>>>>>>> L_2 Error: 0.111111
>>>>>>>>>>>>>> Residual:
>>>>>>>>>>>>>> Vec Object: 1 MPI processes
>>>>>>>>>>>>>> type: seq
>>>>>>>>>>>>>> 0
>>>>>>>>>>>>>> 0
>>>>>>>>>>>>>> 0
>>>>>>>>>>>>>> 0
>>>>>>>>>>>>>> 0
>>>>>>>>>>>>>> 0
>>>>>>>>>>>>>> 0
>>>>>>>>>>>>>> 0
>>>>>>>>>>>>>> 0
>>>>>>>>>>>>>> Initial Residual
>>>>>>>>>>>>>> Vec Object: 1 MPI processes
>>>>>>>>>>>>>> type: seq
>>>>>>>>>>>>>> 0
>>>>>>>>>>>>>> L_2 Residual: 0
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Okay, now run with -start_in_debugger, and give me a stack
>>>>>>>>>>>>> trace using 'where'.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Matt
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>> [0]PETSC ERROR:
>>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation
>>>>>>>>>>>>>> Violation, probably memory access out of range
>>>>>>>>>>>>>> [0]PETSC ERROR: Try option -start_in_debugger or
>>>>>>>>>>>>>> -on_error_attach_debugger
>>>>>>>>>>>>>> [0]PETSC ERROR: or see
>>>>>>>>>>>>>> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSCERROR: or try
>>>>>>>>>>>>>> http://valgrind.org on GNU/linux and Apple Mac OS X to find
>>>>>>>>>>>>>> memory corruption errors
>>>>>>>>>>>>>> [0]PETSC ERROR: likely location of problem given in stack
>>>>>>>>>>>>>> below
>>>>>>>>>>>>>> [0]PETSC ERROR: --------------------- Stack Frames
>>>>>>>>>>>>>> ------------------------------------
>>>>>>>>>>>>>> [0]PETSC ERROR: Note: The EXACT line numbers in the stack are
>>>>>>>>>>>>>> not available,
>>>>>>>>>>>>>> [0]PETSC ERROR: INSTEAD the line number of the start of
>>>>>>>>>>>>>> the function
>>>>>>>>>>>>>> [0]PETSC ERROR: is given.
>>>>>>>>>>>>>> [0]PETSC ERROR: [0] DMPlexComputeJacobianFEM line 871
>>>>>>>>>>>>>> /home/salaza11/petsc/src/dm/impls/plex/plexfem.c
>>>>>>>>>>>>>> [0]PETSC ERROR: [0] SNESComputeJacobian_DMLocal line 94
>>>>>>>>>>>>>> /home/salaza11/petsc/src/snes/utils/dmlocalsnes.c
>>>>>>>>>>>>>> [0]PETSC ERROR: [0] SNES user Jacobian function line 2244
>>>>>>>>>>>>>> /home/salaza11/petsc/src/snes/interface/snes.c
>>>>>>>>>>>>>> [0]PETSC ERROR: [0] SNESComputeJacobian line 2203
>>>>>>>>>>>>>> /home/salaza11/petsc/src/snes/interface/snes.c
>>>>>>>>>>>>>> [0]PETSC ERROR: --------------------- Error Message
>>>>>>>>>>>>>> --------------------------------------------------------------
>>>>>>>>>>>>>> [0]PETSC ERROR: Signal received
>>>>>>>>>>>>>> [0]PETSC ERROR: See http://
>>>>>>>>>>>>>> http://www.mcs.anl.gov/petsc/documentation/faq.html for
>>>>>>>>>>>>>> trouble shooting.
