We're Hiring!

Upgrade from 5.0.2 to 5.1.3 with home-brew faild

Having a problem deploying OMERO? Please ask new questions at https://forum.image.sc/tags/omero
Please note:
Historical discussions about OMERO. Please look for and ask new questions at https://forum.image.sc/tags/omero

The OMERO.server installation documentation begins here and you can find OMERO.web deployment documentation here.

Re: Upgrade from 5.0.2 to 5.1.3 with home-brew faild

Postby Lipplab » Wed Sep 30, 2015 5:02 pm

Hey Sebastien,

thank you a lot for your help. I'm sorry for making so much trouble.
Omero is working!! Yeah!

Just a last question.
I have a Drobo for the uploaded files. It's now nearly full. I want to add an additional Drobo to the server.
How can I integrate the second hard drive capacity to the omero?

Thanks
Julia


bash-3.2$ omero admin start
Creating directory /usr/local/Cellar/omero/5.1.4/var
WARNING: lock files in /Volumes/Drobo16TB/OMERO_DATA_PIC/
----------------------------------------
/Volumes/Drobo16TB/OMERO_DATA_PIC/.omero/repository/0497ffb4-4f1c-4016-845e-254cc9e84520/.lock
/Volumes/Drobo16TB/OMERO_DATA_PIC/.omero/repository/66ed886d-11a1-4f1b-af00-0274a44991b2/.lock
----------------------------------------

You may want to stop all server processes and remove
these files manually. Lock files can remain after an
abrupt server outage and are especially frequent on
remotely mounted filesystems like NFS.

Creating /usr/local/Cellar/omero/5.1.4/var/master
Initializing /usr/local/Cellar/omero/5.1.4/var/log
Creating /usr/local/Cellar/omero/5.1.4/var/registry
No descriptor given. Using etc/grid/default.xml
Waiting on startup. Use CTRL-C to exit
bash-3.2$
Lipplab
 
Posts: 54
Joined: Thu Sep 12, 2013 9:56 am

Re: Upgrade from 5.0.2 to 5.1.3 with home-brew faild

Postby mtbc » Thu Oct 01, 2015 11:08 am

Dear Julia,

It's great that you have OMERO working. :)

In your FS server configuration -- http://www.openmicroscopy.org/site/supp ... ation.html -- there is the setting "omero.managed.dir" to set the root of the Managed Repository for image files. The setting "omero.fs.repo.path" defines a path within the Managed Repository that is used for each set of newly imported files. You can create a directory within the Managed Repository and mount your second drive there and prefix your "omero.fs.repo.path" with that directory -- as shown in https://downloads.openmicroscopy.org/pr ... kshop/#/16 -- so that all new imports go into directories created on that second drive. You should be aware that images that require pyramids (e.g., large JPEGs) still have those created outside the Managed Repository in "omero.data.dir", as with thumbnails, but with luck the bulk of your data is the original image files.

Do feel free to ask if you need me to clarify anything in the above.

Cheers,

Mark
User avatar
mtbc
Team Member
 
Posts: 282
Joined: Tue Oct 23, 2012 10:59 am
Location: Dundee, Scotland

Re: Upgrade from 5.0.2 to 5.1.3 with home-brew faild

Postby Lipplab » Fri Oct 02, 2015 9:01 am

Dear Mark,

thank you a lot for the advice. I'll try it next week.

Have a nice week and greetings to Sebastien.

best wishes

Julia
Lipplab
 
Posts: 54
Joined: Thu Sep 12, 2013 9:56 am

Re: Upgrade from 5.0.2 to 5.1.3 with home-brew faild

Postby Lipplab » Mon Jan 18, 2016 4:59 pm

Dear Mark,
I have serveral questions
1)
I tried to figure out how to write a new directory within the Managed Repository.
I've mounted a second hard drive /Volumes/Drobo_Ex01.
How do I integrate it into the managed repository in that way that the new files are stored there instead of the old destination /Volumes/Drobo16TB/OMERO_DATA_PIC
These are my settings:

