Virtual import throws GC overhead limit exceeded error

Support
1

Hi ,

trying to do a mapping from a postgres table query to stardog. I have done the query with a LIMIT 100 and it works. Otherwise, I keep getting the GC overhead limit exceeded.

Here is the query:

    rdfs:label "{\"title\"}";
    linkedct:outcome_description "{\"description\"}";
    sm:map [
        sm:query "
        SELECT 
            CONCAT(outcomes.id, design_outcomes.id)                                 AS id,
            COALESCE(outcomes.nct_id, design_outcomes.nct_id)                       AS nct_id,
            LOWER(COALESCE(outcomes.outcome_type, design_outcomes.outcome_type))    AS outcome_type, 
            COALESCE(outcomes.title, design_outcomes.measure)                       AS title, 
            COALESCE(outcomes.description, design_outcomes.description)             AS description 
            FROM ctgov.design_outcomes 
            FULL OUTER JOIN ctgov.outcomes ON ctgov.design_outcomes.nct_id = ctgov.outcomes.nct_id" ;
    ] .

Here is the stack trace:

The detailed stack trace for the error is:
com.complexible.stardog.cli.CliException: GC overhead limit exceeded
        at com.complexible.stardog.cli.impl.ConnectionCommand.call(ConnectionCommand.java:82)
        at com.complexible.stardog.cli.CLIBase.execute(CLIBase.java:55)
        at com.complexible.stardog.cli.admin.CLI.main(CLI.java:186)
Caused by: com.complexible.stardog.protocols.http.client.BaseHttpClient$HttpClientException: GC overhead limit exceeded
        at com.complexible.stardog.protocols.http.client.BaseHttpClient.checkResponseCode(BaseHttpClient.java:537)
        at com.complexible.stardog.protocols.http.client.BaseHttpClient.execute(BaseHttpClient.java:363)
        at com.complexible.stardog.protocols.http.client.HttpClientImpl.update(HttpClientImpl.java:279)
        at com.complexible.stardog.protocols.http.client.HttpConnection._update(HttpConnection.java:194)
        at com.complexible.stardog.api.impl.AbstractConnection.executeUpdate(AbstractConnection.java:471)
        at com.complexible.stardog.api.impl.UpdateQueryImpl.execute(UpdateQueryImpl.java:42)
        at com.complexible.stardog.api.impl.UpdateQueryImpl.execute(UpdateQueryImpl.java:22)
        at com.complexible.stardog.virtual.cli.VirtualGraphImport.execute(VirtualGraphImport.java:138)
        at com.complexible.stardog.cli.impl.ConnectionCommand.call(ConnectionCommand.java:70)

I have also tried to increase the memory via the STARDOG_JAVA_ARGS variable like so

STARDOG_JAVA_ARGS="-Xmx12g" /opt/stardog/bin/stardog-admin virtual import ctDB -g http://www.b2p2.com/graph/CTGOV -u admin -p ******** -v /stardog/bix-ct-psql.properties  /data/ct-sms-mapping-tmp.ttl

Any help here would be appreciated on this. Please let me know if more clarification is necessary.

Best Regards

Matt

2

Hi Matt,

You will need to change the memory setting in STARDOG_SERVER_JAVA_ARGS before (re-)starting the server.

Jess

3

So, I might be getting the error, because I am running stardog in a docker container on my mbp. It seems that when I give too much memory to STARDOG_SERVER_JAVA_ARGS the I get connection refused. I am not exactly sure what's going on here. It seems to me that the stardog instance just cannot access the requested resources and then refuses to take any more connections?

4

Is the server refusing to start? Do you see any new message in the server log after changing the memory setting?

5

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