Open Microscopy Environment

I have installed Omero 4.1 onto an Ubuntu 8.04 server edition linux virtual machine following the sticky guide posted on this forum. It was all working well until I tried to move the /OMERO folder onto an NFS mount and start using a NIS user login. Now when you upload a photo using the client editor you get the following error:

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java.lang.Exception: org.openmicroscopy.shoola.env.data.DSAccessException: Cannot access data.
Cannot load hierarchy for class pojos.DatasetData.
   at org.openmicroscopy.shoola.env.data.OMEROGateway.handleException(OMEROGateway.java:333)
   at org.openmicroscopy.shoola.env.data.OMEROGateway.loadContainerHierarchy(OMEROGateway.java:1452)
   at org.openmicroscopy.shoola.env.data.OmeroDataServiceImpl.loadContainerHierarchy(OmeroDataServiceImpl.java:639)
   at org.openmicroscopy.shoola.env.data.views.calls.DMLoader$1.doCall(DMLoader.java:86)
   at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:145)
   at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
   at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
   at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
   at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
   at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
   at java.lang.Thread.run(Unknown Source) Caused by: Ice.MarshalException
    reason = (null)
   at IceInternal.BasicStream.typeToClass(BasicStream.java:2287)
   at IceInternal.BasicStream.findClass(BasicStream.java:2204)
   at IceInternal.BasicStream.loadObjectFactory(BasicStream.java:2071)
   at IceInternal.BasicStream.readObject(BasicStream.java:1450)
   at omero.model.Image.__read(Image.java:2023)
   at IceInternal.BasicStream.readObject(BasicStream.java:1500)
   at IceInternal.BasicStream.readPendingObjects(BasicStream.java:1632)
   at omero.api._IContainerDelM.loadContainerHierarchy(_IContainerDelM.java:611)
   at omero.api.IContainerPrxHelper.loadContainerHierarchy(IContainerPrxHelper.java:730)
   at omero.api.IContainerPrxHelper.loadContainerHierarchy(IContainerPrxHelper.java:702)
   at org.openmicroscopy.shoola.env.data.OMEROGateway.loadContainerHierarchy(OMEROGateway.java:1449)
   ... 9 more

   at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.showErrorDialog(UserNotifierImpl.java:128)
   at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:179)
   at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:168)
   at org.openmicroscopy.shoola.agents.treeviewer.DataBrowserLoader.handleException(DataBrowserLoader.java:133)
   at org.openmicroscopy.shoola.env.data.events.DSCallAdapter.eventFired(DSCallAdapter.java:84)
   at org.openmicroscopy.shoola.env.data.views.BatchCallMonitor$1.run(BatchCallMonitor.java:124)
   at java.awt.event.InvocationEvent.dispatch(Unknown Source)
   at java.awt.EventQueue.dispatchEvent(Unknown Source)
   at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
   at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
   at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
   at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
   at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
   at java.awt.EventDispatchThread.run(Unknown Source)

I have checked the permissions on /OMERO and have (as root) run both chown -R omero:users /OMERO and chmod -R 755 /OMERO.

I can also do the following which shows the file permissions are correct:

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omero@omeroserv:~$ ls -alh / | grep OMERO
drwxr-xr-x 12 omero users 4.0K 2010-04-09 13:50 OMERO
<removed> on /OMERO type nfs (rw,tcp,bg,intr,addr=<removed>)
omero@omeroserv:~$ touch /OMERO/file
omero@omeroserv:~$ ls -alh
total 179M
drwxr-xr-x 12 omero users 4.0K 2010-04-09 13:50 .
drwxr-xr-x 23 root  root  4.0K 2010-04-08 10:59 ..
-rw-------  1 omero users  465 2010-04-09 10:02 .bash_history
-rw-r--r--  1 omero users    0 2010-04-09 13:50 file
drwxr-xr-x  2 omero users 4.0K 2010-04-07 17:23 Files
drwxr-xr-x  2 omero users 4.0K 2010-04-08 16:15 FullText
drwxr-xr-x  3 omero users 4.0K 2010-04-09 09:58 .java
-rw-------  1 omero users    0 2010-04-09 10:02 .lock_test1TZR_P.tmp
-rw-------  1 omero users    0 2010-04-09 10:00 .lock_test4fq0BK.tmp
-rw-------  1 omero users    0 2010-04-09 09:58 .lock_testAdVEx6.tmp
-rw-------  1 omero users    0 2010-04-09 10:02 .lock_testrqev9_.tmp
-rw-------  1 omero users    0 2010-04-09 09:59 .lock_testtn-9hR.tmp
-rw-------  1 omero users    0 2010-04-09 10:01 .lock_testVp_DRa.tmp
-rw-------  1 omero users    0 2010-04-09 09:58 .lock_testwK2ZEw.tmp
-rw-------  1 omero users    0 2010-04-09 10:02 .lock_testZZWBA1.tmp
drwxr-xr-x  4 omero users 4.0K 2010-04-08 09:59 old_omero
drwxr-xr-x  3 omero users 4.0K 2010-04-07 11:56 omero
drwxr-xr-x  3 omero users 4.0K 2010-04-08 15:17 .omero
-rwxr-xr-x  1 omero users 178M 2009-12-02 12:05 omero-Beta4.1.1.tar
drwxr-xr-x  9 omero users 4.0K 2010-04-07 11:56 omero_dist
drwxr-xr-x  2 omero users 4.0K 2010-04-07 15:33 Pixels
drwxrwxrwx 10 root  root  4.0K 2010-04-09 12:00 .snapshot
drwxr-xr-x  2 omero users 4.0K 2010-04-07 17:23 Thumbnails
omero@omeroserv:~$ rm file

