[ome-users] Omero restart
Joshua Moore
josh.moore at gmx.de
Sat Jul 25 13:17:52 BST 2009
Forwarding to list incognito... :)
Best wishes,
~Josh
-------- Original-Nachricht --------
> Datum: Fri, 24 Jul 2009 08:05:29 -0400
> Von: Gordon Laurie <gwl6s at cms.mail.virginia.edu>
> An: josh.moore at gmx.de
> Betreff: Omero restart
> Dear Josh:
>
> I have had Omero working nicely in the lab for several weeks
> (thanks to your help) and have data entered, but found it not working
> this morning (likely an IP address issue that I will fix). I need to
> restart Omero. Could you kindly check my planned restart procedure
> below and let me know if it is correct? All is backed up on a remote
> server.
>
> Many thanks,
> Gordon.
>
>
>
> gordonlaurie$ export PATH=/opt/Ice-3.3/bin:$PATH
> gordonlaurie$ export
> DYLD_LIBRARY_PATH=/opt/Ice-3.3/lib:$DYLD_LIBRARY_PATH
> gordonlaurie$ export
> PYTHONPATH=/opt/Ice-3.3/python:$PYTHONPATHd-128-15-155:~ gordonlaurie$
>
> bin/omero admin start
>
>
>
>
>
> >Gordon W. Laurie writes:
> > > Dear Josh:
> >
> >Hi Gordon,
> >
> > > Going to another computer with Insight, I am getting a login
> > > failure. Reading the troubleshooting about remote clients not
> > > connecting to my OMERO installation, I read about the /etc/hosts
> > > misconfiguration issue. /etc/hosts: Local Host Database did not
> > > work and looking in /etc, I do not see a hosts directory.
> >
> >Copying from:
> >
> > https://www.openmicroscopy.org/site/support/omero4/troubleshooting
> >
> >you may need a file (not a directory) named /etc/hosts with the
> >following contents:
> >
> > 127.0.0.1 localhost
> > 192.168.0.100 my-hostname.lifesci.example.com my-hostname
> >
> >where "192.168.0.100" is your actual IP, and my-hostname...etc is your
> >actual hostname.
> >
> > > In the meantime, I am now having a problem restarting the server.
> > > Apparently used the same sequence as was just successful.
> > > Attached is the zip.log file. An error message came up in the
> > > restart (below). I left out the password.
> >
> >These steps you were taking were for a complete install. Not that you
> >have them working, you don't need all of them.
> >
> > > d-128-15-155:~ gordonlaurie$ export PATH=/opt/Ice-3.3/bin:$PATH
> > > d-128-15-155:~ gordonlaurie$ export
> > > DYLD_LIBRARY_PATH=/opt/Ice-3.3/lib:$DYLD_LIBRARY_PATH
> > > d-128-15-155:~ gordonlaurie$ export
> > > PYTHONPATH=/opt/Ice-3.3/python:$PYTHONPATHd-128-15-155:~
> gordonlaurie$
> >
> >These setup your environment. Always needed.
> >
> >
> > > /usr/share/omero/omero_dist/bin/omero config set omero.db.pass
> > >
> > > d-128-15-155:~ gordonlaurie$ cd /usr/share/omero/omero_dist
> > > d-128-15-155:omero_dist gordonlaurie$
> /usr/share/omero/omero_dist/bin/omero
> > > db script
> > > Please enter omero.db.version [OMERO4]:
> > > Please enter omero.db.patch [0]:
> > > Please enter password for new OMERO root user:
> > > Please re-enter password for new OMERO root user:
> > > Saving to /usr/share/omero/omero_dist/OMERO4__0.sql
> > > d-128-15-155:omero_dist gordonlaurie$
> /Library/PostgreSQL/8.3/bin/psql -h
> > > localhost -U omero omero < /usr/share/omero/omero_dist/OMERO4__0.sql
> > > Password for user omero:
> > > BEGIN
> > > ERROR: relation "acquisitionmode" already exists
> > > ERROR: current transaction is aborted, commands ignored until end of
> > > transaction block
> >
> >These create the database. Only needed (successfully) once. If you
> >remove them from the script you are using, then more will succeed. In
> >general, though, once the server is installed and your environment
> >variables are correct, you don't need anything more than:
> >
> > bin/omero admin stop
> >
> >and
> >
> > bin/omero admin start
> >
> >Best wishes,
> >~Josh.
> >
> >
> > > On Fri, 26 Jun 2009 12:51:47 +0200
> > > josh.moore at gmx.de wrote:
> > > >
> > > > Gordon W. Laurie writes:
> > > > > Dear Josh:
> > > > >
> > > > > Thanks, that worked.
> > > >
> > > > Ah, splendid! Glad to help.
> > > >
> > > > > How do I set PATH, DYLD_LIBRARY_PATH, and PYTHONPATH
> > > > > permanently in my environment?
> > > >
> > > > Perhaps see:
> > > >
> >http://tldp.org/LDP/Bash-Beginners-Guide/html/sect_03_01.html#sect_03_01_02
> > > >
> > > > Cheers,
> > > > ~Josh.
> > > >
> > > > > Gordon.
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > On Fri, 26 Jun 2009 09:15:55 +0200
> > > > > josh.moore at gmx.de wrote:
> > > > > >
> > > > > > Gordon W. Laurie writes:
> > > > > > > Dear Josh:
> > > > > >
> > > > > > Hi Gordon.
