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The same problem suddenly started happening for us too with matrix child jobs on Jenkins 1.532.2 when I upgraded the Git client plugin to v1.6.5 and the Git plugin to v2.0.4.
We were previously running Git plugin v1.4.0. Unfortunately I don't know what version of the Git client plugin we were using but it will have been contemporary with that. We didn't see this problem with those versions.
The Jenkins master has been restarted several times (which seems to cause the slaves to be restarted too.) I haven't tried rebooting the slave but I see no reason why this would make any difference.
23:09:39 Started by upstream project "nightly-brightsign-master" build number 895
23:09:39 originally caused by:
23:09:39 Started by timer
23:09:41 Building remotely on bob in workspace /home/jenkins/workspace/nightly-brightsign-master/MACHINE/panther_puma/label/nightly
23:09:41 Checkout:nightly / /home/jenkins/workspace/nightly-brightsign-master/MACHINE/panther_puma/label/nightly - hudson.remoting.Channel@5e4c03d4:bob
23:09:41 Using strategy: Default
23:09:41 Last Built Revision: Revision 3ed2f7fb57edea2411d450caac3a53cf54323a59 (origin/master)
23:09:41 Using shallow clone
23:09:41 Wiping out workspace first.
23:09:41 Cloning the remote Git repository
23:09:41 Cloning repository gitolite@cam-git:bcm7425/bcm7425-oe
23:09:41 git --version
23:09:41 git version 1.7.10.4
23:09:41 ERROR: Error cloning remote repo 'origin' : Could not clone gitolite@cam-git:bcm7425/bcm7425-oe
23:09:41 hudson.plugins.git.GitException: Could not clone gitolite@cam-git:bcm7425/bcm7425-oe
23:09:41 at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.clone(CliGitAPIImpl.java:220)
23:09:41 at hudson.plugins.git.GitSCM$2.invoke(GitSCM.java:1006)
23:09:41 at hudson.plugins.git.GitSCM$2.invoke(GitSCM.java:942)
23:09:41 at hudson.FilePath$FileCallableWrapper.call(FilePath.java:2439)
23:09:41 at hudson.remoting.UserRequest.perform(UserRequest.java:118)
23:09:41 at hudson.remoting.UserRequest.perform(UserRequest.java:48)
23:09:41 at hudson.remoting.Request$2.run(Request.java:328)
23:09:41 at hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:72)
23:09:41 at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
23:09:41 at java.util.concurrent.FutureTask.run(FutureTask.java:166)
23:09:41 at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
23:09:41 at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
23:09:41 at java.lang.Thread.run(Thread.java:724)
23:09:41 Caused by: hudson.plugins.git.GitException: Command "git clone --progress -o origin --depth 1 gitolite@cam-git:bcm7425/bcm7425-oe /home/jenkins/workspace/nightly-brightsign-master/MACHINE/panther_puma/label/nightly" returned status code 128:
23:09:41 stdout:
23:09:41 stderr: fatal: Could not get current working directory: No such file or directory
23:09:41
23:09:41 at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommandIn(CliGitAPIImpl.java:774)
23:09:41 at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.clone(CliGitAPIImpl.java:218)
23:09:41 ... 12 more