Hi,
I'm trying to manually parse a dataset stored in a file. The data should be
converted into Python objects.
Here is an example of a single line of a (small) dataset:
3 13 17 19 -626177023 -1688330994 -834622062 -409108332 297174549 955187488
589884464 -1547848504 857311165 585616830 -749910209 194940864 -1102778558
-1282985276 -1220931512 792256075 -340699912 1496177106 1760327384
-1068195107 95705193 1286147818 -416474772 745439854 1932457456 -1266423822
-1150051085 1359928308 129778935 1235905400 532121853
The first integer specifies the length of a tuple object. In this case, the
tuple has three element: (13, 17, 19)
The other values (-626177023 to 532121853) are elements of a Set.
I use the following code to process a file:
from time import time
from sets import Set
from string import split
file = 'pathtable_ht.dat'
result = []
start_time = time ()
f=open(file,'r')
for line in f:
splitres = line.split()
tuple_size = int(splitres[0])+1
path_tuple = tuple(splitres[1:tuple_size])
conflicts = Set(map(int,splitres[tuple_size:-1]))
# do something with 'path_tuple' and 'conflicts'
# ... do some processing ...
result.append(( path_tuple, conflicts))
f.close()
print time() - start_time
The elements (integer objects) in these Sets are being shared between the
sets, in fact, there are as many distinct element as there are lines in the
file (eg 1000 lines -> 1000 distinct set elements). AFAIK, the elements are
stored only once and each Set contains a pointer to the actual object
This works fine with relatively small datasets, but it doesn't work at all
with large datasets (4500 lines, 45000 chars per line).
After a few seconds of loading, all main memory is consumed by the Python
process and the computer starts swapping. After a few more seconds, CPU
usage drops from 99% to 1% and all swap memory is consumed:
Mem: 386540k total, 380848k used, 4692k free, 796k buffers
Swap: 562232k total, 562232k used, 0k free, 27416k cached
At this point, my computer becomes unusable.
I'd like to know if I should buy some more memory (a few GB?) or if it is
possible to make my code more memory efficient.
Thanks in advance,
Stan.
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