* Virtuoso　配置

* Load performance

• Allie upload
• PDBJ upload
• Uniprot upload
• DDBJ upload

* Sparql query performance

• Allie query
• PDBJ query
• Uniprot query
• DDBJ query

Virtuoso 配置

* NumberOfBuffers?: the amount of RAM used by Virtuoso to cache database files. This has a critical performance impact and thus the value should be fairly high for large databases. Exceeding physical memory in this setting will have a significant negative impact. For a database-only server about 65% of available RAM could be configured for database buffers. Each buffer caches one 8K page of data and occupies approximately 8700 bytes of memory.

* MaxCheckpointRemap:to avoid out of memory error, you should make sure the values for the paramaters NumberOfBuffers? and MaxCheckpointRemap? are not set with the same values.

* AsyncQueueMaxThreads?: the size of a pool of extra threads that can be used for query parallelization. This should be set to either 1.5 * the number of cores or 1.5 * the number of core threads; see which works better.

* ThreadsPerQuery?: the maximum number of threads a single query will take. This should be set to either the number of cores or the number of core threads; see which works better.

* IndexTreeMaps?: the number of mutexes over which control for buffering an index tree is split. This can generally be left at default (256 in normal operation; valid settings are powers of 2 from 2 to 1024), but setting to 64, 128, or 512 may be beneficial. A low number will lead to frequent contention; upwards of 64 will have little contention.

* ThreadCleanupInterval? & ResourcesCleanupInterval?: Set both to 1 in order to reduce memory leaking.

NumberOfBuffers          = 6500000
MaxDirtyBuffers          = 5000000
MaxCheckpointRemap       = 1000000
AsyncQueryMaxThreads     = 18
ThreadsPerQuery          = 18
IndexTreeMaps            = 512
ThreadCleanupInterval    = 1
ResourcesCleanupInterval = 1

Please refer to attachment:virtuoso.ini.2 for the detailed parameter in the test.

More information please refer to  http://docs.openlinksw.com/virtuoso/databaseadmsrv.html  http://www.openlinksw.com/weblog/oerling/?id=1665

it is generally recommended with the Virtuoso 6.x release 16GB of memory is required per billion triples.

Load Performance

Allie upload

Data: 94,420,989 tripples, n3 format.

* Approach 1:

Load the big file in one stream.

Result:

2hours.

Step:

$ nohup $VIRTUOSO_HOME/bin/isql 1111 dba dba <$VIRTUOSO_HOME/scripts/load.list.isql &

load.list.isql script:

log_enable (2);
DB.DBA.TTLP (file_to_string_output('file path'),' ','http://mydbcls.jp', 0);
checkpoint;

* Approach 2:

Use one stream per core (not per core thread). Split the big file into 12 small files(precisely, 13(12+1)files, #linesPerFiles=#totleLines/12).

Result: 46mins22secs.

Step 1. load file into ld_dir:

$nohup $VIRTUOSO_HOME/bin/isql 1111 dba dba <$VIRTUOSO_HOME/scripts/load.list.isql &

load.list.isql script:

 delete from load_list;
 ld_dir('data directory','*.rdf.nt','http://allie.dbcls.jp');
 select * from load_list;

Step 2. upload the file into virtuoso:

$ nohup $VIRTUOSO_HOME/bin/isql 1111 dba dba <$VIRTUOSO_HOME/scripts/load.data.isql &

load.data.isql script:

--record CPU time
select getrusage ()[0] + getrusage ()[1];

rdf_loader_run () &
...(omit 10 times)
rdf_loader_run () &
checkpoint;

-- Record CPU time
select getrusage ()[0] + getrusage ()[1];

PDBJ upload

Data: .rdf.gz, 77878 files, 589,987,335 triples from  ftp://ftp.pdbj.org/XML/rdf/.

Upload with 12 streams.

Result:103min31s.

Uniprot upload

DDBJ upload

Sparql query performance

Cell cycle query

Query\time(ms)	time 1	time 2	time 3	time 4	time 5
case1	23	23	24	24	24
case2	2	2	2	2	2
case3	22368	23440	22961	23655	23655
case4	2	3	10	4	4
case5	43265	42911	42172	42459	42459
case6	13062	13057	13069	13102	13102
case7	3	3	3	12	12
case8	7683	7479	7455	7656	7656
case9	40	38	36	51	51
case10	1	8	1	3	3
case11	120	119	118	123	123
case12	521	18	17	20	20
case13	24	4	2	7	7
case14	1	1	1	1	1
case15	55065	57530	56760	56203	56203
case16	36	34	46	65	65
case17	14	23	18	13	13
case18	23	17	16	16	16
case19	16980	17064	16643	16631	16631

Allie query

The time cost for the five use case (please refer to  http://kiban.dbcls.jp/togordf/wiki/survey#data)

Query\time(ms)	time 1	time 2	time 3	time 4	time 5
case1	269	27	21	22	21
case2	1350	1273	1729	1300	1381
case3	395	145	138	155	172
case4	171	81	71	101	127
case5	26934	28107	27204	28276	26781

PDBJ query

Query\time(ms)	time 1	time 2	time 3	time 4	time 5
case1	184	156	150	152	131
case2	2	1	2	1	2
case3	6	3	2	1	1
case4	114	157	121	164	161

Uniprot query

DDBJ query