[ome-users] import error
Damir Sudar
dsudar at lbl.gov
Thu Jan 24 00:00:42 GMT 2013
Hi Josh,
Thanks again. I just moved the binary repository to a different
filesystem (local ext4) and now the import of the offending file works
fine. So indeed a clear indication that one should stay away from
network filesystems. Might be a good idea to put a very clear warning in
the OMERO System Administrator Documentation to that effect.
I appreciate your help and for guiding me quickly to the solution.
- Damir
On 1/23/2013 1:09 PM, Josh Moore wrote:
> On Jan 23, 2013, at 7:42 PM, Damir Sudar wrote:
>
>> Hi Josh,
> Hi Damir,
>
> my apologies for letting this slip. Please do try to CC ome-users since the rest of the team won't let me forget! :)
>
>> Based on your initial question about what filesystem, I looked a little further and tried to import the same offending file into a different OMERO installation that we set up for testing. This test installation is also on Ubuntu 12.04LTS but uses a xfs Linux filesystem for the omero.data.dir. And that one had no trouble with the offending file. Have you seen others have trouble with using a CIFS filesystem?
> NFS & Samba filesystems have all shown problems in some if not most cases. The base requirement is that the posix locking semantics are guaranteed. A couple other threads on this topic:
>
> * http://lists.openmicroscopy.org.uk/pipermail/ome-users/2012-September/003287.html
> * https://www.openmicroscopy.org/community/viewtopic.php?f=5&t=386&start=20#p1172
>
>> On 1/21/2013 11:37 AM, Damir Sudar wrote:
>>> Hi Josh,
>>>
>>> Thanks much for looking into this.
>>>
>>> The server which runs stock Ubuntu 12.04 LTS uses an ext4 filesystem for all regular partitions. My omero.data.dir points to a mounted filesystem that resides on a NetApp filer and that is presented to the world as a cifs filesystem. (For future use of the DropBox functionality, I've changed the "omero.fs.watchDir" to /home/omero/DropBox)
>>>
>>> I've attached the master.err file and the master.out is empty. Which server log(s) would be most useful? Here is the output from "omero admin diagnostics".
> Other than the network mount, the rest of your installation looks reasonably healthy.
> Best wishes,
> ~Josh.
>
>
>
>>> ================================================================================
>>> OMERO Diagnostics 4.4.5-ice34-b20
>>> ================================================================================
>>>
>>> Commands: java -version 1.7.0 (/usr/bin/java)
>>> Commands: python -V 2.7.3 (/usr/bin/python)
>>> Commands: icegridnode --version 3.4.2 (/usr/bin/icegridnode)
>>> Commands: icegridadmin --version 3.4.2 (/usr/bin/icegridadmin)
>>> Commands: psql --version 9.1.5 (/usr/bin/psql -- 2 others)
>>>
>>> Server: icegridnode running
>>> Server: Blitz-0 active (pid = 2166, enabled)
>>> Server: DropBox active (pid = 2167, enabled)
>>> Server: FileServer active (pid = 2168, enabled)
>>> Server: Indexer-0 active (pid = 2170, enabled)
>>> Server: MonitorServer active (pid = 2171, enabled)
>>> Server: OMERO.Glacier2 active (pid = 2173, enabled)
>>> Server: OMERO.IceStorm active (pid = 2176, enabled)
>>> Server: PixelData-0 active (pid = 2197, enabled)
>>> Server: Processor-0 active (pid = 2195, enabled)
>>> Server: Tables-0 active (pid = 2196, enabled)
>>> Server: TestDropBox inactive (enabled)
>>>
>>> Log dir: /home/omero/OMERO.server/var/log exists
>>>
>>> Log files: Blitz-0.log 339.0 MB errors=140 warnings=768
>>> Log files: DropBox.log 20.0 KB errors=0 warnings=61