>>>>>>>>>>>>>> [0]PETSC ERROR: Petsc Development GIT revision:
>>>>>>>>>>>>>> v3.4.3-4705-gfb6b3bc GIT Date: 2014-03-03 08:23:43 -0600
>>>>>>>>>>>>>> [0]PETSC ERROR: ./ex12 on a linux-gnu-c-debug named maya by
>>>>>>>>>>>>>> salaza11 Mon Mar 3 11:49:15 2014
>>>>>>>>>>>>>> [0]PETSC ERROR: Configure options --download-mpich
>>>>>>>>>>>>>> --download-scientificpython --download-triangle --download-ctetgen
>>>>>>>>>>>>>> --download-chaco --with-c2html=0
>>>>>>>>>>>>>> [0]PETSC ERROR: #1 User provided function() line 0 in
>>>>>>>>>>>>>> unknown file
>>>>>>>>>>>>>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>>>>>>>>>>>>>> [unset]: aborting job:
>>>>>>>>>>>>>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Sun, Mar 2, 2014 at 7:11 PM, Matthew Knepley <
>>>>>>>>>>>>>> knepley at gmail.com> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Sun, Mar 2, 2014 at 6:54 PM, Miguel Angel Salazar de
>>>>>>>>>>>>>>> Troya <salazardetroya at gmail.com> wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Hi everybody
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I am trying to run example ex12.c without much success. I
>>>>>>>>>>>>>>>> specifically run it with the command options:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> We need to start narrowing down differences, because it runs
>>>>>>>>>>>>>>> for me and our nightly tests. So, first can
>>>>>>>>>>>>>>> you confirm that you are using the latest 'next' branch?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Matt
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> ./ex12 -run_type test -refinement_limit 0.0 -bc_type
>>>>>>>>>>>>>>>> dirichlet -interpolate 0 -petscspace_order 1 -show_initial
>>>>>>>>>>>>>>>> -dm_plex_print_fem 1
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> And I get this output
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Local function:
>>>>>>>>>>>>>>>> Vec Object: 1 MPI processes
>>>>>>>>>>>>>>>> type: seq
>>>>>>>>>>>>>>>> 0
>>>>>>>>>>>>>>>> 1
>>>>>>>>>>>>>>>> 1
>>>>>>>>>>>>>>>> 2
>>>>>>>>>>>>>>>> 1
>>>>>>>>>>>>>>>> 2
>>>>>>>>>>>>>>>> 2
>>>>>>>>>>>>>>>> 3
>>>>>>>>>>>>>>>> Initial guess
>>>>>>>>>>>>>>>> Vec Object: 1 MPI processes
>>>>>>>>>>>>>>>> type: seq
>>>>>>>>>>>>>>>> L_2 Error: 0.625
>>>>>>>>>>>>>>>> Residual:
>>>>>>>>>>>>>>>> Vec Object: 1 MPI processes
>>>>>>>>>>>>>>>> type: seq
>>>>>>>>>>>>>>>> 0
>>>>>>>>>>>>>>>> 0
>>>>>>>>>>>>>>>> 0
>>>>>>>>>>>>>>>> 0
>>>>>>>>>>>>>>>> 0
>>>>>>>>>>>>>>>> 0
>>>>>>>>>>>>>>>> 0
>>>>>>>>>>>>>>>> 0
>>>>>>>>>>>>>>>> Initial Residual
>>>>>>>>>>>>>>>> Vec Object: 1 MPI processes
>>>>>>>>>>>>>>>> type: seq
>>>>>>>>>>>>>>>> L_2 Residual: 0
>>>>>>>>>>>>>>>> [0]PETSC ERROR:
>>>>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>>>>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation
>>>>>>>>>>>>>>>> Violation, probably memory access out of range
>>>>>>>>>>>>>>>> [0]PETSC ERROR: Try option -start_in_debugger or
>>>>>>>>>>>>>>>> -on_error_attach_debugger
>>>>>>>>>>>>>>>> [0]PETSC ERROR: or see
>>>>>>>>>>>>>>>> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSCERROR: or try
>>>>>>>>>>>>>>>> http://valgrind.org on GNU/linux and Apple Mac OS X to
>>>>>>>>>>>>>>>> find memory corruption errors
>>>>>>>>>>>>>>>> [0]PETSC ERROR: likely location of problem given in stack
>>>>>>>>>>>>>>>> below
>>>>>>>>>>>>>>>> [0]PETSC ERROR: --------------------- Stack Frames
>>>>>>>>>>>>>>>> ------------------------------------
>>>>>>>>>>>>>>>> [0]PETSC ERROR: Note: The EXACT line numbers in the stack
>>>>>>>>>>>>>>>> are not available,
>>>>>>>>>>>>>>>> [0]PETSC ERROR: INSTEAD the line number of the start
>>>>>>>>>>>>>>>> of the function
>>>>>>>>>>>>>>>> [0]PETSC ERROR: is given.
>>>>>>>>>>>>>>>> [0]PETSC ERROR: [0] DMPlexComputeJacobianFEM line 867
>>>>>>>>>>>>>>>> /home/salaza11/petsc/src/dm/impls/plex/plexfem.c
>>>>>>>>>>>>>>>> [0]PETSC ERROR: [0] SNESComputeJacobian_DMLocal line 94
>>>>>>>>>>>>>>>> /home/salaza11/petsc/src/snes/utils/dmlocalsnes.c
>>>>>>>>>>>>>>>> [0]PETSC ERROR: [0] SNES user Jacobian function line 2244
>>>>>>>>>>>>>>>> /home/salaza11/petsc/src/snes/interface/snes.c
>>>>>>>>>>>>>>>> [0]PETSC ERROR: [0] SNESComputeJacobian line 2203
>>>>>>>>>>>>>>>> /home/salaza11/petsc/src/snes/interface/snes.c
>>>>>>>>>>>>>>>> [0]PETSC ERROR: --------------------- Error Message
>>>>>>>>>>>>>>>> ------------------------------------
>>>>>>>>>>>>>>>> [0]PETSC ERROR: Signal received!
>>>>>>>>>>>>>>>> [0]PETSC ERROR:
>>>>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>>>>> [0]PETSC ERROR: Petsc Development GIT revision:
>>>>>>>>>>>>>>>> v3.4.3-3453-g0a94005 GIT Date: 2014-03-02 13:12:04 -0600
>>>>>>>>>>>>>>>> [0]PETSC ERROR: See docs/changes/index.html for recent
>>>>>>>>>>>>>>>> updates.
