To further your cause for information, it might help if you showed Perl/Digest::MD5 and md5sum producing different results. Eg. c&p the shell output.

That would show which combination is producing the wrong results.

Given sisyphus' recent problems with using integers on 64-bit platforms, one possibility is the conversion of the 128-bit integer to hex there has issues.

Another possibility is that you aren't binmodeing the file before reading it. A more common mistake on win32, but with the advent of unicode, maybe that is affecting the results?

Example: The first perl command doesn't binmode the file, the second does:

C:\test>perl -MDigest::MD5=md5_hex 
-wle"print md5_hex( do{local $/; <> } )" 1Mx4096.db
22502b12bc292ae0a0aa1f4a33942662

C:\test>perl -MDigest::MD5=md5_hex 
-wle"open I, '<:raw', $ARGV[ 0 ]; print md5_hex(do{local $/; <I>})" 1M
+x4096.db
66bff1dfd44db7d4402171056d494b2d

C:\test>md5sum 1Mx4096.db
66bff1dfd44db7d4402171056d494b2d *1Mx4096.db
[download]

Update: As ikegami alludes to below, in the light of Using ":raw" layer in open() vs. calling binmode(), whether it's broken documentation or a bug in PerlIO, it seems that you need '<:raw:perlio' to achieve the same as binmode via open, which is important if performance is a consideration.