[petsc-users] Problems running ex12.c
Miguel Angel Salazar de Troya
salazardetroya at gmail.com
Mon Mar 3 13:39:11 CST 2014
This is what I get at gdb when I type 'where'.
#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
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