[ome-devel] TempFileManager:rmtree error

[Simon Li]

Hi Andrii

Presumably /homes/andrii is an NFS directory? We've had problems with file locking on network filesystems so we strongly recommend against using it, particularly for your main server directory.

Several people have successfully used NFS for their OMERO repository, but in general they've had to use custom NFS settings to get it to work.

Simon


On 13 November 2015 at 13:33, Andrii Iudin <andrii at ebi.ac.uk<mailto:andrii at ebi.ac.uk>> wrote:
Dear OMERO developers,

I am running OMERO 5.2 on Linux and am getting the following error
message when doing bin/omero web start:

ERROR:omero.util.TempFileManager:rmtree error:
rmdir('/homes/andrii/omero/tmp/omero_andrii/21187') => [Errno 39]
Directory not empty: '/homes/andrii/omero/tmp/omero_andrii/21187'

The content of 21187 directory is a .nfs file that seems to be created
when the original file is removed but is still being accessed by a
process. The .nfs file is removed when bin/omero web stop is performed,
but the directory remains.

This does not affect the work of OMERO, however it creates empty
directories in /homes/andrii/omero/tmp/omero_andrii/ which can slow down
the system unless handled. A similar issue is mentioned here:
http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2014-September/002990.html

Permissions and ownership on such directories are the same as the rest,
however the Apache server is running under a different user. Can this be
the cause of this problem as it is mentioned here:
https://www.openmicroscopy.org/community/viewtopic.php?f=5&t=386#p1064
?

If so, is there any other solution except running the Apache server and
OMERO as the same user or setting a script to regularly remove empty
folders in tmp?

Thank you and best regards,
Andrii
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The University of Dundee is a registered Scottish Charity, No: SC015096
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