[petsc-users] Problems running ex12.c
Miguel Angel Salazar de Troya
salazardetroya at gmail.com
Mon Mar 3 12:39:45 CST 2014
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
[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]PETSC ERROR:
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
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