Open Microscopy Environment

Hi

I am trying to follow the procedure "Node in multiple hosts" outlined in
http://www.openmicroscopy.org/site/supp ... /grid.html

but when running the command "omero node omero-slave start" on the slave machine I get:

==========
Traceback (most recent call last):
File "C:\OMERO.server-5.1.3-ice34-b52\bin\\omero", line 125, in <module>
rv = omero.cli.argv()
File "C:\OMERO.server-5.1.3-ice34-b52\lib\python\omero\cli.py", line 1431, in
argv
cli.invoke(args[1:])
File "C:\OMERO.server-5.1.3-ice34-b52\lib\python\omero\cli.py", line 945, in i
nvoke
stop = self.onecmd(line, previous_args)
File "C:\OMERO.server-5.1.3-ice34-b52\lib\python\omero\cli.py", line 1022, in
onecmd
self.execute(line, previous_args)
File "C:\OMERO.server-5.1.3-ice34-b52\lib\python\omero\cli.py", line 1104, in
execute
args.func(args)
File "C:\OMERO.server-5.1.3-ice34-b52\lib\python\omero\plugins\node.py", line
55, in __call__
c(args)
File "C:\OMERO.server-5.1.3-ice34-b52\lib\python\omero\plugins\node.py", line
78, in start
command = command + ["--install", "OMERO."+args.node]
AttributeError: 'Namespace' object has no attribute 'node'
==========

My configuration is

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

OMERO Diagnostics 5.1.3-ice34-b52
================================================================================

Commands: java -version 1.7.0 (C:\Windows\system32\java.E
XE)
Commands: python -V 2.6.6 (C:\Python26\python.EXE)
Commands: icegridnode --version 3.4.2 (C:\Program Files (x86)\Zer
oC\Ice-3.4.2\bin\x64\icegridnode.EXE)
Commands: icegridadmin --version 3.4.2 (C:\Program Files (x86)\Zer
oC\Ice-3.4.2\bin\x64\icegridadmin.EXE)
Commands: psql --version not found

Server: icegridnode not started

==========

Any idea greatly appreciated! Thanks
Thomas

Hi Thomas

I'm afraid we've only tested multi-node grid configurations on Linux, and we don't currently have the resources to setup a Windows cluster. However we should be able to check it still works on Linux, though it may take a few days as this isn't one of our regular test setups.

Do you have the option of running OMERO on Linux (or other Unix-based system)? If not, are you able to run OMERO in the normal single-node configuration? Could you tell us what you're trying to achieve, and we can see if there's an easier way to do it?

Thanks, Simon

Hi Simon,

we are in the process of scaling up our OMERO setup. At the moment it is running on a single VM (Windows, 8-core, 32GB). The actual files are on a NAS. It works great for single fields-of-view (<3000 pixels width). Our most problematic images are the huge mosaics output by our slide scanners and our automated fluo microscopes. The issue is the rendering is painfully slow for these images (a minute to render the whole image). Increasing the number of cores has helped but has reached a plateau. I also tried increasing the number of service instances for the Processor and the PixelData.

At the source these images are already stored as pyramids, which is fast on a pyramid-enabled viewer. As I understand it, OMERO also generates a pyramid. Is there a way to maybe tweak the generated pyramid to make it faster? Or amp up the rendering service?

My windefault config is now:

<node name="master">
<server-instance template="Glacier2Template"
client-endpoints="ssl -p ${ROUTERPORT}:tcp -p 4063"
server-endpoints="tcp -h 127.0.0.1"/>
<server-instance template="BlitzTemplate" index="0" config="default"/>
<server-instance template="IndexerTemplate" index="0"/>
<server-instance template="DropBoxTemplate"/>
<server-instance template="MonitorServerTemplate"/>
<server-instance template="FileServerTemplate"/>
<server-instance template="StormTemplate"/>
<server-instance template="PixelDataTemplate" index="0" dir=""/><!-- assumes legacy -->
<server-instance template="ProcessorTemplate" index="0" dir=""/><!-- assumes legacy -->
<server-instance template="PixelDataTemplate" index="1" dir=""/><!-- assumes legacy -->
<server-instance template="ProcessorTemplate" index="1" dir=""/><!-- assumes legacy -->
<server-instance template="PixelDataTemplate" index="2" dir=""/><!-- assumes legacy -->
<server-instance template="ProcessorTemplate" index="2" dir=""/><!-- assumes legacy -->
<server-instance template="TablesTemplate" index="0" dir=""/><!-- assumes legacy -->
<server-instance template="TestDropBoxTemplate"/>
</node>

Any idea greatly appreciated! Thanks
Thomas

Dear Thomas,

I'm sorry to hear of this slow rendering! How large are these huge images, and in what image format?

Cheers,
Mark

An example from the fluorescence mosaic:

20713 x 17490. 3 16bit channels. Just over 2GB file. ND2 format.

From the slide scanner:

41207 x 48806. RGB. 6.3 GB. TIFF (Pyramidal, Huron Tech)

Thanks
Thomas

Hi Thomas,

Would you be willing to upload either or both files? This would greatly help us to measure the current performance, and verify that any fixes are indeed an improvement. If so, instructions for uploading large files are being sent by private message.

Regards,
-Melissa

Hi Melissa

sure!

I didn't receive the separate email though, didn't even get to the spam-box..

Thanks
Thomas

Hi Thomas,

It's in a private forum message (not an email), should be visible if you click the "1 new messages" link near the top left of any forum page. If you don't see it there, let me know and I'll re-send as an email.

Regards,
-Melissa