This example on Mac M1 - Githubissues

pwalczysko commented 2 years ago

After following the README, I have a working OMERO.web but cannot log in to OMERO.server as it reports server not responding.

My admin diagnostics say

``` 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 activation timed out (pid = 1144, enabled) Server: DropBox inactive (disabled) Server: FileServer active (pid = 1027, enabled) Server: Indexer-0 active (pid = 1039, enabled) Server: MonitorServer active (pid = 1030, enabled) Server: OMERO.Glacier2 active (pid = 1033, enabled) Server: OMERO.IceStorm active (pid = 1135, enabled) Server: PixelData-0 active (pid = 1051, 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 1.4 KB errors=0 warnings=2 Log files: DropBox.log 4.3 KB errors=4 warnings=6 Log files: FileServer.log 114 B Log files: Indexer-0.log 2.9 KB errors=0 warnings=2 Log files: MonitorServer.log 117 B Log files: PixelData-0.log 3.5 KB errors=0 warnings=2 Log files: Processor-0.log 28.1 KB errors=5 warnings=20 Log files: Tables-0.log 29.4 KB errors=5 warnings=20 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 0.07 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-${index} -Xmx1234m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions JVM settings: Indexer-${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 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 ```

My master.err

``` cat master.err OpenJDK 64-Bit Server VM warning: Ignoring option MaxPermSize; support was removed in 8.0 OpenJDK 64-Bit Server VM warning: Ignoring option MaxPermSize; support was removed in 8.0 OpenJDK 64-Bit Server VM warning: Ignoring option MaxPermSize; support was removed in 8.0 WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access by javassist.util.proxy.SecurityActions (file:/opt/omero/server/OMERO.server-5.6.5-ice36-b233/lib/server/javassist.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain) WARNING: Please consider reporting this to the maintainers of javassist.util.proxy.SecurityActions WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access by javassist.util.proxy.SecurityActions (file:/opt/omero/server/OMERO.server-5.6.5-ice36-b233/lib/server/javassist.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain) WARNING: Please consider reporting this to the maintainers of javassist.util.proxy.SecurityActions WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access by javassist.util.proxy.SecurityActions (file:/opt/omero/server/OMERO.server-5.6.5-ice36-b233/lib/server/javassist.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain) WARNING: Please consider reporting this to the maintainers of javassist.util.proxy.SecurityActions WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release -! 09/22/22 14:40:07.263 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier@BlitzAdapters' Reference.cpp:1637: Ice::NoEndpointException: no suitable endpoint available for proxy `BlitzVerifier -t -e 1.1 @ BlitzAdapters' -! 09/22/22 14:40:07.273 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager@BlitzAdapters' Reference.cpp:1637: Ice::NoEndpointException: no suitable endpoint available for proxy `BlitzManager -t -e 1.1 @ BlitzAdapters' !! 09/22/22 14:40:22.772 error: communicator not destroyed during global destruction.!! 09/22/22 14:40:46.682 error: communicator not destroyed during global destruction ```

My Blitz log is very short

2022-09-22 14:39:23,620 INFO  [                ome.services.blitz.Entry] (      main) Creating OMERO.blitz. Please wait...
2022-09-22 14:39:34,078 INFO  [        ome.services.util.ReadOnlyStatus] (      main) read-only status: db=false, repo=false
2022-09-22 14:39:34,549 WARN  [                          omero.security] (      main) trustStore property is empty, not setting
2022-09-22 14:39:34,556 WARN  [                          omero.security] (      main) trustStorePassword property is empty, not setting
2022-09-22 14:39:34,605 INFO  [.s.ShutdownSafeEhcacheManagerFactoryBean] (      main) Initializing EhCache CacheManager
2022-09-22 14:39:35,829 INFO  [          ome.services.util.DBPatchCheck] (      main) Verified database patch: OMERO5.4__0
2022-09-22 14:39:36,170 INFO  [           ome.services.util.DBUserCheck] (      main) User root.id = 0
2022-09-22 14:39:36,171 INFO  [           ome.services.util.DBUserCheck] (      main) User guest.id = 1
2022-09-22 14:39:36,171 INFO  [           ome.services.util.DBUserCheck] (      main) Group system.id = 0
2022-09-22 14:39:36,171 INFO  [           ome.services.util.DBUserCheck] (      main) Group user.id = 1
2022-09-22 14:39:36,172 INFO  [           ome.services.util.DBUserCheck] (      main) Group guest.id = 2
2022-09-22 14:39:39,721 INFO  [  ome.services.fulltext.FullTextAnalyzer] (      main) Initialized FullTextAnalyzer

This works perfectly fine on Mac Book Pro , but on M1 I have probs as above. Any ideas please @joshmoore @sbesson ?

joshmoore commented 2 years ago

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.

will-moore commented 2 years ago

After boosting memory on my Docker settings...

Screenshot 2022-09-23 at 13 04 58

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

pwalczysko commented 2 years ago

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)

will-moore commented 2 years ago

$ docker --version
Docker version 20.10.16, build aa7e414

will-moore commented 2 years ago

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!

will-moore commented 2 years ago

Unfortunately I am back to seeing the xml.etree.ElementTree.ParseError: no element found: line 1, column 0 error above now. 😭

will-moore commented 2 years ago

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?

joshmoore commented 2 years ago

Is this what's causing the server not to start?

Almost definitely since it's a vital file.

will-moore commented 2 years ago

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!)

joshmoore commented 2 years ago

You shouldn't need to do anything; in other words, something is going very wrong (disk space?).

will-moore commented 2 years ago

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:

Screenshot 2022-09-28 at 15 53 35

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..?

joshmoore commented 2 years ago

You could try "docker-compose down -v" in order to remove the volumes. Changing your docker disk image size clobbers everything.

pwalczysko commented 2 years ago

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 ?

will-moore commented 2 years ago

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 ```

will-moore commented 2 years ago

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.s…"   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!

will-moore commented 2 years ago

Oh, VirtualBox isn't supported for M1 Mac (Monterey) 😢

joshmoore commented 2 years ago

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.

sbesson commented 2 years ago

@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.

will-moore commented 2 years ago

So it looks like we're back to Docker.... Any idea why bin/omero admin restart seemed to kill the docker container (https://github.com/ome/docker-example-omero/issues/12#issuecomment-1268274965)?

joshmoore commented 2 years ago

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.

pwalczysko commented 2 years ago

@will-moore Do you want to maybe try this https://github.com/ome/ansible-example-omero-onenode/issues/13#issue-1352041067 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 :))

ome / docker-example-omero

This example on Mac M1 #12