Open Microscopy Environment

Posted: **Thu Sep 29, 2011 7:30 pm**

Hi all,

I want to know if I can run two different OMERO versions on the same machine. Especially OMERO.web with different port.

I have a machine with an OMERO 4.2.1 version running. So I downloaded 4.3.2 server to the machine and tried to follow the installation instruction.

for 4.2.1 version, I set the following configuration.

omero.web.application_host=http://my.inst.edu
omero.web.application_server=fastcgi
omero.web.debug=True

for 4.3.2 version, I set the following so that I can access to this by 14064 port.

>bin/omero admin ports --prefix=1

and use the same configuration as 4.2.1.

But when I tried to access to my omero.web (http://my.inst.edu), it only shows me the 4.2.1 version.
Do I need to do something else?

Thanks in advance,
BK

Posted: **Thu Sep 29, 2011 9:48 pm**

followup questions.

I think I should use different port for the 2nd OMERO.
I guess the first (4.2.1) OMERO is using the default port 80.

1.
Then do I need to use another port?
1.1
If so, do I need to modify some apache configuration (such as httpd.conf) to accept access from different port?
1.2
Consequently, then I guess I need to use different omero config setting such as

omero.web.application_host=http://my.inst.edu:8080

2.
Then, what are the ports 4064 and 14064 for?

BK

Posted: **Fri Sep 30, 2011 6:08 am**

Hi BK,

The "bin/omero admin ports" command only makes modifications for the OMERO.server. The port 4064 is the firewall port used for all access to OMERO.server. 14064 is also the firewall port, but for your second instance of OMERO.

You're right that you also need to change the ports for OMERO.web. (NB: If you were deploying two instances of the same version of OMERO.server, then a single OMERO.web instance could talk to both of them. You only need to have one instance of OMERO.web for each version you want to support)

You don't want to modify "application_host" since it's fine to run both OMERO.web instances behind the same Apache instance (on port 80), but you'll need to change:

Code: Select all: bin/omero config set omero.web.application_server.port 14080

For the 4.3 version of OMERO.web, then, you can run "bin/omero web config apache" and get a stanza to add to your apache configuration:

Code: Select all: ~/git/dist $ bin/omero web config apache ### ### Stanza for OMERO.web created 2011-09-30 08:02:03.989496 ### FastCGIExternalServer "/Users/moore/omero_dist/var/omero.fcgi" -host 0.0.0.0:14080 ... Alias / "/Users/moore/omero_dist/var/omero.fcgi/"

You'll need to properly configure the aliases for your site.

Hope that helps.
Cheers,
~Josh

Posted: **Fri Sep 30, 2011 2:34 pm**

Hi Josh,

bin/omero config set omero.web.application_server.port 14080

is this for the older OMERO.web (4.2.1)?

when I did the following, i got the error.

-bash-3.2$ bin/omero web config apache
Invalid application host: http://my.inst.edu

Is this because I did not properly configure the aliases? If so, could you give me a hint of how to configure the aliases (or which file should I look at)? (Sorry, I'm not familiar with this).

Thanks in advance,
BK

Posted: **Fri Sep 30, 2011 6:59 pm**

bhcho wrote:Hi Josh,

bin/omero config set omero.web.application_server.port 14080
is this for the older OMERO.web (4.2.1)?

No, that's for 4.3.2

bhcho wrote:when I did the following, i got the error.
-bash-3.2$ bin/omero web config apache
Invalid application host: http://my.inst.edu

Looks like something has been mis-entered in the configuration. You could try pasting us the output of:

Code: Select all: bin/omero web -h

Is this because I did not properly configure the aliases? If so, could you give me a hint of how to configure the aliases (or which file should I look at)? (Sorry, I'm not familiar with this).

Thanks in advance,
BK

No. It's not a problem with Apache. The aliases just map from a path like:

Code: Select all: http://myhost:8080/ALIAS1

to a particular handler.

Cheers,
~josh

EDIT: Removed link to mod_alias

Posted: **Fri Sep 30, 2011 8:36 pm**

omero web -h returns the following

-bash-3.2$ bin/omero web -h
usage: bin/omero web [-h] <subcommand> ...

OMERO.web configuration/deployment tools

Configuration:

Configuration for OMERO.web takes place via the
omero config commands. The configuration values
which are checked are as below:

Key Default? 'Current value'
omero.web.admins True []
omero.web.application_host False 'http://omepslid.compbio.cs.cmu.edu'
omero.web.application_server False 'fastcgi'
omero.web.application_server.host True '0.0.0.0'
omero.web.application_server.port False '14080'
omero.web.cache_backend True '(unset)'
omero.web.database_engine True '(unset)'
omero.web.database_host True '(unset)'
omero.web.database_name True '(unset)'
omero.web.database_password True '(unset)'
omero.web.database_port True '(unset)'
omero.web.database_user True '(unset)'
omero.web.debug False True
omero.web.email_host True None
omero.web.email_host_password True None
omero.web.email_host_user True None
omero.web.email_port True None
omero.web.email_subject_prefix True '[OMERO.web] '
omero.web.email_use_tls True False
omero.web.logdir True '/usr0/local/omero.server/OMERO.server-Beta-4.3.2/var/log'
omero.web.public.password True '(unset)'
omero.web.public.user True '(unset)'
omero.web.scripts_to_ignore True ['/omero/figure_scripts/Movie_Figure.py', '/omero/figure_scripts/Split_View_Figure.py', '/omero/figure_scripts/Thumbnail_Figure.py', '/omero/figure_scripts/ROI_Split_Figure.py', '/omero/export_scripts/Make_Movie.py']
omero.web.send_broken_link_emails True True
omero.web.server_email True None
omero.web.server_list True [["localhost", 4064, "omero"]]
omero.web.session_engine True 'django.contrib.sessions.backends.file'
omero.web.use_eman2 True False
omero.web.webgateway_cache True '(unset)'

