[MMTK] netcdf problem

Ramgopal Mettu mettu at ecs.umass.edu
Thu Sep 17 21:39:30 UTC 2009


Hi All,
   I sent the message below earlier and with Konrad's help I think I  
have localized the problem to my NetCDF installation. For those of you  
running MMTK on OSX (10.5.), how did you install NetCDF so that it  
works correctly with the Scientific Python package? Is there perhaps  
dependency of some kind I am missing? I have tried NetCDF 3.6.3 and  
4.0 compiled without HDF to no avail. NetCDF binaries also do not  
work... The install script for Scientific runs without any major  
errors, although I do get this (seemingly) minor one:

[storyville:~/downloads/ScientificPython-2.9.0] ram% sudo python  
setup.py install
Password:
Using netCDF installation in  /usr/local/netcdf
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ 
distutils/dist.py:263: UserWarning: Unknown distribution option:  
'options'
   warnings.warn(msg)
running install
running build
running build_py
running build_ext
running build_scripts
running install_lib
...
running install_egg_info
Writing /Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/ScientificPython-2.9.0-py2.5.egg-info

Below is the error I encounter after installing Scientific when I try  
to import NetCDF:

[storyville:~/downloads/ScientificPython-2.9.0] ram% python
Python 2.5.4 (r254:67917, Dec 23 2008, 14:57:27)
[GCC 4.0.1 (Apple Computer, Inc. build 5363)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
 >>> from Scientific.IO
   File "<stdin>", line 1
     from Scientific.IO
                      ^
SyntaxError: invalid syntax
 >>> from Scientific.IO import NetCDF
Traceback (most recent call last):
   File "<stdin>", line 1, in <module>
   File "Scientific/IO/NetCDF.py", line 169, in <module>
     from Scientific_netcdf import *
ImportError: No module named Scientific_netcdf
 >>> exit()


On Sep 17, 2009, at 11:00 AM, Ramgopal Mettu wrote:

> 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,  
> TrajectoryOutput
>  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/lib/python2.5/site-packages/Scientific/darwin/ 
> Scientific_netcdf.so, 2): Symbol not found: _H5P_CLS_FILE_ACCESS_g
>  Referenced from: /Library/Frameworks/Python.framework/Versions/2.5/ 
> lib/python2.5/site-packages/Scientific/darwin/Scientific_netcdf.so
>  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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