[MMTK] netcdf problem

Konrad Hinsen research at khinsen.fastmail.net
Fri Sep 18 07:35:59 UTC 2009

On 17 Sep 2009, at 23:39, Ramgopal Mettu wrote:

>  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 installed netCDF 4.0.1 from the sources, without the HDF5 options.  
On another machine, I used netCDF from a MacPorts install. Both  
installations worked fine at first try.

> 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

Is this indeed a complete and working netCDF installation? One  
restriction of the ScientificPython installation script is that it  
assumed that there is a single working netCDF installation on the  
computer. If you install and de-install several versions, it can pick  
up the header files for an incomplete one.

> /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ 
> distutils/dist.py:263: UserWarning: Unknown distribution option:  
> 'options'

That is indeed harmless.

> >>> 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

This looks like an incomplete build/install run. I suggest removing  
the build directory (rm -rf build) in the ScientificPython directory  
to re-run the installation from scratch.  If it completes without any  
error message, it should say at some point that it copied  
Scientific_netcdf.so somewhere. That "somewhere" should be /Library/ 
Frameworks/Python.framework/... and should be on Python's search path.

Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research at  khinsen dot fastmail dot net

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