finding duplicate files
This post is about my duplicate finding program available under programs. The program is a little bare, and needs a nicer API, but the method it uses is the most efficient one that I am aware of.
There are a couple of different ways you can find duplicate files:
Compute the hash of all the files, and look for duplicates
This method works well if the files on disk are mostly static, and files are added infrequently. In this case you can compute the hashes once, and keep it around for later scans. However, if you are only running the scan once, this method is not ideal since it requires you to read the full contents of every file
Compute the hash of files with the same size
This is the method that I think fdupes still uses. It first builds a candidate list of files that are the same size, and computes the checksum of each. This method works well if most of the files that are the same size are really duplicates, but otherwise triggers too much unneeded IO.
Compare all files with the same size in parallel
This is the method that my program uses. Like fdupes, I first built up a candidate list of files with the same size. Instead of hashing the files, it simply reads each file at the same time, comparing block by block. This is just like what the cmp(1) program does, but for multiple files at the same time. The benefit of this over calculating the files hash, is that as soon as the files differ, you can stop reading.
There are a couple of things you need to keep in mind to implement this method.
Don't open too many files.
You have to be careful not to try and open too many files at once. If the user has 5,000 files that all have the same size, the program shouldn't try and open all 5,000 at once. My program uses a simple helper class to handle opening and closing files. The default blocksize in my program would probably waste a bit of memory in this case, but that is easily changed.
Correctly handle diverging sets.
Imagine the filesystem contains 4 files of the same size, 'a', 'b','c', and 'd', where a==c, and b==d. While reading through the files, it will become clear that a!=b, a==c, and a!=d. It is important that at this step the program continues searching using (a,c) and (b,d) as possible duplicates. This is implemented using recursion, the sets (a,c) and (b,d) are fed back into the duplicate finding function.
Example run, compared to fdupes.
Here is dupes.py running against fdupes on a modestly sized directory. Notice how dupes.py only needs to read 600K(not counting metadata).
According to iofileb.d from the dtrace toolkit, dupes.py reads 10M of data (which I think includes python), and fdupes reads 517M. This alone explains the 20x speedup seen in dupes.py
justin@pip:~$ du -hs $DIR 15G $DIR justin@pip:~$ time python code/dupes.py $DIR 2896 total files 35 size collisions, max of length 5 bytes read 647168 real 0m1.224s user 0m0.234s sys 0m0.494s justin@pip:~$ time fdupes -r $DIR real 0m41.694s user 0m13.612s sys 0m7.491s justin@pip:~$ time python code/dupes.py $DIR 2896 total files 35 size collisions, max of length 5 bytes read 647168 real 0m3.662s user 0m0.256s sys 0m0.568s justin@pip:~$ time fdupes -r $DIR real 0m55.473s user 0m11.383s sys 0m6.433s
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