* Bigdata　Configuration

* Load performance

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

* Sparql query performance

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

Bigdata Configuration

The journal in Bigdata (please refer to  http://sourceforge.net/apps/mediawiki/bigdata/index.php?title=StandaloneGuide for details.)

The WORM (Write-Once, Read-Many) is the traditional log-structured append only journal. It was designed for very fast write rates and is used to buffer writes for scale-out. This is a good choice for immortal databases where people want access to ALL history. Scaling is to several billions of triples.

The RW store (Read-Write) supports recycling of allocation slots on the backing file. It may be used as a time-bounded version of an immortal database where history is aged off of the database over time. This is a good choice for standalone workloads where updates are continuously arriving and older database states may be released. The RW store is also less sensitive to data skew because it can reuse B+Tree node and leaf revisions within a commit group on large data set loads. Scaling should be better than the WORM for standalone and could reach to 10B+ triples. The default property file is attachment:RWStore.properties .

Load Performance

Approach 1:

Upload data from Bigdata sparql point(NanoSparqlServer?). Post the data every 10000 lines. Please refer to attachment:upload.pl for details.

Approach 2:

Upload with com.bigdata.rdf.store.DataLoader? tools and RW store default parameter.

And test the situation when adding GC in JVM.

-Xmx55G -Xms30G -XX:+UseG1GC -XX:+TieredCompilation? -XX:+HeapDumpOnOutOfMemoryError

Approach 3:

We modified the following two important parameters(In the rest test we use this configure in default):

com.bigdata.btree.writeRetentionQueue.capacity=500000
com.bigdata.rdf.sail.BigdataSail.bufferCapacity=1000000

Approach 4: Split the file into 12 small files.

Allie upload

Approach 1: 26hours

Approach 2: 5.89hours when Setting JVM GC : 6.75hours

Approach 3: 2.61 hours

Approach 4: 1.03 hours

PDBJ upload

Result: 8.95 hours

Uniprot upload

time: over one week(7.48 days): 646336127ms

INFO : 646335942 main com.bigdata.rdf.store.DataLoader??.logCounters(DataLoader??.java:1185): extent=249818775552, stmts=3161144450, bytes/stat=79 Wrote: 241474404352 bytes. Total elapsed=646336127ms

DDBJ upload

Sparql query performance

Allie query performance

Query\time(ms)	time 1	time 2	time 3	time 4	time 5
case1	423	424	424	443	436
case2	4160	4200	4263	4201	4264
case3	3352	3230	2329	2329	2308
case4	568	592	92	92	97
case5	1830742	661710	39296	39296	39784

PDBJ query performance

Query\time(ms)	time 1	time 2	time 3	time 4	time 5
case1	751	213	213	212	213
case2	27	14	15	13	26
case3	188	56	45	53	66
case4	337	58	57	53	59

Uniprot query performance

DDBJ query performance