# Dictionary corrupted **URL:** \ **Category:** Support\ **Created:** [August 1, 2018, 4:57pm UTC](https://community.stardog.com/t/dictionary-corrupted/1172 "2018-08-01T16:57:50Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![rwynne](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.stardog.com/rwynne/32/282_2.png) [@rwynne](https://community.stardog.com/u/rwynne)\ **Post date:** [August 1, 2018, 4:57pm UTC](https://community.stardog.com/t/dictionary-corrupted/1172/1 "2018-08-01T16:57:51Z")
Hi all, My first post (take it easy, ok?!)… I was in the midst of updating our triplestore here at NCI with our most recent data. Shutdown the server, restarted (all for good measure). Then the following stacktrace was thrown. The only thing I could do was to drop the DB, recreate, and then load again - which worked. Just bringing this to your attention for any possible diagnosis. Thanks, Rob [triplestore@ncidb-d174-v bin]$ ./stardog-admin server start Loading Databases: 50% complete in 00:00:19 WARN 2018-08-01 12:23:03,138 [main] com.complexible.stardog.dht.dictionary.HashDictionary:(279): Dictionary is corrupted, will try to repair automatically java.io.IOException: Cannot read header: 11094 != 8719617 at com.complexible.stardog.dht.impl.PagedDiskHashTable.readFreeOverflowPages(PagedDiskHashTable.java:436) ~[stardog-5.2.1.jar:?] at com.complexible.stardog.dht.impl.PagedDiskHashTable.readFooter(PagedDiskHashTable.java:361) ~[stardog-5.2.1.jar:?] at com.complexible.stardog.dht.impl.PagedDiskHashTable.read(PagedDiskHashTable.java:299) ~[stardog-5.2.1.jar:?] at com.complexible.stardog.dht.impl.PagedDiskHashTable.(PagedDiskHashTable.java:205) ~[stardog-5.2.1.jar:?] at com.complexible.stardog.dht.impl.PagedDiskHashTableBuilder.build(PagedDiskHashTableBuilder.java:161) ~[stardog-5.2.1.jar:?] at com.complexible.stardog.dht.dictionary.HashDictionary.(HashDictionary.java:269) [stardog-5.2.1.jar:?] at com.complexible.stardog.index.disk.DefaultDiskIndexReader.toMappingDictionary(DefaultDiskIndexReader.java:146) [stardog-5.2.1.jar:?] at com.complexible.stardog.index.disk.DefaultDiskIndexReader.read(DefaultDiskIndexReader.java:133) [stardog-5.2.1.jar:?] at com.complexible.stardog.index.io.IndexIO.read(IndexIO.java:320) [stardog-5.2.1.jar:?] at com.complexible.stardog.db.DatabaseFactoryImpl.read(DatabaseFactoryImpl.java:126) [stardog-5.2.1.jar:?] at com.complexible.stardog.db.DatabaseFactoryImpl.read(DatabaseFactoryImpl.java:55) [stardog-5.2.1.jar:?] at com.complexible.stardog.StardogKernel.openDatabase(StardogKernel.java:2583) [stardog-5.2.1.jar:?] at com.complexible.stardog.StardogKernel.initDatabases(StardogKernel.java:2316) [stardog-5.2.1.jar:?] at com.complexible.stardog.StardogKernel.start(StardogKernel.java:2251) [stardog-5.2.1.jar:?] at com.complexible.stardog.StardogKernel.initialize(StardogKernel.java:789) [stardog-5.2.1.jar:?] at com.complexible.stardog.Stardog.initKernel(Stardog.java:219) [stardog-5.2.1.jar:?] at com.complexible.stardog.Stardog.(Stardog.java:211) [stardog-5.2.1.jar:?] at com.complexible.stardog.Stardog.(Stardog.java:65) [stardog-5.2.1.jar:?] at com.complexible.stardog.Stardog$StardogBuilder.create(Stardog.java:572) [stardog-5.2.1.jar:?] at com.complexible.stardog.cli.impl.ServerStart.call(ServerStart.java:149) [stardog-cli-5.2.1.jar:?] at com.complexible.stardog.cli.impl.ServerStart.call(ServerStart.java:44) [stardog-cli-5.2.1.jar:?] at com.complexible.stardog.cli.CLIBase.execute(CLIBase.java:55) [stardog-cli-5.2.1.jar:?] at com.complexible.stardog.cli.admin.CLI.main(CLI.java:189) [stardog-cli-5.2.1.jar:?] … WARN 2018-08-01 12:25:04,570 [main] com.complexible.stardog.db.DatabaseFactoryImpl:read(141): Database NCIEVS is invalid and the repair failed: null Loading Databases: 100% complete in 00:02:21 Loading Databases: 100% complete in 00:02:21 Loading Databases finished in 00:02:21.761 ---
