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Those benchmarks are extremely suspicious. I remember comparing Perl and Python for bioinformatic work (non-trivial computational workloads), and finding that
by timr 14y ago
Those benchmarks are extremely suspicious. I remember comparing Perl and Python for bioinformatic work (non-trivial computational workloads), and finding that Perl was about 2x the speed of Python, on average.
Later, I did similar, non-trivial benchmarks with Python and Ruby, and found a similar, 2x factor. Ruby has improved since then, but unless Perl has become dramatically slower in the same interval, I suspect that these benchmarks are either trivial (i.e. simple loops), or badly written.
- sreque 14y agoYour benchmarks are likely very biased. The vast majority of the work done by your bioinformatics programs should be done in C code, with thin wrappers so that the code can be accessed through Perl and Python. If anything, your benchmarks only comparing specific implementations, such as BioPerl vs BioPython.
- timr 14y agoI wasn't using bioperl or biopython. I wrote the algorithms myself.
- igouy 14y ago>> ... extremely suspicious ... I suspect ...<< Please - less FUD and more looking at program source code (which is 2 clicks from the URL you were given).
- timr 14y agoIf you want to debug the metrics they're using, you're more than welcome to do it. I've got plenty of direct experience to question the results shown by a random webpage on the internet, and not much incentive to figure out why this particular set of benchmarks looks wrong. A quick inspection of the tests suggests a high enough bogon count that it already begins to confirm my suspicions: there's a "fasta-redux" test for Perl which dramatically outperforms the "fasta" test that's implemented cross-language. Also, many of these tests are written in least-common-denominator style, which doesn't reflect the way the languages are actually used.
- igouy 14y agoNope -- The Perl fasta program is 109x slower than the C fasta program; and the Perl fasta-redux program is about 112x slower than the C fasta-redux program.