[ome-devel] omero web problem with 4.4.10
Aleksandra Tarkowska
A.Tarkowska at dundee.ac.uk
Wed Jan 29 09:20:49 GMT 2014
Dear Harri,
I am sorry to hear you are having trouble with starting omeroweb.
Could you please send me output of 'bin/omero config get' (please replace
all passwords by ****) and log files from
/opt/OMERO/OMERO.server-4.4.10-ice33-b112/var/log
There seems to be 2 errors in master.err
Kind regards
Ola
On 28/01/2014 14:04, "Harri Jäälinoja" <harri.jaalinoja at helsinki.fi> wrote:
>Hi Simon,
>
>thanks for your quick reply. Here are the diagnostics:
>
>[omero at lmu-omero2 OMERO.server-4.4.10-ice33-b112]$ omero admin diagnostics
>
>==========================================================================
>======
>OMERO Diagnostics 4.4.10-ice33-b112
>==========================================================================
>======
>
>Commands: java -version 1.7.0 (/usr/bin/java)
>Commands: python -V 2.4.3 (/usr/bin/python)
>Commands: icegridnode --version 3.3.1 (/usr/bin/icegridnode)
>Commands: icegridadmin --version 3.3.1 (/usr/bin/icegridadmin)
>Commands: psql --version 9.1.11 (/usr/bin/psql)
>
>Server: icegridnode running
>Server: Blitz-0 active (pid = 4966, enabled)
>Server: DropBox active (pid = 4978, enabled)
>Server: FileServer active (pid = 4979, enabled)
>Server: Indexer-0 active (pid = 4980, enabled)
>Server: MonitorServer active (pid = 4982, enabled)
>Server: OMERO.Glacier2 active (pid = 4983, enabled)
>Server: OMERO.IceStorm active (pid = 4985, enabled)
>Server: PixelData-0 active (pid = 4992, enabled)
>Server: Processor-0 active (pid = 4995, enabled)
>Server: Tables-0 inactive (disabled)
>Server: TestDropBox inactive (enabled)
>
>OMERO: SSL port 4064
>OMERO: TCP port 4063
>
>Log dir: /opt/OMERO/OMERO.server-4.4.10-ice33-b112/var/log exists
>
>Log files: Blitz-0.log 391.0 KB errors=0 warnings=1
>Log files: DropBox.log 3.0 KB errors=0 warnings=1
>Log files: FileServer.log 0.0 KB
>Log files: Indexer-0.log 196.0 KB
>Log files: MonitorServer.log 2.0 KB
>Log files: OMEROweb.log 66.0 KB
>Log files: OMEROweb_request.log 0.0 KB
>Log files: PixelData-0.log 5.0 KB
>Log files: Processor-0.log 2.0 KB errors=0 warnings=1
>Log files: Tables-0.log n/a
>Log files: TestDropBox.log n/a
>Log files: master.err 0.0 KB errors=2 warnings=0
>Log files: master.out 0.0 KB
>Log files: Total size 0.67 MB
>
>
>Environment:OMERO_HOME=/opt/OMERO/OMERO.server-4.4.10-ice33-b112
>Environment:OMERO_NODE=(unset)
>Environment:OMERO_MASTER=(unset)
>Environment:OMERO_TEMPDIR=(unset)
>Environment:PATH=/usr/kerberos/bin:/usr/bin:/bin:/opt/iRODS/current/client
>s/icommands/bin:/opt/iRODS/current/clients/fuse/bin:/home/omero/bin:/opt/O
>MERO/OMERO.server-4.4.10-ice33-b112/bin:/home/omero/bin
>
>Environment:ICE_HOME=/usr/share/Ice-3.3.1
>Environment:LD_LIBRARY_PATH=(unset)
>Environment:DYLD_LIBRARY_PATH=(unset)
>
>OMERO data dir: '/data/OMERO' Exists? True Is writable? True
>OMERO temp dir: '/home/omero/omero/tmp' Exists? True Is writable?
>True (Size: 0)
>OMERO.web status... [NOT STARTED]
>
>
>Here are the omero processes now:
>[omero at lmu-omero2 OMERO.server-4.4.10-ice33-b112]$ ps -u omero
> PID TTY TIME CMD
> 4931 ? 00:00:00 icegridnode
> 4966 ? 00:00:34 java
> 4978 ? 00:00:00 python
> 4979 ? 00:00:00 python
> 4980 ? 00:00:26 java
> 4982 ? 00:00:00 python
> 4983 ? 00:00:00 glacier2router
> 4985 ? 00:00:00 icebox
> 4992 ? 00:00:33 java
> 4995 ? 00:00:00 python
> 5382 pts/0 00:00:00 bash
> 5774 pts/0 00:00:00 ps
>
>
>We run both OMEROweb on the same machine where the OMERO server is, both
>run as user 'omero'. This is the init script for web:
>
>#!/bin/bash
># omero Start/stop script for OMERO web.
