Open Microscopy Environment

Dear all,

In the OMERO client I press the button for "display the available scripts". When selecting one of the script types I receive the message:

Running Script
Cannot load the script: <some id>
Error: "No processor available! [0 response(s)]"
Please contact your administrator.

As I am the administrator I should solve the issue.

Could you give me some hint what is going wrong?

Thanks,
Andreas

Hi Andreas

Unfortunately that's a known issue with OMERO which occasionally occurs, and which we haven't been able to solve. Could you try restarting the Processor server which is used to run scripts:

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bin/omero admin ice "server stop Processor-0"

This will stop and automatically restart it. It should be ready after about 10 seconds, though give it a minute to be sure, then refresh the scripts menu in your client and try running the script again.

If that doesn't work could you provide the output of

Code: Select all

bin/omero admin diagnostics

Thanks, Simon

Hi Simon,

The restart is done, error occurs as before. Please find below the output of the diagnostics command.

Thanks in advance,
Andreas

================================================================================
OMERO Diagnostics 4.4.10-ice35-b112
================================================================================

ERROR:omero.util.UpgradeCheck:<urlopen error [Errno 110] Connection timed out>
Commands: java -version 1.7.0 (/usr/bin/java)
Commands: python -V 2.6.6 (/usr/bin/python)
Commands: icegridnode --version 3.5.1 (/usr/bin/icegridnode)
Commands: icegridadmin --version 3.5.1 (/usr/bin/icegridadmin)
Commands: psql --version 8.4.13 (/usr/bin/psql)

Server: icegridnode running
Server: Blitz-0 active (pid = 26377, enabled)
Server: DropBox inactive (disabled)
Server: FileServer active (pid = 26379, enabled)
Server: Indexer-0 active (pid = 26388, enabled)
Server: MonitorServer active (pid = 26385, enabled)
Server: OMERO.Glacier2 active (pid = 26403, enabled)
Server: OMERO.IceStorm active (pid = 26400, enabled)
Server: PixelData-0 active (pid = 26393, enabled)
Server: Processor-0 active (pid = 12543, enabled)
Server: Tables-0 inactive (disabled)
Server: TestDropBox inactive (enabled)

OMERO: SSL port 4064
OMERO: TCP port 4063

Log dir: /apps/test/omero/var/log exists

Log files: Blitz-0.log 628.0 KB errors=2 warnings=0
Log files: DropBox.log 2.0 KB errors=4 warnings=2
Log files: FileServer.log 0.0 KB
Log files: Indexer-0.log 15.0 MB errors=78 warnings=43922
Log files: MonitorServer.log 0.0 KB
Log files: OMEROweb.log 35.0 KB errors=32 warnings=0
Log files: OMEROweb_request.log 0.0 KB
Log files: PixelData-0.log 2.0 KB
Log files: Processor-0.log 6.0 KB errors=1 warnings=1
Log files: Tables-0.log n/a
Log files: TestDropBox.log n/a
Log files: master.err 0.0 KB errors=1 warnings=2
Log files: master.out 0.0 KB
Log files: Total size 884.70 MB


Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_TEMPDIR=(unset)
Environment:PATH=/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/OV/bin:/opt/OV/bin/OpC:/home/eberleia/bin
Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)

OMERO data dir: '/OMERO' Exists? True Is writable? True
OMERO temp dir: '/home/eberleia/omero/tmp' Exists? True Is writable? True (Size: 0)
OMERO.web status... [RUNNING] (PID 26841)

Hi Andreas

It looks like there are some errors in your log files- could you zip up the var/log directory, and either attach them to a forum post (.zip should be allowed), or if you'd prefer to keep them private upload them to https://www.openmicroscopy.org/qa2/qa/upload/

This should also help us in dealing with your web problems too.

Many thanks, Simon

Hi Simon,

the log files are available in the upload area.

Thanks,
Andreas

Hi Andreas

Most of the scripts require the optional Python dependencies listed under http://www.openmicroscopy.org/site/supp ... -or-higher. If you install numpy and PIL I think the majority of the scripts will work.

The "No processor" error you were seeing is misleading, I've opened a ticket on our tracking system: https://trac.openmicroscopy.org.uk/ome/ticket/12040

Hope this helps!

Simon

Hi Simon,

In the meantime I installed numpy and PIL, including libjpeg. What I see is that the util scripts do work. What should be installed for the other ones, e.g. Batch Image Export?

Thanks in advance,
Andreas

I think Batch Image Export should work, what errors are you seeing?

Well, the same as described below:

Cannot load the script: 8
Please contact our administrator.

Thanks,
Andreas

Could you try the following for me. Start an omero ipython shell:

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bin/omero python shell

Enter the code from the start of the lib/scripts/omero/export_scripts/Batch_Image_Export.py:

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import omero.scripts as scripts
from omero.gateway import BlitzGateway
import omero.util.script_utils as script_utils
import omero
from omero.rtypes import rstring, rlong, robject
from omero.constants.namespaces import NSCREATED, NSOMETIFF
import os

import glob
import zipfile
from datetime import datetime

try:
    from PIL import Image
except ImportError:
    import Image


And tell me if you see any errors. Note you might have to type the last two lines in manually to avoid auto-indentation problems.