> > > > > >
> > > > > > > Thanks. The password is not omero. I rec'd the message
> below.
> > > > > > >
> > > > > > > Looking into pgAdmin III under properties, it appears that
> postgreS
> > > >is
> > > > > >not
> > > > > > > connected.
> > > > > > >
> > > > > > > I wonder if it is best if I start from scratch. Instead of
> using
> > > > > > > Alex's directions, I go with the official OMERO.server
> > > > > > > installation. My uncertainty is getting the Environment
> Variables
> > > > > > > correct.
> > > > > >
> > > > > > I think you're doing quite well. Just missing a step. In one of
> your
> > > > > > previous messages you posted this:
> > > > > >
> > > > > > d-128-15-155:~ gordonlaurie$ export PATH=/opt/Ice-3.3/bin:$PATH
> > > > > > d-128-15-155:~ gordonlaurie$ export
> > > > > > DYLD_LIBRARY_PATH=/opt/Ice-3.3/lib:$DYLD_LIBRARY_PATH
> > > > > > d-128-15-155:~ gordonlaurie$ export
> > > > > > PYTHONPATH=/opt/Ice-3.3/python:$PYTHONPATH
> > > > > > d-128-15-155:~ gordonlaurie$ export
> > > > > > CLASSPATH=/opt/Ice-3.3/lib/Ice.jar:$CLASSPATH
> > > > > > d-128-15-155:~ gordonlaurie$ export
> > > > > > CLASSPATH=/opt/Ice-3.3/lib/db.jar:$CLASSPATHd-128-15-155:~
> > > >gordonlaurie$
> > > > > > export
> PYTHONPATH=/usr/share/omero/omero_dist/lib/python/:$PYTHONPATH
> > > > > > d-128-15-155:~ gordonlaurie$ cd /usr/share/omero/omero_dist
> > > > > > d-128-15-155:omero_dist gordonlaurie$
> > > > > >/usr/share/omero/omero_dist/bin/omero
> > > > > > db script
> > > > > >
> > > > > >
> > > > > > In order to get "bin/omero config set" to work properly
> >you'll have to
> > > > > > do the following:
> > > > > >
> > > > > > export PATH=/opt/Ice-3.3/bin:$PATH
> > > > > > export DYLD_LIBRARY_PATH=/opt/Ice-3.3/lib:$DYLD_LIBRARY_PATH
> > > > > > export PYTHONPATH=/opt/Ice-3.3/python:$PYTHONPATH
> > > > > > /usr/share/omero/omero_dist/bin/omero config set omero.db.pass
> > > > > >YourSecretPassword
> > > > > >
> > > > > > In general, to use the "bin/omero" command, you'll always have
> to set
> > > > > > PATH, DYLD_LIBRARY_PATH, and PYTHONPATH because of how Ice is
> > > > > > installed on your system. You may want to set these permanently
> in
> > > > > > your environment.
> > > > > >
> > > > > > Best wishes,
> > > > > > ~Josh.
> > > > > >
> > > > > > > Gordon.
> > > > > > >
> > > > > > > d-128-15-155:omero_dist gordonlaurie$ bin/omero config set
> > > >omero.db.pass
> > > > > > > MySecretPassword
> > > > > > > Traceback (most recent call last):
> > > > > > > File "bin/omero", line 67, in <module>
> > > > > > > import omero.cli
> > > > > > > File
> "/usr/share/omero/omero_dist/lib/python/omero/__init__.py",
> > > >line
> > > > > >14,
> > > > > > > in <module>
> > > > > > > import Ice, Glacier2
> > > > > > > ImportError: No module named Ice
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > On Thu, 25 Jun 2009 15:50:12 +0200
> > > > > > > josh.moore at gmx.de wrote:
> > > > > > > >
> > > > > > > > > At this point, it's guaranteed that the webclient won't
> be able
> > > >to
> > > > > > > > > connect, since the server couldn't startup. It would help
> to
> > > >have:
> > > > > > > > >
> > > > > > > > > zip logs.zip /usr/share/omero/omero_dist/var/log/*
> > > > > > > >
> > > > > > > > In the logs (sent offlist), there's this error message:
> > > > > > > >
> > > > > > > > Caused by: org.postgresql.util.PSQLException: FATAL:
> password
> > > > > > > > authentication failed for user "omero"
> > > > > > > >
> > > > > > > > If the password is something other than "omero" (hopefully
> it
> > > >is!),
> > > > > > > > did you configure it?
> > > > > > > >
> > > > > > > > bin/omero config set omero.db.pass MySecretPassword
> > > > > > > >
> > > > > > > > Another option would be to use pg_hba.conf to allow
> passwordless
> > > > > > > > login. See:
> > > > > > > >
> > > > > > > >
> > > >
> https://www.openmicroscopy.org/site/support/omero4/server/postgresql
> > > > > > > >
> > > > > > > > for more information.
> > > > > > > >
> > > > > > > > Cheers,
> > > > > > > > ~J.
>
>
> --
> Gordon W. Laurie, Ph.D.
> Associate Professor
> Department of Cell Biology
> Director, UVa Biotechnology Training Program
> P.O. Box 800732, UVa Health System
> University of Virginia
> Charlottesville, VA 22908-0732
>
> For courier:
> 1340 Jefferson Park Avenue, Rm 394
>
> (434) 924-5250 (voice)
> (434) 982-3912 (fax)
> http://www.people.Virginia.EDU/~gwl6s/
> http://faculty.virginia.edu/biotech/index.html
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