[petsc-users] Problems running ex12.c
Matthew Knepley
knepley at gmail.com
Sun Mar 30 14:01:17 CDT 2014
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.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
>
>
--
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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