Open Microscopy Environment

Hi,

I have an installation of OMERO 4.4.8 on a Linux Ubuntu 12.04 LTS 64-bit machine here in UMass Medical School in Worcester.

About 1 month ago, when we still had the 4.4.4 version of the server, a user informed me that the server, after a period of slow responsiveness, it was unreachable. More precisely both insight and the web client were not able to connect to it . Since then I update the server to the version above and I optimized the postgres db as explained in http://www.openmicroscopy.org/site/support/omero4/sysadmins/server-upgrade.html
but the problem presented itself another couple of times, in the same way as explained before.
So I started digging for additional information and I discover the diagnostic tool. When I run it I received the message of a problem with postgres as you can see in the diagnostic report attached.

Have you ever seen this problem? Do you know if there is something I can do to fix it?
I collected all the log files and I’m ready to tell you where they are but I prefer to do it through a pm if it is possible.

Thank you in advance for your help.
Alex Rigano

Hi Alex,

I'm afraid it looks like the forum attachment didn't make it. (Will look into this)

Please feel free to upload the zipped diagnostics output and the collected log files to our QA system, at http://qa.openmicroscopy.org.uk/qa/upload/

Best,

Kenny

It seems that the forum doesn't accept .txt file extension.
I tried without extension too and it's not working.

I uploaded the file here: http://omega.umassmed.edu/diagnostic

Furthermore I'm looking for source code of the OMERO plugin for ImageJ/Fiji because I'm interested in doing something similar, is it available on github? I'm asking because I was not able to find it in the git repo.
Could you please point me in the right direction?
I apologize for this offtopic.

Thanks in advance for your help.
Best

Hi Alex,

It certainly looks like your OMERO user can't connect to Postgres.

Ca you please zip up the contents of /mnt/VolGroup00-LogVol00/OMERO.server-4.4.8-ice34-b256/var/log and upload to our QA system (which should accept .zip no problem).

And also please include the output of

Code: Select all

/mnt/VolGroup00-LogVol00/OMERO.server-4.4.8-ice34-b256/bin/omero config get


Also, please check yourself that the username/password specified in the output of that command can connect independently to the Postgres DB via psql at the command line.

Many thanks,

Kenny

The ImageJ plugin is basically a different build of the Insight client.
I can't tell you much more than that (need to ask Jean-Marie for more details) but the place to start looking is
https://github.com/openmicroscopy/openm ... lugin.java

hi
As Will indicated a new class was introduced to start OMERO.insight as a IJ plugin.
We also modified the container class (

org.openmicroscopy.shoola.env.Container

to allow such thing. I have also converted the code to start the client as an IJ2 plugin (not yet realised)

Regards
Jmarie

Hi,

Thank for your answers.
I will try to investigate it during the next week.

In the meanwhile I sent a PM with a link to files to Kenneth.
Trying to psql to the db with that username gave me :

Peer authentication failed for user "*"

That made me even more confused.
Could this be an error due to some miscofiguration during the installation phase?

Thanks for your help
Best,

Hi Alex

That certainly looks like the pg_hba.conf Postgres conf file needs a bit of configuring.

OMERO needs to be prompted for a password by Postgres on a tcp/ip socket, and from that error it appears that pg_hba.conf is set with "peer" authentication for that user.

I'd double check there are lines as follows in the pg_hba.conf:

On the system I'm looking at, that file resides in: /var/lib/pgsql/data/pg_hba.conf

Code: Select all

# TYPE  DATABASE    USER        CIDR-ADDRESS          METHOD

# "local" is for Unix domain socket connections only
local   all         all                               ident
# IPv4 local connections:
host    all         all         127.0.0.1/32          md5
# IPv6 local connections:
host    all         all         ::1/128               md5

Reference: https://www.openmicroscopy.org/site/support/omero4/sysadmins/unix/server-postgresql.html

If there's an IPv6 localhost interface make sure the ipv6 local connections line is set to md5 as well.

That may well get you past this hurdle.

Best,

Kenny

Hi,

I looked for that file and I found 3 of them inside the following folders:
- etc/
- omero/etc
- etc/postgresql/9.1/main

I tried to modify each one of them indepentely and then all of them, restarting the server with:
cd /etc/init.d/
sudo ./postgresql restart

My files had peer instead of ident at the end of the first "non comment" line

And after each modify I tried to do:
psql name_db username

But I'm always getting the same error.

Am I doing something wrong?

Thanks for your help
Best,

Alex

Hi Alex

Could you paste the entire contents of /etc/postgresql/9.1/main/pg_hba.conf here? Thanks.