[Numpy-discussion] Reading a big netcdf file

Gökhan Sever gokhansever@gmail....
Wed Aug 3 15:57:19 CDT 2011


This is what I get here:

In [1]: a = np.zeros((21601, 10801), dtype=np.uint16)

In [2]: a.tofile('temp.npa')

In [3]: del a

In [4]: timeit a = np.fromfile('temp.npa', dtype=np.uint16)
1 loops, best of 3: 251 ms per loop


On Wed, Aug 3, 2011 at 10:50 AM, Christopher Barker
<Chris.Barker@noaa.gov>wrote:

> On 8/3/11 9:30 AM, Kiko wrote:
> > I'm trying to read a big netcdf file (445 Mb) using netcdf4-python.
>
> I've never noticed that netCDF4 was particularly slow for reading
> (writing can be pretty slow some times). How slow is slow?
>
> > The data are described as:
>
> please post the results of:
>
> ncdump -h the_file_name.nc
>
> So we can see if there is anything odd in the structure (though I don't
> know what it might be)
>
> Post your code (in the simnd pplest form you can).
>
> and post your timings and machine type
>
> Is the file netcdf4 or 3 format? (the python lib will read either)
>
> As a reference, reading that much data in from a raw file into a numpy
> array takes 2.57 on my machine (a rather old Mac, but disks haven't
> gotten much  faster). YOu can test that like this:
>
> a = np.zeros((21601, 10801), dtype=np.uint16)
>
> a.tofile('temp.npa')
>
> del a
>
> timeit a = np.fromfile('temp.npa', dtype=np.uint16)
>
> (using ipython's timeit)
>
> -Chris
>
>
>
> --
> Christopher Barker, Ph.D.
> Oceanographer
>
> Emergency Response Division
> NOAA/NOS/OR&R            (206) 526-6959   voice
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>
> Chris.Barker@noaa.gov
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>



-- 
Gökhan
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