StarDog Frozen

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s.ar...@geophy.com

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Oct 4, 2016, 7:44:19 AM10/4/16
to Stardog
Stardog is frozen. I cannot stop or restart. 

Here is the log of events. 

Any idea how to recover from this?

INFO  2016-10-03 17:13:56,594 [Stardog.Executor-62] com.complexible.stardog.StardogKernel:stop(326): 
INFO  2016-10-03 17:13:56,594 [Stardog.Executor-62] com.complexible.stardog.StardogKernel:stop(329): Creating index finished in 00:04:44.412
WARN  2016-10-03 17:30:05,153 [RDFStreamProcessor-0] com.complexible.common.rdf.rio.RDFStreamProcessor:setException(557): Error during loading /home/samur/tools/stardog-4.1.3/../d2rq-0.8.1/entities.ttl.gz: java.lang.OutOfMemoryError: GC overhead limit exceeded
java.lang.RuntimeException: java.lang.OutOfMemoryError: GC overhead limit exceeded
at com.complexible.common.rdf.rio.RDFStreamProcessor$ProducerThread.work(RDFStreamProcessor.java:781) [stardog-utils-rdf-4.1.3.jar:?]
at com.complexible.common.rdf.rio.RDFStreamProcessor$Worker.call(RDFStreamProcessor.java:737) [stardog-utils-rdf-4.1.3.jar:?]
at com.complexible.common.rdf.rio.RDFStreamProcessor$Worker.call(RDFStreamProcessor.java:726) [stardog-utils-rdf-4.1.3.jar:?]
at java.util.concurrent.FutureTask.run(FutureTask.java:266) [?:1.8.0_91]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [?:1.8.0_91]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [?:1.8.0_91]
at java.lang.Thread.run(Thread.java:745) [?:1.8.0_91]
Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded
at java.util.Arrays.copyOfRange(Arrays.java:3664) ~[?:1.8.0_91]
at java.lang.String.<init>(String.java:207) ~[?:1.8.0_91]
at java.lang.String.substring(String.java:1933) ~[?:1.8.0_91]
at info.aduna.net.ParsedURI._parseAuthority(ParsedURI.java:525) ~[sesame-util-4.0.0.jar:?]
at info.aduna.net.ParsedURI._parse(ParsedURI.java:462) ~[sesame-util-4.0.0.jar:?]
at info.aduna.net.ParsedURI.<init>(ParsedURI.java:89) ~[sesame-util-4.0.0.jar:?]
at com.complexible.common.rdf.rio.parser.AbstractRDFParser.resolveURI(AbstractRDFParser.java:411) ~[stardog-utils-rdf-4.1.3.jar:?]
at com.complexible.common.rdf.rio.parser.TurtleParser.parseURI(TurtleParser.java:1002) ~[stardog-utils-rdf-4.1.3.jar:?]
at com.complexible.common.rdf.rio.parser.TurtleParser.parseValue(TurtleParser.java:628) ~[stardog-utils-rdf-4.1.3.jar:?]
at com.complexible.common.rdf.rio.parser.TurtleParser.parseQuotedLiteral(TurtleParser.java:715) ~[stardog-utils-rdf-4.1.3.jar:?]
at com.complexible.common.rdf.rio.parser.TurtleParser.parseValue(TurtleParser.java:640) ~[stardog-utils-rdf-4.1.3.jar:?]
at com.complexible.common.rdf.rio.parser.TurtleParser.parseObject(TurtleParser.java:516) ~[stardog-utils-rdf-4.1.3.jar:?]
at com.complexible.common.rdf.rio.parser.TurtleParser.parseObjectList(TurtleParser.java:442) ~[stardog-utils-rdf-4.1.3.jar:?]
at com.complexible.common.rdf.rio.parser.TurtleParser.parsePredicateObjectList(TurtleParser.java:413) ~[stardog-utils-rdf-4.1.3.jar:?]
at com.complexible.common.rdf.rio.parser.TurtleParser.parseTriples(TurtleParser.java:398) ~[stardog-utils-rdf-4.1.3.jar:?]
at com.complexible.common.rdf.rio.parser.TurtleParser.parseStatement(TurtleParser.java:248) ~[stardog-utils-rdf-4.1.3.jar:?]
at com.complexible.common.rdf.rio.parser.TurtleParser.parse(TurtleParser.java:230) ~[stardog-utils-rdf-4.1.3.jar:?]
at com.complexible.common.rdf.rio.RDFStreamBuilder$RDFAbstractStream.parse(RDFStreamBuilder.java:230) ~[stardog-utils-rdf-4.1.3.jar:?]
at com.complexible.common.rdf.rio.RDFStreamBuilder$RDFAbstractStream.parse(RDFStreamBuilder.java:197) ~[stardog-utils-rdf-4.1.3.jar:?]
at com.complexible.common.rdf.rio.RDFStreamProcessor$ProducerThread.work(RDFStreamProcessor.java:773) ~[stardog-utils-rdf-4.1.3.jar:?]
... 6 more
