BH12.12/SPARQLthon10/DDBJ
提供：TogoWiki
目次 |
DDBJ/SW
DDBJエントリーRDF化
DDBJ release 93をRDF化した (SPARQLthon前に準備）
- 424ファイル、870175MB
- DDBJ/Division 毎にファイルが生成されている
| Division | トリプル数 |
|---|---|
| htc | 26415372 |
| pat | 884902311 |
| tsa | 433895526 |
| gss | 1426527901 |
| hum | 122700779 |
| pln | 296267558 |
| vrt | 117076826 |
| inv | 182803780 |
| vrl | 160349238 |
| con | 1937771600 |
| bct | 573891151 |
| mam | 36026615 |
| una | 25005 |
| pri | 10844907 |
| rod | 95120648 |
| phg | 8880161 |
| env | 315899525 |
| htg | 72319257 |
| est | 2956573095 |
| sts | 76468372 |
| syn | 27636486 |
| 合計 | 9762396113 |
virtuoso7インポート
bct divisionデータ5.7億トリプル、インポートに2.5-3時間程度
SQL> select * from DB.DBA.LOAD_LIST where ll_file like '/home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct%'; ll_file ll_graph ll_state ll_started ll_done ll_host ll_work_time ll_error VARCHAR NOT NULL VARCHAR INTEGER TIMESTAMP TIMESTAMP INTEGER INTEGER VARCHAR _______________________________________________________________________________ /home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct1.ttl http://ddbj.nig.ac.jp/sequence/ 2 2013.7.31 13:26.1 0 2013.7.31 13:30.40 0 0 NULL NULL /home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct10.ttl http://ddbj.nig.ac.jp/sequence/ 2 2013.7.31 13:26.1 0 2013.7.31 13:30.55 0 0 NULL NULL /home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct11.ttl http://ddbj.nig.ac.jp/sequence/ 2 2013.7.31 13:26.1 0 2013.7.31 13:30.36 0 0 NULL NULL /home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct12.ttl http://ddbj.nig.ac.jp/sequence/ 2 2013.7.31 13:26.1 0 2013.7.31 13:30.42 0 0 NULL NULL /home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct13.ttl http://ddbj.nig.ac.jp/sequence/ 2 2013.7.31 13:30.36 0 2013.7.31 13:56.18 0 0 NULL NULL /home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct14.ttl http://ddbj.nig.ac.jp/sequence/ 2 2013.7.31 13:30.40 0 2013.7.31 13:53.35 0 0 NULL NULL /home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct15.ttl http://ddbj.nig.ac.jp/sequence/ 2 2013.7.31 13:30.42 0 2013.7.31 13:56.27 0 0 NULL NULL /home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct16.ttl http://ddbj.nig.ac.jp/sequence/ 2 2013.7.31 13:30.55 0 2013.7.31 13:34.33 0 0 NULL NULL /home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct2.ttl http://ddbj.nig.ac.jp/sequence/ 2 2013.7.31 13:34.33 0 2013.7.31 14:1.22 0 0 NULL NULL /home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct3.ttl http://ddbj.nig.ac.jp/sequence/ 2 2013.7.31 13:53.35 0 2013.7.31 14:30.18 0 0 NULL NULL /home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct4.ttl http://ddbj.nig.ac.jp/sequence/ 2 2013.7.31 13:56.18 0 2013.7.31 14:30.8 0 0 NULL NULL /home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct5.ttl http://ddbj.nig.ac.jp/sequence/ 2 2013.7.31 13:56.27 0 2013.7.31 14:30.42 0 0 NULL NULL /home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct6.ttl http://ddbj.nig.ac.jp/sequence/ 2 2013.7.31 14:1.22 0 2013.7.31 14:35.29 0 0 NULL NULL /home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct7.ttl http://ddbj.nig.ac.jp/sequence/ 2 2013.7.31 14:30.8 0 2013.7.31 16:8.36 0 0 NULL NULL /home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct8.ttl http://ddbj.nig.ac.jp/sequence/ 2 2013.7.31 14:30.18 0 2013.7.31 16:24.26 0 0 NULL NULL /home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct9.ttl http://ddbj.nig.ac.jp/sequence/ 2 2013.7.31 14:30.42 0 2013.7.31 16:41.51 0 0 NULL NULL 16 Rows. -- 2805 msec.
