Sample conditions in parallel, and shorten the loop-search limit - #13
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--merge combines the tables of separate per-condition runs, so the conditions can be sampled as one job each. The limit on the search for cyclic reactions drops from 15 to 5 minutes: it normally takes one or two.
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Sampling all five conditions in one process took hours, because the conditions run one
after another and the search for cyclic reactions that precedes each one is
single-threaded and occasionally stalls.
--merge:python -m overflow.run_sampling --merge runs/CN4 runs/CN22 ...combinesthe tables of separate per-condition runs into one set, so each condition can be one
Slurm job and all five run in parallel. In
altExchangeFluxa condition that does notsecrete a byproduct above the detection threshold is left empty for that row. Runs
sampled on different reactions are refused.
and an occasional seed runs for hours) now has a five-minute limit, down from fifteen,
and retries with a new seed. It normally takes one to two minutes.
Tests: two for the merge (columns, the empty entries, and the refusal on different
reactions). The sampling and comparison tests pass on Gurobi.