The web admin interface works except when you click on drive space it produces a server error (which I have submited through the form).

Any suggestions on a possible fix would be greatly appreciated.

Can you let us have a look at your server logs?

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cd /OMERO/omero_dist
tar jcvf omero_logs.tar.bz2 var/log


Then attach the archive here.

Logs are attached. I did have an issue with it having forgotten DB user and password which I resolved but will be showing in the logs.

Well that's a new one. What's happening is that during use space calculation (which happens whenever a new file system service is created) something is failing quite catastrophically. We have several deployments with OMERO binary repositories on NFS so something really odd is going on.

I've created a ticket for this and CC'd you on it:

http://trac.openmicroscopy.org.uk/omero/ticket/2157

Can you run df -k and df -h for me and paste the output here?

Output as requested... we have no other application issues using the filer, we run most things from here.

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root@omeroserv:~# df -h
Filesystem            Size  Used Avail Use% Mounted on
/dev/sda1             1.9G  461M  1.4G  26% /
varrun                506M   84K  506M   1% /var/run
varlock               506M     0  506M   0% /var/lock
udev                  506M   56K  506M   1% /dev
devshm                506M     0  506M   0% /dev/shm
/dev/sda3             1.9G   35M  1.8G   2% /tmp
/dev/sda6             5.6G  730M  4.6G  14% /usr
/dev/sda2             1.9G  1.3G  566M  69% /var
<removed>:/vol/users/unix_users
                      1.7T  314G  1.3T  20% /mnt/filer/users
<removed>:/vol/service_support
                      1.9T  295G  1.6T  16% /mnt/filer/service_support
<removed>:/vol/users/local-linux-shared
                      1.7T  314G  1.3T  20% /usr/local/shared_bin
<removed>:/vol/groups/omero
                      540G  353G  188G  66% /OMERO
root@omeroserv:~# df -k
Filesystem           1K-blocks      Used Available Use% Mounted on
/dev/sda1              1936396    471352   1367452  26% /
varrun                  517612        84    517528   1% /var/run
varlock                 517612         0    517612   0% /var/lock
udev                    517612        56    517556   1% /dev
devshm                  517612         0    517612   0% /dev/shm
/dev/sda3              1936428     35764   1803072   2% /tmp
/dev/sda6              5809336    747384   4769172  14% /usr
/dev/sda2              1936428   1259908    578928  69% /var
<removed>:/vol/users/unix_users
                     1717986944 329251136 1388735808  20% /mnt/filer/users
<removed>:/vol/service_support
                     1932735296 308936704 1623798592  16% /mnt/filer/service_support
<removed>:/vol/users/local-linux-shared
                     1717986944 329251136 1388735808  20% /usr/local/shared_bin
<removed>:/vol/groups/omero
                     566231040 369743040 196488000  66% /OMERO


The ticket has been updated. It would be useful to find out the actual file and/or directory that's causing the problem by running the test, after downloading and extracting the build, as outlined on the ticket.

Thanks for the feedback!

I have attempted running the command sent to me via the ticket after upgrading to the version suggested, this is the output I get.

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omero@omeroserv:~/omero_dist/lib/server$ java -cp  server.jar:libs/commons-logging.jar:libs/log4j.jar:libs/commons-io.jar ome.tools.FileSystem /OMEROjava -cp  server.jar:libs/commons-logging.jar:libs/log4j.jar:libs/commons-io.jar ome.tools.FileSystem /OMERO
log4j:WARN No appenders could be found for logger (ome.tools.FileSystem).
log4j:WARN Please initialize the log4j system properly.


I moved the old install out of the way and re-used the original folder name.

Okay, we'll need the log4j configuration file then. Grab this:

http://users.openmicroscopy.org.uk/~cxa ... properties

This should do it:

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cd ~/omero_dist/lib/server
wget http://users.openmicroscopy.org.uk/~cxallan/log4j.properties
java -cp .:server.jar:libs/commons-logging.jar:libs/log4j.jar:libs/commons-io.jar ome.tools.FileSystem /OMERO


Note the differing .: at the beginning of the classpath.