[petsc-users] Problems running ex12.c
Yaakoub El Khamra
yelkhamra at gmail.com
Tue Jan 28 10:31:38 CST 2014
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?
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
>
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