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
Without garbage collecting it took 35 minutes to upload Allie.
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 with UseG1GC;
35 minutes with automatic garbage collection (vm.swappiness =10); 38 minutes with automatic garbage collection (vm.swappiness =60);
Approach 4: 1.03 hours with UseG1GC;
35 minutes with automatic garbage collection;
PDBJ upload
Result: 8.95 hours with UseG1GC;
7.15 hours(429 minutes) with automatic garbage collection (vm.swappiness =10);
Uniprot upload
uniprot.rdf.gz
We firstly uploaded the file uniprot.rdf.gz (3.16 billion triples):
time: over one week(7.48 days): 646336127ms with UseG1GC
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
with automatic garbage collection： 74.3hours(4458 minutes)
INFO : 267385254 main com.bigdata.rdf.store.DataLoader?.logCounters(DataLoader?.java:1185): extent=249818775552, stmts=3161144450, bytes/stat=79
Wrote: 241489608704 bytes. Total elapsed=267385843ms
uniref.rdf.gz
When adding uniref.rdf.gz, it took over 11 days to import 411800000 statements, and we stopped the procedure for the bad performance.
INFO : 1032251699 main com.bigdata.rdf.store.DataLoader?$2.processingNotification(DataLoader?.java:1018): 411800000 stmts buffered in 1032247.664 secs, rate= 398, baseURL= http://purl.uniprot.org, t otalStatementsSoFar=411800000
uniprot.rdf.gz （2nd）
INFO : 349235249 main com.bigdata.rdf.store.DataLoader?.logCounters(DataLoader?.java:1185): extent=249818775552, stmts=3161144450, bytes/stat=79 Wrote: 241707974656 bytes. Total elapsed=349235466ms INFO : 349235324 main com.bigdata.rdf.store.DataLoader?.main(DataLoader?.java:1545): Total elapsed=349235466ms
Load performance
In the result we configured the setting as vm.swappiness = 60, automatic garbage collection.
| loadtime | Cell Cycle Ontology | Allie | PDBj | UniProt?* |
| 1st time | 3mins | 35mins | 429mins | 4458mins |
| 2nd time | 3mins | 38mins | 412 mins | 5820 mins |
| average | 3mins | 37 mins | 421mins | 5139 mins |
UniProt?*: We only uploaded uniprot.rdf.gz, 3.16 billion triples.
Sparql query performance
Cell cycle query
| Query\time(ms) | time 1 | time 2 | time 3 | time 4 | time 5 |
| case1 | 341 | 353 | 327 | 328 | 327 |
| case2 | 46 | 43 | 41 | 45 | 39 |
| case3 | 3361 | 3039 | 2855 | 3284 | 3416 |
| case4 | 32 | 21 | 9 | 22 | 10 |
| case5 | 416 | 574 | 404 | 401 | 433 |
| case6 | 1216 | 1295 | 1135 | 1277 | 1134 |
| case7 | 21 | 21 | 19 | 23 | 21 |
| case8 | 105 | 113 | 83 | 108 | 93 |
| case9 | 44 | 43 | 44 | 45 | 40 |
| case10 | 14 | 14 | 14 | 14 | 14 |
| case11 | 25 | 29 | 24 | 29 | 14 |
| case12 | 44 | 49 | 45 | 50 | 32 |
| case13 | 7 | 21 | 19 | 9 | 18 |
| case14 | 3 | 17 | 15 | 18 | 15 |
| case15 | 19456 | 19229 | 18670 | 19016 | 19583 |
| case16 | X | X | X | X | X |
| case17 | X | X | X | X | X |
| case18 | X | X | X | X | X |
| case19 | 44 | 36 | 29 | 46 | 37 |
note: do not support count query in case16,17 and 18.
Allie query
| 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
| 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 |
