Error loading database

Sorry for the vague title. I'm not quite sure how to describe exactly what's wrong here other than something seems to have gone terribly wrong. I was loading the thompson/reuters (now Rveteve or some crazy new name) permid data and during loading I got the following error.

    WARN  2019-11-07 20:17:16,994 [Stardog.Executor-0] com.complexible.common.rdf.rio.RDFStreamProcessor:setException(599): Error during loading /home/centos/Downloads/OpenPermID-bulk-person-20191103_092405.ttl.gz: Namespace prefix 'skos' used but not defined [L9]
    WARN  2019-11-07 20:17:16,994 [Stardog.Executor-0] com.complexible.common.rdf.rio.RDFStreamProcessor:setException(606): Parse process creator: 
    java.lang.Exception: null
            at com.complexible.common.rdf.rio.RDFStreamProcessor.<init>(RDFStreamProcessor.java:137) ~[stardog-utils-rdf-7.0.2.jar:?]
            at com.complexible.common.rdf.rio.RDFStreamProcessor.create(RDFStreamProcessor.java:113) ~[stardog-utils-rdf-7.0.2.jar:?]
            at com.complexible.stardog.index.StardogIndexLoader.loader(StardogIndexLoader.java:76) ~[stardog-7.0.2.jar:?]
            at com.complexible.stardog.StardogKernel.bulkLoad(StardogKernel.java:1211) ~[stardog-7.0.2.jar:?]
            at com.complexible.stardog.StardogKernel.createDatabase(StardogKernel.java:1381) ~[stardog-7.0.2.jar:?]
            at com.complexible.stardog.protocols.http.server.AdminDatabaseService.createNewDatabase(AdminDatabaseService.java:539) ~[stardog-protocols-http-server-7.0.2.jar:?]
            at com.stardog.http.server.undertow.jaxrs.ExtractRoutes.lambda$handleIt$5(ExtractRoutes.java:192) ~[stardog-protocols-http-server-7.0.2.jar:?]
            at org.apache.shiro.subject.support.SubjectRunnable.doRun(SubjectRunnable.java:120) ~[shiro-core-1.3.0.jar:1.3.0]
            at org.apache.shiro.subject.support.SubjectRunnable.run(SubjectRunnable.java:108) ~[shiro-core-1.3.0.jar:1.3.0]
            at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [?:1.8.0_222]
            at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [?:1.8.0_222]
            at java.lang.Thread.run(Thread.java:748) [?:1.8.0_222]

No biggie. So there's an undefined prefix in there. It powered on....

    INFO  2019-11-07 20:17:28,043 [Stardog.Executor-0] com.complexible.stardog.index.Index:printInternal(314): Parsing triples: 0% complete in 00:00:11 (2.0M triples - 178.7K triples/sec)
    INFO  2019-11-07 20:17:32,406 [Stardog.Executor-0] com.complexible.stardog.index.Index:printInternal(314): Parsing triples: 1% complete in 00:00:15 (2.5M triples - 163.3K triples/sec)

Then Stardog just crashed with nothing in the logs but when I went to start it up again and try loading the data again I get the following errors in the logs

ERROR 2019-11-07 20:23:27,482 [stardog-user-1] com.complexible.stardog.StardogKernel:bulkLoad(1197): Unable to create loader for database.
com.complexible.mvcc.api.WriteConflictException: Drop conflicts with other create operation
        at com.stardog.starrocks.index.VersionedDatabaseManager.drop(VersionedDatabaseManager.java:199) ~[stardog-7.0.2.jar:?]
        at com.stardog.starrocks.NativeStorageKernel.drop(NativeStorageKernel.java:200) ~[stardog-7.0.2.jar:?]
        at com.complexible.stardog.index.disk.rocks.RocksConcurrentIndexLoader.<init>(RocksConcurrentIndexLoader.java:156) ~[stardog-7.0.2.jar:?]
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[?:1.8.0_222]
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) ~[?:1.8.0_222]
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[?:1.8.0_222]
        at java.lang.reflect.Constructor.newInstance(Constructor.java:423) ~[?:1.8.0_222]
        at com.google.inject.internal.DefaultConstructionProxyFactory$2.newInstance(DefaultConstructionProxyFactory.java:86) ~[guice-4.0.jar:?]
        at com.google.inject.internal.ConstructorInjector.provision(ConstructorInjector.java:105) ~[guice-4.0.jar:?]
        at com.google.inject.internal.ConstructorInjector.construct(ConstructorInjector.java:85) ~[guice-4.0.jar:?]
        at com.google.inject.internal.ConstructorBindingImpl$Factory.get(ConstructorBindingImpl.java:267) ~[guice-4.0.jar:?]
        at com.google.inject.internal.InjectorImpl$2$1.call(InjectorImpl.java:1016) ~[guice-4.0.jar:?]
        at com.google.inject.internal.InjectorImpl.callInContext(InjectorImpl.java:1092) ~[guice-4.0.jar:?]
        at com.google.inject.internal.InjectorImpl$2.get(InjectorImpl.java:1012) ~[guice-4.0.jar:?]
        at com.google.inject.assistedinject.FactoryProvider2.invoke(FactoryProvider2.java:770) ~[guice-assistedinject-4.0.jar:?]
        at com.sun.proxy.$Proxy38.createDiskIndexBulkLoader(Unknown Source) ~[?:?]
        at com.complexible.stardog.StardogKernel.bulkLoad(StardogKernel.java:1194) ~[stardog-7.0.2.jar:?]
        at com.complexible.stardog.StardogKernel.createDatabase(StardogKernel.java:1381) ~[stardog-7.0.2.jar:?]
        at com.complexible.stardog.protocols.http.server.AdminDatabaseService.createNewDatabase(AdminDatabaseService.java:539) ~[stardog-protocols-http-server-7.0.2.jar:?]
        at com.stardog.http.server.undertow.jaxrs.ExtractRoutes.lambda$handleIt$5(ExtractRoutes.java:192) ~[stardog-protocols-http-server-7.0.2.jar:?]
        at org.apache.shiro.subject.support.SubjectRunnable.doRun(SubjectRunnable.java:120) [shiro-core-1.3.0.jar:1.3.0]
        at org.apache.shiro.subject.support.SubjectRunnable.run(SubjectRunnable.java:108) [shiro-core-1.3.0.jar:1.3.0]
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [?:1.8.0_222]
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [?:1.8.0_222]
        at java.lang.Thread.run(Thread.java:748) [?:1.8.0_222]
ERROR 2019-11-07 20:23:27,505 [stardog-user-1] com.stardog.http.server.undertow.ErrorHandling:writeError(138): Unexpected error on the server
com.complexible.stardog.StardogException: Unable to create loader for database.

It seems like something is in a bad state. I couldn't quite follow the logs but I what I think was happening was I was loading from multiple *.gz files and they were loading in parallel so I'm not quite sure when exactly it failed.

Yes, we're aware of the problem and working on a fix. Meanwhile the only option is to use a different name for the database.

Crashing while bulk loading is a separate issue. Was it a JVM crash? Is there a crash dump file?

Thanks,
Pavel

I hadn't realized that it was related to that previous report where you suggested renaming the database. I can't seem to find it although I remember reading it just a couple of days ago.

It looks like I ran out of heap space. I allocated more space and it loaded. I am a little curious what Stardog did with "Namespace prefix 'skos' used but not defined" error. It completed loading but did it just skip the entire file or just the triples that referenced the skos: namespace?