[petsc-users] Problems running ex12.c

Matthew Knepley knepley at gmail.com
Tue Jan 28 10:37:23 CST 2014 

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
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