[petsc-users] Problems running ex12.c
Matthew Knepley
knepley at gmail.com
Tue Mar 4 12:01:28 CST 2014
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.
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
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