[MMTK] netcdf problem

Ramgopal Mettu mettu at ecs.umass.edu
Thu Sep 17 15:00:51 UTC 2009

Hi All,
   I have recently installed MMTK 2.6 (with Scientific 2.8, running  
Python 2.5.2). The installation runs without errors, but when I  
attempt to run one of the Example scripts (e.g. Proteins/rotamers.py)  
I get the following error:

[gargantua:MMTK-2.6.0/Examples/Proteins] mettu% python rotamers.py
Traceback (most recent call last):
   File "rotamers.py", line 6, in <module>
     from MMTK.Trajectory import Trajectory, SnapshotGenerator,  
   File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/MMTK/Trajectory.py", line 24, in <module>
     "because the netCDF module is missing.")
MMTK.Utility.MMTKError: Trajectories are not available because the  
netCDF module is missing.
[gargantua:MMTK-2.6.0/Examples/Proteins] mettu%

When just trying to load NetCDF in python, I get the following error:

[gargantua:~] mettu% python
Python 2.5.2 (r252:60911, Feb 22 2008, 07:57:53)
[GCC 4.0.1 (Apple Computer, Inc. build 5363)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
 >>> import MMTK
 >>> from Scientific.IO import NetCDF
Traceback (most recent call last):
   File "<stdin>", line 1, in <module>
   File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/Scientific/IO/NetCDF.py", line 165, in <module>
     from Scientific_netcdf import *
ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/2.5/ 
2): Symbol not found: _H5P_CLS_FILE_ACCESS_g
   Referenced from: /Library/Frameworks/Python.framework/Versions/2.5/ 
   Expected in: dynamic lookup

 >>> quit()

I have installed netcdf v4.0.1 using binaries for OSX and the install  
scripts for Scientific run fine (I set the NETCDF_PATH and get no  
errors). Is there a particular version of NetCDF that Scientific  
expects?? Thanks for your help!

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