WiP: Install omero #232
WiP: Install omero #232
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Interestingly, for e5e4ba2 (expose OMERO.web in Ansible install case on CentOS 7 docker) I had to add to the web config inside the docker: This finally exposed the OMERO.web outside of the docker on localhost:4080. I wonder if the completely empty config with respect to OMERO.web after installing omero using Ansible as per playbook in ansible..-onenode example is not a bug of the workflow. We probably should not claim it works out of the box in OMERO.web case for |
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@pwalczysko Sorry, in answer to your question, I don't know what's going on or where to look. I guess the code that's responsible is in https://github.com/ome/ansible-role-omero-web somewhere but I've not used ansible yet or edited a playbook/role. |
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Can someone explain the difference between this new page and the main installation document? |
The idea was to have a very simple quick walkthrough, something based on https://downloads.openmicroscopy.org/presentations/2020/Dundee/Workshops/OME2020-OMERO-Installation/#/ , which can be used in workshop situations (this PR). Target audience is a sysadmin who wants to have a quick check, look and feel about what OMERO install entails. The main installation document is for sysadmins who already know that they will want to use manual install and not ansible, and want to go "the hard way" as explained in https://downloads.openmicroscopy.org/presentations/2020/Dundee/Workshops/OME2020-OMERO-Installation/#/ - much less streamlined, much more work, much less explanation about options, no mention of |
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Other than the "quick check" which I can see in terms of an intro before a sysadmin wants to jump into the deep-end (i.e. what are my options), I'd raise the question whether |
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We discussed several times adding the |
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@pwalczysko: thoughts? |
I am using the work to get more familiar with the ansible ecosystem and to be able to answer the questions of sysadmins at outreach opportunities. The guide would be kind of a necessary first step, as it will be necessarily minimal. It also would have the overview of options (ansible, docker, manual) in a much more lighweight manner than the serious doc and would be an easy link to point to when the installation questions come (they do not necessarily come from sysadmins, but from men-in-the-middle). So I would vote for both, first this walkthrough, and when I see that it works and makes sense in the overall and simple cases, then inclusion in the main doc. |
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Ok. I'll hold my horses then. |
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| $ docker-compose pull | ||
| $ docker-compose up -d | ||
| $ docker-compose logs -f |
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This works so far... and gets to:
omeroserver_1 | 2022-09-22 13:08:48,441 [ omego.db] INFO Database is already at OMERO5.4__0
omeroserver_1 | Running /startup/99-run.sh
omeroserver_1 | Starting OMERO.server
but then seems to stop.
Webclient is available at http://localhost:4080/webclient but says server is not responding.
How do I access server logs to see if anything went wrong?
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I have:
$ docker ps
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
4e63dfd4de54 openmicroscopy/omero-server:5 "/usr/local/bin/entr…" 5 days ago Up 8 minutes 0.0.0.0:4063-4064->4063-4064/tcp docker-example-omero_omeroserver_1
7bb7d25fb5f7 openmicroscopy/omero-web-standalone:5 "/usr/local/bin/entr…" 5 days ago Up 8 minutes 0.0.0.0:4080->4080/tcp docker-example-omero_omeroweb_1
acb5f42fa4cf postgres:11 "docker-entrypoint.s…" 5 days ago Up 8 minutes 5432/tcp docker-example-omero_database_1
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OK, so I managed to ssh into server...
$ docker exec -it docker-example-omero_omeroserver_1 /bin/bash
I don't know where $OMERO_HOME is, thought maybe I could find something like grid.xml...
