Open Microscopy Environment

Hello,

I've successfully (I think?) installed Omero server on my Windows 7 (64-bit) machine.

However, when I try to start the service, I get the following error:

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D:\OmeroServer>bin\omero admin start
No descriptor given. Using etc\grid\windefault.xml
Installing OMERO.master Windows service.
Successfully installed OMERO.master Windows service.
OMERO.master service startup failed: (2) The system cannot find the file specified.
OMERO.master service deleted.


Could it be related to the non-default installation directory (D:\OmeroServer)?

If any help, see the diagnostic log below:

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===============================================================================

OMERO Diagnostics 4.4.9-ice34-b98
===============================================================================

Commands:   java -version                  1.7.0     (C:\Windows\system32\java.
XE -- 2 others)
Commands:   python -V                      2.6.6     (C:\Python26x64\python.EXE

Commands:   icegridnode --version          3.4.0     (C:\Ice-3.4.0\bin\x64\iceg
idnode.EXE -- 2 others)
Commands:   icegridadmin --version         3.4.0     (C:\Ice-3.4.0\bin\x64\iceg
idadmin.EXE -- 2 others)
Commands:   psql --version                 not found

Server:     icegridnode                    not started

Cannot list deployed applications.

Log dir:    D:\OmeroServer\var\log         exists

Log files:  Blitz-0.log                    n/a
Log files:  DropBox.log                    n/a
Log files:  FileServer.log                 n/a
Log files:  Indexer-0.log                  n/a
Log files:  MonitorServer.log              n/a
Log files:  OMEROweb.log                   n/a
Log files:  Processor-0.log                n/a
Log files:  Tables-0.log                   n/a
Log files:  TestDropBox.log                n/a
Log files:  Total size                     0.00 MB

Error while parsing logs

Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_TEMPDIR=(unset)
Environment:PATH=C:\Python26x64\;C:\Program Files (x86)\NVIDIA Corporation\Phys
\Common;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Program File
(x86)\QuickTime\QTSystem\;C:\Program Files (x86)\ATI Technologies\ATI.ACE\Core
Static;C:\Program Files\MATLAB\R2013a\runtime\win64;C:\Program Files\MATLAB\R20
3a\bin;C:\Program Files (x86)\MATLAB\R2012b\runtime\win32;C:\Program Files (x86
\MATLAB\R2012b\bin;C:\Program Files\MATLAB\R2012b\runtime\win64;C:\Program File
\MATLAB\R2012b\bin;C:\Program Files\MATLAB\R2011b\runtime\win64;C:\Program File
\MATLAB\R2011b\bin;C:\Program Files\MATLAB\R2011a\runtime\win64;C:\Program File
\MATLAB\R2011a\bin;C:\Program Files (x86)\Java\jre6\bin;c:\Program Files (x86)\
icrosoft SQL Server\100\Tools\Binn\;c:\Program Files\Microsoft SQL Server\100\T
ols\Binn\;c:\Program Files\Microsoft SQL Server\100\DTS\Binn\;C:\Program Files\
likSvn\bin\;C:\Program Files\SlikSvn\bin;C:\Program Files\IVI Foundation\VISA\W
n64\Bin\;C:\Program Files (x86)\IVI Foundation\VISA\WinNT\Bin\;C:\Program Files
(x86)\IVI Foundation\VISA\WinNT\Bin;C:\Program Files\Java\jdk1.6.0_29\bin;C:\Pr
gram Files\TortoiseSVN\bin;C:\Program Files\MATLAB\MATLAB Compiler Runtime\v716
runtime\win64;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Windows\System32\W
ndowsPowerShell\v1.0\;C:\Ice-3.4.0\bin\x64;C:\Ice-3.4.0\bin
Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)

OMERO data dir: 'D:\\OMERO'     Exists? True    Is writable? True
OMERO temp dir: 'C:\Users\Install\AppData\Roaming\omero\tmp'    Exists? True
Is writable? True   (Size: 0)
OMERO.web status... [NOT STARTED]



Thanks.

Nicolas

Hi Nicolas,

could this be the same error as under viewtopic.php?f=5&t=881?

i.e.

• Are java.exe, icegridnode.exe etc. on the system PATH as opposed to the user path?
• Did you restart after setting them?
• Are you running this in a console as admin?

Cheers,
~Josh.

I am running the command line as an administrator. I also think all the paths are set correctly (I assume it is the case as the previous steps in the documentation worked fine?).

By restart, did you mean opening a new command line or restart the whole computer (if the latter, why is it necessary?).

Is there a way to know which file it can't locate?

Thanks for your help!

Nicolas

nicjac wrote:By restart, did you mean opening a new command line or restart the whole computer (if the latter, why is it necessary?).

The reason it's necessary is that OMERO doesn't run as your user but as the "Local Service" user. The only way to have his/her/its PATH updated is a restart. Alternatively, you can try running it as your own user, but your mileage may vary. See http://www.openmicroscopy.org/site/support/omero4/sysadmins/windows/service-tools.html#custom-user for more information.

Cheers,
~Josh

I think the permission thing was the trick, I can start the admin now. However, I then encounter the error that was mentioned in the link from your first post:

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D:\OmeroServer>bin\omero admin start
No descriptor given. Using etc\grid\windefault.xml
Installing OMERO.master Windows service.
Successfully installed OMERO.master Windows service.
Starting OMERO.master Windows service.
Waiting on startup. Use CTRL-C to exit
.............................
Failed to startup some components after 300 seconds
Calling "stop" on remaining components
OMERO.master service deleted.
Waiting on shutdown. Use CTRL-C to exit


Looking at the logs, it seems Blitz can't start properly. Could that be the cause?

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org.springframework.beans.factory.access.BootstrapException: Unable to return specified BeanFactory instance: factory key [OMERO.blitz], from group with resource name [classpath*:beanRefContext.xml]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'OMERO.blitz' defined in URL [jar:file:/D:/OmeroServer/lib/server/blitz.jar!/beanRefContext.xml]: Cannot resolve reference to bean 'ome.server' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'ome.server' defined in URL [jar:file:/D:/OmeroServer/lib/server/server.jar!/beanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [ome.system.OmeroContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'groupChmodStrategy' defined in class path resource [ome/services/sec-primitives.xml]: Cannot resolve reference to bean 'omeroSessionFactory' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'omeroSessionFactory' defined in class path resource [ome/services/hibernate.xml]: Cannot resolve reference to bean 'sessionFactory' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory' defined in class path resource [ome/services/hibernate.xml]: Invocation of init method failed; nested exception is org.hibernate.HibernateException: could not init listeners


Regards,

Nicolas

No matter, as per another forum post I tried again and it worked fine. It seems to only fail on the first try.

Thanks!

Nicolas

Interesting. Haven't heard of any "fail on first try" issues, but we'll look into it. Glad to hear it's working for you.

Cheers,
~Josh