Fast string search in a very large file

Question

What is the fastest method for searching lines in a file containing a string. I have a file containing strings to search. This small file (smallF) contains about 50,000 lines and looks like:

stringToSearch1
stringToSearch2
stringToSearch3

I have to search all of these strings in a larger file (about 100 million lines). If any line in this larger file contains the search string the line is printed.

The best method I have come up with so far is

grep -F -f smallF largeF

But this is not very fast. With just 100 search strings in smallF it takes about 4 minutes. For over 50,000 search strings it will take a lot of time.

Is there a more efficient method?

Answer 1

I once noticed that using -E or multiple -e parameters is faster than using -f. Note that this might not be applicable for your problem as you are searching for 50,000 string in a larger file. However I wanted to show you what can be done and what might be worth testing:

Here is what I noticed in detail:

Have 1.2GB file filled with random strings.

>ls -has | grep string
1,2G strings.txt

>head strings.txt
Mfzd0sf7RA664UVrBHK44cSQpLRKT6J0
Uk218A8GKRdAVOZLIykVc0b2RH1ayfAy
BmuCCPJaQGhFTIutGpVG86tlanW8c9Pa
etrulbGONKT3pact1SHg2ipcCr7TZ9jc
.....

Now I want to search for strings "ab", "cd" and "ef" using different grep approaches:

1. Using grep without flags, search one at a time:

    grep "ab" strings.txt > m1.out  
    2,76s user 0,42s system 96% cpu 3,313 total
    
    grep "cd" strings.txt >> m1.out  
    2,82s user 0,36s system 95% cpu 3,322 total
    
    grep "ef" strings.txt >> m1.out  
    2,78s user 0,36s system 94% cpu 3,360 total

So in total the search takes nearly 10 seconds.

2. Using grep with -f flag with search strings in search.txt

    >cat search.txt
     ab
     cd
     ef
   
    >grep -F -f search.txt strings.txt > m2.out  
    31,55s user 0,60s system 99% cpu 32,343 total
   

For some reasons this takes nearly 32 seconds.

3. Now using multiple search patterns with -e

    grep -E "ab|cd|ef" strings.txt > m3.out  
    3,80s user 0,36s system 98% cpu 4,220 total
   

   or

    grep --color=auto -e "ab" -e "cd" -e "ef" strings.txt > /dev/null  
    3,86s user 0,38s system 98% cpu 4,323 total
   

The third methode using -E only took 4.22 seconds to search through the file.

Now lets check if the results are the same:

cat m1.out | sort | uniq > m1.sort  
cat m3.out | sort | uniq > m3.sort
diff m1.sort m3.sort
#

The diff produces no output, which means the found results are the same.

Maybe want to give it a try, otherwise I would advise you to look at the thread "Fastest possible grep", see comment from Cyrus.

Answer 2

You may want to try sift or ag. Sift in particular lists some pretty impressive benchmarks versus grep.

Answer 3

Note: I realise the following is not a bash based solution, but given your large search space, a parallel solution is warranted.

---

If your machine has more than one core/processor, you could call the following function in Pythran, to parallelize the search:

#!/usr/bin/env python

#pythran export search_in_file(string, string)
def search_in_file(long_file_path, short_file_path):
    _long = open(long_file_path, "r")

    #omp parallel for schedule(guided)
    for _string in open(short_file_path, "r"):
        if _string in _long:
            print(_string)

if __name__ == "__main__":
    search_in_file("long_file_path", "short_file_path")

Note: Behind the scenes, Pythran takes Python code and attempt to aggressively compile it into very fast C++.