[petsc-users] Problems running ex12.c
Jones,Martin Alexander
MAJones2 at mdanderson.org
Fri Jan 17 11:06:54 CST 2014
________________________________
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<mailto: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<mailto:knepley at gmail.com>]
Sent: Thursday, January 16, 2014 6:35 PM
To: Jones,Martin Alexander
Cc: petsc-users at mcs.anl.gov<mailto: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<mailto: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]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] 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<mailto:knepley at gmail.com>]
Sent: Thursday, January 16, 2014 4:37 PM
To: Jones,Martin Alexander
Cc: petsc-users at mcs.anl.gov<mailto: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<mailto: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<mailto:knepley at gmail.com>]
Sent: Thursday, January 16, 2014 4:06 PM
To: Jones,Martin Alexander
Cc: petsc-users at mcs.anl.gov<mailto: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<mailto: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<mailto:knepley at gmail.com>]
Sent: Thursday, January 16, 2014 3:58 PM
To: Jones,Martin Alexander
Cc: petsc-users at mcs.anl.gov<mailto: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<mailto:MAJones2 at mdanderson.org>> wrote:
Thanks!
You built with PETSC_ARCH=arch-linux2-cxx-debug
Matt
________________________________
From: Matthew Knepley [knepley at gmail.com<mailto:knepley at gmail.com>]
Sent: Thursday, January 16, 2014 3:31 PM
To: Jones,Martin Alexander
Cc: petsc-users at mcs.anl.gov<mailto: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<mailto: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<mailto:knepley at gmail.com>]
Sent: Thursday, January 16, 2014 2:48 PM
To: Jones,Martin Alexander
Cc: petsc-users at mcs.anl.gov<mailto: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<mailto: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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