Open Microscopy Environment

Is there any way to avoid the "nasty locking issues with files in OMERO root and JVM directories" in my circumstances?

I can re-install the OMERO server anyway to the server. but changing the circumstances is not an option now.

Do I need to wait for the version 4.2?

I don't see a particular reason to wait for 4.2 as it applies to this particular problem, no. First step would be to ensure that permissions are correct on the folders where the temporary and lock files are. Here are some of these errors from the log:

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2010-04-30 15:32:13,651 ERROR [              omero.util.TempFileManager] (MainThread) rmtree error: remove('/afs/cs.cmu.edu/user/bhcho/omero/tmp/omero_bhcho/9360/.lock') => [Errno 13] Permission denied: '/afs/cs.cmu.edu/user/bhcho/omero/tmp/omero_bhcho/9360/.lock'
2010-04-30 15:32:13,651 ERROR [              omero.util.TempFileManager] (MainThread) rmtree error: rmdir('/afs/cs.cmu.edu/user/bhcho/omero/tmp/omero_bhcho/9360') => [Errno 13] Permission denied: '/afs/cs.cmu.edu/user/bhcho/omero/tmp/omero_bhcho/9360'
...
2010-04-30 15:25:23,317 WARN  [        ome.services.util.ServiceHandler] (l.Server-8) Unknown exception thrown.

java.lang.SecurityException: Could not lock User prefs.Lock file access denied.
        at java.util.prefs.FileSystemPreferences.checkLockFile0ErrorCode(FileSystemPreferences.java:919)
        at java.util.prefs.FileSystemPreferences.lockFile(FileSystemPreferences.java:908)
        at java.util.prefs.FileSystemPreferences.sync(FileSystemPreferences.java:714)
...
Exception in thread "Timer-0" java.lang.SecurityException: Could not lock User prefs.Lock file access denied.
        at java.util.prefs.FileSystemPreferences.checkLockFile0ErrorCode(FileSystemPreferences.java:919)
        at java.util.prefs.FileSystemPreferences.lockFile(FileSystemPreferences.java:908)
        at java.util.prefs.FileSystemPreferences.sync(FileSystemPreferences.java:714)
        at java.util.prefs.FileSystemPreferences.flush(FileSystemPreferences.java:807)
        at java.util.prefs.FileSystemPreferences.syncWorld(FileSystemPreferences.java:451)
        at java.util.prefs.FileSystemPreferences.access$1200(FileSystemPreferences.java:33)
        at java.util.prefs.FileSystemPreferences$4.run(FileSystemPreferences.java:419)
        at java.util.TimerThread.mainLoop(Timer.java:512)
        at java.util.TimerThread.run(Timer.java:462)
Exception in thread "Timer-0" java.lang.SecurityException: Could not lock User prefs.Lock file access denied.
        at java.util.prefs.FileSystemPreferences.checkLockFile0ErrorCode(FileSystemPreferences.java:919)
        at java.util.prefs.FileSystemPreferences.lockFile(FileSystemPreferences.java:908)
        at java.util.prefs.FileSystemPreferences.sync(FileSystemPreferences.java:714)
        at java.util.prefs.FileSystemPreferences.flush(FileSystemPreferences.java:807)
        at java.util.prefs.FileSystemPreferences.syncWorld(FileSystemPreferences.java:451)
        at java.util.prefs.FileSystemPreferences.access$1200(FileSystemPreferences.java:33)
        at java.util.prefs.FileSystemPreferences$4.run(FileSystemPreferences.java:419)
        at java.util.TimerThread.mainLoop(Timer.java:512)
        at java.util.TimerThread.run(Timer.java:462)

Should be in /afs/cs.cmu.edu/user/bhcho/.java/...


It also may help to examine the global preferences directory here:

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2010-04-30 10:29:24,408 WARN  [                         java.util.prefs] (      main) Prefs file removed in background /afs/cs.cmu.edu/misc/java/amd64_f10/jdk1.6.0_16/libexec/jdk1.6.0_16-64bit/jre/.systemPrefs/prefs.xml
...


The locking and shared storage semantics on AFS are unfortunately not something I'm very familiar with (though my recollection is that it does not support many POSIX locking features) so this is something you're going to have ask whomever set the system up for you.