Example Nginx usage:

FYI,

-bash-3.2$ bin/omero config get
omero.data.dir=/xxx/xxx
omero.db.name=yyy
omero.db.pass=zzz
omero.db.user=aaa
omero.web.application_host=http://omepslid.compbio.cs.cmu.edu
omero.web.application_server=fastcgi
omero.web.application_server.port=14080
omero.web.debug=True

BK

Posted: **Mon Oct 03, 2011 5:41 pm**

followup question.
Do I need to match the port in the configuration like this?

-bash-3.2$ bin/omero config set omero.web.application_server.port 14080
-bash-3.2$ bin/omero config set omero.web.application_host 'http://omepslid.compbio.cs.cmu.edu:14080'

Then, I got

-bash-3.2$ bin/omero web config apache
###
### Stanza for OMERO.web created 2011-10-03 13:00:23.450032
###
FastCGIExternalServer "/usr0/local/omero.server/OMERO.server-Beta-4.3.2/var/omero.fcgi" -socket "/usr0/local/omero.server/OMERO.server-Beta-4.3.2/var/django_fcgi.sock"

<Directory "/usr0/local/omero.server/OMERO.server-Beta-4.3.2/var">
Options -Indexes FollowSymLinks
Order allow,deny
Allow from all
</Directory>

<Directory "/usr0/local/omero.server/OMERO.server-Beta-4.3.2/lib/python/omeroweb/media">
Options -Indexes FollowSymLinks
Order allow,deny
Allow from all
</Directory>

Alias /appmedia /usr0/local/omero.server/OMERO.server-Beta-4.3.2/lib/python/omeroweb/media
Alias / "/usr0/local/omero.server/OMERO.server-Beta-4.3.2/var/omero.fcgi/"

But I still cannot logon by http://omepslid.compbio.cs.cmu.edu:14080/

Do I need to modify the "/etc/apache2/httpd.conf" file so that it can listen to port 14080?
Currently, it is

# The following directives control the set of IP addresses and ports
# that the server will listen on. The default is to listen on the
# standard HTTP port (port 80), and if SSL support is enabled, also
# listen on the standard HTTP-over-SSL port (port 443).
Listen 80
<IfDefine SSL>
Listen 443
</IfDefine>

BK

Posted: **Tue Oct 04, 2011 4:16 pm**

Lets back up a little bit as using mod_alias is not supported with OMERO.web and we are assuming a lot of things about your Apache configuration. If you want to run two OMERO.web instances on the same machine you have many options, here are a few:

Use name based virtual hosting with Apache (two hostnames pointing to the same machine omepslid.compbio.cs.cmu.edu and omepslid43.compbio.cs.cmu.edu for example); configuring name based virtual hosting is beyond the scope of what we can help you with, you will need to investigate this yourself
Use address based virtual hosting with Apache (two IP addresses or ports on the same machine; omepslid.compbio.cs.cmu.edu:80 and omepslid.compbio.cs.cmu.edu:8080 for example); again configuring address based virtual hosting is beyond the scope of what we can help you with
Use another web server (for example nginx) on another port; you can configure this easily by installing nginx and using the OMERO.web nginx configuration template
Start the OMERO.web development server for one of your OMERO instances on a different port

The Apache stanzas that OMERO.web prints out for you when you run bin/omero web config apache can be placed inside <VirtualHost> blocks if that is the route you decide to go down. Depending on which Linux distribution you are running on there should be ample documentation on any of the above options.

Posted: **Wed Oct 05, 2011 5:07 pm**

Thanks,
I think I'm almost there.
I am now able to see the front pages for both versions with different domain names. (omepslid.xxx and omepslid2.xxx)

1.
But for omepslid2 OMERO.web, I cannot logon by the root account (i'm sure i'm using the correct password).
I think it's related to the port. from the front page, I can see the only option of (omero:4064). But I expected omero:14064 (since I set the prefix of 1). Should I do something more?

2.
i think this is related to the question 1. It seems like I can still logon to new version of OMERO server via OMERO.insight using the address of "omepslid.xxx" (not omepslid2.xxx) with port 14064. Is this normal?

Thanks in advance,
BK

Posted: **Wed Oct 05, 2011 5:31 pm**

bhcho wrote:I am now able to see the front pages for both versions with different domain names. (omepslid.xxx and omepslid2.xxx)

1.
But for omepslid2 OMERO.web, I cannot logon by the root account (i'm sure i'm using the correct password).
I think it's related to the port. from the front page, I can see the only option of (omero:4064). But I expected omero:14064 (since I set the prefix of 1). Should I do something more?

Yes. You must modify omero.web.server_list. By default this is [["localhost", 4064, "omero"]] so you'll want to do something like the following for your server running on 14064:

Code: Select all: bin/omero config set omero.web.server_list '[["localhost", 14064, "omero"]]'

bhcho wrote:2.
i think this is related to the question 1. It seems like I can still logon to new version of OMERO server via OMERO.insight using the address of "omepslid.xxx" (not omepslid2.xxx) with port 14064. Is this normal?

Yes, that's normal. All that the hostname does is resolve to an IP address and OMERO.server is listening on that IP address. It is not bound to a hostname like your Apache virtual host configuration will be.

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