[CIG-SHORT] Trouble Updating PyLith Pt. 2
Brad Aagaard
baagaard at usgs.gov
Mon Sep 13 16:15:11 PDT 2010
Jeff-
This error is consistent with updated SWIG and/or gcc since SWIG
generated the module files. Please rebuild spatialdata and then rebuild
pylith. Be sure to remove the .py and _wrap.cxx files from your
spatialdata and pylith modulesrc/* directories.
Brad
On 9/13/10 2:44 PM, Jeffrey Thompson wrote:
> Hi CIG-Short,
>
> I followed the advice Brad gave me, and I was able to "make" and "make
> install" PyLith. However, when I run pylith, I get the error shown
> below. This happens independent of the problem I try to run, and occurs
> when I use "pylith --help" or "pylith --version" or even just "pylith."
> The error message is:
>
> /home/jeffremt/tools/cig/gcc-4.1.1_64/lib/python2.5/site-packages/pythia-0.8.1.10-py2.5.egg/pyre/inventory/odb/Curator.py:200:
> UserWarning: Module spatialdata was already imported from
> /home/jeffremt/tools/cig/gcc-4.1.1_64/lib64/python2.5/site-packages/spatialdata/__init__.pyc,
> but /home/jeffremt/tools/cig/gcc-4.1.1_64/lib/python2.5/site-packages is
> being added to sys.path
> from pkg_resources import resource_listdir, resource_isdir,
> resource_exists, resource_filename, Requirement
> /home/jeffremt/tools/cig/gcc-4.1.1_64/lib/python2.5/site-packages/pythia-0.8.1.10-py2.5.egg/pyre/inventory/odb/Curator.py:200:
> UserWarning: Module pylith was already imported from
> /home/jeffremt/tools/cig/gcc-4.1.1_64/lib64/python2.5/site-packages/pylith/__init__.pyc,
> but /home/jeffremt/tools/cig/gcc-4.1.1_64/lib/python2.5/site-packages is
> being added to sys.path
> from pkg_resources import resource_listdir, resource_isdir,
> resource_exists, resource_filename, Requirement
> /home/jeffremt/tools/cig/gcc-4.1.1_64/lib/python2.5/site-packages/pythia-0.8.1.10-py2.5.egg/pyre/inventory/odb/Curator.py:200:
> UserWarning: Module pkg_resources was already imported from
> /home/jeffremt/tools/cig/gcc-4.1.1_64/lib/python2.5/site-packages/setuptools-0.6c9-py2.5.egg/pkg_resources.py,
> but
> /home/jeffremt/tools/cig/gcc-4.1.1_64/lib/python2.5/site-packages/merlin-1.7.egg
> is being added to sys.path
> from pkg_resources import resource_listdir, resource_isdir,
> resource_exists, resource_filename, Requirement
> /home/jeffremt/tools/cig/gcc-4.1.1_64/lib/python2.5/site-packages/pythia-0.8.1.10-py2.5.egg/pyre/inventory/odb/Curator.py:200:
> UserWarning: Module site was already imported from
> /usr/lib64/python2.5/site.pyc, but
> /home/jeffremt/tools/cig/gcc-4.1.1_64/lib/python2.5/site-packages/merlin-1.7.egg
> is being added to sys.path
> from pkg_resources import resource_listdir, resource_isdir,
> resource_exists, resource_filename, Requirement
> ERROR: An unexpected error occurred while tokenizing input
> The following traceback may be corrupted or invalid
> The error message is: ('EOF in multi-line statement', (12, 0))
>
> ERROR: An unexpected error occurred while tokenizing input
> The following traceback may be corrupted or invalid
> The error message is: ('EOF in multi-line statement', (12, 0))
>
> ERROR: An unexpected error occurred while tokenizing input
> The following traceback may be corrupted or invalid
> The error message is: ('EOF in multi-line statement', (12, 0))
>
> ERROR: An unexpected error occurred while tokenizing input
> The following traceback may be corrupted or invalid
> The error message is: ('EOF in multi-line statement', (12, 0))
>
> ERROR: An unexpected error occurred while tokenizing input
> The following traceback may be corrupted or invalid
> The error message is: ('EOF in multi-line statement', (13, 0))
>
> Error in sys.excepthook:
> Traceback (most recent call last):
> File "/usr/lib/python2.5/site-packages/IPython/ultraTB.py", line 885,
> in __call__
> self.handler((etype, evalue, etb))
> File "/usr/lib/python2.5/site-packages/IPython/ultraTB.py", line 875,
> in handler
> print >> Term.cerr, self.text(etype, evalue, etb)
> File "/usr/lib/python2.5/site-packages/IPython/ultraTB.py", line 931,
> in text
> return VerboseTB.text(self,etype, value, tb,context=5)
> File "/usr/lib/python2.5/site-packages/IPython/ultraTB.py", line 818,
> in text
> __IPYTHON__.hooks.synchronize_with_editor(filepath, lnum, 0)
> NameError: global name '__IPYTHON__' is not defined
>
> Original exception was:
> Traceback (most recent call last):
> File "/home/jeffremt/tools/cig/gcc-4.1.1_64/bin/pylith", line 39, in
> <module>
> start(applicationClass=PyLithApp)
> File
> "/home/jeffremt/tools/cig/gcc-4.1.1_64/lib/python2.5/site-packages/pythia-0.8.1.10-py2.5.egg/pyre/applications/__init__.py",
> line 41, in start
> shell.run(**kwds)
