How to handle setting a time limit on reduce2 when harnessed from Phenix?

[russell-taylor]

The function run_reduce_with_timeout() in mmtbx.init.py is used to harness calls to the original reduce. It will presumably be changed to run reduce2.

This function includes a default timeout of 200 seconds that depends on the size of the input file and that depends on the size of the input file.

However, reduce2 has no parameter to limit its runtime. Unfortunately, hydrogen placement (not optimization) is often the bulk of the run time in reduce2, so it is not clear how helpful placing such a timer would be -- stopping things early would result in no hydrogens rather than unoptimized hydrogens.

Determine how to handle this.