[CIG-SHORT] Not able to run dynamic fault (step11) with Pylith-1.9.0 installed from source
Birendra jha
bjha7333 at yahoo.com
Mon Sep 2 19:32:47 PDT 2013
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?
Should I start from configure again, or can I run make clean and make? For latter, should I clean only under pylith-build or do I need to do it for everything?
thanks
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, 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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