OMERO web error

[phm]

Hi,
I have an python error when I start te service for omero web (version 5.3) :

Code: Select all

-bash-4.2$ /home/omero/omerowebvenv/bin/python /home/omero/OMERO.py/bin/omero web start
Post-processed 'omeroweb.viewer.min.css' as 'omeroweb.viewer.min.css'
Post-processed 'omeroweb.viewer.min.js' as 'omeroweb.viewer.min.js'

0 static files copied to '/home/omero/OMERO.py/lib/python/omeroweb/static', 611 unmodified, 2 post-processed.
Clearing expired sessions. This may take some time... [OK]
Starting OMERO.web... Traceback (most recent call last):
  File "/home/omero/OMERO.py/bin/omero", line 125, in <module>
    rv = omero.cli.argv()
  File "/home/omero/OMERO.py/lib/python/omero/cli.py", line 1507, in argv
    cli.invoke(args[1:])
  File "/home/omero/OMERO.py/lib/python/omero/cli.py", line 992, in invoke
    stop = self.onecmd(line, previous_args)
  File "/home/omero/OMERO.py/lib/python/omero/cli.py", line 1069, in onecmd
    self.execute(line, previous_args)
  File "/home/omero/OMERO.py/lib/python/omero/cli.py", line 1151, in execute
    args.func(args)
  File "/home/omero/OMERO.py/lib/python/omero/install/windows_warning.py", line 26, in wrapper
    return func(self, *args, **kwargs)
  File "/home/omero/OMERO.py/lib/python/omero/plugins/web.py", line 80, in wrapper
    return func(self, *args, **kwargs)
  File "/home/omero/OMERO.py/lib/python/omero/plugins/web.py", line 588, in start
    rv = self.ctx.popen(args=runserver, cwd=location)  # popen
  File "/home/omero/OMERO.py/lib/python/omero/cli.py", line 1242, in popen
    stdout=stdout, stderr=stderr)
  File "/usr/lib64/python2.7/subprocess.py", line 711, in __init__
    errread, errwrite)
  File "/usr/lib64/python2.7/subprocess.py", line 1327, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory


And it seems that in the config file there is an error in the path, see inbold:

Code: Select all

[Unit]
Description=OMERO.web
# Not mandatory, Nginx may be running on a different server
Requires=nginx.service
After=network.service

[Service]
User=omero
Type=forking
PIDFile=/home/omero/OMERO.py/var/django.pid
Restart=no
RestartSec=10
Environment="PATH=/home/omero/omerowebvenv/[b]venv[/b]/bin:/bin:/usr/bin" "WEBBINDIR=/home/omero/OMERO.py/bin"
ExecStart=/home/omero/omerowebvenv/[b]venv[/b]/python $WEBBINDIR/omero web start
ExecStop=/home/omero/omerowebvenv/[b]venv[/b]/python $WEBBINDIR/omero web stop

[Install]
WantedBy=multi-user.target


Philippe

[manics]

Hi Philippe

Can you give us some background. Is this a new installation, or an upgrade and if so, can you give us details of exactly what you did?

[phm]

Hi Philippe

Can you give us some background. Is this a new installation, or an upgrade and if so, can you give us details of exactly what you did?

Hi,
It's a "fresh" installation because I was on CentOS 6 and I would like to upgrade my Omero server version from 5.2 to 5.3 (and mostly able to go to 5.4). So I install a fresh CentOS 7 and start the Omero 5.3 version as mentioned in our doc. For the Omero server part the omero server is running correctly. However for the web installation I follow the instruction as describe in the doc(OMERO.web walkthrough installation CentOS 7 and IcePy 3.6) and I get this error when I start the web server.