**Author:** ![zachary.whitley](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.stardog.com/zachary.whitley/32/94_2.png) [@zachary.whitley](https://community.stardog.com/u/zachary.whitley)\ **Post date:** [August 1, 2018, 5:24pm UTC](https://community.stardog.com/t/dictionary-corrupted/1172/2 "2018-08-01T17:24:24Z")
> [@rwynne](#): > > My first post (take it easy, ok?!)… OH MY GOD WHAT DID YOU DO!!! Just kidding. Nice to see you here. NCI? National Cancer Institute? It would be interesting to hear what you're doing with Stardog. > [@rwynne](#): > > updating our triplestore What version were you upgrading from? Did it shutdown cleanly? You might want to check your disk space to make sure you hadn't accidentally filled the drive that it's on. ---
**Author:** ![rwynne](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.stardog.com/rwynne/32/282_2.png) [@rwynne](https://community.stardog.com/u/rwynne)\ **Post date:** [August 1, 2018, 5:57pm UTC](https://community.stardog.com/t/dictionary-corrupted/1172/3 "2018-08-01T17:57:10Z")
We’re currently supporting a Clinical Trials Search API, and using it as the Triplestore of choice for our new EVS RESTAPI. Stardog Version 5.2.1. This error occurred after updating the graphs in each DB. 11G used on the mount with 88G free. Shutdown command hung and had to kill the server. Logs are set to rotate, and I don’t see them as being a space hog. We do the following for our _data_ updates (ignore params that don’t look like links, I can only post up to 5 right now): ./stardog data remove -g …ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl NCIEVS -u $USER -p $PASSWORD ./stardog data add NCIEVS -g …ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl .owl -u $USER -p $PASSWORD ./stardog data remove -g …ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.rdf NCIEVS -u $USER -p $PASSWORD ./stardog data add NCIEVS -g …ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.rdf .rdf -u $USER -p $PASSWORD ./stardog data remove -g …NCIt CTRP -u $USER -p $PASSWORD ./stardog data add CTRP -g …NCIt .owl -u $USER -p $PASSWORD ./stardog data remove -g …NCIt\_Flattened CTRP -u $USER -p $PASSWORD ./stardog data add CTRP -g …NCIt\_Flattened .rdf -u $USER -p $PASSWORD So since the startup threw the error, I did the following: ./stardog-admin db drop NCIEVS ./stardog-admin db drop CTRP ./stardog-admin db create -u \*\*\*\*\*\* -p \*\*\*\* -n NCIEVS ./stardog-admin db create -u \*\*\*\*\* -p \*\*\*\*\* -n CTRP and then ran our update script above. Startup was then clean. Everything seems to be fine now. All relevant params in properties file: query.all.graphs = true logging.audit.enabled = true logging.audit.type = text logging.audit.rotation.type = size logging.audit.rotation.limit = 1000000 leading.wildcard.search.enabled = true; search.enabled = true; search.wildcard.search.enabled = true; HTH, Rob ---
**Author:** ![hmottestad](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.stardog.com/hmottestad/32/19_2.png) [@hmottestad](https://community.stardog.com/u/hmottestad)\ **Post date:** [August 1, 2018, 7:53pm UTC](https://community.stardog.com/t/dictionary-corrupted/1172/4 "2018-08-01T19:53:19Z")
We have had trouble upgrading from 5.1.0 to 5.3.x. Always ended up corrupted. We have discovered that running optimize before upgrading helps prevent corruption. Håvard ---
**Author:** ![hmottestad](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.stardog.com/hmottestad/32/19_2.png) [@hmottestad](https://community.stardog.com/u/hmottestad)\ **Post date:** [August 1, 2018, 7:54pm UTC](https://community.stardog.com/t/dictionary-corrupted/1172/5 "2018-08-01T19:54:43Z")
Also, if you restore from disk (block based) backup, you have to insert a statement into stardog (anything will do) otherwise optimize will crash. ---
**Author:** ![rwynne](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.stardog.com/rwynne/32/282_2.png) [@rwynne](https://community.stardog.com/u/rwynne)\ **Post date:** [August 2, 2018, 1:56pm UTC](https://community.stardog.com/t/dictionary-corrupted/1172/6 "2018-08-02T13:56:13Z")
This makes sense. We just upgraded on our Dev tier. Thanks! ---
**Author:** ![system](https://canada1.discourse-cdn.com/flex030/uploads/stardog/original/2X/e/ed66b48a616f505106a4acde3c9cee7e6da9bc67.svg) [@system](https://community.stardog.com/u/system)\ **Post date:** [August 16, 2018, 1:56pm UTC](https://community.stardog.com/t/dictionary-corrupted/1172/7 "2018-08-16T13:56:19Z")
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