wait_from_nonmem() helper

[seth127]

Summary

There are situations where we want to monitor whether a NONMEM run has completed. Note that we don't care (in these situations) whether it finished successfully in any sense, just whether it is still running. This is not trivial because these models are often submitted to run on worker nodes in a grid, so we can't just check for the process ID.

Notes

Initial idea is to check the .lst file for "Stop Time". This seems to work for most cases, but there are some things to consider.

• Need to check whether this works if you kill a model
  • submitted locally and killed with process ID kill -9 <pid>
  • submitted to SGE and killed with qdel
• Need to check if it works in all NONMEM failures
  • if it dies early (i.e. can't find the data set) does it still print "Stop Time"?

Requirements

• Should be able to take multiple models
• Should be a helper check_nonmem_finished() (also exported) to check a single model one-off
• Should take an arg for interval to check
• Should take an arg for total time limit (so this doesn't hang indefinitely)

[barrettk]

Stories:

MGMT-S019:
  name: wait_for_nonmem
  description: As a user, I want to be able to freeze my R console while a model is executing on the grid or otherwise
  ProductRisk: Medium
  Requirements:
     - MGMT-R010

Requirements:

MGMT-R010:
  description: wait_for_nonmem() will freeze the console until a stop time is found or the allotted time is reached
  tests: 
     - BBR-UTL-012
     - BBR-UTL-013