Code: Select all

[Unit]
Description=OMERO.web
# Not mandatory, Nginx may be running on a different server
Requires=nginx.service
After=network.service

[Service]
User=omero
Type=forking
PIDFile=/home/omero/OMERO.py/var/django.pid
Restart=no
RestartSec=10
Environment="PATH=/home/omero/omerowebvenv/venv/bin:/bin:/usr/bin" "WEBBINDIR=/home/omero/OMERO.py/bin"
ExecStart=/home/omero/omerowebvenv/venv/python $WEBBINDIR/omero web start
ExecStop=/home/omero/omerowebvenv/venv/python $WEBBINDIR/omero web stop

[Install]
WantedBy=multi-user.target


Environment="PATH=/home/omero/omerowebvenv/venv/bin:/bin:/usr/bin" "WEBBINDIR=/home/omero/OMERO.py/bin"
The path seems not correct because /home/omero/omerowebvenv/venv/bin: do not exist on my install
So I change to /home/omero/omerowebvenv/bin

Philippe

[manics]

Hi Philippe

I think you've found an error in the docs. Did changing the path fix OMERO.web for you?

[phm]

Hi,
Unfortunately changing the path didn't fix the problem. Should we did to use the virtual environment I did it but it's optional in the doc.
Philippe

[manics]

Are you seeing the same error as in your first post, or a different one? Can you run

Code: Select all

pip freeze

inside your virtualenv?

[phm]

Are you seeing the same error as in your first post, or a different one? Can you run

Code: Select all

pip freeze

inside your virtualenv?

if i am outside virtualenv :

Code: Select all

-bash-4.2$ pip freeze
Babel==0.9.6
backports.ssl-match-hostname==3.4.0.2
configobj==4.7.2
decorator==3.4.0
Django==1.6.11.6
iniparse==0.4
javapackages==1.0.0
Jinja2==2.8
lxml==3.2.1
MarkupSafe==0.11
nose==1.3.0
numexpr==2.5.2
numpy==1.7.1
omero-figure==3.1.1
omero-fpbioimage==0.2.0
omero-iviewer==0.2.0
perf==0.1
Pillow==2.0.0
pycurl==7.19.0
pygobject==3.14.0
pygpgme==0.3
pyliblzma==0.5.3
pyparsing==1.5.6
pyudev==0.15
pyxattr==0.5.1
PyYAML==3.10
scipy==0.12.1
six==1.9.0
slip==0.4.0
slip.dbus==0.4.0
tables==3.2.0rc3
urlgrabber==3.10
virtualenv==15.1.0
yum-metadata-parser==1.1.4
zeroc-ice==3.6.3


And inside virtualenv :

Code: Select all

(omerowebvenv) -bash-4.2$ pip freeze
Babel==0.9.6
backports.ssl-match-hostname==3.4.0.2
configobj==4.7.2
decorator==3.4.0
Django==1.8.18
django-pipeline==1.3.20
futures==3.1.1
gunicorn==19.7.1
importlib==1.0.4
iniparse==0.4
javapackages==1.0.0
Jinja2==2.8
lxml==3.2.1
MarkupSafe==0.11
nose==1.3.0
numexpr==2.5.2
numpy==1.7.1
omero-figure==3.1.1
omero-fpbioimage==0.2.0
omero-iviewer==0.2.0
omero-marshal==0.5.1
perf==0.1
Pillow==2.0.0
pycurl==7.19.0
pygobject==3.14.0
pygpgme==0.3
pyliblzma==0.5.3
pyparsing==1.5.6
pyudev==0.15
pyxattr==0.5.1
PyYAML==3.10
scipy==0.12.1
six==1.9.0
slip==0.4.0
slip.dbus==0.4.0
tables==3.2.0rc3
urlgrabber==3.10
virtualenv==15.1.0
yum-metadata-parser==1.1.4
zeroc-ice==3.6.3


Philippe

[manics]

Does OMERO.web run if you start it manually after activating the virtualenv?

Code: Select all

source /home/omero/omerowebvenv/bin/activate
/home/omero/OMERO.py/bin/omero web start


[phm]

Does OMERO.web run if you start it manually after activating the virtualenv?

