Omero 5.6.3 error

I have omero in a docker-compose and it was working fine with version 5.6.3 but somehow it started to have problems. I was restarting all the time (checked by docker-compose ps)
and it had the following error:
omero-server | certificates created: /OMERO/certs/server.pem /OMERO/certs/server.p12
omero-server | Traceback (most recent call last):
omero-server | File “/opt/omero/server/venv3/bin/omero”, line 11, in
omero-server | sys.exit(main())
omero-server | File “/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/”, line 125, in main
omero-server | rv = omero.cli.argv()
omero-server | File “/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/”, line 1784, in argv
omero-server | cli.invoke(args[1:])
omero-server | File “/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/”, line 1222, in invoke
omero-server | stop = self.onecmd(line, previous_args)
omero-server | File “/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/”, line 1299, in onecmd
omero-server | self.execute(line, previous_args)
omero-server | File “/opt/omero/server/venv3/lib64/python3.6/site-packages/omero/”, line 1381, in execute
omero-server | args.func(args)
omero-server | File “/opt/omero/server/venv3/lib/python3.6/site-packages/omero/plugins/”, line 121, in call
omero-server | self._load_filehandle(fh, args.keep_going)
omero-server | File “/opt/omero/server/venv3/lib/python3.6/site-packages/omero/plugins/”, line 96, in _load_filehandle
omero-server | for line in fh:
omero-server | File “/usr/lib64/python3.6/encodings/”, line 26, in decode
omero-server | return codecs.ascii_decode(input, self.errors)[0]
omero-server | UnicodeDecodeError: ‘ascii’ codec can’t decode byte 0xe2 in position 184: ordinal not in range(128)
omero-server | Traceback (most recent call last):
omero-server | File “/startup/”, line 15, in
omero-server | assert rc == 0
omero-server | AssertionError

I only managed to fix by deleting the image of 5.6.3 and downgrading to 5.6.1
Was there any recent upgrade on the 5.6.3?

Joao Miguel

Hi Joao,

can you confirm which docker image you are using? I recently needed to re-release 5.6.3. 5.6.3-1 has digest sha256:1947bf3cb3a92171455193c970b6d98cc50027d2f40363b1a94a839c126280f2 while 5.6.3-0 has digest sha256:bc563bf255266e59c433c167c952546881f861d8f4875d25737dc2d5d692c98e. You want 5.6.3-1.

Otherwise, this is certainly an odd error. Have you installed any other packages in the docker?


Ok, I will try to provide as much as I can:
Docker version 20.10.2, build 2291f61
docker-compose version 1.28.0, build d02a7b1a

Inside docker compose i am using a modified version fro CRS4 (Luca Lianas) .yml with:

  • postgres:12.5-alpine
  • redis:6.0.10-alpine
  • openmicroscopy/omero-server:5.6.1
  • crs4/ome_seadragon-web:0.7.0-ome5.8.1
  • crs4/ome_seadragon-nginx:0.7.0-ome5.8.1
  • crs4/ome_seadragon_gw-web:0.1.3
  • jwilder/nginx-proxy
  • crs4/ome_seadragon_gw-nginx:0.1.3
  • jrcs/letsencrypt-nginx-proxy-companion

The admin diagnostics is:

OMERO Diagnostics (admin) 5.6.2
Commands:   java -version                  1.8.0     (/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                 11.7      (/usr/bin/psql)
Commands:   openssl version                1.0.2     (/usr/bin/openssl)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 432, enabled)
Server:     DropBox                        active (pid = 441, enabled)
Server:     FileServer                     active (pid = 855, enabled)
Server:     Indexer-0                      active (pid = 461, enabled)
Server:     MonitorServer                  active (pid = 939, enabled)
Server:     OMERO.Glacier2                 active (pid = 487, enabled)
Server:     OMERO.IceStorm                 active (pid = 513, enabled)
Server:     PixelData-0                    active (pid = 604, enabled)
Server:     Processor-0                    active (pid = 658, enabled)
Server:     Tables-0                       active (pid = 761, enabled)
Server:     TestDropBox                    inactive (enabled)

Log dir:    /opt/omero/server/OMERO.server/var/log exists
Log files:  Blitz-0.log                    95.1 MB       errors=0    warnings=91  
Log files:  DropBox.log                    18.8 KB       errors=4    warnings=9   
Log files:  FileServer.log                 1.8 KB        errors=0    warnings=2   
Log files:  Indexer-0.log                  113.0 KB      errors=0    warnings=22  
Log files:  MonitorServer.log              13.6 KB       errors=0    warnings=4   
Log files:  PixelData-0.log                48.6 KB       errors=0    warnings=22  
Log files:  Processor-0.log                771.9 KB      errors=0    warnings=2   
Log files:  Tables-0.log                   13.4 KB       errors=0    warnings=3   
Log files:  TestDropBox.log                n/a
Log files:  master.err                     269.8 KB      errors=3    warnings=0   
Log files:  master.out                     empty
Log files:  Total size                     96.36 MB


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: 11514)

JVM settings: Blitz-${index}                -Xmx8405m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index}              -Xmx5043m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index}            -Xmx8405m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index}           -Xmx5043m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions

The changes in memory were entered manually after reboot.

I am currently unable to shut it down for long as there are colleagues using the files but I can try a different image if you suggest

I hope that helps

Joao MIguel

I gave a trial to 5.6.3-1 and all seems fine with omero. It accepted the configs from both server and web.
Thanks Josh
Joao Miguel

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