[petsc-users] Problems running ex12.c
Matthew Knepley
knepley at gmail.com
Fri Jan 17 11:29:11 CST 2014
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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