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Dear Simon,<br>
<br>
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.<br>
<br>
Best regards,<br>
Andrii<br>
<br>
<br>
<div class="moz-cite-prefix">On 13/11/2015 13:59, Simon Li wrote:<br>
</div>
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cite="mid:CAMvbRBH9Zr57Uu-3rZcDW2HVruJVOeEqw6sAisRWz7+4AB2k_g@mail.gmail.com"
type="cite">
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<div>Hi Andrii<br>
<br>
</div>
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.<br>
<br>
</div>
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.<br>
<br>
</div>
Simon<br>
<div><br>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 13 November 2015 at 13:33, Andrii
Iudin <span dir="ltr">
<<a moz-do-not-send="true" href="mailto:andrii@ebi.ac.uk"
target="_blank">andrii@ebi.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear OMERO developers,<br>
<br>
I am running OMERO 5.2 on Linux and am getting the following
error<br>
message when doing bin/omero web start:<br>
<br>
ERROR:omero.util.TempFileManager:rmtree error:<br>
rmdir('/homes/andrii/omero/tmp/omero_andrii/21187') =>
[Errno 39]<br>
Directory not empty:
'/homes/andrii/omero/tmp/omero_andrii/21187'<br>
<br>
The content of 21187 directory is a .nfs file that seems to
be created<br>
when the original file is removed but is still being
accessed by a<br>
process. The .nfs file is removed when bin/omero web stop is
performed,<br>
but the directory remains.<br>
<br>
This does not affect the work of OMERO, however it creates
empty<br>
directories in /homes/andrii/omero/tmp/omero_andrii/ which
can slow down<br>
the system unless handled. A similar issue is mentioned
here:<br>
<a moz-do-not-send="true"
href="http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2014-September/002990.html"
rel="noreferrer" target="_blank">http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2014-September/002990.html</a><br>
<br>
Permissions and ownership on such directories are the same
as the rest,<br>
however the Apache server is running under a different user.
Can this be<br>
the cause of this problem as it is mentioned here:<br>
<a moz-do-not-send="true"
href="https://www.openmicroscopy.org/community/viewtopic.php?f=5&t=386#p1064"
rel="noreferrer" target="_blank">https://www.openmicroscopy.org/community/viewtopic.php?f=5&t=386#p1064</a><br>
?<br>
<br>
If so, is there any other solution except running the Apache
server and<br>
OMERO as the same user or setting a script to regularly
remove empty<br>
folders in tmp?<br>
<br>
Thank you and best regards,<br>
Andrii<br>
_______________________________________________<br>
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target="_blank">ome-devel@lists.openmicroscopy.org.uk</a><br>
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rel="noreferrer" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a><br>
<br>
The University of Dundee is a registered Scottish Charity,
No: SC015096<br>
</blockquote>
</div>
<br>
</div>
<br>
<span style="font-size:10pt;">The University of Dundee is a
registered Scottish Charity, No: SC015096</span>
<br>
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