[CIG-SHORT] Problems compiling pylith

Fabrizio Pistagna fabrizio.pistagna at gmail.com
Thu Jun 19 06:40:55 PDT 2008


Hi all,i must install pylith on a Scientific Linux CERN SLC release 4.6
(Beryllium) 2.6.9-55.0.6.EL.cern1smp kernel on x86_64 architecture,
boosting four Dual-Core AMD Opteron(tm) Processor 2218.

I followed the "installation from source" chapter from official pylith book,
using MPI implementation mpich-1.2.7 for gcc4 compiler.
.
Here is my configuration in order of installation:
- Python2.5.2
- last petsc-dev from cig site
- nemesis-1.0
- proj-4.6.0
- numpy-1.1.0
- FIAT-0.3.4
- Pyrex-0.9.8.4
- pyrexembed-0.1.1
- spatialdata-0.3.1
- pylith got from svn

I use the last svn trunk revision because of the version 1.1.2 didn't
compile during make operation, due to a reference to an inexisting
member named "restrict" at line 270-271 of source
files bc/AbsorbingDampers.cc:

bc/AbsorbingDampers.cc:270: error: 'class ALE::Mesh' has no member named
'restrict'

All packages were installed with a --prefix custom path, setting right
variable for PETSC_ARCH and PETSC_DIR.
All gone done, but when i run pylith from terminal, it executes and blocks
itself when it try to imports petsc module, here is the stdout:

$ pylith
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File
"/home/fpistagna/B/packages/lib/python2.5/site-packages/pythia-0.8.1.6-py2.5.egg/mpi/__init__.py",
line 42, in mpistart
    kwds = kwds)
  File
"/home/fpistagna/B/packages/lib/python2.5/site-packages/pythia-0.8.1.6-py2.5.egg/pyre/applications/__init__.py",
line 41, in start
    shell.run(**kwds)
  File
"/home/fpistagna/B/packages/lib/python2.5/site-packages/pythia-0.8.1.6-py2.5.egg/pyre/applications/Shell.py",
line 142, in run
    method(*args, **kwds)
  File
"/home/fpistagna/B/packages/lib/python2.5/site-packages/pythia-0.8.1.6-py2.5.egg/pyre/applications/SuperScript.py",
line 49, in execute
    self.main(*args, **kwds)
  File
"/home/fpistagna/B/packages/lib/python2.5/site-packages/pythia-0.8.1.6-py2.5.egg/pyre/applications/SuperScript.py",
line 58, in main
    self.runSubscript(*args, **kwds)
  File
"/home/fpistagna/B/packages/lib/python2.5/site-packages/pythia-0.8.1.6-py2.5.egg/pyre/applications/SuperScript.py",
line 62, in runSubscript
    self.subscript.run(*args, **kwds)
  File
"/home/fpistagna/B/packages/lib/python2.5/site-packages/pythia-0.8.1.6-py2.5.egg/pyre/applications/Application.py",
line 42, in run
    shell.run(*args, **kwds)
  File
"/home/fpistagna/B/packages/lib/python2.5/site-packages/pythia-0.8.1.6-py2.5.egg/pyre/applications/Shell.py",
line 142, in run
    method(*args, **kwds)
  File
"/home/fpistagna/B/packages/lib/python2.5/site-packages/pythia-0.8.1.6-py2.5.egg/mpi/Application.py",
line 118, in _onComputeNodes
    self.onComputeNodes(*args, **kwds)
  File
"/home/fpistagna/B/packages/lib/python2.5/site-packages/pythia-0.8.1.6-py2.5.egg/mpi/Application.py",
line 124, in onComputeNodes
    self.main(*args, **kwds)
  File "/home/fpistagna/B/files/pylith-1.1.2/pylith/PyLithApp.py", line 79,
in main
    self.petsc.initialize()
  File "/home/fpistagna/B/files/pylith-1.1.2/pylith/utils/PetscManager.py",
line 48, in initialize
    import pylith.utils.petsc as bindings
ImportError: No module named petsc
--pyre-start: mpirun: exit 1

Any ideas?
Thanks in advance
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://geodynamics.org/pipermail/cig-short/attachments/20080619/37c53532/attachment.html 


More information about the CIG-SHORT mailing list