Open Microscopy Environment

Hi all, I am testing omero on a VM with a couple of SVS images. I imported this this morning and the server has been processing them all day long (8 hours now). and so far only a single image has been processed. I expect it to run a little slower on a VM but at this point I am sure I must be doing something wrong. Also the processor has been pegged at 100% all day too

Any suggestions?

Hi Jose,

can you send us the var/log/Blitz-0.log and and PixelData-0.log files? Also, have you modified your memory settings at all? You might read through the "Omero importer fails to create preview after ugrade to 4.3.0" thread for more background info.

Cheers,
~Josh

Hi sorry its taken me so long to get back you, my day job had gotten on the way, but this is taking on a little more significance now that I may be using this for a histology imaging site I am building for a client. In any event please find the attached logs, I hope they can tell you something, also I have not modified any of the memory settings.

The log files are too large to upload so I dropped them in my dropbox account. Please get them from:

http://dl.dropbox.com/u/1185164/log.tar.gz

Thanks again in advance for your help
Jose

Hi Jose,

your PixelData log doesn't have any out of memory exceptions or similar, but increasing the resources for that process may help nonetheless. Would you mind attempting a larger value for the -Xmx option of PixelData in etc/grid/default.xml? An example is show in this thread.

At the same time, we'll take a look at your logs again and see if there's anything obviously wrong. It may be necessary to increase the debugging output to pinpoint the bottleneck, but we'll send instructions on how to do that if it's the case.

Thanks for helping us to track this down!
~Josh.

I increased the memory as you suggested, but its it still taking way to long. Interesting is that my CPU is stuck at 100% and has been the entire time.

Sorry, Jose. My hope was that your issue was garbage collection, and that with more memory, the CPU use would drop. Let us take a look at your logs again and come up with next steps.

Thanks for your patience!
~Josh.

Jose,

it looks like a fix may be in progress: https://trac.openmicroscopy.org.uk/ome/ticket/6500 Would you like to CC'd on that ticket?

Cheers,
~Josh