>>>>>>>>>>>>>>>> [0]PETSC ERROR: See docs/faq.html for hints about trouble
>>>>>>>>>>>>>>>> shooting.
>>>>>>>>>>>>>>>> [0]PETSC ERROR: See docs/index.html for manual pages.
>>>>>>>>>>>>>>>> [0]PETSC ERROR:
>>>>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>>>>> [0]PETSC ERROR: ./ex12 on a linux-gnu-c-debug named maya by
>>>>>>>>>>>>>>>> salaza11 Sun Mar 2 17:00:09 2014
>>>>>>>>>>>>>>>> [0]PETSC ERROR: Libraries linked from
>>>>>>>>>>>>>>>> /home/salaza11/petsc/linux-gnu-c-debug/lib
>>>>>>>>>>>>>>>> [0]PETSC ERROR: Configure run at Sun Mar 2 16:46:51 2014
>>>>>>>>>>>>>>>> [0]PETSC ERROR: Configure options --download-mpich
>>>>>>>>>>>>>>>> --download-scientificpython --download-triangle --download-ctetgen
>>>>>>>>>>>>>>>> --download-chaco --with-c2html=0
>>>>>>>>>>>>>>>> [0]PETSC ERROR:
>>>>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>>>>> [0]PETSC ERROR: User provided function() line 0 in unknown
>>>>>>>>>>>>>>>> file
>>>>>>>>>>>>>>>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>>>>>>>>>>>>>>>> [unset]: aborting job:
>>>>>>>>>>>>>>>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Probably my problems could be on my configuration. I attach
>>>>>>>>>>>>>>>> the configure.log. I ran ./configure like this
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> ./configure --download-mpich --download-scientificpython
>>>>>>>>>>>>>>>> --download-triangle --download-ctetgen --download-chaco --with-c2html=0
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Thanks a lot in advance.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On Tue, Jan 28, 2014 at 10:37 AM, Matthew Knepley <
>>>>>>>>>>>>>>>> knepley at gmail.com> wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> On Tue, Jan 28, 2014 at 10:31 AM, Yaakoub El Khamra <
>>>>>>>>>>>>>>>>> yelkhamra at gmail.com> wrote:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> If
>>>>>>>>>>>>>>>>>> ./ex12 -run_type test -dim 3 -refinement_limit 0.0125
>>>>>>>>>>>>>>>>>> -variable_coefficient field -interpolate 1 -petscspace_order 2
>>>>>>>>>>>>>>>>>> -show_initial -dm_plex_print_fem
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> is for serial, any chance we can get the options to run
>>>>>>>>>>>>>>>>>> in parallel?
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Just use mpiexec -n <procs>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Matt
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Regards
>>>>>>>>>>>>>>>>>> Yaakoub El Khamra
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> On Fri, Jan 17, 2014 at 11:29 AM, Matthew Knepley <
>>>>>>>>>>>>>>>>>> knepley at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> On Fri, Jan 17, 2014 at 11:06 AM, Jones,Martin Alexander
>>>>>>>>>>>>>>>>>>> <MAJones2 at mdanderson.org> wrote:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> ------------------------------
>>>>>>>>>>>>>>>>>>>> *From:* Matthew Knepley [knepley at gmail.com]
>>>>>>>>>>>>>>>>>>>> *Sent:* Friday, January 17, 2014 11:04 AM
>>>>>>>>>>>>>>>>>>>> *To:* Jones,Martin Alexander
>>>>>>>>>>>>>>>>>>>> *Cc:* petsc-users at mcs.anl.gov
>>>>>>>>>>>>>>>>>>>> *Subject:* Re: [petsc-users] Problems running ex12.c
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> On Fri, Jan 17, 2014 at 11:00 AM, Jones,Martin
>>>>>>>>>>>>>>>>>>>> Alexander <MAJones2 at mdanderson.org> wrote:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> These examples all seem to run excepting the
>>>>>>>>>>>>>>>>>>>>> following command,
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> ex12 -run_type test -dim 3 -refinement_limit 0.0125
>>>>>>>>>>>>>>>>>>>>> -variable_coefficient field -interpolate 1 -petscspace_order 2
>>>>>>>>>>>>>>>>>>>>> -show_initial -dm_plex_print_fem
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> I get the following ouput:
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> ./ex12 -run_type test -dim 3 -refinement_limit 0.0125
>>>>>>>>>>>>>>>>>>>>> -variable_coefficient field -interpolate 1 -petscspace_order 2
>>>>>>>>>>>>>>>>>>>>> -show_initial -dm_plex_print_fem
>>>>>>>>>>>>>>>>>>>>> Local function:
>>>>>>>>>>>>>>>>>>>>> ./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
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>>>>>> persists, I would just switch to
>>>>>>>>>>>>>>>>>>>> --download-f-blas-lapack.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Thanks. I have some advice on options
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> --with-precision=single # I would not use this unless
>>>>>>>>>>>>>>>>>>> you are doing something special, like CUDA
>>>>>>>>>>>>>>>>>>> --with-clanguage=C++ # I would recommend switching to
>>>>>>>>>>>>>>>>>>> C, the build is much faster
>>>>>>>>>>>>>>>>>>> --with-mpi-dir=/usr --with-mpi4py=0
>>>>>>>>>>>>>>>>>>> --with-shared-libraries --CFLAGS=-O0 --CXXFLAGS=-O0
>>>>>>>>>>>>>>>>>>> --with-fc=0
>>>>>>>>>>>>>>>>>>> --with-etags=1 # This is unnecessary
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> --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
>>>>>>>>>>>>>>>>>>> --download-metis
