[ome-users] Query re the OMERO upgrade to OMERO 4.2.0 on a Mac server - images are completely dark

Taylor, Ronald C ronald.taylor at pnl.gov
Fri Aug 20 22:34:17 BST 2010

Forgot to include diagnostics output - so, resending my help request with diags output at bottom.

-----Original Message-----
From: Taylor, Ronald C 
Sent: Friday, August 20, 2010 2:22 PM
To: 'Josh Moore'; ome-users at lists.openmicroscopy.org.uk
Cc: ronald.taylor24 at gmail.com; Taylor, Ronald C; Wiley, Steven
Subject: RE: [ome-users] need help with the OMERO upgrade to OMERO 4.2.0 on a Mac server - images are completely dark

Hi Josh, everybody,

Got 4.2.0 up and running on our Mac server, but initial testing shows that all our images come up completely dark. The images are still there - the file names get listed on-screen, but they appear on-screen as completely dark image boxes - no way to actually see them.

So - this problem did not occur in the 4.2.0 upgrade on our Linux box. But the problem is definitely there on our Mac. Even when I do a "launch full viewer" the images come up black. Any ideas on what I should check? 

Does this perhaps have something to do with telling OMERO where its data directory is? I have checked the

 file, which shows
  omero.data.dir set to "/OMERO/"

 which appears to be correct - that was the previous setting for 4.1.1, and the subdirs in /OMERO/ show dates of "Aug20" (today), so Omero must have been accessing those directories today when I was testing the system. However, I see that all the thumbnail files have dates of today. Is that correct, or is something going wrong? The image files were previously in 4.1.1, so should not the thumbnails have been created long ago?

Anyhoo - could use more guidance.

Ronald Taylor, Ph.D.
Computational Biology & Bioinformatics Group Pacific Northwest National Laboratory
902 Battelle Boulevard
P.O. Box 999, Mail Stop J4-33
Richland, WA  99352 USA
Office:  509-372-6568
Email: ronald.taylor at pnl.gov


bash-3.2$ omero admin diagnostics

OMERO Diagnostics Beta-4.2.0-r7571-b29

Commands:   java -version                  1.6.0     (/usr/bin/java -- 2 others)
Commands:   python -V                      2.6.1     (/usr/bin/python)
Commands:   icegridnode --version          3.3.1     (/Library/Ice/Versions/3.3.1/bin/icegridnode)
Commands:   icegridadmin --version         3.3.1     (/Library/Ice/Versions/3.3.1/bin/icegridadmin)
Commands:   psql --version                 8.3.11    (/Postgres/bin/psql)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 21006, enabled)
Server:     DropBox                        active (pid = 21007, enabled)
Server:     FileServer                     active (pid = 21008, enabled)
Server:     Indexer-0                      active (pid = 21009, enabled)
Server:     MonitorServer                  active (pid = 21010, enabled)
Server:     OMERO.Glacier2                 active (pid = 21011, enabled)
Server:     OMERO.IceStorm                 active (pid = 21012, enabled)
Server:     Processor-0                    active (pid = 21013, enabled)
Server:     Repository-1                   error: node `repo' couldn't be reached:
the node is not active
Server:     Tables-0                       active (pid = 21014, enabled)
Server:     TestDropBox                    inactive (enabled)

Log dir:    /Library/Omero/Versions/4.2.0/omero_dist/var/log exists

Log files:  Blitz-0.log                    1.0 MB        errors=15   warnings=14
Log files:  DropBox.log                    2.0 KB        errors=1    warnings=3
Log files:  FileServer.log                 0.0 KB
Log files:  Indexer-0.log                  5.0 KB        errors=0    warnings=9
Log files:  MonitorServer.log              2.0 KB        errors=1    warnings=2
Log files:  OMEROweb.log                   8.0 KB        errors=22   warnings=0
Log files:  Processor-0.log                0.0 KB
Log files:  Tables-0.log                   0.0 KB
Log files:  TestDropBox.log                n/a
Log files:  master.err                     0.0 KB
Log files:  master.out                     0.0 KB
Log files:  Total size                     1.22 MB

Parsing Blitz-0.log:[line:17] => Server restarted <=




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