Comments (21)
will-moore
commented on July 29, 2024
2
After trying again with docker compose down then docker-compose up -d and docker-compose logs -f again, it worked - I can log into webclient and connect via cli to localhost:4064!
from docker-example-omero.
joshmoore
commented on July 29, 2024
JVM settings: Blitz-${index} -Xmx1234m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index} -Xmx823m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index} -Xmx1234m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index} -Xmx823m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
I'm going to guess that your Docker isn't configured with enough memory.
from docker-example-omero.
will-moore
commented on July 29, 2024
After boosting memory on my Docker settings...
I still see no server...
and no logs...
$ docker exec -it docker-example-omero_omeroserver_1 bash
bash-4.2$ cd /opt/omero/server/OMERO.server
bash-4.2$ ls var/log
ls: cannot access var/log: No such file or directory
bash-4.2$ bin/omero admin diagnostics
================================================================================
OMERO Diagnostics (admin) 5.11.2
================================================================================
Traceback (most recent call last):
File "/opt/omero/server/venv3/bin/omero", line 8, in <module>
sys.exit(main())
File "/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/main.py", line 125, in main
rv = omero.cli.argv()
File "/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/cli.py", line 1784, in argv
cli.invoke(args[1:])
File "/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/cli.py", line 1222, in invoke
stop = self.onecmd(line, previous_args)
File "/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/cli.py", line 1299, in onecmd
self.execute(line, previous_args)
File "/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/cli.py", line 1381, in execute
args.func(args)
File "/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/install/windows_warning.py", line 26, in wrapper
return func(self, *args, **kwargs)
File "/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/plugins/prefs.py", line 79, in open_and_close_config
return func(*args, **kwargs)
File "/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/plugins/admin.py", line 1235, in diagnostics
template_xml = XML(templates.text())
File "/usr/lib64/python3.6/xml/etree/ElementTree.py", line 1315, in XML
return parser.close()
xml.etree.ElementTree.ParseError: no element found: line 1, column 0
from docker-example-omero.
pwalczysko
commented on July 29, 2024
But I do, so the boosting did it for me, thanks @joshmoore - I guess @will-moore must have a different setup somehow. My docker is
docker --version
Docker version 20.10.17, build 100c701
(sorry, edited mine, the previous one was from the older Mac - now it is correct)
from docker-example-omero.
will-moore
commented on July 29, 2024
$ docker --version
Docker version 20.10.16, build aa7e414
from docker-example-omero.
will-moore
commented on July 29, 2024
Unfortunately I am back to seeing the xml.etree.ElementTree.ParseError: no element found: line 1, column 0 error above now. š
from docker-example-omero.
will-moore
commented on July 29, 2024
Tried again - same error on bin/omero admin diagnostics
To start from scratch...
docker compose down
docker system prune
Total reclaimed space: 0B
$ docker-compose pull
$ docker-compose up -d
$ docker-compose logs -f
Web failed login again...
In another terminal...
$ docker exec -it docker-example-omero_omeroserver_1 bash
$ cd /opt/omero/server/OMERO.server
$ bin/omero admin diagnostics
================================================================================
OMERO Diagnostics (admin) 5.11.2
================================================================================
Traceback (most recent call last):
File "/opt/omero/server/venv3/bin/omero", line 8, in <module>
sys.exit(main())
File "/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/main.py", line 125, in main
rv = omero.cli.argv()
File "/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/cli.py", line 1784, in argv
cli.invoke(args[1:])
File "/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/cli.py", line 1222, in invoke
stop = self.onecmd(line, previous_args)
File "/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/cli.py", line 1299, in onecmd
self.execute(line, previous_args)
File "/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/cli.py", line 1381, in execute
args.func(args)
File "/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/install/windows_warning.py", line 26, in wrapper
return func(self, *args, **kwargs)
File "/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/plugins/prefs.py", line 79, in open_and_close_config
return func(*args, **kwargs)
File "/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/plugins/admin.py", line 1235, in diagnostics
template_xml = XML(templates.text())
File "/usr/lib64/python3.6/xml/etree/ElementTree.py", line 1315, in XML
return parser.close()
xml.etree.ElementTree.ParseError: no element found: line 1, column 0
That failure at https://github.com/ome/omero-py/blob/7f979ce44b1fcbebfceb92cf51bf7c354a28ec57/src/omero/plugins/admin.py#L1235
seems to be because templates.xml is not being read...
bash-4.2$ ls -alh etc/grid/
total 20K
drwxr-xr-x 1 omero-server omero-server 4.0K Sep 27 12:24 .
drwxr-xr-x 1 omero-server omero-server 4.0K Jun 29 08:56 ..
-rw-r--r-- 1 omero-server omero-server 2.4K Sep 27 12:24 config.xml
-rw-r--r-- 1 omero-server omero-server 0 Sep 27 12:22 templates.xml
-rw-r--r-- 1 omero-server omero-server 0 Sep 27 12:22 templates.xml.lock
It exists but seems empty:
bash-4.2$ cat etc/grid/templates.xml
bash-4.2$
Is this what's causing the server not to start?
from docker-example-omero.
joshmoore
commented on July 29, 2024
Is this what's causing the server not to start?
Almost definitely since it's a vital file.
from docker-example-omero.
will-moore
commented on July 29, 2024
So where does it come from? How could it be that it's empty for me?
Could I copy one from somewhere else?
Also, at one point above, the server did start for me, so it must have been there at some point (after the first time I saw the error for it being empty!)
from docker-example-omero.
joshmoore
commented on July 29, 2024
You shouldn't need to do anything; in other words, something is going very wrong (disk space?).
from docker-example-omero.
will-moore
commented on July 29, 2024
I would have thought that 80 GB was enough for an empty server, but I boosted it to 120 GB and a few other settings too:
Then did a full stop, prune and restart as before...
It worked, and I could log in to the webclient...
So, now I wanted to run without the webclient (since it interferes with running my dev web server).
docker compose down then I commented -out the web section from compose.yml and started everything up.
$ docker-compose pull
Pulling database ... done
Pulling omeroserver ... done
$ docker-compose up -d
Creating network "docker-example-omero_omero" with the default driver
Creating docker-example-omero_omeroserver_1 ... done
Creating docker-example-omero_database_1 ... done
$ docker-compose logs -f
But I can't seem to log in via the CLI or my dev omero-web.