>>>>>>>>>>>>>>>>>>> --download-fiat=yes --download-generator
>>>>>>>>>>>>>>>>>>> --download-scientificpython # Get rid of these, they are obsolete
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Your MKL needs another library for the OpenMP symbols. I
>>>>>>>>>>>>>>>>>>> would recommend switching to --download-f2cblaslapack,
>>>>>>>>>>>>>>>>>>> or you can try and find that library.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Matt
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Matt
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> ------------------------------
>>>>>>>>>>>>>>>>>>>>> *From:* Matthew Knepley [knepley at gmail.com]
>>>>>>>>>>>>>>>>>>>>> *Sent:* Thursday, January 16, 2014 6:35 PM
>>>>>>>>>>>>>>>>>>>>> *To:* Jones,Martin Alexander
>>>>>>>>>>>>>>>>>>>>> *Cc:* petsc-users at mcs.anl.gov
>>>>>>>>>>>>>>>>>>>>> *Subject:* Re: [petsc-users] Problems running ex12.c
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> On Thu, Jan 16, 2014 at 5:43 PM, Jones,Martin
>>>>>>>>>>>>>>>>>>>>> Alexander <MAJones2 at mdanderson.org> wrote:
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Hi, This is the next error message after
>>>>>>>>>>>>>>>>>>>>>> configuring and building with the triangle package when trying to run ex12
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> This is my fault for bad defaults. I will fix. Try
>>>>>>>>>>>>>>>>>>>>> running
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> ./ex12 -run_type test -refinement_limit 0.0
>>>>>>>>>>>>>>>>>>>>> -bc_type dirichlet -interpolate 0 -petscspace_order 1 -show_initial
>>>>>>>>>>>>>>>>>>>>> -dm_plex_print_fem 1
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> for a representative run. Then you could try 3D
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> ex12 -run_type test -dim 3 -refinement_limit
>>>>>>>>>>>>>>>>>>>>> 0.0125 -variable_coefficient field -interpolate 1 -petscspace_order 2
>>>>>>>>>>>>>>>>>>>>> -show_initial -dm_plex_print_fem
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> or a full run
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> ex12 -refinement_limit 0.01 -bc_type dirichlet
>>>>>>>>>>>>>>>>>>>>> -interpolate -petscspace_order 1
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> ex12 -refinement_limit 0.01 -bc_type dirichlet
>>>>>>>>>>>>>>>>>>>>> -interpolate -petscspace_order 2
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Let me know if those work.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Matt
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> ./ex12
>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR:
>>>>>>>>>>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: Caught signal number 8 FPE: Floating
>>>>>>>>>>>>>>>>>>>>>> Point Exception,probably divide by zero
>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: Try option -start_in_debugger or
>>>>>>>>>>>>>>>>>>>>>> -on_error_attach_debugger
>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: or see
>>>>>>>>>>>>>>>>>>>>>> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSCERROR: or try
>>>>>>>>>>>>>>>>>>>>>> http://valgrind.org on GNU/linux and Apple Mac OS X
>>>>>>>>>>>>>>>>>>>>>> to find memory corruption errors
>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: likely location of problem given in
>>>>>>>>>>>>>>>>>>>>>> stack below
>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: --------------------- Stack Frames
>>>>>>>>>>>>>>>>>>>>>> ------------------------------------
>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: Note: The EXACT line numbers in the
>>>>>>>>>>>>>>>>>>>>>> stack are not available,
>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: INSTEAD the line number of the
>>>>>>>>>>>>>>>>>>>>>> start of the function
>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: is given.
>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: [0] DMPlexComputeResidualFEM line 531
>>>>>>>>>>>>>>>>>>>>>> /home/mjonesa/PETSc/petsc/src/dm/impls/plex/plexfem.c
>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: [0] SNESComputeFunction_DMLocal line
>>>>>>>>>>>>>>>>>>>>>> 63 /home/mjonesa/PETSc/petsc/src/snes/utils/dmlocalsnes.c
>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: [0] SNES user function line 2088
>>>>>>>>>>>>>>>>>>>>>> /home/mjonesa/PETSc/petsc/src/snes/interface/snes.c
>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: [0] SNESComputeFunction line 2076
>>>>>>>>>>>>>>>>>>>>>> /home/mjonesa/PETSc/petsc/src/snes/interface/snes.c
>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: [0] SNESSolve_NEWTONLS line 144
>>>>>>>>>>>>>>>>>>>>>> /home/mjonesa/PETSc/petsc/src/snes/impls/ls/ls.c
>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: [0] SNESSolve line 3765
>>>>>>>>>>>>>>>>>>>>>> /home/mjonesa/PETSc/petsc/src/snes/interface/snes.c
>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: --------------------- Error Message
>>>>>>>>>>>>>>>>>>>>>> ------------------------------------
>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: Signal received!
