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I finally got around to trying it again. The important point is that the operation that fails is checkout.
I created a job to check out a reference copy on each node and that worked for an hour and succeeded just fine the first time around. But I set it with sparse checkout of just a few files.
Then I've set up the actual job. It succeeded building some configurations, but not others. It has problems specifically on one slave node. It might be that it's disks are slower and the repository is so large that checking it out takes just over 10 minutes on that node and just under 10 minutes on the other or that that node happened to be more loaded or something.
It should also be noted, that killing the checkout operation leaves the lock behind, so Jenkins won't recover from this without serious manual surgery.
Below is relevant log. Note, that the build took 26 minutes in total, but it clearly says it timed out after 10 minutes, so the limit was not applied cumulatively. It is possible, that the checkout code indeed took 10 minutes.
Building remotely on Win8-builder (various labels) in workspace D:\Jenkins\workspace\Project\LABEL\Android
Cloning the remote Git repository
Using shallow clone
Cloning repository g...@git.company.com:project
> git init D:\Jenkins\workspace\Project\LABEL\Android\src
Fetching upstream changes from g...@git.company.com:project
> git --version
using GIT_SSH to set credentials jenkins key for git
> git fetch --tags --progress g...@git.company.com:project +refs/heads/:refs/remotes/origin/ --depth=1
> git config remote.origin.url g...@git.company.com:project
> git config remote.origin.fetch +refs/heads/:refs/remotes/origin/
> git config remote.origin.url g...@git.company.com:project
Pruning obsolete local branches
Fetching upstream changes from g...@git.company.com:project
using GIT_SSH to set credentials jenkins key for git
> git fetch --tags --progress g...@git.company.com:project +refs/heads/:refs/remotes/origin/ --prune
Checking out Revision 159bc2b21669bc7b5217341fc8de9cd6b48439b2 (origin/dev/jan.hudec/pu)
> git config core.sparsecheckout
> git checkout -f 159bc2b21669bc7b5217341fc8de9cd6b48439b2
ERROR: Timeout after 10 minutes
FATAL: Could not checkout null with start point 159bc2b21669bc7b5217341fc8de9cd6b48439b2
hudson.plugins.git.GitException: Could not checkout null with start point 159bc2b21669bc7b5217341fc8de9cd6b48439b2
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl$8.execute(CliGitAPIImpl.java:1479)
at org.jenkinsci.plugins.gitclient.RemoteGitImpl$CommandInvocationHandler$1.call(RemoteGitImpl.java:153)
at org.jenkinsci.plugins.gitclient.RemoteGitImpl$CommandInvocationHandler$1.call(RemoteGitImpl.java:146)
at hudson.remoting.UserRequest.perform(UserRequest.java:118)
at hudson.remoting.UserRequest.perform(UserRequest.java:48)
at hudson.remoting.Request$2.run(Request.java:326)
at hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:72)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at hudson.remoting.Engine$1$1.run(Engine.java:63)
at java.lang.Thread.run(Unknown Source)
Caused by: hudson.plugins.git.GitException: Command "git checkout -f 159bc2b21669bc7b5217341fc8de9cd6b48439b2" returned status code -1:
stdout:
stderr:
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommandIn(CliGitAPIImpl.java:1307)
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommandIn(CliGitAPIImpl.java:1283)
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommandIn(CliGitAPIImpl.java:1279)
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommand(CliGitAPIImpl.java:1084)
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommand(CliGitAPIImpl.java:1094)
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl$8.execute(CliGitAPIImpl.java:1474)
... 11 more