$ omero login
Previously logged in to localhost:4064 as root
Server: [localhost:4064]
Username: [root]
Password:
internal server error
I don't see anything in the server var/log/Blitz-0.log while this is happening. $ omero admin diagnostics nothing obvious...
2022-09-28 15:06:22,343 INFO [ ome.services.util.DBUserCheck] ( main) Group guest.id = 2
2022-09-28 15:06:26,848 INFO [ ome.services.fulltext.FullTextAnalyzer] ( main) Initialized FullTextAnalyzer
tail: inotify cannot be used, reverting to polling: Function not implemented
Tried docker compose down and up again...
Now I see the xml.etree.ElementTree.ParseError: no element found: line 1, column 0 from empty templates.xml again!
I wonder if docker compose down is part of the problem. That's the only thing I'm doing that's not in the docs..?
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joshmoore
commented on July 29, 2024
You could try "docker-compose down -v" in order to remove the volumes. Changing your docker disk image size clobbers everything.
from docker-example-omero.
pwalczysko
commented on July 29, 2024
Maybe slightly brutish idea @will-moore : If I understand correctly, you are able to start all components successfully after some sequence of commands ? The only thing which is not according to your needs is the interference of the by-default-included omero-web with your development omero-web server ? If so, why not to run everything (postgres, server, web-server) and stop the interference by doing an exec into the web docker and stopping the web manually, which will stop it interfering with your development web-server ?
from docker-example-omero.
will-moore
commented on July 29, 2024
After the last change of docker disk image size, it started OK then after docker compose down and start again I go the templates.xml error, so that doesn't seem to be caused by the settings change.
I tried docker compose down -v just now...
full logs
(omeroweb) Williams-MacBook-Pro:docker-example-omero wmoore$ docker-compose down -v
Stopping docker-example-omero_omeroserver_1 ... done
Stopping docker-example-omero_database_1 ... done
Removing docker-example-omero_omeroserver_1 ... done
Removing docker-example-omero_database_1 ... done
Removing network docker-example-omero_omero
Removing volume docker-example-omero_database
Removing volume docker-example-omero_omero
(omeroweb) Williams-MacBook-Pro:docker-example-omero wmoore$
(omeroweb) Williams-MacBook-Pro:docker-example-omero wmoore$ docker-compose up -d
Creating network "docker-example-omero_omero" with the default driver
Creating volume "docker-example-omero_database" with default driver
Creating volume "docker-example-omero_omero" with default driver
Creating docker-example-omero_database_1 ... done
Creating docker-example-omero_omeroserver_1 ... done
(omeroweb) Williams-MacBook-Pro:docker-example-omero wmoore$ docker-compose logs -f
Attaching to docker-example-omero_database_1, docker-example-omero_omeroserver_1
omeroserver_1 | Running /startup/50-config.py
omeroserver_1 | INFO:omero_certificates.certificates:Setting omero.glacier2.IceSSL.DefaultDir=/OMERO/certs
omeroserver_1 | INFO:omero_certificates.certificates:Setting omero.certificates.commonname=localhost
omeroserver_1 | INFO:omero_certificates.certificates:Setting omero.certificates.owner=/L=OMERO/O=OMERO.server
omeroserver_1 | INFO:omero_certificates.certificates:Setting omero.certificates.key=server.key
omeroserver_1 | INFO:omero_certificates.certificates:Setting omero.glacier2.IceSSL.CertFile=server.p12
omeroserver_1 | INFO:omero_certificates.certificates:Setting omero.glacier2.IceSSL.CAs=server.pem
omeroserver_1 | INFO:omero_certificates.certificates:Setting omero.glacier2.IceSSL.Password=secret
omeroserver_1 | INFO:omero_certificates.certificates:Setting omero.glacier2.IceSSL.Ciphers=HIGH
omeroserver_1 | INFO:omero_certificates.certificates:Setting omero.glacier2.IceSSL.ProtocolVersionMax=TLS1_2
omeroserver_1 | INFO:omero_certificates.certificates:Setting omero.glacier2.IceSSL.Protocols=TLS1_0,TLS1_1,TLS1_2
omeroserver_1 | INFO:omero_certificates.certificates:Executing: openssl version
omeroserver_1 | OpenSSL 1.0.2k-fips 26 Jan 2017
omeroserver_1 | INFO:omero_certificates.certificates:Using existing key: /OMERO/certs/server.key
omeroserver_1 | INFO:omero_certificates.certificates:Creating self-signed certificate: /OMERO/certs/server.pem
omeroserver_1 | INFO:omero_certificates.certificates:Executing: openssl req -new -x509 -subj /L=OMERO/O=OMERO.server/CN=localhost -days 365 -key /OMERO/certs/server.key -out /OMERO/certs/server.pem -extensions v3_ca
omeroserver_1 | INFO:omero_certificates.certificates:Creating PKCS12 bundle: /OMERO/certs/server.p12
omeroserver_1 | INFO:omero_certificates.certificates:Executing: openssl pkcs12 -export -out /OMERO/certs/server.p12 -inkey /OMERO/certs/server.key -in /OMERO/certs/server.pem -name server -password pass:secret
omeroserver_1 | certificates created: /OMERO/certs/server.pem /OMERO/certs/server.p12
database_1 | The files belonging to this database system will be owned by user "postgres".
database_1 | This user must also own the server process.
database_1 |
database_1 | The database cluster will be initialized with locale "en_US.utf8".
database_1 | The default database encoding has accordingly been set to "UTF8".
database_1 | The default text search configuration will be set to "english".
database_1 |
database_1 | Data page checksums are disabled.
database_1 |
database_1 | fixing permissions on existing directory /var/lib/postgresql/data ... ok
database_1 | creating subdirectories ... ok
database_1 | selecting default max_connections ... 100
database_1 | selecting default shared_buffers ... 128MB
database_1 | selecting default timezone ... Etc/UTC
database_1 | selecting dynamic shared memory implementation ... posix
database_1 | creating configuration files ... ok
database_1 | running bootstrap script ... ok
database_1 | performing post-bootstrap initialization ... ok
database_1 | syncing data to disk ... ok
database_1 |
database_1 | Success. You can now start the database server using:
database_1 |
database_1 | pg_ctl -D /var/lib/postgresql/data -l logfile start
database_1 |
database_1 |
database_1 | WARNING: enabling "trust" authentication for local connections
database_1 | You can change this by editing pg_hba.conf or using the option -A, or
database_1 | --auth-local and --auth-host, the next time you run initdb.
