[petsc-users] Problems running ex12.c
Matthew Knepley
knepley at gmail.com
Mon Mar 3 12:48:56 CST 2014
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
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