Code: Select all

source /home/omero/omerowebvenv/bin/activate
/home/omero/OMERO.py/bin/omero web start


Yes it start but not outside the virtualenv :

Code: Select all

(omerowebvenv) -bash-4.2$ /home/omero/OMERO.py/bin/omero web start
Post-processed 'omeroweb.viewer.min.css' as 'omeroweb.viewer.min.css'
Post-processed 'omeroweb.viewer.min.js' as 'omeroweb.viewer.min.js'

0 static files copied to '/home/omero/OMERO.py/lib/python/omeroweb/static', 611 unmodified, 2 post-processed.
Clearing expired sessions. This may take some time... [OK]
Starting OMERO.web... [OK]


Code: Select all

-bash-4.2$ omero admin diagnostics

================================================================================
OMERO Diagnostics 5.3.3-ice36-b63
================================================================================
       
Commands:   java -version                  1.8.0     (/usr/bin/java)
Commands:   python -V                      2.7.5     (/usr/bin/python)
Commands:   icegridnode --version          3.6.3     (/usr/bin/icegridnode)
Commands:   icegridadmin --version         3.6.3     (/usr/bin/icegridadmin)
Commands:   psql --version                 9.6.4     (/usr/bin/psql)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 17310, enabled)
Server:     DropBox                        active (pid = 17332, enabled)
Server:     FileServer                     active (pid = 17336, enabled)
Server:     Indexer-0                      active (pid = 17341, enabled)
Server:     MonitorServer                  active (pid = 17342, enabled)
Server:     OMERO.Glacier2                 active (pid = 17344, enabled)
Server:     OMERO.IceStorm                 active (pid = 17355, enabled)
Server:     PixelData-0                    active (pid = 17356, enabled)
Server:     Processor-0                    active (pid = 17703, enabled)
Server:     Tables-0                       active (pid = 18093, enabled)
Server:     TestDropBox                    inactive (enabled)

Log dir:    /home/omero/OMERO.server/var/log exists
Log files:  Blitz-0.log                    22.0 MB       errors=35   warnings=223
Log files:  DropBox.log                    27.0 KB       errors=20   warnings=14 
Log files:  FileServer.log                 4.0 KB       
Log files:  Indexer-0.log                  4.0 MB        errors=832  warnings=285
Log files:  MonitorServer.log              9.0 KB       
Log files:  OMEROweb.lock                  0.0 KB       
Log files:  OMEROweb.log                   0.0 KB       
Log files:  PixelData-0.log                2.0 MB        errors=457  warnings=171
Log files:  Processor-0.log                1.0 MB        errors=38   warnings=85 
Log files:  Tables-0.log                   126.0 KB      errors=29   warnings=63 
Log files:  TestDropBox.log                n/a
Log files:  master.err                     4.0 KB        errors=5    warnings=5   
Log files:  master.out                     0.0 KB       
Log files:  Total size                     31.26 MB


Environment:OMERO_HOME=(unset)             
Environment:OMERO_NODE=(unset)             
Environment:OMERO_MASTER=(unset)           
Environment:OMERO_USERDIR=(unset)         
Environment:OMERO_TMPDIR=/tmp             
Environment:PATH=/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/dell/srvadmin/bin:/home/omero/OMERO.server/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:'/tmp'                         Exists? True   Is writable? True   (Size: 143428981)

JVM settings: Blitz-${index}                -Xmx5027m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index}              -Xmx3351m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index}            -Xmx5027m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index}           -Xmx3351m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions

OMERO.web status... [NOT STARTED]
Django version: 1.6.11.6



If I start omero web from the systemctl I got this error :

