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Unfortunately, i experience this (very prominent!) problem as well. Here are some more infos and a possible workaround.
Setup:
The Slave is started via:
java -Xmx512m -jar slave.jar -jnlpUrl http://jenkins/computer/slave/slave-agent.jnlp in order to see the log messages
First off, setting various values to these variables (in catalina on tomcat) did not seem to improve the behaviour:
-Dhudson.remoting.Launcher.pingTimeoutSec
-Dhudson.remoting.Launcher.pingIntervalSec
-Dhudson.slaves.ChannelPinger.pingInterval
I was getting the "channel already closed" exception quite frequently and mostly at the same spot during script execution. The job (between 12h and 16h) on the slave (via windows batch file) generates large amounts of documentation via doxygen and pipes the output into a logfile, so it uses quite some CPU and does not echo progress. Throttling the CPU so that the NIC wont suffer from the overload, did not help the problem though. Also, i performed continuous pings to the slave (from the master and back) and ping requests only seldomly failed (normal network tolerances).
To say this first: allthough jenkins failed with the above mentioned exception, the slave continued to perform its job "in the background", so if the exception came after 1h, i would see the updated documentation after 16h allthough jenkins already declared the job as failed.
For the chronology, these are the log excerpts:
In the live console on the jenkins WebUI i see (THE FIRST LINE IS THE LAST OUTPUT BY MY SCRIPT):