database_1 | waiting for server to start....2022-09-28 21:25:46.154 UTC [48] LOG: listening on Unix socket "/var/run/postgresql/.s.PGSQL.5432"
database_1 | 2022-09-28 21:25:46.165 UTC [49] LOG: database system was shut down at 2022-09-28 21:25:45 UTC
database_1 | 2022-09-28 21:25:46.169 UTC [48] LOG: database system is ready to accept connections
database_1 | done
database_1 | server started
database_1 | CREATE DATABASE
database_1 |
database_1 |
database_1 | /usr/local/bin/docker-entrypoint.sh: ignoring /docker-entrypoint-initdb.d/*
database_1 |
database_1 | 2022-09-28 21:25:46.635 UTC [48] LOG: received fast shutdown request
database_1 | waiting for server to shut down....2022-09-28 21:25:46.637 UTC [48] LOG: aborting any active transactions
database_1 | 2022-09-28 21:25:46.639 UTC [48] LOG: background worker "logical replication launcher" (PID 55) exited with exit code 1
database_1 | 2022-09-28 21:25:46.640 UTC [50] LOG: shutting down
database_1 | 2022-09-28 21:25:46.656 UTC [48] LOG: database system is shut down
database_1 | done
database_1 | server stopped
database_1 |
database_1 | PostgreSQL init process complete; ready for start up.
database_1 |
database_1 | 2022-09-28 21:25:46.748 UTC [1] LOG: listening on IPv4 address "0.0.0.0", port 5432
database_1 | 2022-09-28 21:25:46.748 UTC [1] LOG: listening on IPv6 address "::", port 5432
database_1 | 2022-09-28 21:25:46.751 UTC [1] LOG: listening on Unix socket "/var/run/postgresql/.s.PGSQL.5432"
database_1 | 2022-09-28 21:25:46.761 UTC [76] LOG: database system was shut down at 2022-09-28 21:25:46 UTC
database_1 | 2022-09-28 21:25:46.766 UTC [1] LOG: database system is ready to accept connections
^CERROR: Aborting.
(omeroweb) Williams-MacBook-Pro:docker-example-omero wmoore$ docker-compose up -d
docker-example-omero_database_1 is up-to-date
docker-example-omero_omeroserver_1 is up-to-date
(omeroweb) Williams-MacBook-Pro:docker-example-omero wmoore$ docker-compose logs -f
Attaching to docker-example-omero_database_1, docker-example-omero_omeroserver_1
omeroserver_1 | Running /startup/50-config.py
omeroserver_1 | INFO:omero_certificates.certificates:Setting omero.glacier2.IceSSL.DefaultDir=/OMERO/certs
omeroserver_1 | INFO:omero_certificates.certificates:Setting omero.certificates.commonname=localhost
omeroserver_1 | INFO:omero_certificates.certificates:Setting omero.certificates.owner=/L=OMERO/O=OMERO.server
omeroserver_1 | INFO:omero_certificates.certificates:Setting omero.certificates.key=server.key
omeroserver_1 | INFO:omero_certificates.certificates:Setting omero.glacier2.IceSSL.CertFile=server.p12
omeroserver_1 | INFO:omero_certificates.certificates:Setting omero.glacier2.IceSSL.CAs=server.pem
omeroserver_1 | INFO:omero_certificates.certificates:Setting omero.glacier2.IceSSL.Password=secret
omeroserver_1 | INFO:omero_certificates.certificates:Setting omero.glacier2.IceSSL.Ciphers=HIGH
omeroserver_1 | INFO:omero_certificates.certificates:Setting omero.glacier2.IceSSL.ProtocolVersionMax=TLS1_2
omeroserver_1 | INFO:omero_certificates.certificates:Setting omero.glacier2.IceSSL.Protocols=TLS1_0,TLS1_1,TLS1_2
omeroserver_1 | INFO:omero_certificates.certificates:Executing: openssl version
omeroserver_1 | OpenSSL 1.0.2k-fips 26 Jan 2017
omeroserver_1 | INFO:omero_certificates.certificates:Using existing key: /OMERO/certs/server.key
omeroserver_1 | INFO:omero_certificates.certificates:Creating self-signed certificate: /OMERO/certs/server.pem
omeroserver_1 | INFO:omero_certificates.certificates:Executing: openssl req -new -x509 -subj /L=OMERO/O=OMERO.server/CN=localhost -days 365 -key /OMERO/certs/server.key -out /OMERO/certs/server.pem -extensions v3_ca
omeroserver_1 | INFO:omero_certificates.certificates:Creating PKCS12 bundle: /OMERO/certs/server.p12
omeroserver_1 | INFO:omero_certificates.certificates:Executing: openssl pkcs12 -export -out /OMERO/certs/server.p12 -inkey /OMERO/certs/server.key -in /OMERO/certs/server.pem -name server -password pass:secret
omeroserver_1 | certificates created: /OMERO/certs/server.pem /OMERO/certs/server.p12
omeroserver_1 | Running /startup/60-database.sh
omeroserver_1 | postgres connection established
omeroserver_1 | Initialising database
omeroserver_1 | 2022-09-28 21:26:16,271 [omego.extern] INFO Executing : /opt/omero/server/OMERO.server/bin/omero version
database_1 | The files belonging to this database system will be owned by user "postgres".
database_1 | This user must also own the server process.
database_1 |
database_1 | The database cluster will be initialized with locale "en_US.utf8".
database_1 | The default database encoding has accordingly been set to "UTF8".
database_1 | The default text search configuration will be set to "english".
database_1 |
database_1 | Data page checksums are disabled.
database_1 |
database_1 | fixing permissions on existing directory /var/lib/postgresql/data ... ok
database_1 | creating subdirectories ... ok
database_1 | selecting default max_connections ... 100
database_1 | selecting default shared_buffers ... 128MB
database_1 | selecting default timezone ... Etc/UTC
database_1 | selecting dynamic shared memory implementation ... posix
database_1 | creating configuration files ... ok
database_1 | running bootstrap script ... ok
database_1 | performing post-bootstrap initialization ... ok
database_1 | syncing data to disk ... ok
database_1 |
database_1 | Success. You can now start the database server using:
database_1 |
database_1 | pg_ctl -D /var/lib/postgresql/data -l logfile start
database_1 |
database_1 |
database_1 | WARNING: enabling "trust" authentication for local connections
database_1 | You can change this by editing pg_hba.conf or using the option -A, or
database_1 | --auth-local and --auth-host, the next time you run initdb.