ERROR 2016-10-03 17:30:05,166 [Stardog.Executor-62] com.complexible.tx.api.impl.DefaultTransaction:computePrepareResult(489): There was a fatal failure during preparation of df11ebb4-c4c3-4436-942e-14d5550962ef
com.complexible.tx.api.ResourceTransactionException: There was an error while indexing the new data
at com.complexible.stardog.search.db.ConnectableSearchConnectionImpl$SearchIndexResourceTransaction.prepare(ConnectableSearchConnectionImpl.java:410) ~[stardog-search-waldo-4.1.3.jar:?]
at com.complexible.tx.api.BaseResourceTransaction.prepare(BaseResourceTransaction.java:187) ~[stardog-4.1.3.jar:?]
at com.complexible.tx.api.impl.DefaultTransaction.computePrepareResult(DefaultTransaction.java:473) ~[stardog-4.1.3.jar:?]
at com.complexible.tx.api.impl.DefaultTransaction.runPreparePhase(DefaultTransaction.java:439) ~[stardog-4.1.3.jar:?]
at com.complexible.tx.api.impl.DefaultTransaction.commit(DefaultTransaction.java:330) ~[stardog-4.1.3.jar:?]
at com.complexible.stardog.db.DatabaseConnectionImpl.commit(DatabaseConnectionImpl.java:405) ~[stardog-4.1.3.jar:?]
at com.complexible.stardog.db.DatabaseImpl$DBConnectionWrapper.commit(DatabaseImpl.java:1401) ~[stardog-4.1.3.jar:?]
at com.complexible.stardog.db.DelegatingDatabaseConnection.commit(DelegatingDatabaseConnection.java:279) ~[stardog-4.1.3.jar:?]
at com.complexible.stardog.StardogKernel$KernelDbConnection.commit(StardogKernel.java:2753) ~[stardog-4.1.3.jar:?]
at com.complexible.stardog.db.DelegatingDatabaseConnection.commit(DelegatingDatabaseConnection.java:279) ~[stardog-4.1.3.jar:?]
at com.complexible.stardog.StardogKernel$NotifyingDatabaseConnection.commit(StardogKernel.java:3058) ~[stardog-4.1.3.jar:?]
at com.complexible.stardog.protocols.server.SPECServerFunction.commitTx(SPECServerFunction.java:373) ~[stardog-protocols-spec-server-4.1.3.jar:?]
at com.complexible.stardog.protocols.server.SPECServerFunction.handleMessage(SPECServerFunction.java:164) ~[stardog-protocols-spec-server-4.1.3.jar:?]
at com.complexible.common.protocols.server.rpc.ServerHandler.lambda$handleMessage$1(ServerHandler.java:338) ~[stardog-protocols-api-server-4.1.3.jar:?]
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) [?:1.8.0_91]
at java.util.concurrent.FutureTask.run(FutureTask.java:266) [?:1.8.0_91]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [?:1.8.0_91]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [?:1.8.0_91]
at java.lang.Thread.run(Thread.java:745) [?:1.8.0_91]
Caused by: com.complexible.stardog.search.IndexingException: java.lang.RuntimeException: java.lang.OutOfMemoryError: GC overhead limit exceeded
at com.complexible.stardog.search.IndexingStrategy.index(IndexingStrategy.java:104) ~[stardog-search-waldo-4.1.3.jar:?]
at com.complexible.stardog.search.db.ConnectableSearchIndex.reindex(ConnectableSearchIndex.java:521) ~[stardog-search-waldo-4.1.3.jar:?]
at com.complexible.stardog.search.db.ConnectableSearchConnectionImpl$SearchIndexResourceTransaction.prepare(ConnectableSearchConnectionImpl.java:380) ~[stardog-search-waldo-4.1.3.jar:?]
... 18 more
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.lang.OutOfMemoryError: GC overhead limit exceeded
at java.util.concurrent.FutureTask.report(FutureTask.java:122) ~[?:1.8.0_91]
at java.util.concurrent.FutureTask.get(FutureTask.java:192) ~[?:1.8.0_91]
at com.complexible.common.util.concurrent.ExecutionGroup$1.executeAndWait(ExecutionGroup.java:78) ~[stardog-utils-common-4.1.3.jar:?]
at com.complexible.stardog.search.IndexingStrategy.index(IndexingStrategy.java:98) ~[stardog-search-waldo-4.1.3.jar:?]
at com.complexible.stardog.search.db.ConnectableSearchIndex.reindex(ConnectableSearchIndex.java:521) ~[stardog-search-waldo-4.1.3.jar:?]
at com.complexible.stardog.search.db.ConnectableSearchConnectionImpl$SearchIndexResourceTransaction.prepare(ConnectableSearchConnectionImpl.java:380) ~[stardog-search-waldo-4.1.3.jar:?]
... 18 more
