To answer this question, still some details are important. I'll assume some things, based on the information that was given:
- you want to copy files from one filesystem to another, then erase then from the original place.
- you could mount one filesystem on the other computer (be it on computer A or B)
- you have a fast network
- you have even faster processors, so dealing with compression / decompression won't be a problem
- you said it's a supercomputer, so I'll consider that "hard-disk" isn't a bottleneck and you're using some kind of storage.
Rsync have some advantage over a mounted fylesystem: it can compress data while copying. So it'll use less network, and will be faster.
But your problem isn't that: is that you have almost 1TB of files to copy. That will take some time, even in a fast network. Let's do very simple math about it:
- 1 TB = 1,000 GB = 1,000,000 MB of data.
- ethernet at 100 Mbits = 12,5 MB of data, per second.
- 1,000,000 / 12,5 = 80,000 seconds = 1,333 min = 22 hours.
Real-life network speed is a bit lower than that - ethernet 100 Mbips would be 8 MB of real transfer - so you would take a bit more than one day doing that.
One solution would be compressing your files before copying - for example, .tar.gz inside each dir - and then mouting one filesystem inside the other computer, and then simply copying / moving all files. In one TB of data, probably you'll achieve some compression by doing a tar before, better than compressing each file alone.
Edit: another idea: take a look at this site, it sugests using bbcp instead. BBCP can use multiple streams at the same time, filling your network completly.