>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR:
>>>>>>>>>>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: Petsc Development GIT revision:
>>>>>>>>>>>>>>>>>>>>>> v3.4.3-2317-gcd0e7f7 GIT Date: 2014-01-15 20:33:42 -0600
>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: See docs/changes/index.html for
>>>>>>>>>>>>>>>>>>>>>> recent updates.
>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: See docs/faq.html for hints about
>>>>>>>>>>>>>>>>>>>>>> trouble shooting.
>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: See docs/index.html for manual pages.
>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR:
>>>>>>>>>>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: ./ex12 on a arch-linux2-cxx-debug
>>>>>>>>>>>>>>>>>>>>>> named maeda by mjonesa Thu Jan 16 17:41:23 2014
>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: Libraries linked from
>>>>>>>>>>>>>>>>>>>>>> /home/mjonesa/local/lib
>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: Configure run at Thu Jan 16 17:38:33
>>>>>>>>>>>>>>>>>>>>>> 2014
>>>>>>>>>>>>>>>>>>>>>> [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
>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR:
>>>>>>>>>>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: User provided function() line 0 in
>>>>>>>>>>>>>>>>>>>>>> unknown file
>>>>>>>>>>>>>>>>>>>>>> application called MPI_Abort(MPI_COMM_WORLD, 59) -
>>>>>>>>>>>>>>>>>>>>>> process 0
>>>>>>>>>>>>>>>>>>>>>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>> *From:* Matthew Knepley [knepley at gmail.com]
>>>>>>>>>>>>>>>>>>>>>> *Sent:* Thursday, January 16, 2014 4:37 PM
>>>>>>>>>>>>>>>>>>>>>> *To:* Jones,Martin Alexander
>>>>>>>>>>>>>>>>>>>>>> *Cc:* petsc-users at mcs.anl.gov
>>>>>>>>>>>>>>>>>>>>>> *Subject:* Re: [petsc-users] Problems running ex12.c
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> On Thu, Jan 16, 2014 at 4:33 PM, Jones,Martin
>>>>>>>>>>>>>>>>>>>>>> Alexander <MAJones2 at mdanderson.org> wrote:
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> 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:
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Great! Its running. You can reconfigure like this:
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> $PETSC_DIR/$PETSC_ARCH/conf/reconfigure-$PETSC_ARCH.py --download-triangle
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> and then rebuild
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> make
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> and then rerun. You can load meshes, but its much
>>>>>>>>>>>>>>>>>>>>>> easier to have triangle create them.
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Thanks for being patient,
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Matt
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: --------------------- Error
>>>>>>>>>>>>>>>>>>>>>>> Message ------------------------------------
>>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: No support for this operation for
>>>>>>>>>>>>>>>>>>>>>>> this object type!
>>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: Mesh generation needs external
>>>>>>>>>>>>>>>>>>>>>>> package support.
>>>>>>>>>>>>>>>>>>>>>>> Please reconfigure with --download-triangle.!
>>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR:
>>>>>>>>>>>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: Petsc Development GIT revision:
>>>>>>>>>>>>>>>>>>>>>>> v3.4.3-2317-gcd0e7f7 GIT Date: 2014-01-15 20:33:42 -0600
>>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: See docs/changes/index.html for
>>>>>>>>>>>>>>>>>>>>>>> recent updates.
>>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: See docs/faq.html for hints about
>>>>>>>>>>>>>>>>>>>>>>> trouble shooting.
>>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: See docs/index.html for manual pages.
