[Bigdata-developers] "No space left on device" importing Wikidata

[Rune S. <rs...@un...>]

Hi list

I have setup an AWS instance using the blazegraph-ami-2.1.5. I have done the setup using a one disc configuration with 1 terabyte of space. After this I use the biodata.jar to import the full Wikidata dataset:

> sudo java -cp bigdata.jar com.bigdata.rdf.store.DataLoader -namespace wikidata -defaultGraph http://www.wikidata.org fullfeat
> ure.properties latest-all.ttl


After running 4 days the import terminates with an exception saying “no more space left on device”. There’s plenty of space left so what can I do to make this work?

> [ec2-user@ip-10-10-0-189 ~]$ df -h
> Filsystem      Størr Brugt  Tilb Brug% Monteret på
> devtmpfs         15G   60K   15G    1% /dev
> tmpfs            15G     0   15G    0% /dev/shm
> /dev/xvda1     1008G  305G  703G   31% /


> [ec2-user@ip-10-10-0-189 ~]$ ls -la ~/blazegraph --block-size=GB
> totalt 119GB
> drwxrwxr-x 2 ec2-user ec2-user   1GB 29 nov 10:53 .
> drwx------ 6 ec2-user ec2-user   1GB 29 nov 10:52 ..
> -rw-r--r-- 1 root     root     124GB  2 dec 10:14 blazegraph.jnl