># Harri Jäälinoja <harri.jaalinoja at helsinki.fi> Apr. 2012.
>Rev: 20120430
>#
># chkconfig: 345 98 4
># description: OMERO web
>
>OMERO_USER=omero
>OMERO_HOME=/opt/OMERO/OMERO.server-4.4.10-ice33-b112
>
>. /etc/init.d/functions
>RETVAL=0
>
>case "$1" in
> start )
> runuser -s /bin/bash - $OMERO_USER -c \
> "ulimit -c 81920; $OMERO_HOME/bin/omero web start"
>
> RETVAL=$?; echo; [ $RETVAL -eq 0 ] && touch
>/var/lock/subsys/`basename $0`
> exit $RETVAL ;;
>
> stop )
> runuser -s /bin/bash - $OMERO_USER -c "$Env $OMERO_HOME/bin/omero
>web stop"
> RETVAL=$?; echo; [ $RETVAL -eq 0 ] && rm -f
>/var/lock/subsys/`basename $0`
> exit $RETVAL ;;
>
> restart )
> runuser -s /bin/bash - $OMERO_USER -c "$Env $OMERO_HOME/bin/omero
>web stop"
> RETVAL=$?; echo; [ $RETVAL -eq 0 ] && rm -f
>/var/lock/subsys/`basename $0`
>
> runuser -s /bin/bash - $OMERO_USER -c \
> "ulimit -c 81920; $OMERO_HOME/bin/omero admin start"
>
> RETVAL=$?; echo; [ $RETVAL -eq 0 ] && touch
>/var/lock/subsys/`basename $0`
> exit $RETVAL ;;
>
> status )
> runuser -s /bin/bash - $OMERO_USER -c "$Env $OMERO_HOME/bin/omero
>web status"
> RETVAL=$?; echo
> exit $RETVAL ;;
> * )
> echo "Usage: $0 {start|stop|status|restart}"
> exit 2 ;;
>esac
>
>
>The script is probably not the problem. I tried also starting OMEROweb
>directly as user omero with "omero web start" with the same result.
>
>Best,
>Harri
>
>
>
>On 28/01/14 15:43, Simon Li wrote:
>> Hi Harri
>>
>> Could you run
>>
>> omero admin diagnostics
>>
>> from your OMERO_SERVER/bin directory and either copy the output here,
>>or save it to a file and put it somewhere we can download it?
>>
>> Could you give us a bit more information about your setup, for example
>>are you running both OMERO.server and OMERO.web under the 'omero' user,
>>are they running on the same/different servers. Finally is your omeroweb
>>init.d file one that you've written yourself?
>>
>> Best wishes
>>
>> Simon
>>
>>
>> On 28 Jan 2014, at 13:29, Harri Jäälinoja <harri.jaalinoja at helsinki.fi>
>> wrote:
>>
>>> Hi,
>>> we installed OMERO 4.4.10. The server started ok, but there is
>>>something wrong with the web component. There are no errors when
>>>starting it up, but no processes are started:
>>>
>>> [root at lmu-omero2 ~]# ps -u omero
>>> PID TTY TIME CMD
>>>
>>> [root at lmu-omero2 ~]# service omeroweb start
>>> INFO:__main__:Application Starting...
