[CIG-SHORT] Not able to run dynamic fault (step11) with Pylith-1.9.0 installed from source
Brad Aagaard
baagaard at usgs.gov
Mon Sep 2 20:10:26 PDT 2013
On 9/2/13 7:32 PM, Birendra jha wrote:
> Brad
>
> Running ldd lists the correct pylith version:
> libpylith.so.0 => /data/bjha/pylith-1.9.0/lib/libpylith.so.0 (0x00007f5460452000)
>
> How should I check python unit tests?
Start by not cleaning, just run the tests.
To be safe, start with the libtests
cd pylith-build/unittests/libtests
make check
and if they pass, do the python unit tests (note that these often don't
stop even if there is an error, so you need to actually check the
output). Pay particular attention to the friction and fault unit tests.
cd pylith-build/unittests/pytests
make check
If these pass, then look at all of the environment variables in
config.log and compare them against the output of "env". If the tests
pass then something must be different between the environment when you
built and now.
Brad
> --------------------------------------------
> On Tue, 9/3/13, Brad Aagaard <baagaard at usgs.gov> wrote:
>
> Subject: Re: [CIG-SHORT] Not able to run dynamic fault (step11) with Pylith-1.9.0 installed from source
> To: cig-short at geodynamics.org
> Date: Tuesday, September 3, 2013, 7:23 AM
>
> Birendra,
>
> The error you are getting with "import
> pylith.faults.FaultCohesiveDyn"
> indicates that the friction module is missing a symbol for
> pylith::friction::SlipWeakeningTimeStable. This was added in
> v1.9, so
> either the module or pylith library didn't build properly or
> your
> environment when you run the examples is finding the pylith
> library from
> v1.8.
>
> Run "ldd
> /data/bjha/pylith-1.9.0/lib/python2.7/site-packages/pylith/friction/_frictionmodule.so".
>
> If it lists libpylith.so from v1.8, then you need to fix
> your
> environment (check it against the variables from setup.sh).
> If it shows
> libpylith.so from v1.9, then your pylith build has a
> problem. Check the
> python unit tests again.
>
> Brad
>
> On 9/2/13 6:27 PM, Birendra jha wrote:
> > Brad
> >
> > I agree something is wrong with my installation.
> However, all the tests passed when I built pylith using the
> installer.
> > Here is the result of running nemesis:
> >
> > [bjha at login refined]$ nemesis
> > Python 2.7.2 (default, Jul 12 2011, 10:24:30)
> > [GCC 4.6.0 20110530 (Red Hat 4.6.0-9)] on linux2
> > Type "help", "copyright", "credits" or "license" for
> more information.
> >>>> import pylith.faults.FaultCohesiveDyn
> > Traceback (most recent call last):
> > File "<stdin>", line 1, in
> <module>
> > File
> "/data/bjha/pylith-1.9.0/lib/python2.7/site-packages/pylith/faults/FaultCohesiveDyn.py",
> line 34, in <module>
> > class
> FaultCohesiveDyn(FaultCohesive, Integrator,
> ModuleFaultCohesiveDyn):
> > File
> "/data/bjha/pylith-1.9.0/lib/python2.7/site-packages/pylith/faults/FaultCohesiveDyn.py",
> line 75, in FaultCohesiveDyn
> > from pylith.friction.StaticFriction
> import StaticFriction
> > File
> "/data/bjha/pylith-1.9.0/lib/python2.7/site-packages/pylith/friction/StaticFriction.py",
> line 26, in <module>
> > from friction import StaticFriction
> as ModuleStaticFriction
> > File
> "/data/bjha/pylith-1.9.0/lib/python2.7/site-packages/pylith/friction/friction.py",
> line 26, in <module>
> > _friction = swig_import_helper()
> > File
> "/data/bjha/pylith-1.9.0/lib/python2.7/site-packages/pylith/friction/friction.py",
> line 22, in swig_import_helper
> > _mod = imp.load_module('_friction',
> fp, pathname, description)
> > ImportError:
> /data/bjha/pylith-1.9.0/lib/python2.7/site-packages/pylith/friction/_frictionmodule.so:
> undefined symbol:
> _ZN6pylith8friction23SlipWeakeningTimeStableC1Ev
> >>>> pylith.faults.FaultCohesiveDyn.__file__
> > Traceback (most recent call last):
> > File "<stdin>", line 1, in
> <module>
> > NameError: name 'pylith' is not defined
> >>>>
> >
> > I checked PATH, PYTHONPATH and they are exclusively
> pointing to Pylith-1.9.0, not Pylith-1.8.0.
> >
> > What do you suggest?