>>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR:
>>>>>>>>>>>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: ./ex12 on a arch-linux2-cxx-debug
>>>>>>>>>>>>>>>>>>>>>>> named maeda by mjonesa Thu Jan 16 16:28:20 2014
>>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: Libraries linked from
>>>>>>>>>>>>>>>>>>>>>>> /home/mjonesa/local/lib
>>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: Configure run at Thu Jan 16 16:25:53
>>>>>>>>>>>>>>>>>>>>>>> 2014
>>>>>>>>>>>>>>>>>>>>>>> [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]"
>>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR:
>>>>>>>>>>>>>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: DMPlexGenerate() line 4332 in
>>>>>>>>>>>>>>>>>>>>>>> /home/mjonesa/PETSc/petsc/src/dm/impls/plex/plex.c
>>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: DMPlexCreateBoxMesh() line 600 in
>>>>>>>>>>>>>>>>>>>>>>> /home/mjonesa/PETSc/petsc/src/dm/impls/plex/plexcreate.c
>>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: CreateMesh() line 295 in
>>>>>>>>>>>>>>>>>>>>>>> /home/mjonesa/PETSc/petsc/src/snes/examples/tutorials/ex12.c
>>>>>>>>>>>>>>>>>>>>>>> [0]PETSC ERROR: main() line 659 in
>>>>>>>>>>>>>>>>>>>>>>> /home/mjonesa/PETSc/petsc/src/snes/examples/tutorials/ex12.c
>>>>>>>>>>>>>>>>>>>>>>> application called MPI_Abort(MPI_COMM_WORLD, 56) -
>>>>>>>>>>>>>>>>>>>>>>> process 0
>>>>>>>>>>>>>>>>>>>>>>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>> *From:* Matthew Knepley [knepley at gmail.com]
>>>>>>>>>>>>>>>>>>>>>>> *Sent:* Thursday, January 16, 2014 4:06 PM
>>>>>>>>>>>>>>>>>>>>>>> *To:* Jones,Martin Alexander
>>>>>>>>>>>>>>>>>>>>>>> *Cc:* petsc-users at mcs.anl.gov
>>>>>>>>>>>>>>>>>>>>>>> *Subject:* Re: [petsc-users] Problems running ex12.c
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jan 16, 2014 at 4:05 PM, Jones,Martin
>>>>>>>>>>>>>>>>>>>>>>> Alexander <MAJones2 at mdanderson.org> wrote:
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Hi. I changed the ENV variable to the correct
>>>>>>>>>>>>>>>>>>>>>>>> entry. when I type make ex12 I get this:
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> mjonesa at maeda:~/PETSc/petsc-3.4.3/src/snes/examples/tutorials$
>>>>>>>>>>>>>>>>>>>>>>>> make ex12
>>>>>>>>>>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>>>>>>>>>> ex12.c:14:18: fatal error: ex12.h: No such file or
>>>>>>>>>>>>>>>>>>>>>>>> directory
>>>>>>>>>>>>>>>>>>>>>>>> compilation terminated.
>>>>>>>>>>>>>>>>>>>>>>>> make: *** [ex12.o] Error 1
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Any help of yours is very much appreciated.
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Yes, this relates to my 3). This is not going to
>>>>>>>>>>>>>>>>>>>>>>> work for you with the release. Please see the link I sent.
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Matt
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>> *From:* Matthew Knepley [knepley at gmail.com]
>>>>>>>>>>>>>>>>>>>>>>>> *Sent:* Thursday, January 16, 2014 3:58 PM
>>>>>>>>>>>>>>>>>>>>>>>> *To:* Jones,Martin Alexander
>>>>>>>>>>>>>>>>>>>>>>>> *Cc:* petsc-users at mcs.anl.gov
>>>>>>>>>>>>>>>>>>>>>>>> *Subject:* Re: [petsc-users] Problems running
>>>>>>>>>>>>>>>>>>>>>>>> ex12.c
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jan 16, 2014 at 3:55 PM, Jones,Martin
>>>>>>>>>>>>>>>>>>>>>>>> Alexander <MAJones2 at mdanderson.org> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Thanks!
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> You built with PETSC_ARCH=arch-linux2-cxx-debug
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Matt
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>> *From:* Matthew Knepley [knepley at gmail.com]
>>>>>>>>>>>>>>>>>>>>>>>>> *Sent:* Thursday, January 16, 2014 3:31 PM
>>>>>>>>>>>>>>>>>>>>>>>>> *To:* Jones,Martin Alexander
>>>>>>>>>>>>>>>>>>>>>>>>> *Cc:* petsc-users at mcs.anl.gov
>>>>>>>>>>>>>>>>>>>>>>>>> *Subject:* Re: [petsc-users] Problems running
>>>>>>>>>>>>>>>>>>>>>>>>> ex12.c
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jan 16, 2014 at 3:11 PM, Jones,Martin
>>>>>>>>>>>>>>>>>>>>>>>>> Alexander <MAJones2 at mdanderson.org> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Now I went to the directory where ex12.c sits
>>>>>>>>>>>>>>>>>>>>>>>>>> and just did a 'make ex12.c' with the following error if this helps? :
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> mjonesa at maeda:~/PETSc/petsc-3.4.3/src/snes/examples/tutorials$
>>>>>>>>>>>>>>>>>>>>>>>>>> make ex12.c
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> /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
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> /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
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> make: *** No rule to make target
>>>>>>>>>>>>>>>>>>>>>>>>>> `/home/mjonesa/PETSc/petsc-3.4.3/linux-gnu-cxx-debug/conf/petscrules'.
>>>>>>>>>>>>>>>>>>>>>>>>>> Stop.
