Hi Python Tutor,
I keep receiving a memory error when processing many netcdf files. I assume
it has something to do with how I loop things and maybe need to close things
off properly.???
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.
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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