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Posted to jira@jena.apache.org by "R Pope (Jira)" <ji...@apache.org> on 2022/03/23 20:29:00 UTC
[jira] [Commented] (JENA-2314) tdb2.tdbloader performance issue
[ https://issues.apache.org/jira/browse/JENA-2314?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17511476#comment-17511476 ]
R Pope commented on JENA-2314:
------------------------------
Thank you Andy and Rob for your responses. Unfortunately, no luck.
My inkling here is that as Rob mentioned, there's a huge I/O bottleneck happening with the way that Singularity (a container built from our Docker image) is accessing the parallel file system (while running a job) in our HPC environment. Which as Rob will know, the compute nodes (the machines you get given to run big workloads) are often located elsewhere from the login node (where you request work from). We are going the Singularity route since their system engineers suggest that it will be easier as opposed to using a native Java and getting jena & fuseki in the appropriate places to be used in a compute node.
Our project has relied on jena and particularly HPC for the last 2 years.. unfortunately however it will be coming to an end soon so there isn't real capacity to investigate an appropriate setup.
Using our local machines to do the load will do, which is much faster. The queries, updates and indexing sections of our pipeline will continue to run in our HPC environment. There is definitely an appetite to solve this problem, however government funding for big projects in New Zealand being the way they are, it may be a while until we are able to fix it.
In conclusion, as Andy had alluded to, the problem does not lie with Jena, but the way it is used by Singularity, inside all these environments where there is little visibility, for now.
Thanks team :)
> tdb2.tdbloader performance issue
> --------------------------------
>
> Key: JENA-2314
> URL: https://issues.apache.org/jira/browse/JENA-2314
> Project: Apache Jena
> Issue Type: Question
> Components: TDB2
> Affects Versions: Jena 4.0.0, Jena 4.2.0, Jena 4.4.0
> Environment: Java maximum memory: 12884901888
> symbol:http://jena.apache.org/ARQ#regexImpl = symbol:http://jena.apache.org/ARQ#javaRegex
> symbol:http://jena.apache.org/ARQ#registryFunctions = org.apache.jena.sparql.function.FunctionRegistry@1536602f
> symbol:http://jena.apache.org/ARQ#constantBNodeLabels = true
> symbol:http://jena.apache.org/ARQ#registryPropertyFunctions = org.apache.jena.sparql.pfunction.PropertyFunctionRegistry@4ebea12c
> symbol:http://jena.apache.org/ARQ#stageGenerator = org.apache.jena.tdb2.solver.StageGeneratorDirectTDB@2a1edad4
> symbol:http://jena.apache.org/ARQ#enablePropertyFunctions = true
> symbol:http://jena.apache.org/ARQ#strictSPARQL = false
> 13:02:36 INFO loader :: Loader = LoaderParallel
> 13:02:36 INFO loader :: Start: 6 files
> 13:02:48 INFO loader :: Add: 500,000 bdmhistoricalrecords.nq (Batch: 40,361 / Avg: 40,361)
> 13:03:00 INFO loader :: Add: 1,000,000 bdmhistoricalrecords.nq (Batch: 44,907 / Avg: 42,513)
> 13:03:10 INFO loader :: Add: 1,500,000 bdmhistoricalrecords.nq (Batch: 47,980 / Avg: 44,191)
> 13:03:25 INFO loader :: Add: 2,000,000 bdmhistoricalrecords.nq (Batch: 32,486 / Avg: 40,539)
> 13:33:06 INFO loader :: Add: 2,500,000 bdmhistoricalrecords.nq (Batch: 280 / Avg: 1,366)
> 14:30:30 INFO loader :: Add: 3,000,000 bdmhistoricalrecords.nq (Batch: 145 / Avg: 568)
> 14:52:29 INFO loader :: Add: 3,500,000 bdmhistoricalrecords.nq (Batch: 378 / Avg: 530)
> Reporter: R Pope
> Priority: Major
>
> Kia ora, Hi there,
> We have been using tdb2.tdbloader to load ~400,000,000 triples into our triplestore - all the data is in nq format being previoiusly converted from JSONLD. The files we are loading range from ~10GB to ~50GB producing a triplestore ~180GB including a text index. We run the loader in an HPC environment so we can request as much memory as we need, often using 1TB to do the load. The job is run in a Singularity image (similar to docker) and slurm is the chosen workload manager.
> All that aside, the load typically takes ~12-16hours but no more than 24 hours with --loader=parallel and an average rate of ~5,000 triples per second. We haven't needed to run the loader since October 2021, so upon recently running the load job again we are getting a grand average of about ~500triples per second. Haven't been able to wait and see if it even finishes.
> Has anyone else experienced such a big performance loss with tdb2.tdbloader in the current or recent versions of jena? Apart from the potential investigation that can be done on the slurm/HPC side does anyone have advice around performance?
> Thanks in advance
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