ファイルインポート毎に時間が増えていく問題。 - checkpointの頻度を上げるコメントをいただいた。
チューニング
- checkpoint_interval(10)に変更
- MaxCheckpointRemapを増やす 参考リンク
[Database] MaxCheckpointRemap = 625000 # set this to 1/4th of NumberOfBuffers
- ４並列 参考リンク
ld_dir('/home/sw/tf/ddbj/release_93_rdf_v1/','ddbj*.ttl', 'http://ddbj.nig.ac.jp/sequence/'); した後 bulk_load.sh
isql 1111 dba dba exec="rdf_loader_run();" & isql 1111 dba dba exec="rdf_loader_run();" & isql 1111 dba dba exec="rdf_loader_run();" & isql 1111 dba dba exec="rdf_loader_run();" & wait isql 111 dba dba exec="checkpoint;"
結果
SQL> select * from DB.DBA.LOAD_LIST where ll_file like '/home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct%'; ll_file ll_graph ll_state ll_started ll_done ll_host ll_work_time ll_error VARCHAR NOT NULL VARCHAR INTEGER TIMESTAMP TIMESTAMP INTEGER INTEGER VARCHAR _______________________________________________________________________________ /home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct1.ttl http://ddbj.nig.ac.jp/sequence/ 2 2013.7.31 17:38.29 0 2013.7.31 17:43.48 0 0 NULL NULL /home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct10.ttl http://ddbj.nig.ac.jp/sequence/ 2 2013.7.31 17:38.29 0 2013.7.31 17:44.51 0 0 NULL NULL /home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct11.ttl http://ddbj.nig.ac.jp/sequence/ 2 2013.7.31 17:38.29 0 2013.7.31 17:44.51 0 0 NULL NULL /home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct12.ttl http://ddbj.nig.ac.jp/sequence/ 2 2013.7.31 17:38.29 0 2013.7.31 17:44.37 0 0 NULL NULL /home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct13.ttl http://ddbj.nig.ac.jp/sequence/ 2 2013.7.31 17:43.49 0 2013.7.31 17:56.55 0 0 NULL NULL /home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct14.ttl http://ddbj.nig.ac.jp/sequence/ 2 2013.7.31 17:44.37 0 2013.7.31 17:57.10 0 0 NULL NULL /home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct15.ttl http://ddbj.nig.ac.jp/sequence/ 2 2013.7.31 17:44.51 0 2013.7.31 17:57.12 0 0 NULL NULL /home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct16.ttl http://ddbj.nig.ac.jp/sequence/ 2 2013.7.31 17:44.51 0 2013.7.31 17:47.22 0 0 NULL NULL /home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct2.ttl http://ddbj.nig.ac.jp/sequence/ 2 2013.7.31 17:47.22 0 2013.7.31 17:58.31 0 0 NULL NULL /home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct3.ttl http://ddbj.nig.ac.jp/sequence/ 2 2013.7.31 17:56.55 0 2013.7.31 18:0.16 0 0 NULL NULL /home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct4.ttl http://ddbj.nig.ac.jp/sequence/ 2 2013.7.31 17:57.10 0 2013.7.31 18:0.51 0 0 NULL NULL /home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct5.ttl http://ddbj.nig.ac.jp/sequence/ 2 2013.7.31 17:57.12 0 2013.7.31 18:1.8 0 0 NULL NULL /home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct6.ttl http://ddbj.nig.ac.jp/sequence/ 2 2013.7.31 17:58.31 0 2013.7.31 18:2.44 0 0 NULL NULL /home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct7.ttl http://ddbj.nig.ac.jp/sequence/ 2 2013.7.31 18:0.16 0 2013.7.31 18:4.39 0 0 NULL NULL /home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct8.ttl http://ddbj.nig.ac.jp/sequence/ 2 2013.7.31 18:0.51 0 2013.7.31 18:5.4 0 0 NULL NULL /home/sw/tf/ddbj/release_93_rdf_v1//ddbjbct9.ttl http://ddbj.nig.ac.jp/sequence/ 2 2013.7.31 18:1.8 0 2013.7.31 18:5.22 0 0 NULL NULL 16 Rows. -- 395 msec. SQL>
ファイルインポート毎に時間が増えていく問題は解決してインポート時間が大幅に短縮した。約27分!
