[petsc-users] Problems running ex12.c
Matthew Knepley
knepley at gmail.com
Mon Mar 3 13:40:38 CST 2014
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20140303/a276ff7f/attachment-0001.html>
More information about the petsc-users
mailing list