[R-pkgs] New version of package ff

From: Jens Oehlschlägel <jens.oehlschlaegel_at_truecluster.com>
Date: Fri, 22 Jan 2010 17:49:10 +0100


Dear R community,

Package bit version 1.1-3 and ff version 2.1.2 is available on CRAN and should be useful to handle large datasets.

It adds convenient utilities for managing ff objects and files (see ?ffsave) and removes some performance bottlenecks.

In case you experience unexpected performance problems with ff, here is a couple of recommendations based on FAQs:

  1. Compare the size of data to be written at the same time to available RAM for your filesystem cache. If the data exceeds available RAM, then consider using caching="mmeachflush" instead of caching="mmnoflush", this will make write operations predictably slower but prevent write storms stalling some systems (observed under NTFS win32+64). You can set ff's caching option either with options(ffcaching="mmeachflush") before creating ff objects or create ff objects with ffobj <- ff(..., caching="mmeachflush") or open your existing ff object with open(ffobj, caching="mmeachflush") (while it is closed) ff objects will remember this setting
  2. If you use caching="mmnoflush": check the writeback cache configuration of your filesystem (e.g. set data=writeback for ext3, tune limits for dirty pages, consider different filesystem, consider different OS).
  3. Choose a reasonable size for options("ffbatchbytes"), which limits the amount of RAM used for one chunk. With too small chunks you pay more performance overhead. Note that bigger chunks are not always better, for example if you distribute chunked processing on many cores or if some operation involved does not scale well with chunk size.

Final remark: testing ff access functionality on a Core i7 920 (4 cores, 8 cores with HT) shows that hyperthreading with 8 parallel processes (snowfall, sockets) gives about 5x the performance of a single process, but already 7 processes with HT perform worse than 4 processes without HT. Conclusion: if a machine is dedicated to R for RAM-critical applications, try switching hyperthreading off.

Hope you find this useful. We appreciate any feedback.

Jens & Daniel



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https://stat.ethz.ch/mailman/listinfo/r-packages Received on Mon 25 Jan 2010 - 18:41:40 EST

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