ファイル毎のトリプル数集計
processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjbct1.ttl: 36366031 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjbct10.ttl: 38830578 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjbct11.ttl: 38871853 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjbct12.ttl: 38107674 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjbct13.ttl: 37735419 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjbct14.ttl: 34719263 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjbct15.ttl: 35276584 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjbct16.ttl: 16172124 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjbct2.ttl: 31491748 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjbct3.ttl: 35387649 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjbct4.ttl: 38802177 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjbct5.ttl: 38940930 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjbct6.ttl: 38978882 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjbct7.ttl: 38244313 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjbct8.ttl: 37641433 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjbct9.ttl: 38324493 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjcon1.ttl: 77811394 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjcon10.ttl: 41779310 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjcon11.ttl: 38282163 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjcon12.ttl: 43708089 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjcon13.ttl: 44429161 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjcon14.ttl: 43280575 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjcon15.ttl: 46705978 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjcon16.ttl: 50088779 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjcon17.ttl: 50662338 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjcon18.ttl: 61477145 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjcon19.ttl: 79315620 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjcon2.ttl: 63745193 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjcon20.ttl: 66045120 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjcon21.ttl: 113991338 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjcon22.ttl: 78793514 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjcon23.ttl: 69620162 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjcon24.ttl: 63698167 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjcon25.ttl: 68685530 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjcon26.ttl: 58716344 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjcon27.ttl: 90684332 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjcon28.ttl: 70821723 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjcon29.ttl: 65896806 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjcon3.ttl: 69466463 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjcon30.ttl: 69153630 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjcon31.ttl: 55495555 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjcon32.ttl: 40277590 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjcon4.ttl: 67631310 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjcon5.ttl: 34154376 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjcon6.ttl: 57454067 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjcon7.ttl: 51911962 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjcon8.ttl: 51963958 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjcon9.ttl: 52023908 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjenv1.ttl: 33278079 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjenv10.ttl: 20362839 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjenv2.ttl: 34460268 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjenv3.ttl: 34917200 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjenv4.ttl: 34226984 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjenv5.ttl: 38235373 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjenv6.ttl: 32423611 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjenv7.ttl: 27223912 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjenv8.ttl: 34066306 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjenv9.ttl: 26704953 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest1.ttl: 18342882 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest10.ttl: 20080945 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest100.ttl: 25196385 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest101.ttl: 17915415 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest102.ttl: 21881830 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest103.ttl: 18758869 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest104.ttl: 18473457 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest105.ttl: 20681797 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest106.ttl: 22277237 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest107.ttl: 19581489 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest108.ttl: 16480064 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest109.ttl: 18256288 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest11.ttl: 18150150 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest110.ttl: 17116632 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest111.ttl: 17733462 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest112.ttl: 16626686 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest113.ttl: 15676818 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest114.ttl: 17851578 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest115.ttl: 16677287 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest116.ttl: 16759878 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest117.ttl: 17790759 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest118.ttl: 14312569 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest119.ttl: 18414678 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest12.ttl: 15520108 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest120.ttl: 18383194 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest121.ttl: 15547038 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest122.ttl: 18749446 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest123.ttl: 15426094 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest124.ttl: 13764648 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest125.ttl: 16793675 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest126.ttl: 23757265 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest127.ttl: 19261212 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest128.ttl: 19150019 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest129.ttl: 23838499 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest13.ttl: 10457072 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest130.ttl: 20308471 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest131.ttl: 19791444 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest132.ttl: 19919500 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest133.ttl: 21115259 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest134.ttl: 19869746 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest135.ttl: 22045112 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest136.ttl: 21042529 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest137.ttl: 18786897 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest138.ttl: 16726536 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest139.ttl: 17122516 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest14.ttl: 10456463 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest140.ttl: 18666547 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest141.ttl: 15480233 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest142.ttl: 18087239 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest143.ttl: 18125749 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest144.ttl: 17283238 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest145.ttl: 18273837 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest146.ttl: 17107815 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest147.ttl: 18604931 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest148.ttl: 16191927 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest149.ttl: 12330321 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest15.ttl: 13505282 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest150.ttl: 15209583 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest151.ttl: 17537945 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest152.ttl: 18449025 processing... /home/sw/tf/ddbj/release_93_rdf_v1/ddbjest153.ttl: 18377258 processing... 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