/Rune Stilling

> Reading properties: fullfeature.properties
> Will load from: latest-all.ttl
> Journal file: /home/ec2-user/blazegraph/blazegraph.jnl
> ERROR: LexiconConfiguration.java:728: "0000-01-01T00:00:00Z" is not a valid representation of an XML Gregorian Calendar value.: value=0000-01-01T00:00:00Z
> ERROR: LexiconConfiguration.java:728: "0000-01-01T00:00:00Z" is not a valid representation of an XML Gregorian Calendar value.: value=0000-01-01T00:00:00Z
> ERROR: LexiconConfiguration.java:728: "0000-01-01T00:00:00Z" is not a valid representation of an XML Gregorian Calendar value.: value=0000-01-01T00:00:00Z
> ERROR: LexiconConfiguration.java:728: "0000-01-01T00:00:00Z" is not a valid representation of an XML Gregorian Calendar value.: value=0000-01-01T00:00:00Z
> ERROR: LexiconConfiguration.java:728: "0000-01-01T00:00:00Z" is not a valid representation of an XML Gregorian Calendar value.: value=0000-01-01T00:00:00Z
> ERROR: LexiconConfiguration.java:728: "0000-01-01T00:00:00Z" is not a valid representation of an XML Gregorian Calendar value.: value=0000-01-01T00:00:00Z
> ERROR: LexiconConfiguration.java:728: "0000-01-01T00:00:00Z" is not a valid representation of an XML Gregorian Calendar value.: value=0000-01-01T00:00:00Z
> ERROR: LexiconConfiguration.java:728: "0000-12-14T00:00:00Z" is not a valid representation of an XML Gregorian Calendar value.: value=0000-12-14T00:00:00Z
> ERROR: LexiconConfiguration.java:728: "0000-01-01T00:00:00Z" is not a valid representation of an XML Gregorian Calendar value.: value=0000-01-01T00:00:00Z
> ERROR: LexiconConfiguration.java:728: "0000-01-01T00:00:00Z" is not a valid representation of an XML Gregorian Calendar value.: value=0000-01-01T00:00:00Z
> ERROR: LexiconConfiguration.java:728: "0000-01-01T00:00:00Z" is not a valid representation of an XML Gregorian Calendar value.: value=0000-01-01T00:00:00Z
> ERROR: SPORelation.java:2303: java.util.concurrent.ExecutionException: com.bigdata.btree.EvictionError: java.lang.RuntimeException: java.io.IOException: Ikke mere
>  plads på enheden
> java.util.concurrent.ExecutionException: com.bigdata.btree.EvictionError: java.lang.RuntimeException: java.io.IOException: Ikke mere plads på enheden
>         at java.util.concurrent.FutureTask.report(FutureTask.java:122)
>         at java.util.concurrent.FutureTask.get(FutureTask.java:188)
>         at com.bigdata.rdf.spo.SPORelation.logFuture(SPORelation.java:2298)
>         at com.bigdata.rdf.spo.SPORelation.insert(SPORelation.java:2253)
>         at com.bigdata.rdf.store.AbstractTripleStore.addStatements(AbstractTripleStore.java:4405)
>         at com.bigdata.rdf.rio.StatementBuffer$Batch.writeSPOs(StatementBuffer.java:2178)
>         at com.bigdata.rdf.rio.StatementBuffer$Batch.addStatements(StatementBuffer.java:2027)
>         at com.bigdata.rdf.rio.StatementBuffer$Batch.writeNow(StatementBuffer.java:1912)
>         at com.bigdata.rdf.rio.StatementBuffer$Batch.access$1000(StatementBuffer.java:1645)
>         at com.bigdata.rdf.rio.StatementBuffer.incrementalWrite(StatementBuffer.java:1362)
>         at com.bigdata.rdf.rio.StatementBuffer.add(StatementBuffer.java:2240)
>         at com.bigdata.rdf.rio.StatementBuffer.add(StatementBuffer.java:2219)
>         at com.bigdata.rdf.rio.PresortRioLoader.handleStatement(PresortRioLoader.java:162)
>         at org.openrdf.rio.turtle.TurtleParser.reportStatement(TurtleParser.java:1155)
>         at org.openrdf.rio.turtle.TurtleParser.parseObject(TurtleParser.java:505)
>         at org.openrdf.rio.turtle.TurtleParser.parseObjectList(TurtleParser.java:428)
>         at org.openrdf.rio.turtle.TurtleParser.parsePredicateObjectList(TurtleParser.java:400)
>         at org.openrdf.rio.turtle.TurtleParser.parseTriples(TurtleParser.java:385)
>         at org.openrdf.rio.turtle.TurtleParser.parseStatement(TurtleParser.java:261)
>         at org.openrdf.rio.turtle.TurtleParser.parse(TurtleParser.java:216)
>         at com.bigdata.rdf.rio.BasicRioLoader.loadRdf2(BasicRioLoader.java:236)
>         at com.bigdata.rdf.rio.BasicRioLoader.loadRdf(BasicRioLoader.java:176)
>         at com.bigdata.rdf.store.DataLoader.loadData4_ParserErrors_Not_Trapped(DataLoader.java:1595)
>         at com.bigdata.rdf.store.DataLoader.loadFiles(DataLoader.java:1359)
