Open Microscopy Environment

Hi All,

Thanks to the OMERO community for your help on my last thread!

In this thread, I have a more specific question about OS recommendations. In a past thread, I saw that Ubuntu LTS was the recommended OS. In an email conversation with Glencoe, I was told that Red Hat Enterprise or CentOS was preferred by their technicians. Based on this brief discussion with Glencoe, I chose to use CentOS for my test server. I installed the Web Server (no GUI) version of CentOS and was able to get everything up and running; although, it was quite a challenge to learn all of the bash commands. Fortunately, I took copious notes during the installation and I am planning to use a similar CentOS installation for my production server. Before I move forward with the installation, I thought it would be prudent to get an official OS recommendation. I am wondering if I might need a GUI. For instance, I was just informed about JVisualVM on my last thread and I can imagine that this feature requires a GUI. With this topic in mind, here are my questions:

1. The documentation certainly seems to be geared towards an Ubuntu installation. Is this apparent preference related to the greater easy-of-use of Ubuntu or is performance also a factor?

2. What are the major advantages/disadvantages of running OMERO on a Desktop or Minimal Desktop installation of CentOS instead of the Web Server installation?

As always, Thanks!
Blair

Both Ubuntu LTS and Centos 6 should be ideal for running OMERO. The Linux walkthroughs include instructions for both, we just had to choose one to focus on to avoid making the documentation too confusing. Do you have any other people in your department (or know anyone outside) with sysadmin or Linux experience? If so you'd be better off going with what they're familiar with, since if you run into any configuration problems they might be able to help.

The main benefit of going for the Web/Desktop over the minimal install is to save typing, or trying to figure out exactly what packages you need to install. The scripts from the walkthroughs are designed to install everything necessary based on the minimal installation, if they don't it's a bug so let us know!

I've just noticed in your original thread you mentioned CentOS 7. Did you managae to get OMERO working on it? Last time I looked there wasn't a suitable version of Ice available.

Cheers

Simon

Hi Blair,

brossetti wrote:Based on this brief discussion with Glencoe, I chose to use CentOS for my test server.

Good choice! Many of the OME test and production systems are CentOS (6).

brossetti wrote: I am wondering if I might need a GUI. For instance, I was just informed about JVisualVM on my last thread and I can imagine that this feature requires a GUI.

You definitely don't need a GUI installation on your OMERO server. If I was running JVisualVM on one of our servers, I'd run it with a remote X session, on a local X Window server on my Mac. All you need is xauth installed on the server, to 'stream' the UI part of the application to your desktop machine. [1] For ongoing monitoring, you may be better off using JMX [2] [3].

brossetti wrote:1. The documentation certainly seems to be geared towards an Ubuntu installation. Is this apparent preference related to the greater easy-of-use of Ubuntu or is performance also a factor?

We are always updating our documentation - there was no reason for the Ubuntu focus, just the last time it was documented likely Ubuntu was used. CentOS really is a good choice. We now have great walkthroughs with specific installation shell script for both Ubuntu and CentOS [4] - the latter I've used to set up our last few OMERO servers for the OME team!

brossetti wrote:2. What are the major advantages/disadvantages of running OMERO on a Desktop or Minimal Desktop installation of CentOS instead of the Web Server installation?

I don't see any advantages running a Desktop version of CentOS for your server. A couple of disadvantages I can think off from the top of my head:

* When using the Desktop versions of CentOS you are loading extra resources into RAM which may be better of given to OMERO, depending on how much RAM you have.
* The system will take a little longer to start up, too. Also, the more you have installed, the more you are exposed to vulnerabilities and the more you have to patch, making the system less stable.

As for the minimal versions, Simon has already addressed that. Thanks Simon!

brossetti wrote:As always, Thanks!
Blair

You're more than welcome! Hope that was of some use.

[1] https://www.google.co.uk/webhp?q=runnin ... plications

[2] https://www.openmicroscopy.org/site/sup ... ation.html - see "JMX Configuration"

[3] http://java.dzone.com/articles/visualvm ... remote-jvm

[4] https://www.openmicroscopy.org/site/sup ... rough.html

Thanks Simon and Kenny! These are very helpful tips.

@Simon
Good catch! CentOS 7 was a typo -- I will edit that. I created my test server with CentOS 6.5. Now that you mention Ice, I want to share a bit of confusion I had while going through the installation documents. The Ice section says the following:

If possible, install one of the following packages:
System | Package
BSD Ports | devel/ice
Debian | zeroc-ice
Homebrew | ice
RedHat | N/A

I was following along with the RedHat recommendation because my test server was running CentOS. I interpreted the previous section to mean that I did not need to install Ice because there is not a version available for RedHat. Based on my notes, I did the following once I realized my mistake:

46.) Install Ice 3.4 (I didn’t do this earlier because the OMERO site says N/A for Ice). To do this you need to setup the zeroc repo then install packages using yum

Code: Select all

[tech@omerobox /]$ cd /etc/yum.repos.d/
[tech@omerobox yum.repos.d]$ sudo wget http://www.zeroc.com/download/Ice/3.4/rhel5/zeroc-ice.repo
[tech@omerobox yum.repos.d]$ sudo yum install ice-php ice-php-devel
[tech@omerobox yum.repos.d]$ sudo yum install ice-python
[tech@omerobox yum.repos.d]$ sudo yum install ice-python-devel
[tech@omerobox yum.repos.d]$ sudo yum install ice-sqldb

FYI: My test server is running OMERO.server-5.0.2-ice34-b26

@Kenny
Thanks for the tip about the remote X session. I will play around with this to get familiar.

Thanks,
Blair

To reduce the confusion in the docs, we can certainly replace "N/A" with something more explicit like "Install ZeroC RPMs" if that would be clearer?


Regards,
Roger Leigh

Hi Roger,

I think that would be very helpful for novices like me.

Thanks!
Blair

Thanks. The changes are in: https://github.com/openmicroscopy/ome-d ... n/pull/950