[petsc-users] Problems running ex12.c

Miguel Angel Salazar de Troya salazardetroya at gmail.com
Tue Mar 4 11:51:48 CST 2014


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.

[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
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