[petsc-users] Problems running ex12.c
Matthew Knepley
knepley at gmail.com
Fri Jan 17 11:04:35 CST 2014
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,
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
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