Meridian Discovery has a great step by step guide on how to use the md5deep utility to compare hash values in two sets of files. See the instructions on this web page: http://www.meridiandiscovery.com/how-to/validating-copy-results-using-md5deep/ . Meridian's instructions are excellent, but I'll provide a quick summary of them:
1. We begin by downloading md5deep from this site. , and copying the md5deep.exe file to this folder, C:\Windows\System32 , assuming you're running Windows 7. On the github site, click on the releases tab and then choose md5deep-4.4.zip. If you have a 64 bit OS, use md5deep64.exe instead of md5deep.exe
2. Press Ctrl + SHIFT, plus right click in a folder which contains your original set of files. Enter the command
md5deep -rel * > “C:\Temp\InputHashes.md5”
OR if you're using a 64 bit OS:
md5deep64 -rel * > “C:\Temp\InputHashes.md5”
3. Then presss Ctrl + SHIFT, plus right click inside a folder which contains the copy of the original set of files. As noted on the Meridian site, you enter this command:
md5deep -rel * > “C:\Temp\OutputHashes.md5”
The two files that are generated by these commands are simply lists of MD5 hash values on the left, with the corresponding file names on the right.
4. Now, as explained by Meridian, you enter two commands to generate hash values for the files which contain the lists of hash values, and put the two new hash values in a single text file. If there is any difference, it's a sign that the two data sets are not identical.
md5deep “C:\Temp\InputHashes.md5” > “C:\Temp\Comparison.txt”
md5deep “C:\Temp\OutputHashes.md5” >> “C:\Temp\Comparison.txt”