On 01/15/2015 01:45 PM, Stewart Morris wrote:
Hi, I am dealing with very large datasets and it takes a long time to save a workspace image. The options to save compressed data are: "gzip", "bzip2" or "xz", the default being gzip. I wonder if it's possible to include the pbzip2 (http://compression.ca/pbzip2/) algorithm as an option when saving. "PBZIP2 is a parallel implementation of the bzip2 block-sorting file compressor that uses pthreads and achieves near-linear speedup on SMP machines. The output of this version is fully compatible with bzip2 v1.0.2 or newer" I tested this as follows with one of my smaller datasets, having only read in the raw data: ============ # Dumped an ascii image save.image(file='test', ascii=TRUE) # At the shell prompt: ls -l test -rw-rw-r--. 1 swmorris swmorris 1794473126 Jan 14 17:33 test time bzip2 -9 test 364.702u 3.148s 6:14.01 98.3% 0+0k 48+1273976io 1pf+0w time pbzip2 -9 test 422.080u 18.708s 0:11.49 3836.2% 0+0k 0+1274176io 0pf+0w ============ As you can see, bzip2 on its own took over 6 minutes whereas pbzip2 took 11 seconds, admittedly on a 64 core machine (running at 50% load). Most modern machines are multicore so everyone would get some speedup. Is this feasible/practical? I am not a developer so I'm afraid this would be down to someone else...
Take a look at the gdsfmt package. It supports the superfast Lz4 compression algorithm + it provides highly optimized functions to write to/read from disk.
https://github.com/zhengxwen/gdsfmt
Thoughts? Cheers, Stewart
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