database_1 | waiting for server to start....2022-09-28 21:25:46.154 UTC [48] LOG: listening on Unix socket "/var/run/postgresql/.s.PGSQL.5432"
database_1 | 2022-09-28 21:25:46.165 UTC [49] LOG: database system was shut down at 2022-09-28 21:25:45 UTC
database_1 | 2022-09-28 21:25:46.169 UTC [48] LOG: database system is ready to accept connections
database_1 | done
database_1 | server started
database_1 | CREATE DATABASE
database_1 |
database_1 |
database_1 | /usr/local/bin/docker-entrypoint.sh: ignoring /docker-entrypoint-initdb.d/*
database_1 |
database_1 | 2022-09-28 21:25:46.635 UTC [48] LOG: received fast shutdown request
database_1 | waiting for server to shut down....2022-09-28 21:25:46.637 UTC [48] LOG: aborting any active transactions
database_1 | 2022-09-28 21:25:46.639 UTC [48] LOG: background worker "logical replication launcher" (PID 55) exited with exit code 1
database_1 | 2022-09-28 21:25:46.640 UTC [50] LOG: shutting down
database_1 | 2022-09-28 21:25:46.656 UTC [48] LOG: database system is shut down
database_1 | done
database_1 | server stopped
database_1 |
database_1 | PostgreSQL init process complete; ready for start up.
database_1 |
database_1 | 2022-09-28 21:25:46.748 UTC [1] LOG: listening on IPv4 address "0.0.0.0", port 5432
database_1 | 2022-09-28 21:25:46.748 UTC [1] LOG: listening on IPv6 address "::", port 5432
database_1 | 2022-09-28 21:25:46.751 UTC [1] LOG: listening on Unix socket "/var/run/postgresql/.s.PGSQL.5432"
database_1 | 2022-09-28 21:25:46.761 UTC [76] LOG: database system was shut down at 2022-09-28 21:25:46 UTC
database_1 | 2022-09-28 21:25:46.766 UTC [1] LOG: database system is ready to accept connections
database_1 | 2022-09-28 21:26:14.846 UTC [84] ERROR: relation "dbpatch" does not exist at character 15
database_1 | 2022-09-28 21:26:14.846 UTC [84] STATEMENT: select * from dbpatch
omeroserver_1 | OMERO.py version:
omeroserver_1 | OMERO.server version:
omeroserver_1 | 5.6.5-ice36-b233
omeroserver_1 | 5.11.2
omeroserver_1 | 2022-09-28 21:26:23,123 [omego.extern] INFO Completed [6.847 s]
omeroserver_1 | 2022-09-28 21:26:23,125 [ omego.db] INFO DbAdmin: DbAdmin OMERO.server ...
omeroserver_1 | 2022-09-28 21:26:23,126 [omego.extern] INFO Running [current environment]: /opt/omero/server/OMERO.server/bin/omero config get --show-password
omeroserver_1 | 2022-09-28 21:26:23,126 [omego.extern] INFO Executing : /opt/omero/server/OMERO.server/bin/omero config get --show-password
omeroserver_1 | 2022-09-28 21:26:28,906 [omego.extern] INFO Completed [5.780 s]
omeroserver_1 | 2022-09-28 21:26:28,909 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d omero -h database -U omero -w -A -t --version
omeroserver_1 | 2022-09-28 21:26:28,945 [omego.extern] INFO Completed [0.036 s]
omeroserver_1 | 2022-09-28 21:26:28,946 [ omego.db] INFO psql version: psql (PostgreSQL) 11.16
omeroserver_1 |
omeroserver_1 | 2022-09-28 21:26:28,947 [omego.extern] INFO Running [current environment]: /opt/omero/server/OMERO.server/bin/omero config get --show-password
omeroserver_1 | 2022-09-28 21:26:28,947 [omego.extern] INFO Executing : /opt/omero/server/OMERO.server/bin/omero config get --show-password
omeroserver_1 | 2022-09-28 21:26:34,936 [omego.extern] INFO Completed [5.987 s]
omeroserver_1 | 2022-09-28 21:26:34,940 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d omero -h database -U omero -w -A -t -c \conninfo
omeroserver_1 | 2022-09-28 21:26:35,009 [omego.extern] INFO Completed [0.068 s]
omeroserver_1 | 2022-09-28 21:26:35,013 [ omego.db] INFO Creating SQL: omero-20220928-212635-011281.sql
omeroserver_1 | 2022-09-28 21:26:35,014 [omego.extern] INFO Running [current environment]: /opt/omero/server/OMERO.server/bin/omero db script -f omero-20220928-212635-011281.sql omero
omeroserver_1 | 2022-09-28 21:26:35,014 [omego.extern] INFO Executing : /opt/omero/server/OMERO.server/bin/omero db script -f omero-20220928-212635-011281.sql omero
omeroserver_1 | 2022-09-28 21:26:51,879 [omego.extern] INFO Completed [16.864 s]
omeroserver_1 | 2022-09-28 21:26:51,880 [ omego.db] INFO Creating database using omero-20220928-212635-011281.sql
omeroserver_1 | 2022-09-28 21:26:51,881 [omego.extern] INFO Running [current environment]: /opt/omero/server/OMERO.server/bin/omero config get --show-password
omeroserver_1 | 2022-09-28 21:26:51,881 [omego.extern] INFO Executing : /opt/omero/server/OMERO.server/bin/omero config get --show-password
omeroserver_1 | 2022-09-28 21:26:57,797 [omego.extern] INFO Completed [5.915 s]
omeroserver_1 | 2022-09-28 21:26:57,799 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d omero -h database -U omero -w -A -t -f omero-20220928-212635-011281.sql
omeroserver_1 | 2022-09-28 21:27:00,150 [omego.extern] INFO Completed [2.350 s]
omeroserver_1 | 2022-09-28 21:27:00,152 [ omego.db] WARNI stderr: b'psql:omero-20220928-212635-011281.sql:2842: NOTICE: identifier "fkcontraststretchingcontext_codomainmapcontext_id_codomainmapcontext" will be truncated to "fkcontraststretchingcontext_codomainmapcontext_id_codomainmapco"\npsql:omero-20220928-212635-011281.sql:4712: NOTICE: identifier "fklogicalchannel_photometricinterpretation_photometricinterpretation" will be truncated to "fklogicalchannel_photometricinterpretation_photometricinterpret"\npsql:omero-20220928-212635-011281.sql:5697: NOTICE: identifier "fkreverseintensitycontext_codomainmapcontext_id_codomainmapcontext" will be truncated to "fkreverseintensitycontext_codomainmapcontext_id_codomainmapcont"\n'
omeroserver_1 | Running /startup/99-run.sh
omeroserver_1 | Starting OMERO.server
This gives me...