>>> Log files: FileServer.log 1.0 KB
>>> Log files: Indexer-0.log 99.0 MB errors=313 warnings=19
>>> Log files: MonitorServer.log 41.0 KB
>>> Log files: OMEROweb.log 2.0 MB errors=6 warnings=25
>>> Log files: OMEROweb.log.1 31.0 KB
>>> Log files: OMEROweb.log.2 21.0 KB
>>> Log files: OMEROweb.log.3 25.0 KB errors=0 warnings=1
>>> Log files: OMEROweb.log.4 4.0 KB errors=0 warnings=1
>>> Log files: OMEROweb.log.5 34.0 KB errors=0 warnings=2
>>> Log files: OMEROweb_request.log 64.0 KB errors=46 warnings=83
>>> Log files: PixelData-0.log 83.0 KB errors=18 warnings=32
>>> Log files: Processor-0.log 2.0 MB errors=0 warnings=65
>>> Log files: Tables-0.log 6.0 KB errors=0 warnings=2
>>> Log files: TestDropBox.log n/a
>>> Log files: master.err 6.0 KB errors=2 warnings=0
>>> Log files: master.out 0.0 KB
>>> Log files: Total size 443.50 MB
>>>
>>> Parsing Blitz-0.log:[line:118] => Server restarted <=
>>> Parsing Blitz-0.log:[line:14565] Your postgres hostname and/or port is invalid
>>> Parsing Blitz-0.log:[line:14676] Your postgres hostname and/or port is invalid
>>> Parsing Blitz-0.log:[line:14787] Your postgres hostname and/or port is invalid
>>> Parsing Blitz-0.log:[line:375526] => Server restarted <=
>>> Parsing Blitz-0.log:[line:411869] => Server restarted <=
>>> Parsing Blitz-0.log:[line:1625787] Your postgres hostname and/or port is invalid
>>> Parsing Blitz-0.log:[line:1625888] => Server restarted <=
>>>
>>> Environment:OMERO_HOME=/home/omero/OMERO.server
>>> Environment:OMERO_NODE=(unset)
>>> Environment:OMERO_MASTER=(unset)
>>> Environment:PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/lib/jvm/jdk1.7.0_11/bin:/usr/share/Ice-3.4.2:/usr/lib/postgresql/9.1/bin:/home/omero/OMERO.server/bin
>>> Environment:ICE_HOME=/usr/share/Ice-3.4.2
>>> Environment:LD_LIBRARY_PATH=/usr/share/java:/usr/lib:
>>> Environment:DYLD_LIBRARY_PATH=(unset)
>>>
>>> OMERO data dir: '/mnt/netapp/OMERO' Exists? True Is writable? True
>>> OMERO.web status... [RUNNING] (PID 2507)
>>>
>>>
>>> ---------------------------
>>> Thanks,
>>> - Damir
>>>
>>> On 1/21/2013 1:38 AM, Josh Moore wrote:
>>>> On Jan 18, 2013, at 9:54 PM, Damir Sudar wrote:
>>>>
>>>>> Hi,
>>>> Hi Damir,
>>>>
>>>>> Using the Insight Importer I get the error below with one specific large
>>>>> (3.8GB) LSM file acquired using a Zeiss LSM710. The file has 3 color
>>>>> channels, 26 Z planes, and is 5120 by 5120 pixels (we used 5 x 5 tiling).
>>>>> I'll be happy to upload the file somewhere if you have a site that will
>>>>> accept a ~4GB upload. Note that other (somewhat smaller LSM files acquired
>>>>> the same way import fine. The offending file is just a bit bigger but ZEN
>>>>> has no trouble with it.
>>>>> Enclosed is the log file that describes my environment. Server runs on
>>>>> Ubuntu 12.04LTS with Java 1.7.0_u11 (all 64-bit).
>>>>> Any suggestions?
>>>> This isn't something I've seen before. What type of file system do you have OMERO running on? Also, would it be possible to also get the server log, and possibly the output of master.err and master.out?
>>>>
>>>> Thanks,
>>>> ~Josh.
>>>>
>>>>> Thanks,
>>>>> - Damir
--
Damir Sudar - Staff Scientist and Deputy for Technology
Lawrence Berkeley Laboratory / Life Sciences Division
One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
T: 510/486-5346 - F: 510/486-5586 - E: DSudar at lbl.gov
WWW: http://www.lbl.gov/lsd/People_&_Organization/Scientific_Staff_Directory/Sudar_Lab.html
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