A clue: this may not end well - for a start you could have > 200GB of data....
Anyhow, some hints.
- ulimit -n 4096
- run on a machine with a lot of memory or
- xia2 image=/path/to/master.h5:1:100800:3600
First increases the OS limit on the allowed number of file handles a process is entitled to. You will probably need a lot of RAM for e.g. indexing (because a lot of reflections) or split into evenly sized chunks with the syntax above (e.g. 1:360000:3600 if you did 100 turns, into one turn chunks) - this will make the processing much more swift though the scaling will still take a little while.
Whatever happens, with xia2 this is unlikely to be fast... if using 3d/i/ii pipeline, the use of the neggia plugin with XDS will appear in the next release with DIALS 1.7, which is due real soon now...