Free up memory

[rosemckeon]

@rosemckeon Whoa! That is quite memory heavy. Too late for this now I suspect, but if you build on these simulations for a future project, it might make sense to get rid of unused memory during the simulation (e.g., by printing prior generations to a file, then removing them from the R environment). The gc() function might be able to free up a bit by garbage collection.

I've got 16 GB to work with here. I'll start with one run to see how things look, then start trying everything in parallel.

Originally posted by @bradduthie in #61 (comment)

[rosemckeon]

I think the seedoutput data is a contender for getting removed from the R environment. This one has substantially more rows than any of the others and the model only needs the last generation to work with at any given time.

[rosemckeon]

Useful how to here for reading in and binding loads of files: https://stackoverflow.com/a/32888918
I could save each gen as a tmp file, so I don't need to keep adding to a huge R object, then bind them all together at the end.

[rosemckeon]

See use of tmpdir() in unlink() examples with dir_to_clean: https://www.rdocumentation.org/packages/base/versions/3.6.1/topics/unlink

[bradduthie]

@rosemckeon All three simulations still running on Generations 106, 119, and 154. Memory is near maxed out at 16 GB.

[rosemckeon]

@bradduthie Seems like the manual gc() might only be a small help. Are those generations you mentioned for the first set of tests? (the simulation files have multiple different tests to go through). You can see quickly by looking in each data folder to see how many files end in *10.rds

[bradduthie]

Ah, okay @rosemckeon -- I do have 5-10 of each in the data folders now. Suspect this should be fine. Memory usage is quite high, but nothing seems to be slowing down my computer.

[rosemckeon]

@bradduthie excellent! That may be a fair bit faster / it could just be that quite a few have finished because you're running the most disturbed first. Really good to know they're running OK anyway!

[bradduthie]

@rosemckeon Now with 7-12 files saved, all still running.

[rosemckeon]

Brill, thanks @bradduthie Can you push some tomorrow?