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Firstly, I did perform a search on this problem in these forums, but didn't quite get what I was looking for. So I hope I don't yelled at for making a duplicate post.
So I used rsync to backup my webroot to another nix machine. du -hs gave me 1.3 G on the source machine and 1.1 G on the backup machine. I tried to compare the individual files and noticed a trend. The files on backup machine were always smaller than the files on source machine.
The source uses SATA drive, destination uses IDE. So this time I rsynced locally to another folder on the source machine. Same size anomaly. So i did a simple cp file ~/file and same size anomaly. So it's not a rsync issue.
I took a file and ran md5sum on both, the source file and destination file. To my surprise, even though the file size was different, they had the same md5sum.
Now, let it be known that the source machine is a production server and the dir i rsynced was being used, serving pages to the web. I googled about this and came up with stuff like open descriptors and holes. I don't understand this stuff and was wondering if this was really the case. What are those if it is the case? And my backup copy is 100% identical right? There are thousands of files and I ran md5sum only on couple. Can I take comfort that when time comes, I can restore using my backup without any problems?