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> 1) You would type 'make ex12'
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> 2) Either you PETSC_DIR (
>>>>>>>>>>>>>>>>>>>>>>>>> /home/mjonesa/PETSc/petsc-3.4.3) or PETSC_ARCH (
>>>>>>>>>>>>>>>>>>>>>>>>> linux-gnu-cxx-debug) environment variables
>>>>>>>>>>>>>>>>>>>>>>>>> do not match what you built. Please send
>>>>>>>>>>>>>>>>>>>>>>>>> configure.log and make.log
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> 3) Since it was only recently added, if you want
>>>>>>>>>>>>>>>>>>>>>>>>> to use the FEM functionality, you must use the development version:
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> http://www.mcs.anl.gov/petsc/developers/index.html
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Matt
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> *From:* Matthew Knepley [mailto:knepley at gmail.com]
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> *Sent:* Thursday, January 16, 2014 2:48 PM
>>>>>>>>>>>>>>>>>>>>>>>>>> *To:* Jones,Martin Alexander
>>>>>>>>>>>>>>>>>>>>>>>>>> *Cc:* petsc-users at mcs.anl.gov
>>>>>>>>>>>>>>>>>>>>>>>>>> *Subject:* Re: [petsc-users] Problems running
>>>>>>>>>>>>>>>>>>>>>>>>>> ex12.c
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jan 16, 2014 at 2:35 PM, Jones,Martin
>>>>>>>>>>>>>>>>>>>>>>>>>> Alexander <MAJones2 at mdanderson.org> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Hello To Whom it Concerns,
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> I am trying to run the tutorial ex12.c by running 'bin/pythonscripts/PetscGenerateFEMQuadrature.py
>>>>>>>>>>>>>>>>>>>>>>>>>> dim order dim 1 laplacian dim order dim 1 boundary
>>>>>>>>>>>>>>>>>>>>>>>>>> src/snes/examples/tutorials/ex12.h'
>>>>>>>>>>>>>>>>>>>>>>>>>> but getting the following error:
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> $ bin/pythonscripts/PetscGenerateFEMQuadrature.py
>>>>>>>>>>>>>>>>>>>>>>>>>> dim order dim 1 laplacian dim order dim 1 boundary
>>>>>>>>>>>>>>>>>>>>>>>>>> src/snes/examples/tutorials/ex12.h
>>>>>>>>>>>>>>>>>>>>>>>>>> Traceback (most recent call last):
>>>>>>>>>>>>>>>>>>>>>>>>>> File
>>>>>>>>>>>>>>>>>>>>>>>>>> "bin/pythonscripts/PetscGenerateFEMQuadrature.py", line 15, in <module>
>>>>>>>>>>>>>>>>>>>>>>>>>> from FIAT.reference_element import
>>>>>>>>>>>>>>>>>>>>>>>>>> default_simplex
>>>>>>>>>>>>>>>>>>>>>>>>>> ImportError: No module named
>>>>>>>>>>>>>>>>>>>>>>>>>> FIAT.reference_element
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> I have removed the requirement of generating the
>>>>>>>>>>>>>>>>>>>>>>>>>> header file (its now all handled in C). I thought
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> I changed the documentation everywhere (including
>>>>>>>>>>>>>>>>>>>>>>>>>> the latest tutorial slides). Can you try running
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> with 'master' (or 'next'), and point me toward
>>>>>>>>>>>>>>>>>>>>>>>>>> the old docs?
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Matt
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>>>>>>> What most experimenters take for granted before
>>>>>>>>>>>>>>>>>>>>>>>>>> they begin their experiments is infinitely more interesting than any
>>>>>>>>>>>>>>>>>>>>>>>>>> results to which their experiments lead.
>>>>>>>>>>>>>>>>>>>>>>>>>> -- Norbert Wiener
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>>>>>> What most experimenters take for granted before
>>>>>>>>>>>>>>>>>>>>>>>>> they begin their experiments is infinitely more interesting than any
>>>>>>>>>>>>>>>>>>>>>>>>> results to which their experiments lead.
>>>>>>>>>>>>>>>>>>>>>>>>> -- Norbert Wiener
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>>>>> What most experimenters take for granted before
>>>>>>>>>>>>>>>>>>>>>>>> they begin their experiments is infinitely more interesting than any
>>>>>>>>>>>>>>>>>>>>>>>> results to which their experiments lead.
>>>>>>>>>>>>>>>>>>>>>>>> -- Norbert Wiener
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>>>> What most experimenters take for granted before they
>>>>>>>>>>>>>>>>>>>>>>> begin their experiments is infinitely more interesting than any results to
>>>>>>>>>>>>>>>>>>>>>>> which their experiments lead.
>>>>>>>>>>>>>>>>>>>>>>> -- Norbert Wiener
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>>> What most experimenters take for granted before they
>>>>>>>>>>>>>>>>>>>>>> begin their experiments is infinitely more interesting than any results to
>>>>>>>>>>>>>>>>>>>>>> which their experiments lead.
>>>>>>>>>>>>>>>>>>>>>> -- Norbert Wiener
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>> What most experimenters take for granted before they
>>>>>>>>>>>>>>>>>>>>> begin their experiments is infinitely more interesting than any results to
>>>>>>>>>>>>>>>>>>>>> which their experiments lead.
>>>>>>>>>>>>>>>>>>>>> -- Norbert Wiener
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>> What most experimenters take for granted before they
>>>>>>>>>>>>>>>>>>>> begin their experiments is infinitely more interesting than any results to
>>>>>>>>>>>>>>>>>>>> which their experiments lead.
>>>>>>>>>>>>>>>>>>>> -- Norbert Wiener
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>> What most experimenters take for granted before they
>>>>>>>>>>>>>>>>>>> begin their experiments is infinitely more interesting than any results to
>>>>>>>>>>>>>>>>>>> which their experiments lead.
