[CIG-SHORT] Problem running Pylith binary on 64-bit Mac OS X
Brad Aagaard
baagaard at usgs.gov
Sun Dec 6 12:37:29 PST 2009
Isabelle-
Another difference between the 3d/hex8 examples and the twocells/twohex8
example, is the
[pylithapp.mesh_generator]
debug = 1
in twocells/twohex8/pylithapp.cfg. Change this to
[pylithapp.mesh_generator]
debug = 0
and let me know if this resolves the issue.
Brad
Matthew Knepley wrote:
> On Sun, Dec 6, 2009 at 1:37 PM, Isabelle Ryder <izryder at googlemail.com
> <mailto:izryder at googlemail.com>> wrote:
>
> Hi Matt
>
> Thanks for responding. You're right, there was a part of the message
> omitted in my initial email; I think the omitted part (pasted at the
> bottom of this message) was just to do with the debugger.
>
> Regarding your make test request - is the $PETSC_DIR meant to be
> opt/petsc-dev? The only thing in this directory is the
> darwin8.9.1-cxx-opt directory, and make test gives the following:
>
>
> The binary install is missing the PETSc tests evidently.
>
>
> bash-3.2$ make test
> make: *** No rule to make target `test'. Stop.
>
> I tried Brad's suggestion of running the viscoelastic examples in
> 3d/hex8, and they ran to completion.
>
>
> It looks like it is trying to launch gdb. Check that the .cfg file does
> not have the
>
> --petsc.start_in_debugger
>
> option defined. However, we can also use it to debug this by giving
>
> --petsc.display=:0.0
>
> Matt
>
>
> Isabelle
>
> --------
> bash-3.2$ pylith axialdisp.cfg
> >>
> /Users/buildbot/install/x86_darwin_single_nosched_binbot/lib/python2.3/site-packages/pylith/utils/PetscManager.py:48:initialize
> -- petsc(info)
> -- Initializing PETSc.
> [0]PETSC ERROR: PETSC: Attaching gdb to
> /Users/isabelleryder/research/fem/pylith/pylith-1.4.2-darwin-i386/bin/mpinemesis
> of pid 8755 on display /tmp/launch-WUqdAn/:0 on machine
> Isabelle-Ryders-MacBook-Pro.local
> ^CTraceback (most recent call last):
> Traceback (most recent call last):
> File
> "/Users/isabelleryder/research/fem/pylith/pylith-1.4.2-darwin-i386/bin/pylith",
> line 33, in ?
> start(applicationClass=PyLithApp)
> File "<string>", line 1, in ?
> File
> "/Users/buildbot/install/x86_darwin_single_nosched_binbot/lib/python2.3/site-packages/pythia-0.8.1.9-py2.3.egg/pyre/applications/__init__.py",
> line 41, in start
>
>
> On 12/6/09, Matthew Knepley <knepley at mcs.anl.gov
> <mailto:knepley at mcs.anl.gov>> wrote:
> > Did you send the whole error message? It looks like there is a
> ... after
> > PETSC ERROR. However,
> > we can debug PETSc separately. Can you
> >
> > cd $PETSC_DIR
> > make test
> >
> > and send the output?
> >
> > Thanks,
> >
> > Matt
> >
> > On Sat, Dec 5, 2009 at 12:43 PM, Isabelle Ryder
> > <izryder at googlemail.com <mailto:izryder at googlemail.com>>wrote:
> >
> >> Hi
> >>
> >> I am running Pylith on Mac OS X 10.6.2 from the pre-compiled binary
> >> distribution pylith-1.4.2-darwin-i386. The elastic example
> problems run ok
> >> but with the viscoelastic problems in the twohex8 directory I
> run into
> >> "PETSC ERROR". The start of the Traceback is pasted below.
> >>
> >> I found what looked like a similar problem in the CIG-Short
> archive (Sept
> >> 2008) and this was a 32 v. 64 bit issue on Linux. However, if
> this is the
> >> problem, I'm not sure how to implement the workaround for Mac OS X.
> >>
> >> Many thanks
> >>
> >> Isabelle Ryder
> >> --------------
> >> bash-3.2$ pylith axialdisp.cfg
> >> >>
> >>
> /Users/buildbot/install/x86_darwin_single_nosched_binbot/lib/python2.3/si
> >> packages/pylith/utils/PetscManager.py:48:initialize
> >> -- petsc(info)
> >> -- Initializing PETSc.
> >> [0]PETSC ERROR: ...
> >>
> >> Traceback (most recent call last):
> >> File "<string>", line 1, in ?
> >> File
> >>
> "/Users/buildbot/install/x86_darwin_single_nosched_binbot/lib/python2.
> >>
> ite-packages/pythia-0.8.1.9-py2.3.egg/pyre/schedulers/__init__.py", line
> >> 53,
> >> jobstart
> >> File
> >>
> "/Users/buildbot/install/x86_darwin_single_nosched_binbot/lib/python2.
> >>
> ite-packages/pythia-0.8.1.9-py2.3.egg/pyre/applications/__init__.py",
> line
> >> 41
> >> n start
> >> File
> >>
> "/Users/buildbot/install/x86_darwin_single_nosched_binbot/lib/python2.
> >>
> ite-packages/pythia-0.8.1.9-py2.3.egg/pyre/applications/Shell.py", line
> >> 142,
> >> run
> >> File
> >>
> "/Users/buildbot/install/x86_darwin_single_nosched_binbot/lib/python2.
> >>
> ite-packages/pythia-0.8.1.9-py2.3.egg/pyre/applications/SuperScript.py",
> >> line
> >> , in execute
> >> File
> >>
> "/Users/buildbot/install/x86_darwin_single_nosched_binbot/lib/python2.
> >>
> ite-packages/pythia-0.8.1.9-py2.3.egg/pyre/applications/SuperScript.py",
> >> line
> >> , in main
> >>
> >>
> >> _______________________________________________
> >> CIG-SHORT mailing list
> >> CIG-SHORT at geodynamics.org <mailto:CIG-SHORT at geodynamics.org>
> >> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
> >>
> >>
> >
> >
> > --
> > 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
> >
>
>
> --
> Dr Isabelle Ryder
> Lecturer in Geophysics
> Dept of Earth & Ocean Sciences
> University of Liverpool
> L69 3GP
> tel: 0151 7945143
>
>
>
>
> --
> 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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>
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