Parsing very slow on larger files

[ijdickinson]

I'm reading in a bunch of RDF files, each into their own RdfContext::Graph. The results below show the timings I'm getting. Small files load just fine; larger files take disproportionately long. One file takes 8.5 minutes to load 38k triples. I'm running on a quad-core 64 bit Ubuntu system with 8Gb memory and using ruby 1.9.1, so I don't think the raw performance of the machine is an issue.

log file output:

loading concept definitions...
Initializing coins_concept with target/def/sector.nt
... parsing complete in 0.1s producing 39 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/sector
Initializing coins_concept with target/def/data-type.nt
... parsing complete in 1.6s producing 487 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/data-type
Initializing coins_concept with target/def/programme-admin.nt
... parsing complete in 0.2s producing 47 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/programme-admin
Initializing coins_concept with target/def/cga-body-type.nt
... parsing complete in 0.2s producing 47 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/cga-body-type
Initializing coins_concept with target/def/resource-capital.nt
... parsing complete in 0.1s producing 39 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/resource-capital
Initializing coins_concept with target/def/pesa-transfer.nt
... parsing complete in 0.3s producing 87 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/pesa-transfer
Initializing coins_concept with target/def/account-code.nt
... parsing complete in 20.2s producing 4711 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/account-code
Initializing coins_concept with target/def/estimate-number.nt
... parsing complete in 2.5s producing 503 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/estimate-number
Initializing coins_concept with target/def/cofog.nt
... parsing complete in 4.5s producing 1271 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/cofog
Initializing coins_concept with target/def/department-code.nt
... parsing complete in 3.3s producing 847 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/department-code
Initializing coins_concept with target/def/budget-capital-current.nt
... parsing complete in 0.3s producing 47 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/budget-capital-current
Initializing coins_concept with target/def/request-for-resources-next-year.nt
... parsing complete in 0.2s producing 63 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/request-for-resources-next-year
Initializing coins_concept with target/def/counterparty-code.nt
... parsing complete in 1.7s producing 431 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/counterparty-code
Initializing coins_concept with target/def/pesa-delivery.nt
... parsing complete in 0.1s producing 31 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/pesa-delivery
Initializing coins_concept with target/def/income-category.nt
... parsing complete in 0.5s producing 111 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/income-category
Initializing coins_concept with target/def/estimate-line.nt
... parsing complete in 2.1s producing 615 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/estimate-line
Initializing coins_concept with target/def/programme-object-group-code.nt
... parsing complete in 125.7s producing 15895 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/programme-object-group-code
Initializing coins_concept with target/def/estimates-aina.nt
... parsing complete in 0.1s producing 39 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/estimates-aina
Initializing coins_concept with target/def/estimates-capital-current.nt
... parsing complete in 2.1s producing 63 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/estimates-capital-current
Initializing coins_concept with target/def/activity-code.nt
... parsing complete in 6.0s producing 1375 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/activity-code
Initializing coins_concept with target/def/estimate-number-next-year.nt
... parsing complete in 2.4s producing 503 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/estimate-number-next-year
Initializing coins_concept with target/def/accounting-authority.nt
... parsing complete in 0.9s producing 159 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/accounting-authority
Initializing coins_concept with target/def/pesa-current-grants.nt
... parsing complete in 1.0s producing 215 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/pesa-current-grants
Initializing coins_concept with target/def/estimate-line-next-year.nt
... parsing complete in 2.8s producing 615 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/estimate-line-next-year
Initializing coins_concept with target/def/request-for-resources.nt
... parsing complete in 0.2s producing 63 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/request-for-resources
Initializing coins_concept with target/def/pesa-services.nt
... parsing complete in 0.4s producing 39 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/pesa-services
Initializing coins_concept with target/def/estimate-line-last-year.nt
... parsing complete in 2.6s producing 575 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/estimate-line-last-year
Initializing coins_concept with target/def/nac.nt
... parsing complete in 4.0s producing 951 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/nac
Initializing coins_concept with target/def/estimate-number-last-year.nt
... parsing complete in 2.5s producing 495 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/estimate-number-last-year
Initializing coins_concept with target/def/budget-boundary.nt
... parsing complete in 0.1s producing 39 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/budget-boundary
Initializing coins_concept with target/def/pesa-1.1.nt
... parsing complete in 0.1s producing 31 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/pesa-1.1
Initializing coins_concept with target/def/esa.nt
... parsing complete in 2.6s producing 543 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/esa
Initializing coins_concept with target/def/territory.nt
... parsing complete in 0.2s producing 71 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/territory
Initializing coins_concept with target/def/data-subtype.nt
... parsing complete in 2.3s producing 471 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/data-subtype
Initializing coins_concept with target/def/department-group.nt
... parsing complete in 2.1s producing 439 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/department-group
Initializing coins_concept with target/def/signage.nt
... parsing complete in 0.1s producing 31 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/signage
Initializing coins_concept with target/def/request-for-resources-last-year.nt
... parsing complete in 0.4s producing 63 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/request-for-resources-last-year
Initializing coins_concept with target/def/programme-object-code.nt
... parsing complete in 513.3s producing 38855 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/programme-object-code
Initializing coins_concept with target/def/sbi.nt
... parsing complete in 8.1s producing 455 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/sbi
Initializing coins_concept with target/def/time.nt
... parsing complete in 0.8s producing 119 triples
... indexed as https://finance.data/gov.uk/def/statistical-concept/time
Total time taken 720.9s

The files are in n-triples format: I also tried with Turtle input but gave up after waiting too long! I've tried with :list_store and :memory_store, it doesn't make much difference.

My guess is that something in the parser loop is not scaling linearly with the size of the input file, but that's just a guess. I don't think there's anything special about the input files themselves, but am happy to provide copies if that helps with debugging.

Ian

[gkellogg]

The SQLite3 store will provide persistent storage, and may scale better for even larger graphs, but it is slower for smaller graphs. That would be :store => SQLite3.new(:path => "store.db"). You may have also found a memory leak within the Parser. The NTriples parser is the same as the Turtle/N3, so that could be an issue. Do you have the same problem parsing large files in other serializations?

If you have a script to run through these, I'll check it out.

Also, note that the same parsers and serializers in RdfContext are also available through RDF.rb as rdf-rdfa, rdf-n3 and rdf-rdfxml. RDF.rb has a richer infrastructure for graph storage than RdfContext. I've also noticed that RDF/XML parsing is substantially faster, due to some underlying optimizations in that implementation.