fast md5sum on millions of strings in bash/ubuntu

Question

I need the MD5 sums of 3 million strings or so in a bash script on ubuntu. 3 million strings -> 3 million MD5 hashes. The trivial implementation takes about 0.005sec per string. That's over 4 hours. What faster alternatives exist? Is there a way to pump groups of strings into md5sum?

#time md5sum running 100 times on short strings
#each iteration is ~0.494s/100 = 0.005s
time (for i in {0..99}; do md5sum <(echo $i); done) > /dev/null

real    0m0.494s
user    0m0.120s
sys     0m0.356s

A good solution will include a bash/Perl script that takes a list of strings from stdin and outputs a list of their MD5 hashes.

Answer 1

It's not hard to do in C (or Perl or Python) using any of the many md5 implementations -- at its heart md5 is a hash function that goes from a character vector to a character vector.

So just write a outer program that reads your 3 million strings, and then feed them one by one to the md5 implementation of your choice. That way you have one program startup rather than 3 million, and that alone will save you time.

FWIW in one project I used the md5 implementation (in C) by Christophe Devine, there is OpenSSL's as well and I am sure CPAN will have a number of them for Perl too.

Edit: Ok, couldn't resist. The md5 implementation I mentioned is e.g. inside this small tarball. Take the file md5.c and replace the (#ifdef'ed out) main() at the bottom with this

int main( int argc, char *argv[] ) {
    FILE *f;
    int j;
    md5_context ctx;
    unsigned char buf[1000];
    unsigned char md5sum[16];

    if( ! ( f = fopen( argv[1], "rb" ) ) ) {
        perror( "fopen" );
        return( 1 );
    }

    while( fscanf(f, "%s", buf) == 1 ) {
        md5_starts( &ctx );
        md5_update( &ctx, buf, (uint32) strlen((char*)buf) );
        md5_finish( &ctx, md5sum );

        for( j = 0; j < 16; j++ ) {
            printf( "%02x", md5sum[j] );
        }
        printf( " <- %s\n", buf );
    }
    return( 0 );
}

build a simple standalone program as e.g. in

/tmp$ gcc -Wall -O3 -o simple_md5 simple_md5.c

and then you get this:

# first, generate 300,000 numbers in a file (using 'little r', an R variant)
/tmp$ r -e'for (i in 1:300000) cat(i,"\n")' > foo.txt

# illustrate the output
/tmp$ ./simple_md5 foo.txt | head
c4ca4238a0b923820dcc509a6f75849b <- 1
c81e728d9d4c2f636f067f89cc14862c <- 2
eccbc87e4b5ce2fe28308fd9f2a7baf3 <- 3
a87ff679a2f3e71d9181a67b7542122c <- 4
e4da3b7fbbce2345d7772b0674a318d5 <- 5
1679091c5a880faf6fb5e6087eb1b2dc <- 6
8f14e45fceea167a5a36dedd4bea2543 <- 7
c9f0f895fb98ab9159f51fd0297e236d <- 8
45c48cce2e2d7fbdea1afc51c7c6ad26 <- 9
d3d9446802a44259755d38e6d163e820 <- 10

# let the program rip over it, suppressing stdout
/tmp$ time (./simple_md5 foo.txt > /dev/null)

real    0m1.023s
user    0m1.008s
sys     0m0.012s
/tmp$

So that's about a second for 300,000 (short) strings.