bash-4.2$ cd /
bash-4.2$ find ./ -name grid.xml
find: './var/spool/at': Permission denied
find: './var/spool/cron': Permission denied
find: './var/db/sudo': Permission denied
find: './var/lib/machines': Permission denied
find: './var/lib/yum/history/2020-11-13/2': Permission denied
find: './var/lib/yum/history/2020-11-13/1': Permission denied
find: './var/lib/yum/history/2020-11-13/8': Permission denied
find: './var/lib/yum/history/2020-11-13/11': Permission denied
find: './var/lib/yum/history/2020-11-13/7': Permission denied
find: './var/lib/yum/history/2020-11-13/9': Permission denied
find: './var/lib/yum/history/2020-11-13/6': Permission denied
find: './var/lib/yum/history/2020-11-13/10': Permission denied
find: './var/lib/yum/history/2020-11-13/5': Permission denied
find: './var/lib/yum/history/2020-11-13/3': Permission denied
find: './var/lib/yum/history/2020-11-13/4': Permission denied
find: './etc/pki/CA/private': Permission denied
find: './etc/ssmtp': Permission denied
find: './etc/sudoers.d': Permission denied
find: './proc/tty/driver': Permission denied
find: './run/cryptsetup': Permission denied
find: './run/sudo': Permission denied
find: './root': Permission denied
bash-4.2$ sudo find ./ -name grid.xml
sudo: no tty present and no askpass program specified
bash-4.2$ echo $OMERO_HOME
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Try
docker exec -it docker-example-omero_omeroweb_1 bash
bash-4.2$ vi /opt/omero/web/OMERO.web/var/log/OMEROweb.log
Analogously for omero_server.
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Thanks - using my exec still on omero-server container... This gives me nothing, so something failing before logs created:
ls /opt/omero/server/OMERO.server/var/
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I have:
$ docker ps CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES 4e63dfd4de54 openmicroscopy/omero-server:5 "/usr/local/bin/entr…" 5 days ago Up 8 minutes 0.0.0.0:4063-4064->4063-4064/tcp docker-example-omero_omeroserver_1 7bb7d25fb5f7 openmicroscopy/omero-web-standalone:5 "/usr/local/bin/entr…" 5 days ago Up 8 minutes 0.0.0.0:4080->4080/tcp docker-example-omero_omeroweb_1 acb5f42fa4cf postgres:11 "docker-entrypoint.s…" 5 days ago Up 8 minutes 5432/tcp docker-example-omero_database_1
vs mine which is (I have some additional :: motives in the PORTS bit, but not sure how important this is)
docker ps
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
3d049e9f93a0 postgres:11 "docker-entrypoint.s…" 35 seconds ago Up 34 seconds 5432/tcp docker-example-omero_database_1
8fd37b70d98b openmicroscopy/omero-web-standalone:5 "/usr/local/bin/entr…" 35 seconds ago Up 34 seconds 0.0.0.0:4080->4080/tcp, :::4080->4080/tcp docker-example-omero_omeroweb_1
3e3b742adb6d openmicroscopy/omero-server:5 "/usr/local/bin/entr…" 35 seconds ago Up 34 seconds 0.0.0.0:4063-4064->4063-4064/tcp, :::4063-4064->4063-4064/tcp docker-example-omero_omeroserver_1
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@will-moore I have master.err and Blitz log, but my server is not working on M1. I will open an extra issue, so as not to confuse people.
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When would be the right time to come back to the discussion from early Sep? |
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I am still finding it quite painful to do any work that needs a connection to OMERO, especially when working from home, since I still have not managed to install OMERO on my M1 Mac, even using Docker etc. So I would really appreciate any solution that allows me to run OMERO locally! |
The sooner the better for me. cc @jburel - I should be finishing this by the end of January |
@will-moore the install of OMERO on M1 is on my ToDo list prior to TiM 2023. I have my old Mac with everything running on it, but the M1 machine just became my main working comp. I am afraid though that we had a discrepancy in the experience of spinning up the docker between mine M1 and yours. No idea why. Do you want to please rather discuss on a separate issue on the https://github.com/ome/ansible-example-omero-onenode rather than this PR please ? |
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Rebased this on top of #236 to avoid scc conflitcs |
WiP: As discussed last week with @jburel , adding a workflow guide for OMERO install, based freely on the presentation https://downloads.openmicroscopy.org/presentations/2020/Dundee/Workshops/OME2020-OMERO-Installation/#/
See also
ome/omero-deployment-examples#70
ome/ansible-example-omero-onenode#11
Rebased this on top of #236 to avoid scc conflitcs