[InterMine Dev] data loading errors

Kalpana Karra kkarra at stanford.edu
Tue Oct 27 05:28:12 GMT 2020


Hello,

If loading a data source that takes a while, I see this type of warning and eventually connection timeout, wondering how to get around this.

[dataLoad] [db.production housekeeper] WARN com.zaxxer.hikari.pool.HikariPool - db.production - Thread starvation or clock leap detected (housekeeper delta=58s402ms).
 [dataLoad] [db.production housekeeper] WARN com.zaxxer.hikari.pool.HikariPool - db.production - Thread starvation or clock leap detected (housekeeper delta=46s330ms).


Connection error: 
org.postgresql.util.PSQLException: The connection attempt failed.
	at org.postgresql.Driver$ConnectThread.getResult(Driver.java:403)
	at org.postgresql.Driver.connect(Driver.java:261)
	at java.sql.DriverManager.getConnection(DriverManager.java:664)
	at java.sql.DriverManager.getConnection(DriverManager.java:247)
	at org.postgresql.ds.common.BaseDataSource.getConnection(BaseDataSource.java:94)
	at org.postgresql.ds.common.BaseDataSource.getConnection(BaseDataSource.java:79)
	at com.zaxxer.hikari.pool.PoolBase.newConnection(PoolBase.java:369)
	at com.zaxxer.hikari.pool.PoolBase.newPoolEntry(PoolBase.java:198)
	at com.zaxxer.hikari.pool.HikariPool.createPoolEntry(HikariPool.java:467)
	at com.zaxxer.hikari.pool.HikariPool.access$100(HikariPool.java:71)
	at com.zaxxer.hikari.pool.HikariPool$PoolEntryCreator.call(HikariPool.java:706)
	at com.zaxxer.hikari.pool.HikariPool$PoolEntryCreator.call(HikariPool.java:692)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.net.SocketTimeoutException
	at java.net.SocksSocketImpl.remainingMillis(SocksSocketImpl.java:111)
	at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
	at java.net.Socket.connect(Socket.java:607)
	at org.postgresql.core.PGStream.<init>(PGStream.java:69)
	at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:156)
	at org.postgresql.core.ConnectionFactory.openConnection(ConnectionFactory.java:49)
	at org.postgresql.jdbc.PgConnection.<init>(PgConnection.java:195)
	at org.postgresql.Driver.makeConnection(Driver.java:452)
	at org.postgresql.Driver.access$100(Driver.java:61)
	at org.postgresql.Driver$ConnectThread.run(Driver.java:362)
	... 1 more
Failed to create a Non-Pooling DataSource from PostgreSQL JDBC Driver 42.2.2 for postgres at jdbc:postgresql

Thanks,
-Kalpana



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