>         at com.bigdata.rdf.store.DataLoader.main(DataLoader.java:2085)
> Caused by: com.bigdata.btree.EvictionError: java.lang.RuntimeException: java.io.IOException: Ikke mere plads på enheden
> Caused by: com.bigdata.btree.EvictionError: java.lang.RuntimeException: java.io.IOException: Ikke mere plads på enheden
>         at com.bigdata.btree.DefaultEvictionListener.doEviction(DefaultEvictionListener.java:198)
>         at com.bigdata.btree.DefaultEvictionListener.evicted(DefaultEvictionListener.java:75)
>         at com.bigdata.btree.DefaultEvictionListener.evicted(DefaultEvictionListener.java:37)
>         at com.bigdata.cache.HardReferenceQueue.evict(HardReferenceQueue.java:226)
>         at com.bigdata.cache.HardReferenceQueue.beforeOffer(HardReferenceQueue.java:199)
>         at com.bigdata.cache.RingBuffer.add(RingBuffer.java:159)
>         at com.bigdata.cache.HardReferenceQueue.add(HardReferenceQueue.java:176)
>         at com.bigdata.btree.AbstractBTree.doTouch(AbstractBTree.java:3766)
>         at com.bigdata.btree.AbstractBTree.doSyncTouch(AbstractBTree.java:3722)
>         at com.bigdata.btree.AbstractBTree.touch(AbstractBTree.java:3685)
>         at com.bigdata.btree.Node.insert(Node.java:916)
>         at com.bigdata.btree.Node.insert(Node.java:922)
>         at com.bigdata.btree.Node.insert(Node.java:922)
>         at com.bigdata.btree.AbstractBTree.insert(AbstractBTree.java:2184)
>         at com.bigdata.btree.AbstractBTree.insert(AbstractBTree.java:2108)
>         at com.bigdata.rdf.spo.SPOIndexWriteProc.applyOnce(SPOIndexWriteProc.java:246)
>         at com.bigdata.btree.proc.AbstractKeyArrayIndexProcedure.apply(AbstractKeyArrayIndexProcedure.java:381)
>         at com.bigdata.btree.UnisolatedReadWriteIndex.submit(UnisolatedReadWriteIndex.java:723)
>         at com.bigdata.rdf.spo.SPOIndexWriter.call(SPOIndexWriter.java:363)
>         at com.bigdata.rdf.spo.SPOIndexWriter.call(SPOIndexWriter.java:68)
>         at java.util.concurrent.FutureTask.run(FutureTask.java:262)
>         at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1152)
>         at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:622)
>         at java.lang.Thread.run(Thread.java:748)
> Caused by: java.lang.RuntimeException: java.io.IOException: Ikke mere plads på enheden
>         at com.bigdata.journal.DiskOnlyStrategy.writeOnDisk(DiskOnlyStrategy.java:2292)
>         at com.bigdata.journal.DiskOnlyStrategy.access$100(DiskOnlyStrategy.java:163)
>         at com.bigdata.journal.DiskOnlyStrategy$WriteCache.flush(DiskOnlyStrategy.java:386)
>         at com.bigdata.journal.DiskOnlyStrategy.flushWriteCache(DiskOnlyStrategy.java:506)
>         at com.bigdata.journal.DiskOnlyStrategy.write(DiskOnlyStrategy.java:2093)
>         at com.bigdata.journal.TemporaryRawStore.write(TemporaryRawStore.java:587)
>         at com.bigdata.btree.AbstractBTree.writeNodeOrLeaf(AbstractBTree.java:4416)
>         at com.bigdata.btree.AbstractBTree.writeNodeRecursiveConcurrent(AbstractBTree.java:4131)
>         at com.bigdata.btree.AbstractBTree.writeNodeRecursive(AbstractBTree.java:3844)
>         at com.bigdata.btree.DefaultEvictionListener.doEviction(DefaultEvictionListener.java:139)
>         ... 23 more
> Caused by: java.io.IOException: Ikke mere plads på enheden
>         at sun.nio.ch.FileDispatcherImpl.pwrite0(Native Method)
>         at sun.nio.ch.FileDispatcherImpl.pwrite(FileDispatcherImpl.java:66)
>         at sun.nio.ch.IOUtil.writeFromNativeBuffer(IOUtil.java:89)
>         at sun.nio.ch.IOUtil.write(IOUtil.java:51)
>         at sun.nio.ch.FileChannelImpl.writeInternal(FileChannelImpl.java:771)
>         at sun.nio.ch.FileChannelImpl.write(FileChannelImpl.java:756)
>         at com.bigdata.io.FileChannelUtility.writeAll(FileChannelUtility.java:610)
>         at com.bigdata.io.FileChannelUtility.writeAll(FileChannelUtility.java:509)
>         at com.bigdata.journal.DiskOnlyStrategy.writeOnDisk(DiskOnlyStrategy.java:2287)
>         ... 32 more
> ERROR: Banner.java:160: Uncaught exception in thread
> com.bigdata.btree.IndexInconsistentError: Index is in error state: 0e4d0aa7-6117-40fd-b85f-3932085187b3kb.spo.POS, store: com.bigdata.journal.TemporaryStore{file=
> /tmp/bigdata5787148345791213009.tmp}
>         at com.bigdata.btree.AbstractBTree.assertNotReadOnly(AbstractBTree.java:1429)
