Load Performance
Please refer to http://kiban.dbcls.jp/togordf/wiki/bigdata1.1.0 for the detailed load approach and configuration introduction.
-Xmx60G -Xms50G
and vm.swappiness=10
when setting
com.bigdata.btree.writeRetentionQueue.capacity=500000 com.bigdata.rdf.sail.BigdataSail.bufferCapacity=1000000
as Bigdata1.1.0, it occurred the error
ERROR: 1034 main com.bigdata.rdf.store.AbstractTripleStore.create(AbstractTripleStore.java:1679): com.bigdata.config.ConfigurationException: Must be in [2:50000]:
Therefore we used the following parameters
com.bigdata.btree.writeRetentionQueue.capacity=50000 com.bigdata.rdf.sail.BigdataSail.bufferCapacity=1000000
| loadtime | Cell Cycle Ontology | Allie | PDBj | UniProt? | DDBJ |
| 1st time | 3mins | 237mins | 1175mins(19.58hs) | ||
| 2nd time | 2mins | 307 mins | 1140mins(19hs) | ||
| average | 3mins | 272mins | 1158mins(19.3hs) |
Space used:
| Endpoint | Cell Cycle Ontology | Allie | PDBj | UniProt? | DDBJ |
| bigdata | 0.78G | 6.2G | 34 G |
Uniprot:
ERROR: 743893632 main com.bigdata.Banner$1.uncaughtException(Banner.java:110): Uncaught exception in thread java.lang.RuntimeException?: Allocation size to big: 13940 > 8192: lastRootBlock=rootBlock{ rootBlock=1, challisField=1, version=3, nextOffset=154618830861, localTime=1353304142691
Sparql query performance
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 | 306 | 276 | 272 | 284 | 294 | 282 |
| case2 | 35 | 40 | 33 | 33 | 39 | 35 |
| case3 | 3081 | 3464 | 3016 | 3702 | 3427 | 3247 |
| case4 | 20 | 8 | 19 | 18 | 8 | 13 |
| case5 | 47 | 116 | 48 | 48 | 65 | 52 |
| case6 | 3374 | 3260 | 3278 | 3458 | 3368 | 3320 |
| case7 | 27 | 8 | 19 | 8 | 8 | 11 |
| case8 | 108 | 94 | 78 | 101 | 98 | 93 |
| case9 | 59 | 46 | 43 | 52 | 47 | 47 |
| case10 | 13 | 13 | 2 | 13 | 13 | 10 |
| case11 | 20 | 19 | 21 | 19 | 22 | 20 |
| case12 | 26 | 28 | 27 | 28 | 31 | 27 |
| case13 | 14 | 3 | 4 | 4 | 9 | 5 |
| case14 | 14 | 2 | 15 | 3 | 3 | 6 |
| case15 | 18202 | 18549 | 18129 | 18045 | 18126 | 18126 |
| case19 | 17 | 37 | 44 | 39 | 26 | 30 |
Allie query
| Query\time(ms) | time 1 | time 2 | time 3 | time 4 | time 5 | avg |
| case1 | 358 | 366 | 371 | 375 | 365 | 365 |
| case2 | 681 | 707 | 689 | 705 | 684 | 690 |
| case3 | 1874 | 1756 | 1798 | 1773 | 1788 | 1779 |
| case4 | 101 | 121 | 89 | 107 | 96 | 98 |
| case5 | 38057 | 38749 | 40250 | 38799 | 38488 | 38523 |
PDBJ query
| Query\time(ms) | time 1 | time 2 | time 3 | time 4 | time 5 | avg |
| case1 | 286 | 190 | 187 | 188 | 193 | 190 |
| case2 | 15 | 14 | 13 | 15 | 14 | 14 |
| case3 | 58 | 36 | 30 | 37 | 36 | 35 |
| case4 | 64 | 54 | 57 | 53 | 53 | 54 |