Code: Select all

[root@omero omero]# systemctl restart omero-web.service
Job for omero-web.service failed because the control process exited with error code. See "systemctl status omero-web.service" and "journalctl -xe" for details.
[root@omero omero]# journalctl -xe
août 21 15:50:47 omero snmpd[1746]: Connection from UDP: [192.168.111.245]:42247->[192.168.202.21]:161
août 21 15:50:47 omero snmpd[1746]: Connection from UDP: [192.168.111.245]:42247->[192.168.202.21]:161
août 21 15:50:47 omero snmpd[1746]: Connection from UDP: [192.168.111.245]:42247->[192.168.202.21]:161
août 21 15:50:47 omero snmpd[1746]: Connection from UDP: [192.168.111.245]:42247->[192.168.202.21]:161
août 21 15:50:47 omero snmpd[1746]: Connection from UDP: [192.168.111.245]:42247->[192.168.202.21]:161
août 21 15:50:47 omero snmpd[1746]: Connection from UDP: [192.168.111.245]:42247->[192.168.202.21]:161
août 21 15:50:47 omero snmpd[1746]: Connection from UDP: [192.168.111.245]:42247->[192.168.202.21]:161
août 21 15:50:47 omero snmpd[1746]: Connection from UDP: [192.168.111.245]:42247->[192.168.202.21]:161
août 21 15:50:47 omero snmpd[1746]: Connection from UDP: [192.168.111.245]:42247->[192.168.202.21]:161
août 21 15:50:47 omero snmpd[1746]: Connection from UDP: [192.168.111.245]:42247->[192.168.202.21]:161
août 21 15:50:47 omero snmpd[1746]: Connection from UDP: [192.168.111.245]:42247->[192.168.202.21]:161
août 21 15:50:47 omero snmpd[1746]: Connection from UDP: [192.168.111.245]:42247->[192.168.202.21]:161
août 21 15:50:47 omero snmpd[1746]: Connection from UDP: [192.168.111.245]:55653->[192.168.202.21]:161
août 21 15:50:47 omero snmpd[1746]: Connection from UDP: [192.168.111.245]:55653->[192.168.202.21]:161
août 21 15:50:47 omero snmpd[1746]: Connection from UDP: [192.168.111.245]:49755->[192.168.202.21]:161
août 21 15:50:47 omero snmpd[1746]: Connection from UDP: [192.168.111.245]:49755->[192.168.202.21]:161
août 21 15:50:57 omero sshd[15645]: Connection closed by 192.168.111.247 [preauth]
août 21 15:51:10 omero snmpd[1746]: Connection from UDP: [192.168.111.247]:40850->[192.168.202.21]:161
août 21 15:51:10 omero snmpd[1746]: Connection from UDP: [192.168.111.247]:40850->[192.168.202.21]:161
août 21 15:51:11 omero snmpd[1746]: Connection from UDP: [192.168.111.247]:34879->[192.168.202.21]:161
août 21 15:51:28 omero su[15650]: (to root) omero on pts/0
août 21 15:51:28 omero su[15650]: pam_unix(su:session): session opened for user root by omero(uid=1000)
août 21 15:51:34 omero snmpd[1746]: Connection from UDP: [192.168.111.247]:57995->[192.168.202.21]:161
août 21 15:51:37 omero polkitd[1418]: Registered Authentication Agent for unix-process:15670:25962361 (system bus name :1.212 [/usr/bin/pkttyagent --noti
août 21 15:51:37 omero systemd[1]: Starting OMERO.web...
-- Subject: L'unité (unit) omero-web.service a commencé à démarrer
-- Defined-By: systemd
-- Support: http://lists.freedesktop.org/mailman/listinfo/systemd-devel
--
-- L'unité (unit) omero-web.service a commencé à démarrer.
août 21 15:51:37 omero python[15676]: /home/omero/omerowebvenv/bin/python: can't open file 'web': [Errno 2] No such file or directory
août 21 15:51:37 omero systemd[1]: omero-web.service: control process exited, code=exited status=2
août 21 15:51:37 omero systemd[1]: Failed to start OMERO.web.
-- Subject: L'unité (unit) omero-web.service a échoué
-- Defined-By: systemd
-- Support: http://lists.freedesktop.org/mailman/listinfo/systemd-devel
--
-- L'unité (unit) omero-web.service a échoué, avec le résultat failed.
août 21 15:51:37 omero systemd[1]: Unit omero-web.service entered failed state.
août 21 15:51:37 omero systemd[1]: omero-web.service failed.
août 21 15:51:37 omero polkitd[1418]: Unregistered Authentication Agent for unix-process:15670:25962361 (system bus name :1.212, object path /org/freedes
août 21 15:51:42 omero snmpd[1746]: Connection from UDP: [192.168.111.247]:35888->[192.168.202.21]:161
août 21 15:51:57 omero sshd[15687]: Connection closed by 192.168.111.247 [preauth]



[manics]

Hi, I think there might be another error in our docs, our automated tests didn't detect that web isn't running. I haven't had a chance to test this, but could you try defining the environment variables separately in the systemd service file and let me know if it works?

Code: Select all

Environment="PATH=/home/omero/omerowebvenv/venv/bin:/bin:/usr/bin"
Environment="WEBBINDIR=/home/omero/OMERO.py/bin"


Make sure you run

Code: Select all

systemctl daemon-reload

before

Code: Select all

systemctl start omero-web

Thanks, Simon