Virtual import throws GC overhead limit exceeded error

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 "
            CONCAT(,                                 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.CLIBase.execute(
        at com.complexible.stardog.cli.admin.CLI.main(
Caused by: com.complexible.stardog.protocols.http.client.BaseHttpClient$HttpClientException: GC overhead limit exceeded
        at com.complexible.stardog.protocols.http.client.BaseHttpClient.checkResponseCode(
        at com.complexible.stardog.protocols.http.client.BaseHttpClient.execute(
        at com.complexible.stardog.protocols.http.client.HttpClientImpl.update(
        at com.complexible.stardog.protocols.http.client.HttpConnection._update(
        at com.complexible.stardog.api.impl.AbstractConnection.executeUpdate(
        at com.complexible.stardog.api.impl.UpdateQueryImpl.execute(
        at com.complexible.stardog.api.impl.UpdateQueryImpl.execute(
        at com.complexible.stardog.virtual.cli.VirtualGraphImport.execute(

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 -u admin -p ******** -v /stardog/  /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


Hi Matt,

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


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?

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

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