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

[Birendra jha]

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
 >
 
 _______________________________________________
 CIG-SHORT mailing list
 CIG-SHORT at geodynamics.org
 http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short