[InterMine Dev] data loading errors

Sam Hokin shokin at ncgr.org
Tue Oct 27 15:53:39 GMT 2020


I get that when the database/connections are heavily loaded, like if I'm running post-processors and sources at the same time. 
Sometimes it recovers with just the WARNs, and sometimes it'll drop the connection with a socket timeout as you see. You'll want to 
boost your resources, likely on the database server, but perhaps also on the machine running the IM code.

On 10/26/20 11:28 PM, Kalpana Karra wrote:
> 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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