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I also have this issue on Jenkins 1.625.3 LTS. Using Java 8 on master and slave nodes. I have a Windows Server 2003/XP VM as my slave build node. The problem is intermittent and eventually the slave node regains connection, but the timeout is too short so it just fails the build.
In jenkins.err.log, I get
Jan 06, 2016 3:38:19 PM jenkins.slaves.JnlpSlaveAgentProtocol$Handler$1 onClosed
WARNING: Computer.threadPoolForRemoting [#3599] for cibuilder-8 terminated
java.io.EOFException
at org.jenkinsci.remoting.nio.NioChannelHub$3.run(NioChannelHub.java:613)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at hudson.remoting.SingleLaneExecutorService$1.run(SingleLaneExecutorService.java:112)
at jenkins.util.ContextResettingExecutorService$1.run(ContextResettingExecutorService.java:28)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
On the slave node's build log:
Fetching upstream changes from file: > git --version # timeout=10
> git -c core.askpass=true fetch --tags --progress file:FATAL: java.io.EOFException
hudson.remoting.RequestAbortedException: java.io.EOFException
at hudson.remoting.Request.abort(Request.java:297)
at hudson.remoting.Channel.terminate(Channel.java:847)
at org.jenkinsci.remoting.nio.NioChannelHub$3.run(NioChannelHub.java:613)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at hudson.remoting.SingleLaneExecutorService$1.run(SingleLaneExecutorService.java:112)
at jenkins.util.ContextResettingExecutorService$1.run(ContextResettingExecutorService.java:28)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
at ......remote call to cibuilder-8(Native Method)
at hudson.remoting.Channel.attachCallSiteStackTrace(Channel.java:1416)
at hudson.remoting.Request.call(Request.java:172)
at hudson.remoting.Channel.call(Channel.java:780)
at org.jenkinsci.plugins.gitclient.RemoteGitImpl$CommandInvocationHandler.execute(RemoteGitImpl.java:145)
at sun.reflect.GeneratedMethodAccessor250.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.jenkinsci.plugins.gitclient.RemoteGitImpl$CommandInvocationHandler.invoke(RemoteGitImpl.java:131)
at com.sun.proxy.$Proxy51.execute(Unknown Source)
at hudson.plugins.git.GitSCM.retrieveChanges(GitSCM.java:1003)
at hudson.plugins.git.GitSCM.checkout(GitSCM.java:1043)
at hudson.scm.SCM.checkout(SCM.java:485)
at hudson.model.AbstractProject.checkout(AbstractProject.java:1275)
at hudson.model.AbstractBuild$AbstractBuildExecution.defaultCheckout(AbstractBuild.java:610)
at jenkins.scm.SCMCheckoutStrategy.checkout(SCMCheckoutStrategy.java:86)
at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:532)
at hudson.model.Run.execute(Run.java:1741)
at hudson.matrix.MatrixRun.run(MatrixRun.java:146)
at hudson.model.ResourceController.execute(ResourceController.java:98)
at hudson.model.Executor.run(Executor.java:408)
Caused by: java.io.EOFException
at org.jenkinsci.remoting.nio.NioChannelHub$3.run(NioChannelHub.java:613)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at hudson.remoting.SingleLaneExecutorService$1.run(SingleLaneExecutorService.java:112)
at jenkins.util.ContextResettingExecutorService$1.run(ContextResettingExecutorService.java:28)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
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