Problem installing the netCDF4 module with Python 2.7

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Problem installing the netCDF4 module with Python 2.7

Postby Albert » Tue Nov 26, 2013 5:20 am

Hello. I am starting a new part-time job, and I have to program in Python (I have done a lot of previous scientific programming, mainly in C and Matlab, but I am not a computer scientist). My employer wants me to use version 2 so I have installed Python 2.7. I also need to get the netCDF4 module working. I have some large data files to analyze. I can open these and analyze them in Matlab with no problems at all, so the data files themselves are all OK. I am using my home laptop with Windows 7 installed.

So: what I did is this. I downloaded and installed the 32 bit numpy and netCDF4 packages for Python 2.7 (specifically, numpy-1.8.0-win32-superpack-python2.7 and netCDF4-1.0.7.win32-py2.7). The installation seemed to be successful, and if I type "import numpy" and "import netCDF4" in python it doesn't complain about anything. However, when I run the following short piece of code, I get an error, not in my code, but in the netCDF4.pyx code (I'll post the error below). Here is my code:

Code: Select all
import numpy
from netCDF4 import Dataset

def main():

    dataset = Dataset(infilename)
    kelvin = dataset.variables['tos'][0]
    sst = kelvin - 273.15
    time = dataset.variables['time']
    lat = dataset.variables['latitude']
    lon = dataset.variables['longitude']
    num_months = len(time)
    print 'Loaded %d months of sst' % num_months


Here is the error I get:

Code: Select all
Traceback (most recent call last):
  File "C:\Albert\Python\", line 22, in <module>
  File "C:\Albert\Python\", line 19, in main
    num_months = len(time)
  File "netCDF4.pyx", line 3070, in netCDF4.Variable.__len__ (netCDF4.c:38796)
  File "netCDF4.pyx", line 2485, in netCDF4.Variable.shape.__get__ (netCDF4.c:30870)
  File "netCDF4.pyx", line 2456, in netCDF4.Variable._getdims (netCDF4.c:30508)
RuntimeError: NetCDF: Not a valid ID

I had a read of the docs, and the only thing I could find that might be the problem is that I might need to install the netCDF4 C libraries. So I got the binaries file netCDF4.3.0-NC4-DAP-32 and installed it. It seems to have installed perfectly; but I still get the same error message. I have looked on the internet as best I can and cannot find any help. If anyone out there can help me, I would greatly appreciate it!

Last edited by micseydel on Tue Nov 26, 2013 7:30 am, edited 1 time in total.
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Re: Problem installing the netCDF4 module with Python 2.7

Postby stranac » Tue Nov 26, 2013 10:34 am

Based on some google searching, I think that the problem is with your trying to get len(time) after dataset was closed.
Try putting that line before dataset.close()
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Re: Problem installing the netCDF4 module with Python 2.7

Postby Albert » Wed Nov 27, 2013 12:43 am

Thanks stranac! That worked perfectly! I really appreciate your help. I'm completely new to Python, so my apologies for my ignorance! :D
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