Vocbench and graphdb - connection reset
Katerina Gkirtzou
Dear VocBench community,
we have installed in a local machine the vocbench 9.1.1 and ontotext graph db 9.1.1 using docker-compose. Within vocbench, I have created an Ontolex project with a remote access to the ontotaxt graph db, loaded my data from vocbench into the triple store and everything seemed to have work fine in the setup.
We haven't work on the project due to summer vacations, but now that we have returned, when we try to open/access the project we get "java.lang.IllegalStateException: Transaction URL has not been set". If we press "Ok" and got to data tab, we get "Could not rollback RDF4J transaction; nested exception is org.eclipse.rdf4j.repository.RepositoryException: java.net.SocketException: Connection reset" and I cannot have access to the data via vocbench.
The ontotext graphdb is up and running, I can see that some sparql queries have been initiated, probably from vocbench (eg SELECT ?datatype ?r WHERE { ?datatype a/rdfs:subClassOf* rdfs:Datatype. ?datatype owl:equivalentClass ?r . ?r a rdfs:Datatype . FILTER(isURI(?datatype)) FILTER(isBlank(?r)) } ).
When these queries finished, then I can search the data from vocbench (note that the index does not work in our case, as all our labels are in greek) and it seems that I gain access to the data again. Any ideas what is going on?
The ontotext graph db is up, I can access it, and also if I press ok, I can
Armando Stellato
Dear Katerina,
just a question to clarify as you have probably repeated the version number of GDB by mistake: which is the VB’s version number? I guess it’s 9.0 or 9.1.0 right?
Anyway, has this happened only when you came back, or is this happening once in a while?
Kind Regards,
Armando
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Katerina Gkirtzou
Dear Armando,
I am sorry, you are right, in the installation I have vocbench is 9.1.0 and ontotext graph is 9.1.1. 😁
Anyway, I notice that I got this exception (ie SocketException:
Connection reset) after vacations.But it is not consistent. Today,
when I tried to access the project I got "Could not rollback RDF4J
transaction; nested exception is
org.eclipse.rdf4j.repository.RepositoryException:
org.apache.http.NoHttpResponseException: The target server failed
to respond". In both cases I noticed that some queries were
running in the graphdb, but in the latter case I couldn't access
the date (which is normally given the exception). In the
attachment files you could see the queries that run in graphdb. Do
you think that I need to increase the memory in graphdb to
increase its performance and maybe stop producing such errors? I
know that my dataset is quite big, thus I opted for an external
db, as it is suggested by the VB documentation.
Any help is welcome.
Best regards,
Katerina
"Could not rollback RDF4J transaction; nested exception is
org.eclipse.rdf4j.repository.RepositoryException:
org.apache.http.NoHttpResponseException: The target server failed
to respond"
Armando Stellato
Dear Katerina,
sorry for coming back so late. It might be, what is the size of the dataset (is it only that, or there are several hosted?) and what is the amount of memory given to GDB and ST?
Kind Regards,
Armando
Katerina Gkirtzou
Dear Armando,
As far as the configuration is concerned both GDB and Vocbench run as containers in a VM with 8GB memory and 4 CPUs. Both containers can allocate at maximum this memory. As far as the size of the dataset, which is the only hosted in the GDB, it contains 2,340,164 triples (which is just the basic subset of what our final lexicon will have). The n3 file has 44MB size.
I also checked
the memory and CPU consumption while I tried to open the dataset
from vocbench. And although I still got the initial error of "Could not rollback
RDF4J transaction; nested exception is
org.eclipse.rdf4j.repository.RepositoryException:
org.apache.http.NoHttpResponseException: The target server
failed to respond" and queries were running in GDB, the memory
consumption remained stable. Specifically GDB required
~2.5GB, while vocbench required ~800MB. The CPU consumption
spiked for the GDB to 2-3CPUs, while vocbench left to use the
single available CPU. Maybe more CPU is needed for the GDB ?
Any suggestions are welcome!
King regards,
Katerina
