[ome-users] Re-indexing OMERO's search database

[Sebastien Besson (Staff)]

Hi Niko,

glad to hear re-indexing worked as expected (and faster).
As you mentioned, the metrics at the bottom of this documentation page may be out-of-date as more
optimization of the re-indexing has been included in the codebase. We'll look into re-indexing these DBs
with the latest 5.0.x servers and updating these numbers.

Would it be okay to add your metrics with background re-indexing to the documentation page table with a link to this
thread?  If so, could you let us know which values for the Indexer settings and the omero.search.batch you used?

Best,
Sebastien

On 9 Feb 2015, at 08:48, Niko Ehrenfeuchter <nikolaus.ehrenfeuchter at unibas.ch<mailto:nikolaus.ehrenfeuchter at unibas.ch>> wrote:

Hi all,

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).

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].

Thanks again!
~Niko

[1] https://www.openmicroscopy.org/site/support/omero5/sysadmins/search.html#monitoring-re-indexing



On 06.02.2015 10:13, Niko Ehrenfeuchter wrote:
Hi Sebastien,

thanks for the very quick reply. Indeed, we are still on 5.0.5 as I
mentioned in another email (thanks for the sharp reading!) and your hint
solved this problem. Re-indexing is now in progress.

Thanks again!
~Niko

On 05.02.2015 21:31, Sebastien Besson (Staff) wrote:
Hi Niko,

assuming your server is still 5.0.5, you are likely hitting the same
issue as the one reported in
http://www.openmicroscopy.org/community/viewtopic.php?f=5&t=7673.

You will need to pass the omero.db.pass via environment variable to be
able to connect to the
database, i.e.

$ JAVA_OPTS="-Domero.db.pass=$(bin/omero config get omero.db.pass)"
bin/omero admin reindex --reset 0

After upgrade to 5.0.6 and later, this extra environment will  no longer
necessary since the password
is passed via environment variable in the CLI command directly.

Let us know if this does not work,
Sebastien

On 5 Feb 2015, at 17:20, Niko Ehrenfeuchter
<nikolaus.ehrenfeuchter at unibas.ch<mailto:nikolaus.ehrenfeuchter at unibas.ch>
<mailto:nikolaus.ehrenfeuchter at unibas.ch>> wrote:

Hi all,

we're experiencing some odd behaviour of the search functionality in
OMERO recently, by missing many files when doing a search. So I went
and checked the docs [1] for this, making sure the Indexer is neither
stuck nor running behind.

After checking this, I thought I will "just" do a (background)
re-indexing before I start bothering you again. However, from the
commands listed in the documentation, the third one (--reset 0) keeps
on failing. The output, including the stack traces can be found in the
attached log file.

Am I doing something wrong?

Thanks a lot!
~Niko


[1]
https://www.openmicroscopy.org/site/support/omero5/sysadmins/search.html
--
Niko Ehrenfeuchter | Image Analysis Specialist | Biozentrum,
University of Basel | Klingelbergstr. 50/70 | CH-4056 Basel
Phone: +41 (61) 26 72673 | nikolaus.ehrenfeuchter at unibas.ch<mailto:nikolaus.ehrenfeuchter at unibas.ch>
<mailto:nikolaus.ehrenfeuchter at unibas.ch> | www.biozentrum.unibas.ch<http://www.biozentrum.unibas.ch/>
<http://www.biozentrum.unibas.ch<http://www.biozentrum.unibas.ch/>> | www.microscopynetwork.unibas.ch<http://www.microscopynetwork.unibas.ch/>
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Dr Sébastien Besson
Open Microscopy Environment / Harvard Medical School
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364


The University of Dundee is a registered Scottish Charity, No: SC015096


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--
Niko Ehrenfeuchter | Image Analysis Specialist | Biozentrum, University of Basel | Klingelbergstr. 50/70 | CH-4056 Basel
Phone: +41 (61) 26 72673 | nikolaus.ehrenfeuchter at unibas.ch<mailto:nikolaus.ehrenfeuchter at unibas.ch> | www.biozentrum.unibas.ch<http://www.biozentrum.unibas.ch/> | www.microscopynetwork.unibas.ch<http://www.microscopynetwork.unibas.ch/>
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Dr Sébastien Besson
Open Microscopy Environment / Harvard Medical School
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364


The University of Dundee is a registered Scottish Charity, No: SC015096
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