me-www:bin benjaminS$ omero fs repos
Previously logged in to 134.96.155.200:4064 as benjaminS
Server: [134.96.155.200:4064]
Username: [benjaminS]
Password:
Created session 870b2f83-f494-45c5-a1ab-0f33b6a10329 (benjaminS@134.96.155.200:4064). Idle timeout: 10 min. Current group: LIPPLAB
# | Id | UUID | Type | Path
---+-------+--------------------------------------+---------+-----------------------------------------------------
0 | 12 | 9e67df8e-0e10-4b3c-af0d-7c105f2a7c27 | Public | /Volumes/Drobo16TB/OMERO_DATA_PIC
1 | 13 | ScriptRepo | Script | /usr/local/Cellar/omero/5.1.4/lib/scripts
2 | 51201 | f3f73bc4-1edb-4f8f-9022-118f0e9924f3 | Public | /opt/omero/OMERO_DATA_PIC/ManagedRepository
3 | 51251 | eeb134e0-4c26-445b-96cc-ee70299f0dc9 | Managed | /Volumes/Drobo16TB/OMERO_DATA_PIC/ManagedRepository
(4 rows)
ome-www:bin benjaminS$ omero config get
omero.data.dir=/Volumes/Drobo16TB/OMERO_DATA_PIC/
omero.db.name=omeroDB
omero.db.pass=omeroDBpass
omero.db.user=omeroDBuser
omero.web.application_server=development
omero.web.debug=True

2) Can I just copy the complete Managed repositorxy on a new Drive?

3) And do I manually delete this file with the normal comand "rm"?
WARNING: lock files in /Volumes/Drobo16TB/OMERO_DATA_PIC/
----------------------------------------
/Volumes/Drobo16TB/OMERO_DATA_PIC/.omero/repository/0497ffb4-4f1c-4016-845e-254cc9e84520/.lock
----------------------------------------

You may want to stop all server processes and remove
these files manually. Lock files can remain after an
abrupt server outage and are especially frequent on
remotely mounted filesystems like NFS.


Thank you a lot
Julia
Lipplab
 
Posts: 54
Joined: Thu Sep 12, 2013 9:56 am

Re: Upgrade from 5.0.2 to 5.1.3 with home-brew faild

Postby jmoore » Tue Jan 19, 2016 10:11 am

Hi Julia,

Lipplab wrote:1)
I tried to figure out how to write a new directory within the Managed Repository.


This directory is "Managed" since only the OMERO server should write to it.

I've mounted a second hard drive /Volumes/Drobo_Ex01.
How do I integrate it into the managed repository in that way that the new files are stored there instead of the old destination /Volumes/Drobo16TB/OMERO_DATA_PIC
...


If you can mount Drobo_Ex01 under /Volumes/Drobo16TB/OMERO_DATA_PI/ManagedRepository/SOMETHING then you can use:

Code: Select all
bin/omero config set omero.fs.repo.path 'SOMETHING/%user%_%userId%//%year%-%month%/%day%/%time%'


to prepend the new directory. (At this point, you could change the general layout as explained in the config.) If you can't mount Drobo_Ex01, you can instead make the SOMETHING directory a symlink to /Volumes/Drobo_Ex01.


2) Can I just copy the complete Managed repository on a new Drive?


Yes, you could:
  • shut down the server
  • copy the files over
  • configure omero.managed.dir to point at /Volumes/Drobo_Ex01/ManagedRepository
  • start the server and check that an import goes to Drobo_Ex01
  • clean up Drobo16TB/OMERO_DATA_PIC/ManagedRepository

3) And do I manually delete this file with the normal comand "rm"?
WARNING: lock files in /Volumes/Drobo16TB/OMERO_DATA_PIC/
----------------------------------------
/Volumes/Drobo16TB/OMERO_DATA_PIC/.omero/repository/0497ffb4-4f1c-4016-845e-254cc9e84520/.lock
----------------------------------------

You may want to stop all server processes and remove
these files manually. Lock files can remain after an
abrupt server outage and are especially frequent on
remotely mounted filesystems like NFS.


