[petsc-users] Problems running ex12.c
Matthew Knepley
knepley at gmail.com
Tue Mar 4 23:28:50 CST 2014
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
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