Caused by: java.lang.RuntimeException: java.lang.OutOfMemoryError: GC overhead limit exceeded
at com.complexible.common.rdf.rio.RDFStreamProcessor$ProducerThread.work(RDFStreamProcessor.java:781) ~[stardog-utils-rdf-4.1.3.jar:?]
at com.complexible.common.rdf.rio.RDFStreamProcessor$Worker.call(RDFStreamProcessor.java:737) ~[stardog-utils-rdf-4.1.3.jar:?]
at com.complexible.common.rdf.rio.RDFStreamProcessor$Worker.call(RDFStreamProcessor.java:726) ~[stardog-utils-rdf-4.1.3.jar:?]
... 4 more
Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded
at java.util.Arrays.copyOfRange(Arrays.java:3664) ~[?:1.8.0_91]
at java.lang.String.<init>(String.java:207) ~[?:1.8.0_91]
at java.lang.String.substring(String.java:1933) ~[?:1.8.0_91]
at info.aduna.net.ParsedURI._parseAuthority(ParsedURI.java:525) ~[sesame-util-4.0.0.jar:?]
at info.aduna.net.ParsedURI._parse(ParsedURI.java:462) ~[sesame-util-4.0.0.jar:?]
at info.aduna.net.ParsedURI.<init>(ParsedURI.java:89) ~[sesame-util-4.0.0.jar:?]
at com.complexible.common.rdf.rio.parser.AbstractRDFParser.resolveURI(AbstractRDFParser.java:411) ~[stardog-utils-rdf-4.1.3.jar:?]
at com.complexible.common.rdf.rio.parser.TurtleParser.parseURI(TurtleParser.java:1002) ~[stardog-utils-rdf-4.1.3.jar:?]
at com.complexible.common.rdf.rio.parser.TurtleParser.parseValue(TurtleParser.java:628) ~[stardog-utils-rdf-4.1.3.jar:?]
at com.complexible.common.rdf.rio.parser.TurtleParser.parseQuotedLiteral(TurtleParser.java:715) ~[stardog-utils-rdf-4.1.3.jar:?]
at com.complexible.common.rdf.rio.parser.TurtleParser.parseValue(TurtleParser.java:640) ~[stardog-utils-rdf-4.1.3.jar:?]
at com.complexible.common.rdf.rio.parser.TurtleParser.parseObject(TurtleParser.java:516) ~[stardog-utils-rdf-4.1.3.jar:?]
at com.complexible.common.rdf.rio.parser.TurtleParser.parseObjectList(TurtleParser.java:442) ~[stardog-utils-rdf-4.1.3.jar:?]
at com.complexible.common.rdf.rio.parser.TurtleParser.parsePredicateObjectList(TurtleParser.java:413) ~[stardog-utils-rdf-4.1.3.jar:?]
at com.complexible.common.rdf.rio.parser.TurtleParser.parseTriples(TurtleParser.java:398) ~[stardog-utils-rdf-4.1.3.jar:?]
at com.complexible.common.rdf.rio.parser.TurtleParser.parseStatement(TurtleParser.java:248) ~[stardog-utils-rdf-4.1.3.jar:?]
at com.complexible.common.rdf.rio.parser.TurtleParser.parse(TurtleParser.java:230) ~[stardog-utils-rdf-4.1.3.jar:?]
at com.complexible.common.rdf.rio.RDFStreamBuilder$RDFAbstractStream.parse(RDFStreamBuilder.java:230) ~[stardog-utils-rdf-4.1.3.jar:?]
at com.complexible.common.rdf.rio.RDFStreamBuilder$RDFAbstractStream.parse(RDFStreamBuilder.java:197) ~[stardog-utils-rdf-4.1.3.jar:?]
at com.complexible.common.rdf.rio.RDFStreamProcessor$ProducerThread.work(RDFStreamProcessor.java:773) ~[stardog-utils-rdf-4.1.3.jar:?]
at com.complexible.common.rdf.rio.RDFStreamProcessor$Worker.call(RDFStreamProcessor.java:737) ~[stardog-utils-rdf-4.1.3.jar:?]
at com.complexible.common.rdf.rio.RDFStreamProcessor$Worker.call(RDFStreamProcessor.java:726) ~[stardog-utils-rdf-4.1.3.jar:?]
... 4 more
ERROR 2016-10-03 17:30:06,080 [Stardog.Executor-62] com.complexible.stardog.db.DatabaseConnectionImpl:commit(414): There was an error committing the transaction, all changes were rolled back successfully
com.complexible.tx.api.HeuristicRollbackException: There was a fatal failure during preparation of df11ebb4-c4c3-4436-942e-14d5550962ef There was an error while indexing the new data
at com.complexible.tx.api.impl.DefaultTransaction.runPreparePhase(DefaultTransaction.java:444) ~[stardog-4.1.3.jar:?]
at com.complexible.tx.api.impl.DefaultTransaction.commit(DefaultTransaction.java:330) ~[stardog-4.1.3.jar:?]
at com.complexible.stardog.db.DatabaseConnectionImpl.commit(DatabaseConnectionImpl.java:405) ~[stardog-4.1.3.jar:?]
at com.complexible.stardog.db.DatabaseImpl$DBConnectionWrapper.commit(DatabaseImpl.java:1401) ~[stardog-4.1.3.jar:?]