omero admin diagnostics
bash-4.2$ bin/omero admin diagnostics
================================================================================
OMERO Diagnostics (admin) 5.11.2
================================================================================
Commands: java -version 11.0.15 (/usr/bin/java)
Commands: python -V 3.6.8 (/opt/omero/server/venv3/bin/python -- 2 others)
Commands: icegridnode --version 3.6.5 (/usr/bin/icegridnode)
Commands: icegridadmin --version 3.6.5 (/usr/bin/icegridadmin)
Commands: psql --version 11.16 (/usr/bin/psql)
Commands: openssl version 1.0.2 (/usr/bin/openssl)
Server: icegridnode running
Server: Blitz-0 active (pid = 1086, enabled)
Server: DropBox inactive (disabled)
Server: FileServer active (pid = 1126, enabled)
Server: Indexer-0 active (pid = 1167, enabled)
Server: MonitorServer active (pid = 1153, enabled)
Server: OMERO.Glacier2 active (pid = 1134, enabled)
Server: OMERO.IceStorm active (pid = 1082, enabled)
Server: PixelData-0 active (pid = 1057, enabled)
Server: Processor-0 activating (enabled)
Server: Tables-0 activating (enabled)
Server: TestDropBox inactive (enabled)
Log dir: /opt/omero/server/OMERO.server/var/log exists
Log files: Blitz-0.log 100.5 KB errors=0 warnings=3
Log files: DropBox.log 4.3 KB errors=4 warnings=6
Log files: FileServer.log 114 B
Log files: Indexer-0.log 3.1 KB errors=0 warnings=2
Log files: MonitorServer.log 117 B
Log files: PixelData-0.log 3.6 KB errors=0 warnings=2
Log files: Processor-0.log 21.8 KB errors=4 warnings=16
Log files: Tables-0.log 22.6 KB errors=4 warnings=16
Log files: TestDropBox.log n/a
Log files: master.err 2.7 KB errors=1 warnings=2
Log files: master.out empty
Log files: Total size 0.16 MB
Environment:OMERO_HOME=(unset)
Environment:OMERODIR=/opt/omero/server/OMERO.server/
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_USERDIR=(unset)
Environment:OMERO_TMPDIR=(unset)
Environment:PATH=/opt/omero/server/venv3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
Environment:PYTHONPATH=(unset)
Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)
OMERO SSL port:4064
OMERO TCP port:4063
OMERO data dir:'/OMERO' Exists? True Is writable? True
OMERO temp dir:'/opt/omero/server/omero/tmp' Exists? True Is writable? True (Size: 0)
JVM settings: Blitz-${index} -Xmx1723m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index} -Xmx1148m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index} -Xmx1723m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index} -Xmx1148m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
Jar: lib/server/formats-api.jar Bio-Formats API 6.10.0 31 May 2022 f8b46c2458c43cffdf5bc67cc4bf9dfc6e93167b
Jar: lib/server/formats-bsd.jar BSD Bio-Formats readers and writers 6.10.0 31 May 2022 f8b46c2458c43cffdf5bc67cc4bf9dfc6e93167b
Jar: lib/server/formats-gpl.jar Bio-Formats library 6.10.0 31 May 2022 f8b46c2458c43cffdf5bc67cc4bf9dfc6e93167b
Jar: lib/server/ome-codecs.jar OME Codecs 0.3.2 19 May 2022 5aa67ccc5d04208d5ea78a1f58d49716130f89a6
Jar: lib/server/ome-common.jar OME Common Java 6.0.9 19 May 2022 1a61b42905228d596d80107e7a02853e77e0d7a7
Jar: lib/server/ome-jai.jar OME JAI 0.1.3 3 August 2018 489959cb7d24c279249bc08181aa9f734158ca4e
Jar: lib/server/ome-mdbtools.jar MDB Tools (Java port) 5.3.2 7 August 2018 68ffca2a95750cbb96f0d11785851aa4a554c0a4
Jar: lib/server/ome-poi.jar OME POI 5.3.6 19 May 2022 bb8f9406af613d4d1b088149d979f994f7aa1650
Jar: lib/server/ome-xml.jar OME XML library 6.3.1 19 May 2022 f2abe457b296d37c8d6a5a6774ebcf0017dc51a8
Jar: lib/server/omero-blitz.jar jar 5.5.12
Jar: lib/server/omero-common.jar jar 5.5.10
Jar: lib/server/omero-gateway.jar jar 5.6.10
Jar: lib/server/omero-model.jar jar 5.6.7
Jar: lib/server/omero-renderer.jar jar 5.5.10
Jar: lib/server/omero-romio.jar jar 5.7.0
Jar: lib/server/omero-server.jar jar 5.6.4
Trying to login...
