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...
Thoughts?
Cheers,
Stewart
--
Stewart W. Morris
Centre for Genomic and Experimental Medicine
The University of Edinburgh
United Kingdom
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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