Open Microscopy Environment

Dear forum,
after the installation of OMERO the omero admin start fails. As far as I read the Biltz-Log it's something with the database connection. All the connection data in omero.db is proofed twice so I'm pretty sure it's no simple configuration mistake.

I attach all the logs and and a diagnostics aoutput as tar.

Many thanks for help in advance!

Best,
Marco

Dear Marco,

Many thanks for getting in touch. Thanks also for the log file archive.

The master.err log from has Ice stating ''Address already in use" - which implies that Ice was already running when it was trying to start.

It may have been that Ice hasn't fully shut down from the last time OMERO was started.

I should be possible to stop Ice specifically with the following:

Code: Select all

killall icegridnode

Then retry

Code: Select all

omero admin start

If that doesn't work and if it's possible to restart the server, then please try that.

Best,

Kenny

Hi Kenneth,
thanks for the reply. Unfortunatly this did not help.

The first Error I see in the Blitz is:

Code: Select all

Caused by: org.postgresql.util.PSQLException: FATAL: Passwort-Authentifizierung für Benutzer omero fehlgeschlagen

It's german and means Password authentication for user omero failed. omero is my psql database owner. But if I try

Code: Select all

psql -h localhost -U omero -l

everything works fine.

my pg_hba.conf seems to be fine to:

Code: Select all

cat omero.db/pg_hba.conf
# TYPE  DATABASE        USER            ADDRESS                 METHOD
# "local" is for Unix domain socket connections only
local   all             all                                     peer

# IPv4 local connections:
host    all             all             127.0.0.1/32            md5
host    all             all             ::1/128                 md5


I can do

Code: Select all

psql  -h localhost -u omero omero_database

an do some sql (and pass the init-sql of course which means write access is fine).

Hi Marco,

If possible please try another full shutdown (preferably system restart if possible).

Code: Select all

omero admin stop

If you can't reboot the system, please check if ice is still running and close it down

Code: Select all

kill  $(pgrep -f icegridnode)

then

Code: Select all

pgrep -f icegridnode

(expect no results)

Then can you please run

Code: Select all

omero admin diagnostics

and provide us with the results.

Can you now check for any instances of glacier2router running?

Code: Select all

pgrep -f glacier2router

(expect no results) - however if you see a process id, please kill it with

Code: Select all

kill  $(pgrep -f glacier2router)

Now can you please clear the logs by removing the OMERO server var/log folder (copying them somewhere if you want to keep any of the log data!)

Code: Select all

cp -r OMERO.server/var/log/ ~/OMERO_logs_20121219
rm -rf OMERO.server/var/log

and try to start up the server

Code: Select all

omero admin start

And now please submit another copy of the log output as you have done before.

Many thanks,

Kenny

Hi Marco,

Another thing to try: can you please change 'md5' to 'trust' in the pg_hba.conf, so the file reads

Code: Select all

cat omero.db/pg_hba.conf
# TYPE  DATABASE        USER            ADDRESS                 METHOD
# "local" is for Unix domain socket connections only
local   all             all                                     peer

# IPv4 local connections:
host    all             all             127.0.0.1/32            trust
host    all             all             ::1/128                 trust


zach_marca wrote:

Code: Select all

cat omero.db/pg_hba.conf
# TYPE  DATABASE        USER            ADDRESS                 METHOD
# "local" is for Unix domain socket connections only
local   all             all                                     peer

# IPv4 local connections:
host    all             all             127.0.0.1/32            md5
host    all             all             ::1/128                 md5


Thanks,

Kenny

The update to pg_hba.conf detailed in my previous post was enough to fix Marco's installation.

Sent: Wed Dec 19, 2012 4:02 pm
by zach_marca

Hi Kenneth,
that was it! Now I can do omero login as root, so everything seems to be fine.

Best,

Kenny