Then, you need to come up with other creative solutions, like deep syncing inside the FS tree, etc. Fun times.
Add checksumming, and you probably would like to take a holiday whilst it copies the data :-)
rsync --whole-file --ignore-times
that should turn off the metadata checks and the rsync block checksum algorithm entirely and transfer all of the bits at the source to the dest without any rsync CPU penalty.
also for this purpose it looks like -H is also required to preserve hard links which the man page notes:
"Note that -a does not preserve hardlinks, because finding multiply-linked files is expensive. You must separately specify -H."
be mildly interesting to see a speed test between rsync with these options and cp.
there are also utilities out there to "post-process" and re-hardlink everything that is identical, so that a fast copy without preserving hardlinks and then a slow de-duplication step would get you to the same endpoint, but at an obvious expense.
And the critical aspect from a performance perspective was where the hash table became too large to fit into memory. Performance of all sorts goes pear-shaped when that happens.
rsync is pretty incredible, but, well, quantity has a quality all its own, and the scale involved here (plus the possible in-process disk failure) likely wasn't helping much.
I've had good luck with the -H option, though it is slower than without the option. I have never copied a filesystem with nearly as many files as the OP with -H; the most I've done is probably a couple million, consisting of 20 or so hardlinked snapshots with probably 100,000 or 200,000 files each. rsync -H works fine for that kind of workload.
I regularly rsync machines with millions of files. On a slow portable 2.5" 25MB/sec USB2 connection it's never taken me more than 1hr on completely cold caches to verify that no file needs to be copied. With caches being hot, it's a few minutes. And on faster drives it's faster still.
Unless you are doing something weird and force it to checksum, checksumming mostly kicks in on files that have actually changed and can be transferred efficiently in parts (i.e. network; NOT on local disks). In other cases, it's just a straight copy.
Have you actually used rsync in the setting you describe, or at least read its manual?
- In this scenario, the receiving side is empty, so there is no need to check every single file.
- Since 3.0, rsync walks the dirtree while copying (unless you use some special options). So, in some sense, rsync is already "deep syncing inside the FS tree", as you put it.
Some of the other features in rsync would seem to make it a more logical fit for this task anyway, e.g. it's resumable, it supports on-the-fly compression (though the value of that depends on the types of files being transferred), native logging etc etc.
CPU is cheap.