Optimizations to R ETL process (esp. loading).#4
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concretevitamin wants to merge 1 commit intomitdbg:masterfrom
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Optimizations to R ETL process (esp. loading).#4concretevitamin wants to merge 1 commit intomitdbg:masterfrom
concretevitamin wants to merge 1 commit intomitdbg:masterfrom
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- Directly reads from .txt file instead of saving out to .Rdata first then reading back again. Prototyped for Regression. - Even if the .Rdata step is desired, using fread() has much better performance.
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Sorry this slipped through the cracks and I am only looking at this now. Thanks for submitting your code! Regarding the changes to vanilla_R_benchmark.R, I have done a bit of testing on the 5000x5000 dataset, and it seems that load() on a binary file is faster than fread() on a text file (6.5 seconds v. 11.8 seconds). Under what conditions did you find fread() to be faster? Regarding the changes to generate_Rdata.R, fread() is certainly faster than read.csv(), but it seems to leave the data in a format that doesn't work with the code in vanilla_R_benchmark.R. I haven't done much debugging, but if you have any ideas I'd definitely appreciate them! |
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then reading back again. Prototyped for Regression.
performance.
I've found this to be much more efficient for benchmarking (tested on an EC2 instance). If this approach looks good, I could certainly make corresponding changes for all queries.