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
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
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()