You can but this is likely pointing to a deeper issue with locking on Drobo. See
https://www.openmicroscopy.org/site/support/omero5.2/sysadmins/unix/server-binary-repository.html#locking-and-remote-shares


Cheers,
~Josh

UPDATE: fixed the above command by adding "omero.fs.repo.path " -- `bin/omero config set omero.fs.repo.path ...`
User avatar
jmoore
Site Admin
 
Posts: 1591
Joined: Fri May 22, 2009 1:29 pm
Location: Germany

Re: Upgrade from 5.0.2 to 5.1.3 with home-brew faild

Postby Lipplab » Tue Aug 09, 2016 8:02 am

Dear Josh,

Due to the Drobo properties I had to split one Drobo into two 16 TB partitions called Drobo_Ex01, and Drobo_Ex02.
The Drobo_Ex01 is for backups of the omero server.
I copied the magaed repository to the new harddrive /Volumes/Drobo_Ex02 and I cleaned up the old destination /Volumes/Drobo16TB/OMERO_DATA_PIC.

Now I need more space to add more files. Therfore I want to expant to the /Volumes/Drobo16TB, that all new data are saved on this harddrive.

As you recommended I tried first to mount
If you can mount Drobo_Ex01 under /Volumes/Drobo16TB/OMERO_DATA_PI/ManagedRepository/SOMETHING

but It didn't work.

I have a question for your second suggestion:
If you can't mount Drobo_Ex01, you can instead make the SOMETHING directory a symlink to /Volumes/Drobo_Ex01.


I have to create a Folder for the new data called f.ex. SOMETHING on the new destination /Volumes/Drobo16TB/ and I have to configure it first with
Code: Select all
bin/omero config set 'SOMETHING/%user%_%userId%//%year%-%month%/%day%/%time%'
??
Then I can make the symlink ln -s path to origonal/ /path to link
Code: Select all
ln -s /Volumes/Drobo_Ex02 /Volumes/Drobo16TB/SOMETHING/


and that's it? So all the new data will be saved on Volumes/Drobo16TB/SOMETHING?

Thanks Julia
Lipplab
 
Posts: 54
Joined: Thu Sep 12, 2013 9:56 am

Re: Upgrade from 5.0.2 to 5.1.3 with home-brew faild

Postby cblackburn » Tue Aug 09, 2016 9:17 am

Hi Julia,

It's been a while!

I'll come on to your question later, but first of all I would highly recommend upgrading your OMERO server to the most recent release, 5.2.5. As well as all the improvements in the 5.2 line this includes an important security fix, details at:

https://www.openmicroscopy.org/community/viewtopic.php?f=11&t=8092

Note that as we no longer actively support the 5.1 line we won't be back-porting any further fixes to 5.1.

Upgrade information is available at:

http://www.openmicroscopy.org/site/support/omero5.2/sysadmins/server-upgrade.html

Once you have done this then you should be able to set the destination of the ManagedRepository. However, Josh had a typo in his original config setting command, it should be:

Code: Select all
bin/omero config set omero.fs.repo.path  'SOMETHING/%user%_%userId%//%year%-%month%/%day%/%time%'

and then after that you can symlink as described.

Cheers,

Colin
cblackburn
 
Posts: 85
Joined: Mon May 25, 2009 9:03 pm

Re: Upgrade from 5.0.2 to 5.1.3 with home-brew faild

Postby Lipplab » Tue Aug 09, 2016 11:12 am

Dear Colin,

thanks a lot for your fast reply.
at the moment, the omero server is running on 5.2.2.

I'll first update the server.
Than I'll do the symlink.

cheers,
Julia
Lipplab
 
Posts: 54
Joined: Thu Sep 12, 2013 9:56 am

Re: Upgrade from 5.0.2 to 5.1.3 with home-brew faild

Postby Lipplab » Wed Aug 10, 2016 8:45 am

Dear Colin,

I've tried to update omero with hombrew.
I updated homebrew and i tried to run brew upgarde omero
i got this message:
Code: Select all
ome-www:bin benjaminS$ brew upgrade omero
Error: ome/alt/omero52 not installed


Code: Select all
ome-www:bin benjaminS$ brew update
Already up-to-date.
ome-www:bin benjaminS$ brew upgrade omero
Error: ome/alt/omero52 not installed
ome-www:bin benjaminS$ omero admin diagnostics

================================================================================
OMERO Diagnostics 5.2.2-ice35
================================================================================
       