at com.complexible.stardog.db.DelegatingDatabaseConnection.commit(DelegatingDatabaseConnection.java:279) ~[stardog-4.1.3.jar:?]
at com.complexible.stardog.StardogKernel$KernelDbConnection.commit(StardogKernel.java:2753) ~[stardog-4.1.3.jar:?]
at com.complexible.stardog.db.DelegatingDatabaseConnection.commit(DelegatingDatabaseConnection.java:279) ~[stardog-4.1.3.jar:?]
at com.complexible.stardog.StardogKernel$NotifyingDatabaseConnection.commit(StardogKernel.java:3058) ~[stardog-4.1.3.jar:?]
at com.complexible.stardog.protocols.server.SPECServerFunction.commitTx(SPECServerFunction.java:373) ~[stardog-protocols-spec-server-4.1.3.jar:?]
at com.complexible.stardog.protocols.server.SPECServerFunction.handleMessage(SPECServerFunction.java:164) ~[stardog-protocols-spec-server-4.1.3.jar:?]
at com.complexible.common.protocols.server.rpc.ServerHandler.lambda$handleMessage$1(ServerHandler.java:338) ~[stardog-protocols-api-server-4.1.3.jar:?]
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) [?:1.8.0_91]
at java.util.concurrent.FutureTask.run(FutureTask.java:266) [?:1.8.0_91]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [?:1.8.0_91]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [?:1.8.0_91]
at java.lang.Thread.run(Thread.java:745) [?:1.8.0_91]
ERROR 2016-10-03 17:30:06,081 [Stardog.Executor-62] com.complexible.common.protocols.server.rpc.ServerHandler:exceptionCaught(415): exceptionCaughtServerHandler
com.complexible.stardog.db.DatabaseException: There was a fatal failure during preparation of df11ebb4-c4c3-4436-942e-14d5550962ef There was an error while indexing the new data
at com.complexible.stardog.db.DatabaseConnectionImpl.commit(DatabaseConnectionImpl.java:415) ~[stardog-4.1.3.jar:?]
at com.complexible.stardog.db.DatabaseImpl$DBConnectionWrapper.commit(DatabaseImpl.java:1401) ~[stardog-4.1.3.jar:?]
at com.complexible.stardog.db.DelegatingDatabaseConnection.commit(DelegatingDatabaseConnection.java:279) ~[stardog-4.1.3.jar:?]
at com.complexible.stardog.StardogKernel$KernelDbConnection.commit(StardogKernel.java:2753) ~[stardog-4.1.3.jar:?]
at com.complexible.stardog.db.DelegatingDatabaseConnection.commit(DelegatingDatabaseConnection.java:279) ~[stardog-4.1.3.jar:?]
at com.complexible.stardog.StardogKernel$NotifyingDatabaseConnection.commit(StardogKernel.java:3058) ~[stardog-4.1.3.jar:?]
at com.complexible.stardog.protocols.server.SPECServerFunction.commitTx(SPECServerFunction.java:373) ~[stardog-protocols-spec-server-4.1.3.jar:?]
at com.complexible.stardog.protocols.server.SPECServerFunction.handleMessage(SPECServerFunction.java:164) ~[stardog-protocols-spec-server-4.1.3.jar:?]
at com.complexible.common.protocols.server.rpc.ServerHandler.lambda$handleMessage$1(ServerHandler.java:338) ~[stardog-protocols-api-server-4.1.3.jar:?]
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) [?:1.8.0_91]
at java.util.concurrent.FutureTask.run(FutureTask.java:266) [?:1.8.0_91]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [?:1.8.0_91]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [?:1.8.0_91]
at java.lang.Thread.run(Thread.java:745) [?:1.8.0_91]
Caused by: com.complexible.tx.api.HeuristicRollbackException: There was a fatal failure during preparation of df11ebb4-c4c3-4436-942e-14d5550962ef There was an error while indexing the new data
at com.complexible.tx.api.impl.DefaultTransaction.runPreparePhase(DefaultTransaction.java:444) ~[stardog-4.1.3.jar:?]
at com.complexible.tx.api.impl.DefaultTransaction.commit(DefaultTransaction.java:330) ~[stardog-4.1.3.jar:?]
at com.complexible.stardog.db.DatabaseConnectionImpl.commit(DatabaseConnectionImpl.java:405) ~[stardog-4.1.3.jar:?]
... 13 more
INFO  2016-10-04 08:57:52,206 [Stardog.Executor-204] com.complexible.stardog.StardogKernel:shutdown(2112): Stardog server 4.1.3 shutdown on 2016-10-04T08:57:52.206+0200.


