Re: [dotNetRDF-bugs] Scope of autassigned bland node IDs

[Tomasz P. <tom...@gm...>]

Hi Rob

I finally got back to R2RML to analyze why I am getting that memory
leak. It seems connected to the changes you had to introduce for
SPARQL 1.1.

I have determined that it happens in GraphMatcher#GenerateMappings
method. The graphs are equal and I'm not sure what causes the problem.
As soon as TryBruteForceMapping is reached memory consumption explodes
to gigabytes within minutes.

The low-level problem is the mappings variable in the
GenerateMappings, which within a few iteration contains thousands of
elements.

This problem no longer occurs on trunk. Have you actually been
introducing any fixes around that area?

Tom

On Mon, Jan 14, 2013 at 12:32 PM, Rob Vesse <rv...@do...> wrote:
> Comments inline:
>
> On 1/10/13 7:14 PM, "Tomek Pluskiewicz" <to...@pl...> wrote:
>
>>Hi Rob
>>
>>I have just updated to latest dotNetRDF available on NuGet and I'm
>>experiencing two issues.
>>
>>1. In my unit tests I relied on the way the library assigns blank node
>>identifiers: autos1, autos2 and so on. When I run the tests separately
>>each one passes but when I batch them they fail because in subsequent
>>tests blank nodes are name autos2, autos3, etc. However they don't
>>share the same graph or triple store. Have you changed this behavior
>>delbierately?
>
> Yes this behavior changed in the 0.8.x releases, the change was made in
> order to resolve a bug in SPARQL 1.1 Update support and also uncovered a
> bug in graph isomorphism calculation which was fixed.
>
> You shouldn't rely on an internal implementation detail like how the
> library assigns blank node identifiers.  Blank nodes should always be
> identifiable by the triples they appear in so it should be possible to
> formulate API calls or SPARQL queries that validate that you have produced
> the data you expected.
>
>>
>>2. There is a bad memory leak in during SPARQL execution of this:
>
> Define bad memory leak?
>
> Updates are transactional so it may be a side effect of the library
> maintaining the state necessary to rollback the transaction should it fail
> or be aborted.  Also the fact that you are replacing constant nodes with
> blank nodes will assign a lot of new identifiers and those identifiers
> have to be tracked to prevent collisions.
>
>>
>>PREFIX rr: <http://www.w3.org/ns/r2rml#>
>>DELETE { ?map rr:graph ?value . }
>>INSERT { ?map rr:graphMap [ rr:constant ?value ] . }
>>WHERE { ?map rr:graph ?value } ;
>>
>>DELETE { ?map rr:object ?value . }
>>INSERT { ?map rr:objectMap [ rr:constant ?value ] . }
>>WHERE { ?map rr:object ?value } ;
>>
>>DELETE { ?map rr:predicate ?value . }
>>INSERT { ?map rr:predicateMap [ rr:constant ?value ] . }
>>WHERE { ?map rr:predicate ?value } ;
>>
>>DELETE { ?map rr:subject ?value . }
>>INSERT { ?map rr:subjectMap [ rr:constant ?value ] . }
>>WHERE { ?map rr:subject ?value }
>>
>>The full code is simply:
>>
>>var dataset = new InMemoryDataset(store, R2RMLMappings.BaseUri);
>>            ISparqlUpdateProcessor processor = new
>>LeviathanUpdateProcessor(dataset);
>>            var updateParser = new SparqlUpdateParser();
>>
>>
>>processor.ProcessCommandSet(updateParser.ParseFromString(ShortcutSubmapsRe
>>placeSparql));
>>
>>Is this a know problem and has been already fixed or should I
>>investigate closely?
>
> This is not a known issue, I would also guess that the data being used
> would have some bearing on the severity of the problem.  Please go ahead
> and investigate but I would suspect it is the two things I outlined above
> which are the culprits here.
>
> Rob
>
>>
>>Thanks,
>>Tom
>>
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>
>
>
>
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