Open Microscopy Environment

Hello,

I completed a new installation of OMERO.server and OMERO.web on a Ubuntu server VM and set data directory to local /omero folder. We will install a new NAS next month and want to change data directory to a folder in the new NAS. Migrating data is not important. We are using omero with test data now to familiarize with the system.

All i have to do is mount remote fs, set new data dir and restart OMERO.server? Or i have to do something else with database? What is prefered filesystem?

Thanks

borja8 wrote:Hello,

Hi borja8.

borja8 wrote:All i have to do is mount remote fs, set new data dir and restart OMERO.server? Or i have to do something else with database?

There are several options open to you, and it'll depend if you've invested any effort in your database, like creating local user accounts, for example.

I wouldn't recommend just changing the data dir underneath the server, if you've imported any data like the test data you mention, then the database would be out of sync with the underlying filesystem.

One option (1): Treat this like a backup/restore situation [1]. i.e. connect your new storage, stop the server, rsync the existing data dir to the new storage, update the OMERO config with the new data dir path to your new storage, then start up OMERO.

Another option (2): Start out with a 'fresh' server (provided you don't need your database objects like user accounts etc). i.e. create a new, empty data dir folder structure on the new storage and re-run the database bootstrap step on either a new database, or a re-created database. This way you end up with a brand new, clean server.

borja8 wrote: What is prefered filesystem?

Our system requirements page discusses this - see [2]. This will completely depend on what your organisation or institution either pay for, or have experience running and supporting. It's worth discussing this with your local IT support system who will be running the storage on which OMERO runs upon. It'll also depend how much data you think you'll end up with imported into the server.

[1] https://docs.openmicroscopy.org/latest/ ... store.html
[2] https://docs.openmicroscopy.org/latest/ ... ml#storage

kennethgillen wrote:

borja8 wrote:Hello,

Hi borja8.

borja8 wrote:All i have to do is mount remote fs, set new data dir and restart OMERO.server? Or i have to do something else with database?

There are several options open to you, and it'll depend if you've invested any effort in your database, like creating local user accounts, for example.

I wouldn't recommend just changing the data dir underneath the server, if you've imported any data like the test data you mention, then the database would be out of sync with the underlying filesystem.

One option (1): Treat this like a backup/restore situation [1]. i.e. connect your new storage, stop the server, rsync the existing data dir to the new storage, update the OMERO config with the new data dir path to your new storage, then start up OMERO.

Another option (2): Start out with a 'fresh' server (provided you don't need your database objects like user accounts etc). i.e. create a new, empty data dir folder structure on the new storage and re-run the database bootstrap step on either a new database, or a re-created database. This way you end up with a brand new, clean server.

borja8 wrote: What is prefered filesystem?

Our system requirements page discusses this - see [2]. This will completely depend on what your organisation or institution either pay for, or have experience running and supporting. It's worth discussing this with your local IT support system who will be running the storage on which OMERO runs upon. It'll also depend how much data you think you'll end up with imported into the server.

[1] https://docs.openmicroscopy.org/latest/ ... store.html
[2] https://docs.openmicroscopy.org/latest/ ... ml#storage

Your answer was really helpful. I've folllowed steps provided in option1 and now i have omero storage over an NFS mount.
I would like to know if there are some options recommended to add to fstab file for using with omero.

Thank you very much

borja8 wrote:Your answer was really helpful. I've folllowed steps provided in option1 and now i have omero storage over an NFS mount.
I would like to know if there are some options recommended to add to fstab file for using with omero.

Thank you very much

You're more than welcome.

The only thing I'd personally check is whether the storage returns after a reboot of the server. There's nothing in my personal experience that would be OMERO specific for the fstab - I just use what our research computing team recommend for connecting to NFS mounts on their platform. Your local IT or storage provider may be able to advise what they recommend for their platform.

The greater community might have more to add here, too.

All the best,

Kenny