(omeroweb) Williams-MBP:docker-example-omero wmoore$ omero login
Previously logged in to localhost:4064 as root
Server: [localhost:4064]
Username: [root]
Password:
internal server error
Which gives this in the Blitz log
Blitz log
``` ... 2022-09-28 21:31:15,326 INFO [ ome.services.util.ServiceHandler] ( main) Rslt: (1, 2, 3, ... 3 more) 2022-09-28 21:31:15,327 INFO [ ome.services.util.ServiceHandler] ( main) Executor.doWork -- ensure enum values (rw) 2022-09-28 21:31:15,328 INFO [ ome.services.util.ServiceHandler] ( main) Args: [null, InternalSF@817012565] 2022-09-28 21:31:15,333 INFO [ ome.security.basic.BasicEventContext] ( main) cctx: group=1 2022-09-28 21:31:15,409 INFO [ ome.security.basic.EventHandler] ( main) Auth: user=0,group=1,event=24(Internal),sess=4f7f1630-7232-4ead-93e5-375020028cbc 2022-09-28 21:31:15,477 INFO [ org.perf4j.TimingLogger] ( main) start[1664400675328] time[148] tag[omero.call.success.ome.services.util.EnsureEnum$2.doWork] 2022-09-28 21:31:15,478 INFO [ ome.services.util.ServiceHandler] ( main) Rslt: (1, 2, 3, ... 8 more) 2022-09-28 21:31:15,479 INFO [ ome.services.util.ServiceHandler] ( main) Executor.doWork -- ensure enum values (rw) 2022-09-28 21:31:15,480 INFO [ ome.services.util.ServiceHandler] ( main) Args: [null, InternalSF@817012565] 2022-09-28 21:31:15,491 INFO [ ome.security.basic.BasicEventContext] ( main) cctx: group=1 2022-09-28 21:31:15,545 INFO [ ome.security.basic.EventHandler] ( main) Auth: user=0,group=1,event=25(Internal),sess=4f7f1630-7232-4ead-93e5-375020028cbc 2022-09-28 21:31:15,589 INFO [ org.perf4j.TimingLogger] ( main) start[1664400675480] time[109] tag[omero.call.success.ome.services.util.EnsureEnum$2.doWork] 2022-09-28 21:31:15,591 INFO [ ome.services.util.ServiceHandler] ( main) Rslt: (1, 2, 3, ... 1 more) 2022-09-28 21:31:15,593 INFO [ ome.services.util.ServiceHandler] ( main) Executor.doWork -- ensure enum values (rw) 2022-09-28 21:31:15,593 INFO [ ome.services.util.ServiceHandler] ( main) Args: [null, InternalSF@817012565] 2022-09-28 21:31:15,603 INFO [ ome.security.basic.BasicEventContext] ( main) cctx: group=1 2022-09-28 21:31:15,653 INFO [ ome.security.basic.EventHandler] ( main) Auth: user=0,group=1,event=26(Internal),sess=4f7f1630-7232-4ead-93e5-375020028cbc 2022-09-28 21:31:15,692 INFO [ org.perf4j.TimingLogger] ( main) start[1664400675593] time[98] tag[omero.call.success.ome.services.util.EnsureEnum$2.doWork] 2022-09-28 21:31:15,693 INFO [ ome.services.util.ServiceHandler] ( main) Rslt: (1, 2, 3) 2022-09-28 21:31:15,694 INFO [ ome.services.util.ServiceHandler] ( main) Executor.doWork -- ensure enum values (rw) 2022-09-28 21:31:15,694 INFO [ ome.services.util.ServiceHandler] ( main) Args: [null, InternalSF@817012565] 2022-09-28 21:31:15,701 INFO [ ome.security.basic.BasicEventContext] ( main) cctx: group=1 2022-09-28 21:31:15,732 INFO [ ome.security.basic.EventHandler] ( main) Auth: user=0,group=1,event=27(Internal),sess=4f7f1630-7232-4ead-93e5-375020028cbc 2022-09-28 21:31:15,828 INFO [ org.perf4j.TimingLogger] ( main) start[1664400675694] time[134] tag[omero.call.success.ome.services.util.EnsureEnum$2.doWork] 2022-09-28 21:31:15,829 INFO [ ome.services.util.ServiceHandler] ( main) Rslt: (1, 2, 3, ... 4 more) 2022-09-28 21:31:15,834 INFO [ ome.services.util.ServiceHandler] ( main) Executor.doWork -- ensure enum values (rw) 2022-09-28 21:31:15,834 INFO [ ome.services.util.ServiceHandler] ( main) Args: [null, InternalSF@817012565] 2022-09-28 21:31:15,843 INFO [ ome.security.basic.BasicEventContext] ( main) cctx: group=1 2022-09-28 21:31:15,923 INFO [ ome.security.basic.EventHandler] ( main) Auth: user=0,group=1,event=28(Internal),sess=4f7f1630-7232-4ead-93e5-375020028cbc 2022-09-28 21:31:15,977 INFO [ org.perf4j.TimingLogger] ( main) start[1664400675834] time[142] tag[omero.call.success.ome.services.util.EnsureEnum$2.doWork] 2022-09-28 21:31:15,978 INFO [ ome.services.util.ServiceHandler] ( main) Rslt: (1, 2) 2022-09-28 21:31:16,009 INFO [ ome.services.util.BaseDBCheck] ( main) performed DB check DBMappedEnumCheck: done for OMERO version OMERO5.4__0 2022-09-28 21:31:16,197 INFO [ ome.services.util.DBUnicodeUnitsCheck] ( main) Database has the correctly encoded units of measure. 2022-09-28 21:31:16,227 INFO [ ome.services.util.BaseDBCheck] ( main) performed DB check DBUnicodeUnitsCheck: done 2022-09-28 21:31:16,236 INFO [ ome.services.util.ServerVersionCheck] ( main) ------------------------------------------------- 2022-09-28 21:31:16,237 INFO [ ome.services.util.ServerVersionCheck] ( main) OMERO Version: 5.6.5-ice36-b233 Ready. 2022-09-28 21:31:16,237 INFO [ ome.services.util.ServerVersionCheck] ( main) ------------------------------------------------- 2022-09-28 21:31:18,238 INFO [ ome.system.UpgradeCheck] ( main) no update needed 2022-09-28 21:31:19,597 INFO [ ome.tools.hibernate.ExtendedMetadata] ( main) Calculating ExtendedMetadata... 