Open Microscopy Environment

Hi

Our production server is filling the /tmp directory every 1.5 weeks. Admittedly we use OMERO in a slightly less conventional way with 1 public user serving our images to our website. Is this behaviour normal? Does OMERO only delete these files on reboot? What is the recommended way around this?

once we have 8.9G of temp files OMERO fails as it can't write cache files.

Thanks in advance

Jonathan.

Note we are using OMERO 5.0.4.

Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'pixelDataHandler' defined in class path resource [ome/services/service-ome.io.nio.PixelData.xml]: Cannot resolve reference to bean '/OMERO/Pixels' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '/OMERO/Pixels' defined in class path resource [ome/services/service-ome.io.nio.PixelsService.xml]: Cannot resolve reference to bean 'backOff' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'backOff' defined in class path resource [ome/services/service-ome.io.nio.PixelsService.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [ome.io.nio.SimpleBackOff]: Constructor threw exception; nested exception is java.lang.RuntimeException: javax.imageio.IIOException: Can't create cache file!

For clarification this directory holds session info in files like this: sessionidc1zzyv5i09jsriue6q86a5053wuf...

jwarren wrote:Hi

Hi Jonathan,

Our production server is filling the /tmp directory every 1.5 weeks. Admittedly we use OMERO in a slightly less conventional way with 1 public user serving our images to our website. Is this behaviour normal? Does OMERO only delete these files on reboot? What is the recommended way around this?

once we have 8.9G of temp files OMERO fails as it can't write cache files.

This is certainly a known issue though 9GB of temp files sounds like quite the extreme case. It depends on exactly what you're doing, but it might be possible to optimize some of this by using cookies to re-use sessions where possible.

Note we are using OMERO 5.0.4.

First and foremost I should say that we really can't support 5.0 on the open-source side, and 5.0.4 is even behind in terms of security releases.

If you go to the 5.1 docs though, there's a section on using `clearsessions`: https://www.openmicroscopy.org/site/support/omero5.1/sysadmins/unix/server-linux-walkthrough.html#regular-tasks to periodically get rid of these files.

The current stable documentation (5.2) is under https://www.openmicroscopy.org/site/support/omero/sysadmins/unix/install-web.html#omero-web-maintenance-unix-linux and will give you an idea of a more complete fix.

And in the upcoming 5.3 release, we'll be suggesting putting web sessions into redis in order to completely alleviate this problem.

Thanks in advance
Jonathan.

All the best,
~Josh

Actually sorry we are using 5.1.3! so not quite that bad

Thanks for the prompt reply Josh - I'll have a look and get back to you.

jwarren wrote:Actually sorry we are using 5.1.3! so not quite that bad

Whew. ~Josh.