FATAL: ApplicationImpl$ComponentsSetup

[Benjade Palmero]

Hello,

I am having problem with starting vivo, here's my error:

org.apache.jena.tdb.TDBException: Process ID 11772 can't open database at location ../vivo/home/tdbModels/ because it is already locked by the process with PID 8565. TDB databases do not permit concurrent usage across JVMs so in order to prevent possible data corruption you cannot open this location from the JVM that does not own the lock for the dataset    at org.apache.jena.tdb.StoreConnection._makeAndCache(StoreConnection.java:282)    at org.apache.jena.tdb.StoreConnection.make(StoreConnection.java:244)    at org.apache.jena.tdb.StoreConnection.make(StoreConnection.java:258)    at org.apache.jena.tdb.transaction.DatasetGraphTransaction.(DatasetGraphTransaction.java:69)    at org.apache.jena.tdb.sys.TDBMaker.createDirect(TDBMaker.java:126)    at java.util.concurrent.ConcurrentHashMap.computeIfAbsent(ConcurrentHashMap.java:1660)    at org.apache.jena.tdb.sys.TDBMaker._create(TDBMaker.java:112)

By the way, I'm using version 1.13.

All the best,

BeNPaL

[Dragan Ivanovic]

Hello Benjade,

Thanks for your email. Not so easy to say what might be the problem, but let me try to guess. It looks as the problem is in a not killed process, i.e. it might be that the previous tomcat instance is not shut down properly. You might try to kill the process with PID 8565. 

If your VIVO instance is the new one, meaning you are not upgrading from some previous version and not moving the data, you can even completely delete directory ../vivo/home/tdbModels, it will be created again, but the database will be empty. After successful running of the VIVO instance you can ingest the sample data to test some VIVO functionalities. You can find instructions how to do that at this link - https://wiki.lyrasis.org/display/VIVODOC113x/Sample+Data.

Anyway, do not hesitate to contact me back if you still have problem with running the VIVO. Moreover, you can join our regular weekly calls to discuss with us all your issues - https://wiki.lyrasis.org/display/VIVO/2022+Development+Calls

Regards,

Dragan Ivanovic

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[Benjade Palmero]

Hello,

Thank you for your reply Dragan. I have managed to solve the problem already, it's a tomcat workaround. 

I run the vivo tomcat instance on a separate user and separate port.

I am looking forward to meeting you and the rest of the group through dev calls in the future.

Again, thank you very much.

All the best,

BeNPaL

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