[ome-users] OMERO install on a Mac server - success at last (mostly) but still have questions

Wed Jun 23 23:20:42 BST 2010

Josh,

Well, OMERO is finally running on our Mac server under 10.6. I have started Postgres and the OMERO server and have logged in to OMERO remotely using the Importer and Insight clients. I've created a project, data set, and imported some images. That was successful. Yea!

There remain a couple things:

1) First, the OMERO.web web server refuses to come up. The web settings command
   omero web settings

 appeared to work fine, setting the server to wileyserver2.pnl.gov and the port to 8000

Diagnostics, invoked via
   omero admin diagnostics

says that the web server is up (active and enabled), and I don't see any errors in the very small OMEROweb.log files (I have attached them, in case I missed a clue), but I cannot log in via
   http:/wileyserver2.pnl.gov:8000

The browser says that there is no connection.

Also, 
   telnet wileyserver2.pnl.gov 8000
 gets a "connection refused".

The invocation via

  omero admin ice
  >> server enable Web
  >> server start Web

 did not generate any error msgs and

  >> server state Web
 also says that the web server is active and enabled, and assigned a pid number.

Computer support here swears that there is nothing in the router or intranet that would block any ports, and the wileyserver2 firewall is down, since I have not invoked it since the last reboot. So - the problem should not be that the port is blocked, but something else.

Can you give me any leads as to what I should look for to fix this?

Also, the "omero config set" command still isn't working and I don't know why. I have used your workaround that alters the etc/grid/default.xml file, which appears to work OK. But I'd still like to find out why command line param setting is not working and get this fixed at some point. Doing a "omero config get" still returns nothing at all.

Following up on your comment: 
"There's no need to set "rontaylor" for any OMERO configuration values, unless that were how you accessed PostgreSQL (instead of "psql -U omero"), nor do I think the copied server is expecting an "RT" account, as long as your file permissions are correct. (i.e. all directories needing writing to like var/ and /OMERO belong to "rontaylor")."

My file permissions are, I believe, correct. When I untar'ed, everything got converted to "rontaylor" ownership. Also, my Postgres account for omero is omero all the way - owner, password, db name are all "omero". And I can access that db without error using "psql -U omero". So - it's a stumper.

Ron 

-----Original Message-----
From: Josh Moore [mailto:josh.moore at gmx.de]
Sent: Wednesday, June 23, 2010 12:44 AM
To: Taylor, Ronald C
Cc: ome-users at lists.openmicroscopy.org.uk; 'Arcieri, Kenneth (NIH/NICHD) [V]'
Subject: Re: [ome-users] Failed OMERO install on a Mac server - requesting help on another problem

Hi Ron,

preferences failing to set *without* an error message sounds very problematic, and other than the possibility of your having run the commands under different users, I'm unsure of what could cause it. 
Nevertheless, there is a workaround.

The Java Preferences API used by OMERO 4.1 also doesn't work on Windows. 
As described under the Windows installation[1] it's possible to configure properties in etc/grid/default.xml (or for Windows windefault.xml). Add your settings like this:

<properties id="Profile">
<property name="omero.data.dir"  value="/MyOmeroDir/"/> </properties>

In 4.2, the use of Java Preferences in the server has been removed to prevent issues just like this. Sorry for the incovenience!

Best wishes,
~Josh.

[1]https://www.openmicroscopy.org/site/support/omero4/server/install-windows#section-6

