C# scanner generator tested

There is the gplex scanner generator (http://plas.fit.qut.edu.au/gplex/) for the C#-programming language. Due to the mono runtime environment (http://www.mono-project.com/) C# code can be run on Win32, Linux and Mac-OSX platforms. As our wc sample run below suggests gplex scanner generated code is slower than Java JIT-compiled code but faster than Java-interpreted code. The mono application requires much less memory.

Tool/Queries	1	10	100	1000	10000
wc-flex	0.005	0.011	0.087	0.912	10.426
wc-java	0.197	0.248	0.367	1.549	14.707
wc-java016	0.216	0.263	0.346	1.533	14.806
wc-java064	0.209	0.243	0.364	1.522	14.649
wc-java512	0.216	0.247	0.351	1.542	16.486
wc-javaip	0.193	0.422	2.808	28.353	331.753
wc-mono1.2	0.168	0.282	1.580	15.650	175.863
wc-mono2.0	0.147	0.267	1.676	15.870	187.633
wc-mono2.0-static	0.150	0.272	1.670	16.265	189.411
wc-re2c	0.004	0.006	0.038	0.382	4.301
wc-unix	0.010	0.044	0.453	4.782	54.704

wc-mono-static means that a executable with the mono-runtime linked in was tested. Mono-frameworks were 1.2 and 2.0.1. Different options for java memory were tested. java016 means that java was run with the -Xmx16m option.

OboScanners for GeneOntology Files

Mode/Lines	1	10	100	1000	10000	100000	250000	Memory (M
flex	0.001	0.001	0.001	0.004	0.015	0.182	0.313	2.
java15	0.132	0.135	0.132	0.242	0.623	1.273	2.130	79
java15_x64	0.137	0.133	0.133	0.233	0.581	1.240	2.288
java16	0.131	0.134	0.131	0.205	0.441	1.194	1.963	800
perl	0.031	0.031	0.031	0.032	0.066	0.384	0.961	7
plex2.0_32	0.001	0.001	0.002	0.011	0.109	1.011	2.765	0.8
plex2.2_32	0.001	0.001	0.003	0.012	0.123	1.136	3.136	1
plex2.2_64	0.002	0.001	0.003	0.016	0.155	1.479	3.808	1
tcl	0.090	0.089	0.092	0.123	0.439	3.392	8.724	6

WC-Comparisons

Again the same set of blastfiles was used for testing of a word counting scanner. Flex and re2c based scanners again were performing best.

Mode	1	10	100	1000	10000
wc-flex	0.003	0.011	0.102	1.083	12.459
wc-flexpp	0.026	0.169	1.940	21.193	244.294
wc-gcj-exe	0.097	0.123	0.441	3.934	42.928
wc-gcj	0.087	0.307	2.875	30.163	nd
wc-java14	0.153	0.259	0.481	1.748	15.965
wc-java	0.176	0.257	0.444	1.704	15.682
wc-javaip14	0.122	0.345	2.774	28.982	329.265
wc-javaip	0.120	0.345	2.771	28.769	335.123
wc-perl-hand	0.006	0.018	0.155	1.590	18.132
wc-perl-lex	0.164	0.872	9.108	97.561	nd
wc-plex64	0.008	0.044	0.476	5.106	58.264
wc-plex	0.006	0.043	0.433	4.589	55.773
wc-re2c	0.002	0.005	0.035	0.346	3.975
wc-tcl8532	0.257	1.625	17.440	190.076	nd
wc-tcl8564	0.183	1.071	11.550	126.854	nd
wc-tcl	0.401	2.327	25.212	274.777	nd
wc-unix	0.006	0.026	0.285	2.937	33.792

Comparison of several scanner generators for a simple BLAST scanner

Sample: BlastFile with 1 to 10.000 result items

Mode	1	10	100	1000	10000
flex	0.003	0.015	0.199	1.979	25.548
flex-tcl	0.005	0.018	0.167	1.775	20.701
gcj	0.099	0.149	0.784	7.536	83.421
gij	0.109	0.482	4.917	51.939	nd
java	0.228	0.348	0.753	3.048	27.806
javaip	0.180	0.517	4.715	49.852	nd
plex	0.011	0.082	0.856	9.565	107.987
perl	0.031	0.050	0.235	2.280	23.916
re2c	0.004	0.012	0.076	0.765	8.438
tcl	1.702	12.524	140.249	nd	nd

The Re2c based scanner is the fastest, but the setup and the coding is more complicated than for the other scanners.
Flex-based scanners are 2-3 times slower than Re2c based scanners, regardless if there is an embedded Tcl-interpreter for better string handling (flex-tcl), Jflex code (java), executed with the Sun-Java Hotspot virtual machine (1.5) as well as to machine code compiled Jflex code (java-gcj) and Plex (sbs-plex = Pascal lex) based scanners are about 5 and 10 times slower than Re2c based scanners. Interpreted Java-Code either executed with the Sun-interpreter (java-ip = “java -Xint”) or with the gnu-interpreter (java-gij) is about 50 times slower than Re2c-Code. The Tcl based scanner is about 1000 times slower than the Re2c based. The per scanner is a line based scanner thereof not able to do complicated scanning with more than two states or patterns on the same line.

New Documentation online

Some new documentation about the aim of the bioscanners project is now online.

• Project Presentation 2007-04-05 MPIMP-Golm, Potsdam, Germany
• Project abstract

Initial Setup of the Bioscanners and Bioparsers Webpage

Project Aim 

Write parsers for biological data based on scanner generators like Flex (C), Re2c(C), Jflex (Java) and Ifickle (Tcl). These scanner generators are providing easier maintainance, development and higher speed than hand written scanners.

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