Commands:   java -version                  1.7.0     (/usr/bin/java)
Commands:   python -V                      2.7.7     (/usr/local/bin/python -- 2 others)
Commands:   icegridnode --version          3.5.1     (/usr/local/bin/icegridnode)
Commands:   icegridadmin --version         3.5.1     (/usr/local/bin/icegridadmin)
Commands:   psql --version                 9.3.4     (/usr/local/bin/psql)

Server:     icegridnode                    not started

Log dir:    /usr/local/Cellar/omero/5.2.2/var/log exists
Log files:  Blitz-0.log                    61.0 MB       errors=191  warnings=645
Log files:  Blitz-0.log.1                  524.0 MB      errors=2624 warnings=2110
Log files:  DropBox.log                    19.0 KB       errors=16   warnings=7   
Log files:  FileServer.log                 2.0 KB       
Log files:  Indexer-0.log                  3.0 MB        errors=3    warnings=9   
Log files:  MonitorServer.log              7.0 KB        errors=10   warnings=0   
Log files:  OMEROweb.log                   n/a
Log files:  PixelData-0.log                1.0 MB        errors=0    warnings=16 
Log files:  Processor-0.log                4.0 MB        errors=1164 warnings=1   
Log files:  Processor-0.log.1              4.0 MB        errors=1427 warnings=84 
Log files:  Tables-0.log                   n/a
Log files:  TestDropBox.log                n/a
Log files:  master.err                     13.0 KB       errors=9    warnings=6   
Log files:  master.out                     0.0 KB       
Log files:  Total size                     599.82 MB


Environment:OMERO_HOME=(unset)             
Environment:OMERO_NODE=(unset)             
Environment:OMERO_MASTER=(unset)           
Environment:OMERO_USERDIR=(unset)         
Environment:OMERO_TMPDIR=(unset)           
Environment:PATH=/usr/local/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin
Environment:PYTHONPATH=(unset)             
Environment:ICE_HOME=(unset)               
Environment:LD_LIBRARY_PATH=(unset)       
Environment:DYLD_LIBRARY_PATH=(unset)     

Cannot list deployed applications.
OMERO data dir:'/Volumes/Drobo_Ex02/OMERO_DATA_PIC/' Exists? True   Is writable? True
OMERO temp dir:'/Users/benjaminS/omero/tmp'   Exists? True   Is writable? True   (Size: 18444)

JVM settings: Blitz-${index}                -Xmx2576m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index}              -Xmx1717m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index}            -Xmx2576m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index}           -Xmx1717m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions

OMERO.web not installed!
Django not installed!


should I manually update omero with.....
$ cd ..
$ mv OMERO.server OMERO.server-old
$ unzip OMERO.server-5.2.5-ice3x-byy.zip
$ ln -s OMERO.server-5.2.5-ice3x-byy OMERO.server
$ cp OMERO.server-old/etc/grid/config.xml OMERO.server/etc/grid ....?
Does it cause problems with homebrew?
Many thanks Julia
Lipplab
 
Posts: 54
Joined: Thu Sep 12, 2013 9:56 am

Re: Upgrade from 5.0.2 to 5.1.3 with home-brew faild

Postby sbesson » Wed Aug 10, 2016 9:10 am

Hi Julia,

I can reproduce the [quote]brew upgrade[/quote` issue you are describing which looks like a side-effect of this Pull Request. Previously we used to maintain two duplicate formulas (omero and omero52) but `omero` is now an alias in the Homebrew semantics.

Note in the general case `brew upgrade` will only upgrade the installed package and not perform all the steps of the OMERO.server upgrade in particular it will not handle PSQL database upgrade and copying of configuration files.

From your 5.2.2 installation, the easiest way to upgrade is to:
  • backup the configuration file and optionally logs from your previous installation as you suggested in your thread
  • uninstall the existing package with
    Code: Select all
    brew remove omero
  • install the new OMERO.server with
    Code: Select all
    brew install omero
    NB: this should build the omero52 formula from source code
  • copy the new configuration files and restart the server

Best,
Sebastien
User avatar
sbesson
Team Member
 
Posts: 421
Joined: Tue Feb 28, 2012 7:20 pm

PreviousNext

Return to Installation and Deployment

Who is online

Users browsing this forum: No registered users and 1 guest