On 6/23/10 2:22 AM, Taylor, Ronald C wrote:
>
> Josh, Ken,
>
> I have reinstalled Postgres from source and now
>    psql -h localhost -U omero omero
>
>   does work - it brings up the omero db and I can list the tables, etc.
>
> But OMERO still does not come up and now I've found another problem. I 
> cannot use
>
>    omero config set<param>  <val>
>
> When I try doing something like
>
>    omero config set omero.data.dir /var/lib/omero/data   (following top of p 10 in Ken's manual)
>
>   the command apparently does not do anything. That is, there is no 
> error msg on-screen but when I do
>
>    omero config get
> Or
>    omero config get omero.data.dir
>
> I get nothing back - I just return to the command prompt with no information displayed on the param.
>
> So - it looks like the config setting never gets stored. From Ken's Mac instructions (bottom of p 9), I would expect to see a config file here (working in the rontaylor acct):
>
>     /Users/rontaylor/Library/Preferences/omero.prefs.default.plist
>
> But there is no such file. I need to set omero.data.dir - and also need to set omero.db.port to 5433. I'm thinking if I can do that, OMERO might come up OK. But now I have this config problem. Any guidance? Am I looking for the plist file in the wrong place? Do you have any idea why my config values are not getting stored?
>
> I'm tempted to try altering the ../omero_dist/etc/omero_properties file, but the instructions say not to do that. Besides, need to figure out why "omero config set' is not working.
>
>   Ron
> ___________________________________________
> Ronald Taylor, Ph.D.
> Computational Biology&  Bioinformatics Group Pacific Northwest 
> National Laboratory
> 902 Battelle Boulevard
> P.O. Box 999, Mail Stop J4-33
> Richland, WA  99352 USA
> Office:  509-372-6568
> Email: ronald.taylor at pnl.gov
>
> -----Original Message-----
> From: ome-users-bounces at lists.openmicroscopy.org.uk
> [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of 
> Josh Moore
> Sent: Monday, June 21, 2010 11:27 PM
> To: ome-users at lists.openmicroscopy.org.uk
> Subject: Re: [ome-users] Failed OMERO install on a Mac server - 
> requesting help
>
> Hi Ronald,
>
> it looks like either the connection information for your PostgreSQL 
> server is wrong, or the server itself is not listening to for TCP 
> connections. For debugging this, you might take a look at some of 
> these
> pages:
>
>    * https://www.openmicroscopy.org/site/support/omero4/server/postgresql
>    *
> http://lists.openmicroscopy.org.uk/pipermail/ome-users/2009-April/001596.html
>    *
> http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2007-August/000
> 886.html
>
> Basically, if you can connect to your database with "psql omero" but not "psql -h localhost omero" then most likely TCP is not configuration in postgresql.conf. If you can reach with "psql -h localhost -U omero omero" (or whatever values you configured for omero.db.host, omero.db.user, and omero.db.name), then something else is going on.
>
> Cheers,
> ~Josh
>
>
> On 6/21/10 10:38 PM, Taylor, Ronald C wrote:
>    
>> Hello folks,
>>
>> I have successfully installed OMERO on my MacBook and on my Red hat Linux desktop. I'm now trying to install OMERO on our Mac server, which is the host machine we plan to use for the medium/long term.
>>
>> Our Mac server just got upgraded to Mac OS X Server 10.6, so I was using Ken's OMERO for 10.6 install instructions as my template. I copied over the appropriate subdirectories from /Library and /Library/Frameworks on my MacBook, and then made the additional changes that appeared to be required in Ken's instructions (for example, a couple Python libs that still had to be re-installed from source since they don't have separate subdirectories).
>>
>> I also set the firewall using  Server -->   Server Preferences -->   Security -->   Firewall
>>     to have open ports at 8000 (for OMERO.web) and at 5433 (the port I'm using for Postgres).
>>
>> I then invoked Postgres. It comes up fine. I then tried invoking OMERO using
>>      omero admin start
>>
>> That fails  - it times out after 5 minutes.
>>
>> So - need help again.
>>
>> I have attached a record* file that contains the screen output of the failed start, including the results of
>>      omero admin diagnostics  (which I have also repeated at bottom)
>>
>> I have also attached all the log files in
>>       ../omero_dist/var/log
>>    except for the master.out file, which remained empty.
>>
>> And I have attached my .bash_profile file for the account (/Users/rontaylor) in which I started Postgres and attempted to start OMERO.
>>
>> The Blitz-0 log shows a SQL error msg which I have not seen before. Could that have anything to do with a blocked port to Postgres at the router/intranet level, something I should check out with our network people?
>>
>> As before, any help would be greatly appreciated.
>>      

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