[CIG-SHORT] Not able to run dynamic fault (step11) with Pylith-1.9.0 installed from source

[Brad Aagaard]

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
>   >
>   > _______________________________________________
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>   >
>
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