Doing the full run of 1289 predictions for Tina's dataset (checkpointing still disabled) to benchmark how the file content cache speeds up the run. Because this takes longer, I only did one test per cache size. The speedup is again roughly 2x using a cache size of 400 with diminishing returns when stretched to 800.
Doing the full run of 1289 predictions for Tina's dataset (checkpointing still disabled)
to benchmark how the file content cache speeds up the run. Because this takes longer, I
only did one test per cache size. The speedup is again roughly 2x using a cache size of 400
with diminishing returns when stretched to 800.

For multiprocessing, we would have to think about how reliable the shared data is between
the threads. There should be a thread-safe sharing model. Otherwise, we could cluster jobs
by input PDB before farming them out.

Bumping the default cache size (used unless a user specifies the size using file_content_buffer_size in ~/.my.cnf) to 600.

{'hits': 6996, 'misses': 661, 'size': 800}
Time taken for 1289 predictions: 103.349820137s (0.0802405435846s per prediction).

{'hits': 6290, 'misses': 1367, 'size': 400}
Time taken for 1289 predictions: 112.525548935s (0.0873645566265s per prediction).

{'hits': 30, 'misses': 7627, 'size': 1}
Time taken for 1289 predictions: 211.988888025s (0.164587645982s per prediction).

Kortemme-Lab/kddg,Kortemme-Lab/kddg