Load Performance
Please refer to http://kiban.dbcls.jp/togordf/wiki/OwlimSe4.3 for the detailed load approach and configuration introduction.
Configuration:
-Xmx60G -Xms30G -Druleset=empty -Dentity-index-size=800000000 -Dcache-memory=20000m -Dtuple-index-memory=20000m -DenablePredicateList=false -Dpredicate-memory=0 -Dfts-memory=0 -DftsIndexPolicy=never -Denable-context-index=false -Din-memory-literal-properties=false -Dtransaction-mode=fast -Dtransaction-isolation=false -Drepository-type=file-repository
and vm.swappiness=10
We noticed that for Allie it made no too much difference to spllit the whole file into small file set or adjust the configuration setting.
| loadtime | Cell Cycle Ontology | Allie | PDBj | UniProt? | DDBJ
|
| 1st time | 3mins | 22mins | 141mins | 4000mins(66hs40mins) | 7888mins(131hs28mins)
|
| 2nd time | 3mins | 22mins | 138mins | 3539mins(58hs59mins) | 7612mins(5d6hs52mins)
|
| average | 3mins | 22mins | 140mins | 3770mins(62hs50mins) | 7750mins(129hours10mins)
|
Space used:
| Endpoint | Cell Cycle Ontology | Allie | PDBj | UniProt? | DDBJ
|
| OWLIM-SE | 3.7G | 8.2G | 27 G | 213G | 513G
|
Here we did the query evaluation by executing the whole query mix (composed of the query sequence) five times in each triple store, removed the highest one and then got the average time cost of the other four queries.
Cell cycle query
| Query\time(ms) | time 1 | time 2 | time 3 | time 4 | time 5 | avg
|
| case1 | 120 | 125 | 121 | 122 | 119 | 121
|
| case2 | 10 | 9 | 9 | 8 | 8 | 9
|
| case3 | 2858 | 2833 | 2738 | 2725 | 2663 | 2740
|
| case4 | 5 | 4 | 5 | 5 | 4 | 5
|
| case5 | 149 | 148 | 150 | 150 | 151 | 149
|
| case6 | 1738 | 1782 | 1688 | 1768 | 1694 | 1722
|
| case7 | 3 | 3 | 3 | 3 | 3 | 3
|
| case8 | 38 | 45 | 37 | 41 | 41 | 39
|
| case9 | 26 | 25 | 25 | 25 | 25 | 25
|
| case10 | 1 | 1 | 0 | 1 | 0 | 1
|
| case11 | 6 | 7 | 6 | 7 | 6 | 6
|
| case12 | 47 | 47 | 46 | 47 | 46 | 47
|
| case13 | 2 | 2 | 2 | 2 | 2 | 2
|
| case14 | 1 | 1 | 1 | 1 | 1 | 1
|
| case15 | 54516 | 52675 | 52494 | 54135 | 51811 | 52779
|
| case16 | 7 | 7 | 7 | 9 | 7 | 7
|
| case17 | 5 | 4 | 5 | 4 | 4 | 4
|
| case18 | 24 | 23 | 24 | 24 | 23 | 24
|
| case19 | 17 | 17 | 17 | 17 | 16 | 17
|
Allie query
| Query\time(ms) | time 1 | time 2 | time 3 | time 4 | time 5 | avg
|
| case1 | 136 | 139 | 137 | 136 | 136 | 136
|
| case2 | 1550 | 1531 | 1579 | 1544 | 1530 | 1539
|
| case3 | 1085 | 1080 | 1091 | 1083 | 1091 | 1085
|
| case4 | 28 | 28 | 29 | 29 | 31 | 29
|
| case5 | 77517 | 79261 | 81779 | 78765 | 78942 | 78621
|
PDBJ query
| Query\time(ms) | time 1 | time 2 | time 3 | time 4 | time 5 | avg
|
| case1 | 297 | 53 | 76 | 79 | 78 | 72
|
| case2 | 4 | 2 | 2 | 2 | 3 | 2
|
| case3 | 843 | 177 | 156 | 154 | 160 | 162
|
| case4 | 70 | 7 | 6 | 6 | 7 | 7
|
Uniprot query
| Query\time(ms) | time 1 | time 2 | time 3 | time 4 | time 5 | avg
|
| case1 | 2319 | 12137 | 406 | 473 | 527 | 931
|
| case2 | 6353 | 12227 | 449 | 433 | 444 | 1920
|
| case3 | 12108 | 8517 | 694 | 626 | 672 | 2627
|
| case4 | 1962 | 496 | 17 | 37 | 16 | 142
|
| case5 | 371 | 193 | 17 | 17 | 17 | 61
|
| case6 | 688632 | 79848 | 4357 | 182354 | 91786 | 89586
|
| case7 | 981995 | 72629 | 72055 | 126147 | 74689 | 86380
|
| case8 | 6527 | 677 | 676 | 656 | 687 | 674
|
| case9 | 2519 | 946 | 1051 | 1026 | 953 | 994
|
| case10 | 77283 | 1046 | 1036 | 1020 | 1110 | 1053
|
| case11 | 6925 | 50 | 51 | 48 | 50 | 50
|
| case12 | 348 | 8 | 11 | 10 | 11 | 10
|
| case13 | 36 | 7 | 9 | 9 | 9 | 9
|
| case14 | 7 | 6 | 7 | 7 | 7 | 7
|
| case15 | 92495 | 15134 | 14856 | 15268 | 14889 | 15037
|
| case16 | 39748 | 30756 | 29900 | 35012 | 32551 | 32055
|
| case17 | 4738 | 3467 | 3476 | 2815 | 1513 | 2818
|
| case18 | 10323 | 7404 | 7687 | 9865 | 9234 | 8548
|
DDBJ query
| Query\time(ms) | time 1 | time 2 | time 3 | time 4 | time 5 | avg
|
| case1 | 58113 | 5168 | 4495 | 4659 | 4808 | 4783
|
| case2 | 4617 | 4657 | 4490 | 4326 | 4680 | 4528
|
| case3 | 4824 | 5111 | 5136 | 4765 | 4766 | 4867
|
| case4 | 329 | 9 | 16 | 10 | 11 | 12
|
| case5 | 222 | 20 | 37 | 35 | 6 | 25
|
| case6 | 114 | 3 | 4 | 3 | 4 | 4
|
| case7 | 5980 | 685 | 726 | 418 | 49 | 470
|
| case8 | 12051 | 1818 | 1785 | 512 | 198 | 1078
|
| case9 | 2635 | 25 | 19 | 22 | 20 | 22
|
| case10 | 1 | 1 | 1 | 1 | 1 | 1
|