> File
> "/home/jeffremt/tools/cig/gcc-4.1.1_64/lib/python2.5/site-packages/pythia-0.8.1.10-py2.5.egg/pyre/applications/Shell.py",
> line 125, in run
> app.applyConfiguration(context)
> File
> "/home/jeffremt/tools/cig/gcc-4.1.1_64/lib/python2.5/site-packages/pythia-0.8.1.10-py2.5.egg/pyre/inventory/Configurable.py",
> line 74, in applyConfiguration
> context.configureComponent(self)
> File
> "/home/jeffremt/tools/cig/gcc-4.1.1_64/lib/python2.5/site-packages/pythia-0.8.1.10-py2.5.egg/pyre/inventory/ConfigContext.py",
> line 68, in configureComponent
> component.configureComponents(self)
> File
> "/home/jeffremt/tools/cig/gcc-4.1.1_64/lib/python2.5/site-packages/pythia-0.8.1.10-py2.5.egg/pyre/inventory/Configurable.py",
> line 119, in configureComponents
> self.inventory.configureComponents(context)
> File
> "/home/jeffremt/tools/cig/gcc-4.1.1_64/lib/python2.5/site-packages/pythia-0.8.1.10-py2.5.egg/pyre/inventory/Inventory.py",
> line 99, in configureComponents
> component.applyConfiguration(context)
> File
> "/home/jeffremt/tools/cig/gcc-4.1.1_64/lib/python2.5/site-packages/pythia-0.8.1.10-py2.5.egg/pyre/inventory/Configurable.py",
> line 74, in applyConfiguration
> context.configureComponent(self)
> File
> "/home/jeffremt/tools/cig/gcc-4.1.1_64/lib/python2.5/site-packages/pythia-0.8.1.10-py2.5.egg/pyre/inventory/ConfigContext.py",
> line 68, in configureComponent
> component.configureComponents(self)
> File
> "/home/jeffremt/tools/cig/gcc-4.1.1_64/lib/python2.5/site-packages/pythia-0.8.1.10-py2.5.egg/pyre/inventory/Configurable.py",
> line 119, in configureComponents
> self.inventory.configureComponents(context)
> File
> "/home/jeffremt/tools/cig/gcc-4.1.1_64/lib/python2.5/site-packages/pythia-0.8.1.10-py2.5.egg/pyre/inventory/Inventory.py",
> line 99, in configureComponents
> component.applyConfiguration(context)
> File
> "/home/jeffremt/tools/cig/gcc-4.1.1_64/lib/python2.5/site-packages/pythia-0.8.1.10-py2.5.egg/pyre/inventory/Configurable.py",
> line 74, in applyConfiguration
> context.configureComponent(self)
> File
> "/home/jeffremt/tools/cig/gcc-4.1.1_64/lib/python2.5/site-packages/pythia-0.8.1.10-py2.5.egg/pyre/inventory/ConfigContext.py",
> line 68, in configureComponent
> component.configureComponents(self)
> File
> "/home/jeffremt/tools/cig/gcc-4.1.1_64/lib/python2.5/site-packages/pythia-0.8.1.10-py2.5.egg/pyre/inventory/Configurable.py",
> line 119, in configureComponents
> self.inventory.configureComponents(context)
> File
> "/home/jeffremt/tools/cig/gcc-4.1.1_64/lib/python2.5/site-packages/pythia-0.8.1.10-py2.5.egg/pyre/inventory/Inventory.py",
> line 99, in configureComponents
> component.applyConfiguration(context)
> File
> "/home/jeffremt/tools/cig/gcc-4.1.1_64/lib/python2.5/site-packages/pythia-0.8.1.10-py2.5.egg/pyre/inventory/Configurable.py",
> line 74, in applyConfiguration
> context.configureComponent(self)
> File
> "/home/jeffremt/tools/cig/gcc-4.1.1_64/lib/python2.5/site-packages/pythia-0.8.1.10-py2.5.egg/pyre/inventory/ConfigContext.py",
> line 68, in configureComponent
> component.configureComponents(self)
> File
> "/home/jeffremt/tools/cig/gcc-4.1.1_64/lib/python2.5/site-packages/pythia-0.8.1.10-py2.5.egg/pyre/inventory/Configurable.py",
> line 119, in configureComponents
> self.inventory.configureComponents(context)
> File
> "/home/jeffremt/tools/cig/gcc-4.1.1_64/lib/python2.5/site-packages/pythia-0.8.1.10-py2.5.egg/pyre/inventory/Inventory.py",
> line 99, in configureComponents
> component.applyConfiguration(context)
> File
> "/home/jeffremt/tools/cig/gcc-4.1.1_64/lib/python2.5/site-packages/pythia-0.8.1.10-py2.5.egg/pyre/inventory/Configurable.py",
> line 77, in applyConfiguration
> self._configure()
> File
> "/home/jeffremt/tools/cig/gcc-4.1.1_64/lib64/python2.5/site-packages/pylith/meshio/OutputMatElastic.py",
> line 83, in _configure
> OutputManagerMesh._configure(self)
> File
> "/home/jeffremt/tools/cig/gcc-4.1.1_64/lib64/python2.5/site-packages/pylith/meshio/OutputManagerMesh.py",
> line 73, in _configure
> ModuleOutputManager.coordsys(self, self.inventory.coordsys)
> File
> "/home/jeffremt/tools/cig/gcc-4.1.1_64/lib64/python2.5/site-packages/pylith/meshio/meshio.py",
> line 589, in coordsys
> def coordsys(self, *args): return
> _meshio.MeshOutputManager_coordsys(self, *args)
> TypeError: in method 'MeshOutputManager_coordsys', argument 2 of type
> 'spatialdata::geocoords::CoordSys const *'
>
> I've attached the config.log file from my configuration of PyLith just
> in case that's helpful.
>
> Thank you,
> Jeff Thompson
> California Institute of Technology
>
>
>
>
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