>         at com.bigdata.btree.BTree.setDirtyListener(BTree.java:709)
>         at com.bigdata.journal.Name2Addr.dropIndex(Name2Addr.java:1239)
>         at com.bigdata.journal.TemporaryStore.dropIndex(TemporaryStore.java:333)
>         at com.bigdata.rdf.spo.SPORelation.destroy(SPORelation.java:524)
>         at com.bigdata.rdf.store.AbstractTripleStore.destroy(AbstractTripleStore.java:2052)
>         at com.bigdata.rdf.store.TempTripleStore.close(TempTripleStore.java:155)
>         at com.bigdata.rdf.store.DataLoader.loadData4_ParserErrors_Not_Trapped(DataLoader.java:1715)
>         at com.bigdata.rdf.store.DataLoader.loadFiles(DataLoader.java:1359)
>         at com.bigdata.rdf.store.DataLoader.main(DataLoader.java:2085)
> Caused by: java.lang.RuntimeException: java.io.IOException: Ikke mere plads på enheden
>         at com.bigdata.journal.DiskOnlyStrategy.writeOnDisk(DiskOnlyStrategy.java:2292)
>         at com.bigdata.journal.DiskOnlyStrategy.access$100(DiskOnlyStrategy.java:163)
>         at com.bigdata.journal.DiskOnlyStrategy$WriteCache.flush(DiskOnlyStrategy.java:386)
>         at com.bigdata.journal.DiskOnlyStrategy.flushWriteCache(DiskOnlyStrategy.java:506)
>         at com.bigdata.journal.DiskOnlyStrategy.write(DiskOnlyStrategy.java:2093)
>         at com.bigdata.journal.TemporaryRawStore.write(TemporaryRawStore.java:587)
>         at com.bigdata.btree.AbstractBTree.writeNodeOrLeaf(AbstractBTree.java:4416)
>         at com.bigdata.btree.AbstractBTree.writeNodeRecursiveConcurrent(AbstractBTree.java:4131)
>         at com.bigdata.btree.AbstractBTree.writeNodeRecursive(AbstractBTree.java:3844)
>         at com.bigdata.btree.DefaultEvictionListener.doEviction(DefaultEvictionListener.java:139)
>         at com.bigdata.btree.DefaultEvictionListener.evicted(DefaultEvictionListener.java:75)
>         at com.bigdata.btree.DefaultEvictionListener.evicted(DefaultEvictionListener.java:37)
>         at com.bigdata.cache.HardReferenceQueue.evict(HardReferenceQueue.java:226)
>         at com.bigdata.cache.HardReferenceQueue.beforeOffer(HardReferenceQueue.java:199)
>         at com.bigdata.cache.RingBuffer.add(RingBuffer.java:159)
>         at com.bigdata.cache.HardReferenceQueue.add(HardReferenceQueue.java:176)
>         at com.bigdata.btree.AbstractBTree.doTouch(AbstractBTree.java:3766)
>         at com.bigdata.btree.AbstractBTree.doSyncTouch(AbstractBTree.java:3722)
>         at com.bigdata.btree.AbstractBTree.touch(AbstractBTree.java:3685)
>         at com.bigdata.btree.Node.insert(Node.java:916)
>         at com.bigdata.btree.Node.insert(Node.java:922)
>         at com.bigdata.btree.Node.insert(Node.java:922)
>         at com.bigdata.btree.AbstractBTree.insert(AbstractBTree.java:2184)
>         at com.bigdata.btree.AbstractBTree.insert(AbstractBTree.java:2108)
>         at com.bigdata.rdf.spo.SPOIndexWriteProc.applyOnce(SPOIndexWriteProc.java:246)
>         at com.bigdata.btree.proc.AbstractKeyArrayIndexProcedure.apply(AbstractKeyArrayIndexProcedure.java:381)
>         at com.bigdata.btree.UnisolatedReadWriteIndex.submit(UnisolatedReadWriteIndex.java:723)
>         at com.bigdata.rdf.spo.SPOIndexWriter.call(SPOIndexWriter.java:363)
>         at com.bigdata.rdf.spo.SPOIndexWriter.call(SPOIndexWriter.java:68)
>         at java.util.concurrent.FutureTask.run(FutureTask.java:262)
>         at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1152)
>         at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:622)
>         at java.lang.Thread.run(Thread.java:748)
> Caused by: java.io.IOException: Ikke mere plads på enheden
>         at sun.nio.ch.FileDispatcherImpl.pwrite0(Native Method)
>         at sun.nio.ch.FileDispatcherImpl.pwrite(FileDispatcherImpl.java:66)
>         at sun.nio.ch.IOUtil.writeFromNativeBuffer(IOUtil.java:89)
>         at sun.nio.ch.IOUtil.write(IOUtil.java:51)
>         at sun.nio.ch.FileChannelImpl.writeInternal(FileChannelImpl.java:771)
>         at sun.nio.ch.FileChannelImpl.write(FileChannelImpl.java:756)
>         at com.bigdata.io.FileChannelUtility.writeAll(FileChannelUtility.java:610)
>         at com.bigdata.io.FileChannelUtility.writeAll(FileChannelUtility.java:509)
>         at com.bigdata.journal.DiskOnlyStrategy.writeOnDisk(DiskOnlyStrategy.java:2287)
>         ... 32 more