[ome-users] OMERO-CellProfiler: too many open files

[Mark Woodbridge]

Hi Bram,

Would you consider sharing the changes you made to the 
OMERO/CellProfiler integration code to make it compatible with Beta4 and 
the latest CellProfiler? We're interested in getting this integration 
working, and I guess that others may be too.

I would also be interested to hear if you (or anyone else) has had any 
success compiling the OMERO/CellProfiler integration code using the 
Matlab Compiler so that it can be used on client machines without Matlab 
licenses.

Regards,

Mark.


b.gerritsen at nki.nl wrote:
> Dear all,
> 
> When I analyze many images from the omero db in CellProfiler, the run fails after about 50 to 100 images with an Ice.SocketException. In the same error report a java.io.Exception is shown telling me there are too many open files. Closer inspection of matlab shows there are 16 files opened with every call to "createOmeroJavaService", but these files are not closed during the run, not even after a call to "session.close()". As soon as matlab tries to open more than 1024 files I get the exception.
> 
> Here is some more information about the system I'm running Omero on:
> 
> Red Hat Enterprise Linux 5.3
> Omero Beta 4.0.3
> Postgresql 8.1.4
> ZeroC Ice 3.3.1
> Python 2.4.3
> Matlab 7.8.0 (R2009a)
> CellProfiler (developer version) 1.0.5811 Branch 1.0.6027
> 
> I had to change the OmeroLoader.m, numImages.m, and CPOMEROimread.m files to be able to analyze images from omero beta 4 in cellprofiler (apparently the matlab scripts from "http://svn.openmicroscopy.org.uk/svn/omero/tags/omero-4.0.3/" are not compatible with the beta 4 release nor with recent versions of cellprofiler).
> 
> Thanks in advance!
> Bram Gerritsen
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