Memory error
Jamie Mitchell
jamiemitchell1604 at gmail.com
Mon Mar 24 07:39:47 EDT 2014
On Monday, March 24, 2014 11:32:31 AM UTC, Jamie Mitchell wrote:
> Hello all,
>
>
>
> I'm afraid I am new to all this so bear with me...
>
>
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> I am looking to find the statistical significance between two large netCDF data sets.
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>
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> Firstly I've loaded the two files into python:
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>
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> swh=netCDF4.Dataset('/data/cr1/jmitchel/Q0/swh/controlperiod/averages/swh_control_concat.nc', 'r')
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>
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> swh_2050s=netCDF4.Dataset('/data/cr1/jmitchel/Q0/swh/2050s/averages/swh_2050s_concat.nc', 'r')
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>
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> I have then isolated the variables I want to perform the pearson correlation on:
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>
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> hs=swh.variables['hs']
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> hs_2050s=swh_2050s.variables['hs']
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> Here is the metadata for those files:
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>
>
> print hs
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> <type 'netCDF4.Variable'>
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> int16 hs(time, latitude, longitude)
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> standard_name: significant_height_of_wind_and_swell_waves
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> long_name: significant_wave_height
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> units: m
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> add_offset: 0.0
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> scale_factor: 0.002
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> _FillValue: -32767
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> missing_value: -32767
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> unlimited dimensions: time
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> current shape = (86400, 350, 227)
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>
>
> print hs_2050s
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> <type 'netCDF4.Variable'>
>
> int16 hs(time, latitude, longitude)
>
> standard_name: significant_height_of_wind_and_swell_waves
>
> long_name: significant_wave_height
>
> units: m
>
> add_offset: 0.0
>
> scale_factor: 0.002
>
> _FillValue: -32767
>
> missing_value: -32767
>
> unlimited dimensions: time
>
> current shape = (86400, 350, 227)
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>
>
>
>
> Then to perform the pearsons correlation:
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> from scipy.stats.stats import pearsonr
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> pearsonr(hs,hs_2050s)
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> I then get a memory error:
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> Traceback (most recent call last):
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> File "<stdin>", line 1, in <module>
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> File "/usr/local/sci/lib/python2.7/site-packages/scipy/stats/stats.py", line 2409, in pearsonr
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> x = np.asarray(x)
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> File "/usr/local/sci/lib/python2.7/site-packages/numpy/core/numeric.py", line 321, in asarray
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> return array(a, dtype, copy=False, order=order)
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> MemoryError
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> This also happens when I try to create numpy arrays from the data.
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>
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> Does anyone know how I can alleviate theses memory errors?
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> Cheers,
>
>
>
> Jamie
Just realised that obviously pearson correlation requires two 1D arrays and mine are 3D, silly mistake!
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