[petsc-users] Problems running ex12.c
David Fuentes
fuentesdt at gmail.com
Sun Apr 20 21:26:10 CDT 2014
Hi,
the dev version of ex12 seems to be running with the opencl options:
-petscfe_type opencl -mat_petscfe_type opencl
How are the num_blocks and num_batches options to be used ?
-petscfe_num_blocks 2 -petscfe_num_batches 2
https://bitbucket.org/petsc/petsc/src/64715f0f033346c10c77b73cf58216d111db8789/config/builder.py#cl-337
Thanks,
David
On Fri, Apr 4, 2014 at 10:37 AM, Matthew Knepley <knepley at gmail.com> wrote:
> On Mon, Mar 31, 2014 at 7:08 PM, Matthew Knepley <knepley at gmail.com>wrote:
>
>> On Mon, Mar 31, 2014 at 6:37 PM, Miguel Angel Salazar de Troya <
>> salazardetroya at gmail.com> wrote:
>>
>>> Thanks for your response. Now I am trying to modify this example to
>>> include Dirichlet and Neumann conditions at the same time.
>>>
>>> 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?
>>>
>>
>> Right about the shortcoming, but wrong about the source.
>> DMPlexAddBoundary() takes an argument that is the marker value for the
>> given label, so you can select boundaries.
>> However, DMPlexComputeResidualFEM() currently hardcodes the boundary name
>> ("boundary")
>> and the marker value (1). I wrote this when we had no boundary
>> representation in PETSc. Now that we have DMAddBoundary(), we can
>> loop over the Neumann boundaries. I have put this on my todo list. If you
>> are motivated, you can do it first and I will help.
>>
>
> I pushed this change today, so now you can have multiple Neumann
> boundaries with whatever labels
> you want. I have not written a test for multiple boundaries, but the old
> single boundary tests pass.
>
> Thanks,
>
> Matt
>
>
>> Thanks,
>>
>> Matt
>>
>>
>>> 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?
>>>
>>>
>>> On Sun, Mar 30, 2014 at 7:51 PM, Matthew Knepley <knepley at gmail.com>wrote:
>>>
>>>> On Sun, Mar 30, 2014 at 7:07 PM, Miguel Angel Salazar de Troya <
>>>> salazardetroya at gmail.com> wrote:
>>>>
>>>>> Thanks for your response. Your help is really useful to me.
>>>>>
>>>>> 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?
>>>>>
>>>>
>>>> If it is not purely a function of the coordinates, or you do not know
>>>> that function, there is no option left.
>>>>
>>>>
>>>>> 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.
>>>>>
>>>>
>>>> Its not a vector, which indicates a particular behavior under
>>>> coordinate transformations, but an array
>>>> which can hold any data you want.
>>>>
>>>> Matt
>>>>
>>>>
>>>>> Thanks in advance
>>>>> Miguel
>>>>>
>>>>>
>>>>> On Sun, Mar 30, 2014 at 2:01 PM, Matthew Knepley <knepley at gmail.com>wrote:
>>>>>
>>>>>> On Sun, Mar 30, 2014 at 1:57 PM, Miguel Angel Salazar de Troya <
>>>>>> salazardetroya at gmail.com> wrote:
>>>>>>
>>>>>>> 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.
>>>>>>>
>>>>>>
>>>>>> 1) I wanted to try and make things more automatic for the user
>>>>>>
>>>>>> 2) I needed a way to automatically layout data for coarser/finer
>>>>>> grids in unstructured MG
>>>>>>
>>>>>> Thus, now when you set for PetscFE into the DM using DMSetField(), it
>>>>>> will automatically create
>>>>>> the section on the first call to DMGetDefaultSection().
>>>>>>
>>>>>> I do not have a similar provision now for materials, so you create
>>>>>> your own section. I think this is
>>>>>> alright until we have some idea of a nicer interface.
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Matt
>>>>>>
>>>>>>
>>>>>>> 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.htmlfor 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
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> 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
>
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