Jun-16-2019, 02:30 PM
I've posted a similar question to stackoverflow but unfortunately didn't get any answers there. Maybe this is a more python-specific issue and I'll get some information here.
I got some dataset where I have a bunch of large files (~100) and I want to extract specific lines from those files very efficiently (both in memory and in speed).
My code gets a list of relevant files, the code opens each file with [line 1], then maps the file to memory with [line 2], also, for each file I receives a list of indices and going over the indices I retrieve the relevant information (10 bytes for this example) like so: [line 3-4], finally I close the handles with [line 5-6].
Now to the problem - The code runs well when I limit the indices to be small (meaning - when I ask the code to get information from the beginning of the file). But! when I increase the range of the indices, everything slows down to (almost) a halt AND the buff/cache memory gets full (I'm not sure if the memory issue is related to the slowdown).
So my question is why does it matter if I retrieve information from the beginning or the end of the file and how do I overcome this in order to get instant access to information from the end of the file without slowing down and increasing buff/cache memory use.
PS - some numbers and sizes: so I got ~100 files each about 1GB in size, when I limit the indices to be from the 0%-10% of the file it runs fine, but when I allow the index to be anywhere in the file it stops working.
I got some dataset where I have a bunch of large files (~100) and I want to extract specific lines from those files very efficiently (both in memory and in speed).
My code gets a list of relevant files, the code opens each file with [line 1], then maps the file to memory with [line 2], also, for each file I receives a list of indices and going over the indices I retrieve the relevant information (10 bytes for this example) like so: [line 3-4], finally I close the handles with [line 5-6].
binaryFile = open(path, "r+b") binaryFile_mm = mmap.mmap(binaryFile.fileno(), 0) for INDEX in INDEXES: information = binaryFile_mm[(INDEX):(INDEX)+10].decode("utf-8") binaryFile_mm.close() binaryFile.close()This codes runs in parallel, with thousands of indices for each file, and continuously do that several times a second for hours.
Now to the problem - The code runs well when I limit the indices to be small (meaning - when I ask the code to get information from the beginning of the file). But! when I increase the range of the indices, everything slows down to (almost) a halt AND the buff/cache memory gets full (I'm not sure if the memory issue is related to the slowdown).
So my question is why does it matter if I retrieve information from the beginning or the end of the file and how do I overcome this in order to get instant access to information from the end of the file without slowing down and increasing buff/cache memory use.
PS - some numbers and sizes: so I got ~100 files each about 1GB in size, when I limit the indices to be from the 0%-10% of the file it runs fine, but when I allow the index to be anywhere in the file it stops working.