INFO  2016-10-04 08:59:31,682 [main] com.complexible.stardog.virtual.DefaultVirtualGraphRegistry:syncCache(184): Initializing R2RML registry
INFO  2016-10-04 08:59:31,776 [main] com.complexible.stardog.virtual.DefaultVirtualGraphRegistry:syncCache(193): Loaded R2RML registry with 0 sources
INFO  2016-10-04 08:59:32,521 [main] com.complexible.stardog.StardogKernel:start(1864): Initializing Stardog
WARN  2016-10-04 08:59:32,851 [main] com.complexible.stardog.metadata.MetadataIO:readBytes(260): Unrecognized option in the metadata: search.version
WARN  2016-10-04 08:59:33,364 [main] com.complexible.stardog.metadata.MetadataIO:readBytes(260): Unrecognized option in the metadata: search.version

************************************************************
This copy of Stardog is licensed to samur araujo (sa...@geophy.com), geophy
This is a trial Enterprise license
This license will expire in 12 days on Sun Oct 16 09:33:05 CEST 2016
************************************************************

                                                             :;   
                                      ;;                   `;`:   
  `'+',    ::                        `++                    `;:`  
 +###++,  ,#+                        `++                    .     
 ##+.,',  '#+                         ++                     +    
,##      ####++  ####+:   ##,++` .###+++   .####+    ####++++#    
`##+     ####+'  ##+#++   ###++``###'+++  `###'+++  ###`,++,:     
 ####+    ##+        ++.  ##:   ###  `++  ###  `++` ##`  ++:      
  ###++,  ##+        ++,  ##`   ##;  `++  ##:   ++; ##,  ++:      
    ;+++  ##+    ####++,  ##`   ##:  `++  ##:   ++' ;##'#++       
     ;++  ##+   ###  ++,  ##`   ##'  `++  ##;   ++:  ####+        
,.   +++  ##+   ##:  ++,  ##`   ###  `++  ###  .++  '#;           
,####++'  +##++ ###+#+++` ##`   :####+++  `####++'  ;####++`      
`####+;    ##++  ###+,++` ##`    ;###:++   `###+;   `###++++      
                                                    ##   `++      
                                                   .##   ;++      
                                                    #####++`      
                                                     `;;;.        
************************************************************


