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Hi Niko,
<div><br>
</div>
<div>glad to hear re-indexing worked as expected (and faster).</div>
<div>As you mentioned, the metrics at the bottom of this documentation page may be out-of-date as more</div>
<div>optimization of the re-indexing has been included in the codebase. We'll look into re-indexing these DBs</div>
<div>with the latest 5.0.x servers and updating these numbers.</div>
<div><br>
</div>
<div>Would it be okay to add your metrics with background re-indexing to the documentation page table with a link to this</div>
<div>thread? If so, could you let us know which values for the Indexer settings and the omero.search.batch you used?</div>
<div><br>
</div>
<div>Best,</div>
<div>Sebastien</div>
<div><br>
<div>
<div>On 9 Feb 2015, at 08:48, Niko Ehrenfeuchter <<a href="mailto:nikolaus.ehrenfeuchter@unibas.ch">nikolaus.ehrenfeuchter@unibas.ch</a>> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div style="font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">
Hi all,<br>
<br>
just to let you know, re-indexing the database solved our search issues, at least as far as we can tell for now (in other words, everything that we expected to show up is actually there right now).<br>
<br>
For the record, the indexing of our current ~19 TB binary repository took 8h 36m in background (on-line) mode. That's much much faster that I was expecting from reading the documentation [1].<br>
<br>
Thanks again!<br>
~Niko<br>
<br>
[1]<span class="Apple-converted-space"> </span><a href="https://www.openmicroscopy.org/site/support/omero5/sysadmins/search.html#monitoring-re-indexing">https://www.openmicroscopy.org/site/support/omero5/sysadmins/search.html#monitoring-re-indexing</a><br>
<br>
<br>
<br>
On 06.02.2015 10:13, Niko Ehrenfeuchter wrote:<br>
<blockquote type="cite">Hi Sebastien,<br>
<br>
thanks for the very quick reply. Indeed, we are still on 5.0.5 as I<br>
mentioned in another email (thanks for the sharp reading!) and your hint<br>
solved this problem. Re-indexing is now in progress.<br>
<br>
Thanks again!<br>
~Niko<br>
<br>
On 05.02.2015 21:31, Sebastien Besson (Staff) wrote:<br>
<blockquote type="cite">Hi Niko,<br>
<br>
assuming your server is still 5.0.5, you are likely hitting the same<br>
issue as the one reported in<br>
<a href="http://www.openmicroscopy.org/community/viewtopic.php?f=5&t=7673">http://www.openmicroscopy.org/community/viewtopic.php?f=5&t=7673</a>.<br>
<br>
You will need to pass the omero.db.pass via environment variable to be<br>
able to connect to the<br>
database, i.e.<br>
<br>
$ JAVA_OPTS="-Domero.db.pass=$(bin/omero config get omero.db.pass)"<br>
bin/omero admin reindex --reset 0<br>
<br>
After upgrade to 5.0.6 and later, this extra environment will no longer<br>
necessary since the password<br>
is passed via environment variable in the CLI command directly.<br>
<br>
Let us know if this does not work,<br>
Sebastien<br>
<br>
On 5 Feb 2015, at 17:20, Niko Ehrenfeuchter<br>
<<a href="mailto:nikolaus.ehrenfeuchter@unibas.ch">nikolaus.ehrenfeuchter@unibas.ch</a><br>
<<a href="mailto:nikolaus.ehrenfeuchter@unibas.ch">mailto:nikolaus.ehrenfeuchter@unibas.ch</a>>> wrote:<br>
<br>
<blockquote type="cite">Hi all,<br>
<br>
we're experiencing some odd behaviour of the search functionality in<br>
OMERO recently, by missing many files when doing a search. So I went<br>
and checked the docs [1] for this, making sure the Indexer is neither<br>
stuck nor running behind.<br>
<br>
After checking this, I thought I will "just" do a (background)<br>
re-indexing before I start bothering you again. However, from the<br>
commands listed in the documentation, the third one (--reset 0) keeps<br>
on failing. The output, including the stack traces can be found in the<br>
attached log file.<br>
<br>
Am I doing something wrong?<br>
<br>
Thanks a lot!<br>
~Niko<br>
<br>
<br>
[1]<br>
<a href="https://www.openmicroscopy.org/site/support/omero5/sysadmins/search.html">https://www.openmicroscopy.org/site/support/omero5/sysadmins/search.html</a><br>
--<br>
Niko Ehrenfeuchter | Image Analysis Specialist | Biozentrum,<br>
University of Basel | Klingelbergstr. 50/70 | CH-4056 Basel<br>
Phone: +41 (61) 26 72673 |<span class="Apple-converted-space"> </span><a href="mailto:nikolaus.ehrenfeuchter@unibas.ch">nikolaus.ehrenfeuchter@unibas.ch</a><br>
<<a href="mailto:nikolaus.ehrenfeuchter@unibas.ch">mailto:nikolaus.ehrenfeuchter@unibas.ch</a>> |<span class="Apple-converted-space"> </span><a href="http://www.biozentrum.unibas.ch/">www.biozentrum.unibas.ch</a><br>
<<a href="http://www.biozentrum.unibas.ch/">http://www.biozentrum.unibas.ch</a>> |<span class="Apple-converted-space"> </span><a href="http://www.microscopynetwork.unibas.ch/">www.microscopynetwork.unibas.ch</a><br>
<<a href="http://www.microscopynetwork.unibas.ch/">http://www.microscopynetwork.unibas.ch</a>><br>
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</blockquote>
<br>
<br>
<br>
Dr Sébastien Besson<br>
Open Microscopy Environment / Harvard Medical School<br>
Wellcome Trust Centre for Gene Regulation and Expression,<br>
College of Life Sciences, University of Dundee, Dow Street,<br>
Dundee DD1 5EH Scotland UK Tel: (01382) 386364<br>
<br>
<br>
The University of Dundee is a registered Scottish Charity, No: SC015096<br>
<br>
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</blockquote>
<br>
</blockquote>
<br>
--<span class="Apple-converted-space"> </span><br>
Niko Ehrenfeuchter | Image Analysis Specialist | Biozentrum, University of Basel | Klingelbergstr. 50/70 | CH-4056 Basel<br>
Phone: +41 (61) 26 72673 |<span class="Apple-converted-space"> </span><a href="mailto:nikolaus.ehrenfeuchter@unibas.ch">nikolaus.ehrenfeuchter@unibas.ch</a><span class="Apple-converted-space"> </span>|<span class="Apple-converted-space"> </span><a href="http://www.biozentrum.unibas.ch/">www.biozentrum.unibas.ch</a><span class="Apple-converted-space"> </span>|<span class="Apple-converted-space"> </span><a href="http://www.microscopynetwork.unibas.ch/">www.microscopynetwork.unibas.ch</a><br>
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<br>
<br>
<div><span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px;"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; ">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; ">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
<div>Dr Sébastien Besson</div>
<div>Open Microscopy Environment / Harvard Medical School</div>
<div>Wellcome Trust Centre for Gene Regulation and Expression,</div>
<div>College of Life Sciences, University of Dundee, Dow Street,</div>
<div>Dundee DD1 5EH Scotland UK Tel: (01382) 386364</div>
</div>
</span></div>
</span></span></div>
<br>
<br>
<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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