Autarchy of the Private Cave

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    Compressors galore: pbzip2, lbzip2, plzip, xz, and lrzip tested on a FASTQ file

    28th March 2015

    About 2 years ago I had already reviewed some parallel (and not) compressing utilities, settling at that time on pbzip2 – it scales quasi-linearly with the number of CPUs/cores, stores compressed data in relatively small 900k blocks, is fast, and has good compression ratio. pbzip2 was (and still is) a very good choice.

    Yesterday I got somewhat distracted, and thus found lbzip2 -

    an independent, multi-threaded implementation of bzip2. It is commonly the fastest SMP (and uniprocessor) bzip2 compressor and decompressor

    - as it says in the Debian package description. Is it really “commonly the fastest” one? How does it compare to pbzip2? Should I use lbzip2 instead of pbzip2?

    This minor distraction had grown into a full-scale web-search and comparison, adding to the mix plzip (a parallel version of lzip), xz, and lrzip. After reading thousands of characters, all of these were put to a simple test: compressing an about 2 gigabyte FASTQ file with default options.

    All the external links and benchmarks, as well as my own mini-benchmark results, are provided below.

    The conclusion is that out of all the tested compressors lbzip2 is indeed the best one (for my practical use). It is only slightly better than the trusty pbzip2, which takes the second place. All the other compressors performed so poorly, that they do not get any place in my practical rating…

    So, let us first ask internet wisdom/foolishness, if lbzip2 or pbzip2 is faster/better?
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    Posted in *nix, Comparison, Links, Misc, Software | 6 Comments »

    HospitalityClub.org and CouchSurfing.com

    4th September 2008

    These are the addresses for those who would like to travel lightly, meet new people, get new friends, hang out with interesting people, or just find a shelter for a night in the foreign country.

    I’m now registered in both systems (and getting “verified” in CS), and so far I stayed with three people (at two places) found via HC and CS. Both experiences were highly positive. Actually, my world outlook changed quite a bit after my first stay: I heard from someone that

    it’s better to trust wrong person once, than always distrust all the people

    But building trust, despite being central to HC ans CS, is only one – basic – component. Cultural exchange and knowledge sharing are also important, though so far I was unable to comprehend these components sufficiently to write on them.

    At the CouchSurfing.com website, it appears to be popular to put some test/quiz results into profiles. These are the tests:
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    Posted in Links, Misc, Society | 1 Comment »