[petsc-users] Problems running ex12.c
Miguel Angel Salazar de Troya
salazardetroya at gmail.com
Mon Mar 3 13:44:32 CST 2014
Thanks. This is what I get.
(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
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