Here’s a small script to compare the files in two different directories on a Linux machine. The script uses MD5 checksum to compare the files.

#!/bin/bash
prefix1="/usr/directory1" # First directory without trailing /
prefix2="/usr/directory2" # Second directory without trailing /

find -L "$prefix1" -type f | while read -r filename; do
    name="${filename#$prefix1}"
    sum1="$(md5sum -b "$prefix1$name")"
    sum2="$(md5sum -b "$prefix2$name")"
    if [ "${sum1% *}" = "${sum2% *}" ]; then
        echo "ok: $prefix1$name"
    else
        echo "not ok: $prefix1$name"
    fi
done