Optimize setup performance and memory use by removing MPI.gather

[Baharis]

This is the change to diffBragg discussed during today's and Monday's meeting. It heavily optimizes performance and memory use of diffBragg for experiments with a very large (>100 000 000) total number of reflections. This is achieved by moving previously separate calculations from across ensemble_refine_launcher.py and stage_two_refiner.py into a common class and utilizing MPI.Allreduce and iterators in lieu of MPI.gather and lists. Changes include:

• simtbx/diffBragg/ensemble_refine_launcher.py:
  • Introduced class HiAsu responsible for managing Miller indices;
  • Replaced use of separate dicts, lists, counters with HiAsu;
  • Disabled multiplicity diagnostics _get_unique_Hi until a better implementation is ready;
  • Replaced _mem_usage with new simtbx/diffBragg/utils.py memory_report;
• simtbx/diffBragg/hopper_ensemble_utils.py
  • Moved mem_usage functionality to memory_report + LOGGER.info for more general logging which now correctly reports where it has been called;
• simtbx/diffBragg/refiners/stage_two_refiner.py:
  • Simplified + optimized by passing HiAsu from the launcher instead of recalculating statistics;
• simtbx/diffBragg/utils.py:
  • Introduced memory_report function which can be called anywhere to report memory use.
• simtbx/command_line/stage_two.py:
  • Add max_sigz phil par (defaults to 10.) to reject experiments diverged during stage1

[Baharis]

I took the freedom to ask you all for reviews because:

• @dermen We mostly discussed the changes already, but I want you to be aware of all of them since this is predominantly your code; I made a list of them and minimized the clutter in diff to make it more readable;
• @Trzs GitHub suggested you authored some lines here, so if there is any functionality that needs to be considered e.g. for frontier, you are definitely the most informed;
• @vganapati Similarily to Felix, you authored some lines recently when trying to get the map working for space group C2 with Derek, so I mention you just in case you have any suggestions or worries.

This branch should be probably squash-merged into a single commit, and then can be easily merged to frontier.

[Baharis]

Merged after agreement by @dermen and tacit agreement of @vganapati and @Trzs during the weekly CCTBX meeting.