[ome-devel] TempFileManager:rmtree error

[Andrii Iudin]

Dear Simon,

Thank you for your reply. This is indeed an NFS directory. Luckily the 
issue was just resolved by a colleague of mine, Ingvar Lagerstedt, who 
has suggested to change the settings of OMERO to use local /tmp instead 
of the NFS one. In 5.2 it is possible to do so by setting the 
environmental variable OMERO_TMPDIR. Now the error message is gone.

Best regards,
Andrii


On 13/11/2015 13:59, Simon Li wrote:
> 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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