2022-09-28 21:31:23,843 INFO [ ome.services.graphs.GraphPathBean] ( main) initialized graph path bean with 1291 properties 2022-09-28 21:31:23,979 INFO [ o.s.scheduler.SchedulerFactoryBean] ( main) Starting Quartz Scheduler now 2022-09-28 21:31:24,102 INFO [ ome.services.scripts.ScriptRepoHelper] ( main) Registering MatlabScripts: WildcardFileFilter(*.m) 2022-09-28 21:31:24,105 INFO [ ome.services.scripts.ScriptRepoHelper] ( main) Registering LUTScripts: WildcardFileFilter(*.lut) 2022-09-28 21:31:24,107 INFO [ ome.services.scripts.ScriptRepoHelper] ( main) Registering PythonScripts: WildcardFileFilter(*.py) 2022-09-28 21:31:24,107 INFO [ ome.services.scripts.ScriptRepoHelper] ( main) Registering JythonScripts: WildcardFileFilter(*.jy) 2022-09-28 21:31:26,483 INFO [o.services.blitz.util.BlitzConfiguration] ( main) Initializing Ice.Communicator 2022-09-28 21:31:27,382 INFO [ ome.services.blitz.fire.Ring] ( main) Checking cluster 2022-09-28 21:31:27,468 INFO [ ome.services.blitz.fire.Registry] ( main) Found 0 cluster node(s) : [] 2022-09-28 21:31:27,469 INFO [ ome.services.blitz.fire.Ring] ( main) Got 0 cluster uuids : [] 2022-09-28 21:31:27,480 INFO [ ome.services.util.ServiceHandler] ( main) Executor.doWork -- ome.security.basic.NodeProviderInDb.getManagerList[] 2022-09-28 21:31:27,480 INFO [ ome.services.util.ServiceHandler] ( main) Args: [null, InternalSF@817012565] 2022-09-28 21:31:27,655 INFO [ ome.security.basic.EventHandler] ( main) Auth: user=0,group=0,event=null(Internal),sess=4f7f1630-7232-4ead-93e5-375020028cbc 2022-09-28 21:31:27,898 INFO [ org.perf4j.TimingLogger] ( main) start[1664400687481] time[417] tag[omero.call.success.ome.security.basic.NodeProviderInDb$1.doWork] 2022-09-28 21:31:27,902 INFO [ ome.services.util.ServiceHandler] ( main) Rslt: () 2022-09-28 21:31:27,925 INFO [ ome.services.util.ServiceHandler] ( main) Executor.doWork -- ome.security.basic.NodeProviderInDb.addManager[] 2022-09-28 21:31:27,926 INFO [ ome.services.util.ServiceHandler] ( main) Args: [null, InternalSF@817012565] 2022-09-28 21:31:28,123 INFO [ ome.security.basic.EventHandler] ( main) Auth: user=0,group=0,event=29(Internal),sess=4f7f1630-7232-4ead-93e5-375020028cbc 2022-09-28 21:31:28,201 INFO [ ome.security.basic.CurrentDetails] ( main) Adding log:INSERT,class ome.model.meta.Node,1 2022-09-28 21:31:28,257 INFO [ org.perf4j.TimingLogger] ( main) start[1664400687927] time[330] tag[omero.call.success.ome.security.basic.NodeProviderInDb$4.doWork] 2022-09-28 21:31:28,258 INFO [ ome.services.util.ServiceHandler] ( main) Rslt: ome.model.meta.Node:Id_1 2022-09-28 21:31:28,530 INFO [ ome.services.blitz.fire.Registry] ( main) Added ClusterNode/4f7f1630-7232-4ead-93e5-375020028cbc to registry 2022-09-28 21:31:28,536 INFO [ ome.services.util.ServiceHandler] ( main) Executor.doWork -- ome.services.scripts.ScriptRepoHelper.LoadScripts (rw)[] 2022-09-28 21:31:28,537 INFO [ ome.services.util.ServiceHandler] ( main) Args: [null, InternalSF@817012565] 2022-09-28 21:31:28,591 INFO [ ome.security.basic.EventHandler] ( main) Auth: user=0,group=0,event=30(Internal),sess=4f7f1630-7232-4ead-93e5-375020028cbc 2022-09-28 21:31:28,833 INFO [ ome.security.basic.CurrentDetails] ( main) Adding log:INSERT,class ome.model.core.OriginalFile,1 2022-09-28 21:31:28,912 INFO [ ome.security.basic.CurrentDetails] ( main) Adding log:INSERT,class ome.model.core.OriginalFile,2 2022-09-28 21:31:28,920 INFO [ ome.security.basic.CurrentDetails] ( main) Adding log:UPDATE,class ome.model.core.OriginalFile,1 2022-09-28 21:31:28,975 INFO [ ome.security.basic.CurrentDetails] ( main) Adding log:INSERT,class ome.model.core.OriginalFile,3 2022-09-28 21:31:28,984 INFO [ ome.security.basic.CurrentDetails] ( main) Adding log:UPDATE,class ome.model.core.OriginalFile,2 2022-09-28 21:31:29,044 INFO [ ome.security.basic.CurrentDetails] ( main) Adding log:INSERT,class ome.model.core.OriginalFile,4 2022-09-28 21:31:29,046 INFO [ ome.security.basic.CurrentDetails] ( main) Adding log:UPDATE,class ome.model.core.OriginalFile,3 2022-09-28 21:31:29,080 INFO [ ome.security.basic.CurrentDetails] ( main) Adding log:INSERT,class ome.model.core.OriginalFile,5 2022-09-28 21:31:29,082 INFO [ ome.security.basic.CurrentDetails] ( main) Adding log:UPDATE,class ome.model.core.OriginalFile,4 2022-09-28 21:31:29,111 INFO [ ome.security.basic.CurrentDetails] ( main) Adding log:INSERT,class ome.model.core.OriginalFile,6 2022-09-28 21:31:29,115 INFO [ ome.security.basic.CurrentDetails] ( main) Adding log:UPDATE,class ome.model.core.OriginalFile,5 2022-09-28 21:31:29,136 INFO [ ome.security.basic.CurrentDetails] ( main) Adding log:INSERT,class ome.model.core.OriginalFile,7 2022-09-28 21:31:29,138 INFO [ ome.security.basic.CurrentDetails] ( main) Adding log:UPDATE,class ome.model.core.OriginalFile,6 2022-09-28 21:31:29,170 INFO [ ome.security.basic.CurrentDetails] ( main) Adding log:INSERT,class ome.model.core.OriginalFile,8 2022-09-28 21:31:29,171 INFO [ ome.security.basic.CurrentDetails] ( main) Adding log:UPDATE,class ome.model.core.OriginalFile,7 2022-09-28 21:31:29,198 INFO [ ome.security.basic.CurrentDetails] ( main) Adding log:INSERT,class ome.model.core.OriginalFile,9 2022-09-28 21:31:29,200 INFO [ ome.security.basic.CurrentDetails] ( main) Adding log:UPDATE,class ome.model.core.OriginalFile,8 2022-09-28 21:31:29,219 INFO [ ome.security.basic.CurrentDetails] ( main) Adding log:INSERT,class ome.model.core.OriginalFile,10 2022-09-28 21:31:29,220 INFO [ ome.security.basic.CurrentDetails] ( main) Adding log:UPDATE,class ome.model.core.OriginalFile,9 2022-09-28 21:31:29,237 INFO [ ome.security.basic.CurrentDetails] ( main) Adding log:INSERT,class ome.model.core.OriginalFile,11 2022-09-28 21:31:29,240 INFO [ ome.security.basic.CurrentDetails] ( main) Adding log:UPDATE,class ome.model.core.OriginalFile,10 2022-09-28 21:31:29,257 INFO [ ome.security.basic.CurrentDetails] ( main) Adding log:INSERT,class ome.model.core.OriginalFile,12 2022-09-28 21:31:29,258 INFO [ ome.security.basic.CurrentDetails] ( main) Adding log:UPDATE,class ome.model.core.OriginalFile,11 2022-09-28 21:31:29,272 INFO [ ome.security.basic.CurrentDetails] ( main) Adding log:INSERT,class ome.model.core.OriginalFile,13 2022-09-28 21:31:29,274 INFO [ ome.security.basic.CurrentDetails] ( main) Adding log:UPDATE,class ome.model.core.OriginalFile,12 2022-09-28 21:31:29,294 INFO [ ome.security.basic.CurrentDetails] ( main) Adding log:INSERT,class ome.model.core.OriginalFile,14 2022-09-28 21:31:29,296 INFO [ ome.security.basic.CurrentDetails] ( main) Adding log:UPDATE,class ome.model.core.OriginalFile,13 2022-09-28 21:31:29,327 INFO [ ome.security.basic.CurrentDetails] ( main) Adding log:INSERT,class ome.model.core.OriginalFile,15 2022-09-28 21:31:29,330 INFO [ ome.security.basic.CurrentDetails] ( main) Adding log:UPDATE,class ome.model.core.OriginalFile,14 ```from docker-example-omero.
