Hi All,
I keep receiving a memory error when processing many netcdf files. I assumed
it had something to do with how I loop things and maybe needed to close
things off properly but I recently received an error that made me think it
might be because of matplotlib.
In the code below I am looping through a bunch of netcdf files (each file is
hourly data for one month) and within each netcdf file I am outputting a
*png file every three hours. This works for one netcdf file (therefore one
month) but when it begins to process the next netcdf file I receive a memory
error (see below). Since I have tidied some of my code up it seems to
process partly into the second file but then I still receive the memory
error.
I have tried a few suggestions such as:
-Combining the dataset using MFDataset (using NETCDF4) is not an option
because the files do not have unlimited dimension.
- gc.collect() but that just results in a *GEOS_ERROR: bad allocation error*.
-only open LAT and LON once (which worked)
System Details:
Python 2.7.2 |EPD 7.1-2 (32-bit)| (default, Jul 3 2011, 15:13:59) [MSC
v.1500 32 bit (Intel)] on win32
Any feedback will be greatly appreciated as I seem to keep ending up with
memory errors when working with netcdf files this even happens if I am using
a much better computer.
*Most recent error: *
Traceback (most recent call last):
File "C:\plot_netcdf_merc_multiplot_across_multifolders_TSFC.py", line 78,
in <module>
plt.savefig((os.path.join(outputfolder, 'TSFC'+date_string+'UTC.png')))
File "C:\Python27\lib\site-packages\matplotlib\pyplot.py", line 363, in
savefig
return fig.savefig(*args, **kwargs)
File "C:\Python27\lib\site-packages\matplotlib\figure.py", line 1084, in
savefig
self.canvas.print_figure(*args, **kwargs)
File "C:\Python27\lib\site-packages\matplotlib\backends\backend_wxagg.py",
line 100, in print_figure
FigureCanvasAgg.print_figure(self, filename, *args, **kwargs)
File "C:\Python27\lib\site-packages\matplotlib\backend_bases.py", line
1923, in print_figure
**kwargs)
File "C:\Python27\lib\site-packages\matplotlib\backends\backend_agg.py",
line 438, in print_png
FigureCanvasAgg.draw(self)
File "C:\Python27\lib\site-packages\matplotlib\backends\backend_agg.py",
line 393, in draw
self.renderer = self.get_renderer()
File "C:\Python27\lib\site-packages\matplotlib\backends\backend_agg.py",
line 404, in get_renderer
self.renderer = RendererAgg(w, h, self.figure.dpi)
File "C:\Python27\lib\site-packages\matplotlib\backends\backend_agg.py",
line 59, in __init__
self._renderer = _RendererAgg(int(width), int(height), dpi, debug=False)
RuntimeError: Could not allocate memory for image
*Error when I added gc.collect()*
GEOS_ERROR: bad allocation
*Old error (before adding gc.collect() )*
*Traceback (most recent call last):
File "d:/plot_netcdf_merc_multiplot_across_multifolders__memoryerror.py",
line 44, in <module>
TSFC=ncfile.variables['T_SFC'][1::3]
File "netCDF4.pyx", line 2473, in netCDF4.Variable.__getitem__
(netCDF4.c:23094)
MemoryError*
from netCDF4 import Dataset
import numpy as N
import matplotlib.pyplot as plt
from mpl_toolkits.basemap import Basemap
from netcdftime import utime
from datetime import datetime
import os
import gc
shapefile1="E:/
>
> griddeddatasamples/GIS/DSE_REGIONS"
> MainFolder=r"E:/griddeddatasamples/GriddedData/InputsforValidation/T_SFC/"
> OutputFolder=r"E:/griddeddatasamples/GriddedData/OutputsforValidation"
> fileforlatlon=Dataset("E:/griddeddatasamples/GriddedData/InputsforValidation/T_SFC/TSFC_1974_01/IDZ00026_VIC_ADFD_T_SFC.nc",
> 'r+', 'NETCDF4')
> LAT=fileforlatlon.variables['latitude'][:]
> LON=fileforlatlon.variables['longitude'][:]
>
> for (path, dirs, files) in os.walk(MainFolder):
> for dir in dirs:
> print dir
> path=path+'/'
> for ncfile in files:
> if ncfile[-3:]=='.nc':
> print "dealing with ncfiles:", ncfile
> ncfile=os.path.join(path,ncfile)
> ncfile=Dataset(ncfile, 'r+', 'NETCDF4')
> TSFC=ncfile.variables['T_SFC'][1::3]
> TIME=ncfile.variables['time'][1::3]
> ncfile.close()
> gc.collect()
>
> for TSFC, TIME in zip((TSFC[:]),(TIME[:])):
> cdftime=utime('seconds since 1970-01-01 00:00:00')
> ncfiletime=cdftime.num2date(TIME)
> print ncfiletime
> timestr=str(ncfiletime)
> d = datetime.strptime(timestr, '%Y-%m-%d %H:%M:%S')
> date_string = d.strftime('%Y%m%d_%H%M')
>
> map =
> Basemap(projection='merc',llcrnrlat=-40,urcrnrlat=-33,
>
> llcrnrlon=139.0,urcrnrlon=151.0,lat_ts=0,resolution='i')
> x,y=map(*N.meshgrid(LON,LAT))
> map.drawcoastlines(linewidth=0.5)
> map.readshapefile(shapefile1, 'DSE_REGIONS')
> map.drawstates()
>
> plt.title('Surface temperature at %s UTC'%ncfiletime)
> ticks=[-5,0,5,10,15,20,25,30,35,40,45,50]
> CS = map.contourf(x,y,TSFC, ticks, cmap=plt.cm.jet)
> l,b,w,h =0.1,0.1,0.8,0.8
> cax = plt.axes([l+w+0.025, b, 0.025, h], )
> cbar=plt.colorbar(CS, cax=cax, drawedges=True)
>
> plt.savefig((os.path.join(OutputFolder,
> 'TSFC'+date_string+'UTC.png')))
> plt.close()
> gc.collect()
>
>
>
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