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

Java-Memory Observations

A problem with Java based applications is the hugh memory amount required to run the scanner. Tested were diffeent settings of the maximum memory allocation pool using the commandline option -Xmx.

Mode	1	10	100	1000	10000	Memory (Mb)
java	0.14	0.256	0.453	1.708	15.500	788
java -Xmx16m	0.174	0.260	0.436	1.728	15.598	290
java -Xmx32m	0.175	0.255	0.457	1.713	15.576	308
java -Xmx64m	0.175	0.254	0.456	1.713	15.460	339
java -Xmx128m	0.156	0.255	0.441	1.708	15.607	404
java -Xmx256	0.156	0.253	0.421	1.714	15.520	532
java -Xmx512	0.155	0.253	0.456	1.709	15.507	795

OboScanner

Comparing 64 and 32bit Scanners generated with the tply-lexer for pascal (free pascal) and with the jflex-Lexer for Java. Java programs require about 800Mb of memory whereas the pascal programs require just 1Mb of memory. However the Java programs where faster with the complete gene ontology obofile (about 250000 lines).

Mode/Lines	1	10	100	1000	10000	100000	250000
obo-plex32	0.001	0.001	0.003	0.015	0.142	1.334	3.623
obo-plex64	0.001	0.001	0.003	0.015	0.160	1.448	4.038
obo-java15_x64	0.140	0.135	0.133	0.206	0.623	1.297	2.241
obo-java15	0.133	0.136	0.137	0.208	0.596	1.352	2.028
obo-java16	0.134	0.132	0.134	0.215	0.465	1.117	1.943

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