will-moore
commented on July 29, 2024
Tried to manually restart server... but this ended up stopping the docker container
docker exec -it docker-example-omero_omeroserver_1 bash
cd /opt/omero/server/OMERO.server
bin/omero admin restart
Waiting on shutdown. Use CTRL-C to exit
........
$ docker ps
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
2512db4fd335 postgres:11 "docker-entrypoint.sā¦" 6 days ago Up 6 days 5432/tcp docker-example-omero_database_1
Tried again...
$ docker compose down -v
$ docker compose up
$ omero login
Previously logged in to localhost:4064 as root
Server: [localhost:4064]
Username: [root]
Password:
InternalException: Failed to connect: Ice.ConnectionLostException:
recv() returned zero
$ bin/omero admin diagnostics
================================================================================
OMERO Diagnostics (admin) 5.11.2
================================================================================
Traceback (most recent call last):
File "/opt/omero/server/venv3/bin/omero", line 8, in <module>
sys.exit(main())
File "/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/main.py", line 125, in main
rv = omero.cli.argv()
File "/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/cli.py", line 1784, in argv
cli.invoke(args[1:])
File "/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/cli.py", line 1222, in invoke
stop = self.onecmd(line, previous_args)
File "/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/cli.py", line 1299, in onecmd
self.execute(line, previous_args)
File "/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/cli.py", line 1381, in execute
args.func(args)
File "/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/install/windows_warning.py", line 26, in wrapper
return func(self, *args, **kwargs)
File "/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/plugins/prefs.py", line 79, in open_and_close_config
return func(*args, **kwargs)
File "/opt/omero/server/venv3/lib/python3.6/site-packages/omero/plugins/admin.py", line 1235, in diagnostics
template_xml = XML(templates.text())
File "/usr/lib64/python3.6/xml/etree/ElementTree.py", line 1315, in XML
return parser.close()
xml.etree.ElementTree.ParseError: no element found: line 1, column 0
So, I think it's time to give up with Docker and try VirtualBox or something similar.
Unless there's other Docker options to try..?
I just want to have OMERO running on my laptop somehow!
from docker-example-omero.
will-moore
commented on July 29, 2024
Oh, VirtualBox isn't supported for M1 Mac (Monterey) š¢
from docker-example-omero.
joshmoore
commented on July 29, 2024
I just want to have OMERO running on my laptop somehow!
@sbesson : did you have Ice working on M1 natively? If so, @will-moore, you could omero admin start against the database that's running in docker.
from docker-example-omero.
sbesson
commented on July 29, 2024
@sbesson : did you have Ice working on M1 natively?
Pretty sure I had installed the zeroc-ice 3.6.5 package from conda-forge as they have arm64 builds in an environment. That was allowing me to use omero-py i.e. client-side operations at minimum. I have not spent extra time on getting a native M1 server environment.
from docker-example-omero.
will-moore
commented on July 29, 2024
So it looks like we're back to Docker....
Any idea why bin/omero admin restart seemed to kill the docker container (#12 (comment))?
from docker-example-omero.
joshmoore
commented on July 29, 2024
Yeah, in docker you always need some process that remains running. (In fact, usually there should be exactly one.) When you enter a container, you've added an extra process but when you exit, the main process keeps going. Running restart ran stop and therefore the main process of the docker was gone and so things got cleaned up.
from docker-example-omero.
pwalczysko
commented on July 29, 2024
@will-moore Do you want to maybe try this ome/ansible-example-omero-onenode#13 (comment) workflow ? It seems a bit more commands to run on the first look, but it works fine in my hands, and technically it is less complicated (you will get everything in only one container, not 3 (which you do not need)). It will take a bit of time, but not more than 15 minutes. I cannot see what could go wrong there... (maybe that is the problem :))
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Related Issues (8)
- omero server is failing? HOT 3
- Add example of mounting an extra .omero config file HOT 1
- configuration options for omero docker HOT 15
- Where are Omero Server Log files located? HOT 4
- Image rendering throws exception with java.lang.OutOfMemoryError HOT 5
- OMERO.figure image export options HOT 2
- Server is not responding on Mac M1 HOT 32
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