> > Birendra
> > --------------------------------------------
> > On Tue, 9/3/13, Brad Aagaard <baagaard at usgs.gov>
> wrote:
> >
> > Subject: Re: [CIG-SHORT] Not able to
> run dynamic fault (step11) with Pylith-1.9.0 installed from
> source
> > To: cig-short at geodynamics.org
> > Date: Tuesday, September 3, 2013, 2:29
> AM
> >
> > Birendra,
> >
> > I don't find any problems with
> examples/3d/hex8/step11. It
> > runs fine for
> > me using the binary and building from
> source. My guess is
> > that something
> > is wrong with your installation. Did
> you wipe out all of the
> > old PyLith
> > stuff in your PATH, PYTHONPATH, etc or
> at least adjust your
> > PATH,
> > PYTHONPATH, etc so that they only see
> v1.9.0? Did all of the
> > tests pass
> > when you built pylith using the
> installer?
> >
> > What happens when you do the
> following?
> > nemesis
> > import pylith.faults.FaultCohesiveDyn
> > pylith.faults.FaultCohesiveDyn.__file__
> >
> > You can also try running
> > pylithinfo --verbose step11.cfg
> >
> > The output will be written to
> pylith_parameters.txt. It will
> > show you
> > where every parameter is set. You
> would first need to fix
> > any validation
> > errors to get this far, because those
> are tripped before the
> > parameters
> > can be written.
> >
> > Regards,
> > Brad
> >
> >
> > On 9/1/13 10:26 PM, Birendra jha
> wrote:
> > > Hi Pylith developers
> > >
> > > I installed Pylith-1.9.0 using
> the installer on the
> > pylith website. Installation was
> successful with no error
> > messages except in the beginning when
> I ran configure I got
> > a message about existing software:
> > >
> > > WARNING: Existing version of HDF5
> installed. Found
> > /usr/bin/h5dump
> > > WARNING: Existing version of
> NetCDF installed. Found
> > /usr/bin/ncdump
> > >
> > > configure: error: "Configure
> failed due to conflict
> > with existing software. Existing
> software may interfere with
> > proper installation of PyLith, may be
> configured incorrectly
> > for use with PyLith, or may have been
> built with
> > incompatible compilers. Remove
> existing software
> > (RECOMMENDED) or reconfigure with
> --enable-force-install to
> > override error message. "
> > >
> > > As per suggestion, I reran
> configure with
> > --enable-force-install option, and it
> finished successfully
> > along with 'make'.
> > >
> > > I am able to run successfully all
> examples e.g. step01,
> > step06 except examples with dynamic
> fault e.g. step11:
> > >
> > > [bjha at login hex8]$ pylith
> step11.cfg
> > > Traceback (most recent call
> last):
> > > File
> "/data/bjha/pylith-1.9.0/bin/pylith",
> > line 39, in <module>
> > >
> start(applicationClass=PyLithApp)
> > > File
> > "/data/bjha/pylith-1.9.0/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/pyre/applications/__init__.py",
> > line 41, in start
> > >
> shell.run(**kwds)
> > > File
> > "/data/bjha/pylith-1.9.0/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/pyre/applications/Shell.py",
> > line 125, in run
> > >
> app.applyConfiguration(context)
> > > File
> > "/data/bjha/pylith-1.9.0/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/pyre/inventory/Configurable.py",
> > line 84, in applyConfiguration
> > > raise
> ValueError("%s\nBacktrace -
> > Component %s" % (err.message,
> aliases))
> > > ValueError: Error while
> configuring spatial database
> > reader (simpleioascii, iohandler):
> > > Filename for spatial database not
> specified.
> > > Backtrace - Component
> simpleioascii, iohandler
> > > Backtrace - Component simpledb,
> slip
> > > Backtrace - Component stepslipfn,
> slip_function
> > > Backtrace - Component eqkinsrc,
> rupture
> > > Backtrace - Component
> singlerupture, eq_srcs
> > > Backtrace - Component
> faultcohesivekin, fault
> > > Backtrace - Component interfaces
> > > Backtrace - Component
> timedependent, problem
> > > Backtrace - Component pylithapp
> > >
> > > Why is it saying faultcohesivekin
> when it is
> > FaultCohesiveDyn in the step11.cfg? I
> am able to run this in
> > my Pylith-1.8.0 copy.
> > > Please help.
> > >
> > > Thanks and regards
> > > Birendra
> > >
> > >
> _______________________________________________
> > > CIG-SHORT mailing list
> > > CIG-SHORT at geodynamics.org
> > > http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
> > >
> >
> > _______________________________________________
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> >
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>
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