>>>>>>>>>>>>>>>>>>> -- Norbert Wiener
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>> What most experimenters take for granted before they begin
>>>>>>>>>>>>>>>>> their experiments is infinitely more interesting than any results to which
>>>>>>>>>>>>>>>>> their experiments lead.
>>>>>>>>>>>>>>>>> -- Norbert Wiener
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>> *Miguel Angel Salazar de Troya*
>>>>>>>>>>>>>>>> Graduate Research Assistant
>>>>>>>>>>>>>>>> Department of Mechanical Science and Engineering
>>>>>>>>>>>>>>>> University of Illinois at Urbana-Champaign
>>>>>>>>>>>>>>>> (217) 550-2360
>>>>>>>>>>>>>>>> salaza11 at illinois.edu
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>> What most experimenters take for granted before they begin
>>>>>>>>>>>>>>> their experiments is infinitely more interesting than any results to which
>>>>>>>>>>>>>>> their experiments lead.
>>>>>>>>>>>>>>> -- Norbert Wiener
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> --
>>>>>>>>>>>>>> *Miguel Angel Salazar de Troya*
>>>>>>>>>>>>>> Graduate Research Assistant
>>>>>>>>>>>>>> Department of Mechanical Science and Engineering
>>>>>>>>>>>>>> University of Illinois at Urbana-Champaign
>>>>>>>>>>>>>> (217) 550-2360
>>>>>>>>>>>>>> salaza11 at illinois.edu
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> --
>>>>>>>>>>>>> What most experimenters take for granted before they begin
>>>>>>>>>>>>> their experiments is infinitely more interesting than any results to which
>>>>>>>>>>>>> their experiments lead.
>>>>>>>>>>>>> -- Norbert Wiener
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>> *Miguel Angel Salazar de Troya*
>>>>>>>>>>>> Graduate Research Assistant
>>>>>>>>>>>> Department of Mechanical Science and Engineering
>>>>>>>>>>>> University of Illinois at Urbana-Champaign
>>>>>>>>>>>> (217) 550-2360
>>>>>>>>>>>> salaza11 at illinois.edu
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> What most experimenters take for granted before they begin their
>>>>>>>>>>> experiments is infinitely more interesting than any results to which their
>>>>>>>>>>> experiments lead.
>>>>>>>>>>> -- Norbert Wiener
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> *Miguel Angel Salazar de Troya*
>>>>>>>>>> Graduate Research Assistant
>>>>>>>>>> Department of Mechanical Science and Engineering
>>>>>>>>>> University of Illinois at Urbana-Champaign
>>>>>>>>>> (217) 550-2360
>>>>>>>>>> salaza11 at illinois.edu
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> What most experimenters take for granted before they begin their
>>>>>>>>> experiments is infinitely more interesting than any results to which their
>>>>>>>>> experiments lead.
>>>>>>>>> -- Norbert Wiener
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> *Miguel Angel Salazar de Troya*
>>>>>>>> Graduate Research Assistant
>>>>>>>> Department of Mechanical Science and Engineering
>>>>>>>> University of Illinois at Urbana-Champaign
>>>>>>>> (217) 550-2360
>>>>>>>> salaza11 at illinois.edu
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> What most experimenters take for granted before they begin their
>>>>>>> experiments is infinitely more interesting than any results to which their
>>>>>>> experiments lead.
>>>>>>> -- Norbert Wiener
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> *Miguel Angel Salazar de Troya*
>>>>>> Graduate Research Assistant
>>>>>> Department of Mechanical Science and Engineering
>>>>>> University of Illinois at Urbana-Champaign
>>>>>> (217) 550-2360
>>>>>> salaza11 at illinois.edu
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> What most experimenters take for granted before they begin their
>>>>> experiments is infinitely more interesting than any results to which their
>>>>> experiments lead.
>>>>> -- Norbert Wiener
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> What most experimenters take for granted before they begin their
>>>> experiments is infinitely more interesting than any results to which their
>>>> experiments lead.
>>>> -- Norbert Wiener
>>>>
>>>
>>>
>>>
>>> --
>>> *Miguel Angel Salazar de Troya*
>>> Graduate Research Assistant
>>> Department of Mechanical Science and Engineering
>>> University of Illinois at Urbana-Champaign
>>> (217) 550-2360
>>> salaza11 at illinois.edu
>>>
>>>
>>
>>
>> --
>> What most experimenters take for granted before they begin their
>> experiments is infinitely more interesting than any results to which their
>> experiments lead.
>> -- Norbert Wiener
>>
>
>
>
> --
> *Miguel Angel Salazar de Troya*
> Graduate Research Assistant
> Department of Mechanical Science and Engineering
> University of Illinois at Urbana-Champaign
> (217) 550-2360
> salaza11 at illinois.edu
>
>
--
*Miguel Angel Salazar de Troya*
Graduate Research Assistant
Department of Mechanical Science and Engineering
University of Illinois at Urbana-Champaign
(217) 550-2360
salaza11 at illinois.edu
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