Here's a non-Perl variant.

In directory 1, run

$ find . -type f -print0 | xargs -0 md5sum >checksums
[download]

to create a list of checksums.  Then, form within directory 2, verify the list of checksums

$ md5sum -c checksums 2>&1 | grep -q FAILED\$ && echo FAIL
[download]

(The advantage of using the checksumming technique is that the directories don't need to be accessible from the same machine (as a direct block-by-block comparison would require). You only need to copy the checksums file.)

This assumes that directory 2 isn't a subdirectory of directory 1.  Also, you haven't specified what is supposed to happen, if there are additional files in directory 2, which are not present in directory 1  (they would be ignored by this approach).

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