Stardog server 4.1.3 started on Tue Oct 04 08:59:33 CEST 2016.

Stardog server is listening on all network interfaces.
SNARL server available at snarl://localhost:5820.
HTTP server available at http://localhost:5820.

STARDOG_HOME=/home/samur/tools/stardog-4.1.3/bin/.. 

Michael Grove

unread,
Oct 4, 2016, 7:47:57 AM10/4/16
to stardog
On Tue, Oct 4, 2016 at 7:44 AM, <s.ar...@geophy.com> wrote:
> Stardog is frozen. I cannot stop or restart.
>
> Here is the log of events.
>
> Any idea how to recover from this?
>
> INFO 2016-10-03 17:13:56,594 [Stardog.Executor-62]
> com.complexible.stardog.StardogKernel:stop(326):
> INFO 2016-10-03 17:13:56,594 [Stardog.Executor-62]
> com.complexible.stardog.StardogKernel:stop(329): Creating index finished in
> 00:04:44.412
> WARN 2016-10-03 17:30:05,153 [RDFStreamProcessor-0]
> com.complexible.common.rdf.rio.RDFStreamProcessor:setException(557): Error
> during loading
> /home/samur/tools/stardog-4.1.3/../d2rq-0.8.1/entities.ttl.gz:
> java.lang.OutOfMemoryError: GC overhead limit exceeded
> java.lang.RuntimeException: java.lang.OutOfMemoryError: GC overhead limit
> exceeded

The server ran out of memory; you need to stop the process and
allocate more memory to the JVM.

How big of a dataset are you attempting to load?

Cheers,

Mike
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Samur Araujo

unread,
Oct 4, 2016, 7:56:49 AM10/4/16
to sta...@clarkparsia.com
The dataset is 600MB compressed. It has 82 Million triples.

I will increase memory and run again. 

Best,
Samur

> stardog+unsubscribe@clarkparsia.com

> For more options, visit this group at
> http://groups.google.com/a/clarkparsia.com/group/stardog?hl=en

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Senior Data Scientist 
Geophy 

Nieuwe Plantage 54-55
2611XK  Delft
+31 (0)70 7640725 

1 Fore Street
EC2Y 9DT  London
+44 (0)20 37690760

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