4store 配置
$ cd $4STORE_HOME/bin $ ./4s-backend-setup allie $ ./4s-backend allie ./4s-import -v allie --format ntriples datapath --model http://myURI.com
Configuration consideration (refer to http://4store.org/):
Here specify the cluster and segmentation values:
4s-backend-setup --node 0 --cluster 1 --segments 4 demo
The number of segments should be a power of 2, parallelisation depends on segmentation. As a rule of thumb try a power of 2 close to twice as many segments as there are physical CPUs or CPU cores on the system, but depending on the workload you may find less or more work better.
Load Performance
Allie upload
Approach 1: Default setting (2 segments)
About 12 minutes
Approach 2: 8 segments
About 13 minutes
Segment setting makes little difference.
PDBJ upload
vm.swapniess=60: 6408 minutes(4.45 days) vm.swapniess=10: 4738 minutes(4.45 days)
| loadtime | Cell Cycle Ontology | Allie | PDBj |
| 1st time | 2mins | 12mins | 4738 mins |
| 2nd time | 2mins | 12mins | 4930 mins |
| average | 2mins | 12 mins | 4834 mins |
Sparql query performance
Cell cycle query
| Query\time(ms) | time 1 | time 2 | time 3 | time 4 | time 5 |
| case1 | 54 | 53 | 55 | 65 | 62 |
| case2 | 16 | 17 | 17 | 22 | 23 |
| case3 | 2244 | 1229 | 1246 | 1224 | 1243 |
| case4 | 13 | 13 | 12 | 14 | 15 |
| case5 | 34 | 34 | 34 | 33 | 31 |
| case6 | 68 | 67 | 69 | 65 | 55 |
| case7 | 22 | 21 | 21 | 22 | 25 |
| case8 | 67 | 67 | 67 | 66 | 68 |
| case9 | 2035 | 2035 | 2033 | 2036 | 2036 |
| case10 | 7 | 8 | 8 | 8 | 6 |
| case11 | 6 | 6 | 6 | 6 | 6 |
| case12 | 1064 | 1063 | 2063 | 2063 | 2062 |
| case13 | 9 | 8 | 9 | 8 | 8 |
| case14 | 8 | 8 | 8 | 7 | 6 |
| case15 | * | * | * | * | * |
| case16 | X | X | X | X | X |
| case17 | X | X | X | X | X |
| case18 | X | X | X | X | X |
| case19 | 15 | 16 | 15 | 16 | 15 |
X: parser error: syntax error, unexpected COUNT, expecting '(' or '?' or '$' or '*' on line 4.
*: No response within 2 hours.
Allie query
| Query\time(ms) | time 1 | time 2 | time 3 | time 4 | time 5 |
| case1 | X | X | X | X | X |
| case2 | 220 | 225 | 212 | 222 | 215 |
| case3 | X | X | X | X | X |
| case4 | X | X | X | X | X |
| case5 | 68245 | 64945 | 67070 | 67703 | 60794 |
X: Do not suppot lang() function.
PDBJ query
| Query\time(ms) | time 1 | time 2 | time 3 | time 4 | time 5 |
| case1 | 3639 | 1024 | 1026 | 1024 | 1026 |
| case2 | 1024 | 2027 | 2024 | 1027 | 1024 |
| case3 | 97728 | 131 | 134 | 128 | 134 |
| case4 | 2027 | 1023 | 2027 | 2024 | 1023 |