>>> INFO:root:Processing custom settings for module omeroweb.settings
>>> DEBUG:omeroweb.settings:ADMINS = [] (source:default)
>>> DEBUG:omeroweb.settings:APPLICATION_SERVER = 'fastcgi-tcp'
>>>(source:omero.web.application_server)
>>> DEBUG:omeroweb.settings:APPLICATION_SERVER_HOST = '0.0.0.0'
>>>(source:default)
>>> DEBUG:omeroweb.settings:APPLICATION_SERVER_MAX_REQUESTS = 400
>>>(source:default)
>>> DEBUG:omeroweb.settings:APPLICATION_SERVER_PORT = '4080'
>>>(source:default)
>>> DEBUG:omeroweb.settings:ADDITIONAL_APPS = [] (source:default)
>>> DEBUG:omeroweb.settings:CACHES = {} (source:default)
>>> DEBUG:omeroweb.settings:DATABASES = {} (source:default)
>>> DEBUG:omeroweb.settings:DEBUG = True (source:omero.web.debug)
>>> DEBUG:omeroweb.settings:EMAIL_HOST =
>>>'lmu-omero2.biocenter.helsinki.fi' (source:omero.web.email_host)
>>> DEBUG:omeroweb.settings:EMAIL_HOST_PASSWORD = '********************'
>>>(source:default)
>>> DEBUG:omeroweb.settings:EMAIL_HOST_USER = None (source:default)
>>> DEBUG:omeroweb.settings:EMAIL_PORT = None (source:default)
>>> DEBUG:omeroweb.settings:EMAIL_SUBJECT_PREFIX = '[OMERO.web] '
>>>(source:default)
>>> DEBUG:omeroweb.settings:EMAIL_USE_TLS = False (source:default)
>>> DEBUG:omeroweb.settings:FORCE_SCRIPT_NAME = None (source:default)
>>> DEBUG:omeroweb.settings:INDEX_TEMPLATE = None (source:default)
>>> DEBUG:omeroweb.settings:LOGDIR =
>>>'/opt/OMERO/OMERO.server-4.4.10-ice33-b112/var/log' (source:default)
>>> DEBUG:omeroweb.settings:LOGIN_VIEW = 'weblogin' (source:default)
>>> DEBUG:omeroweb.settings:NANOXML_JAR = 'nanoxml.jar' (source:default)
>>> DEBUG:omeroweb.settings:OPEN_ASTEX_MAX_SIDE = 400 (source:default)
>>> DEBUG:omeroweb.settings:OPEN_ASTEX_MAX_VOXELS = 27000000
>>>(source:default)
>>> DEBUG:omeroweb.settings:OPEN_ASTEX_MIN_SIDE = 20 (source:default)
>>> DEBUG:omeroweb.settings:PING_INTERVAL = 60000 (source:default)
>>> DEBUG:omeroweb.settings:PUBLIC_CACHE_ENABLED = False (source:default)
>>> DEBUG:omeroweb.settings:PUBLIC_CACHE_KEY =
>>>'omero.web.public.cache.key' (source:default)
>>> DEBUG:omeroweb.settings:PUBLIC_CACHE_TIMEOUT = 86400 (source:default)
>>> DEBUG:omeroweb.settings:PUBLIC_ENABLED = False (source:default)
>>> DEBUG:omeroweb.settings:PUBLIC_PASSWORD = '********************'
>>>(source:default)
>>> DEBUG:omeroweb.settings:PUBLIC_SERVER_ID = 1 (source:default)
>>> DEBUG:omeroweb.settings:PUBLIC_URL_FILTER = <_sre.SRE_Pattern object
>>>at 0x1bf29630> (source:default)
>>> DEBUG:omeroweb.settings:PUBLIC_USER = None (source:default)
>>> DEBUG:omeroweb.settings:SCRIPTS_TO_IGNORE =
>>>['/omero/figure_scripts/Movie_Figure.py',
>>>'/omero/figure_scripts/Split_View_Figure.py',
>>>'/omero/figure_scripts/Thumbnail_Figure.py',
>>>'/omero/figure_scripts/ROI_Split_Figure.py',
>>>'/omero/export_scripts/Make_Movie.py',
>>>'/omero/setup_scripts/FLIM_initialise.py',
>>>'/omero/import_scripts/Populate_ROI.py'] (source:default)
>>> DEBUG:omeroweb.settings:SEND_BROKEN_LINK_EMAILS = True (source:default)
>>> DEBUG:omeroweb.settings:SERVER_EMAIL =
>>>'omero at lmu-omero2.biocenter.helsinki.fi' (source:omero.web.server_email)
>>> DEBUG:omeroweb.settings:SERVER_LIST = [['localhost', 4064, 'omero']]
>>>(source:default)
>>> DEBUG:omeroweb.settings:SESSION_ENGINE =
>>>'django.contrib.sessions.backends.file' (source:default)
>>> DEBUG:omeroweb.settings:STATIC_URL = '/static/'
>>>(source:omero.web.static_url)
>>> DEBUG:omeroweb.settings:STATICFILES_DIRS = [] (source:default)
>>> DEBUG:omeroweb.settings:CENTER_PLUGINS = [] (source:default)
>>> DEBUG:omeroweb.settings:RIGHT_PLUGINS = [['Acquisition',
>>>'webclient/data/includes/right_plugin.acquisition.js.html',
>>>'metadata_tab'], ['Preview',
>>>'webclient/data/includes/right_plugin.preview.js.html', 'preview_tab']]
>>>(source:default)
>>> DEBUG:omeroweb.settings:TOP_LINKS = [] (source:default)
>>> DEBUG:omeroweb.settings:VIEWER_INITIAL_ZOOM_LEVEL = None
>>>(source:default)
>>> DEBUG:omeroweb.settings:WEBGATEWAY_CACHE = None (source:default)
>>> DEBUG:omeroweb.settings:WEBSTART_CLASS =
>>>'org.openmicroscopy.shoola.Main' (source:default)
>>> DEBUG:omeroweb.settings:WEBSTART_HEAP = '1024m' (source:default)
>>> DEBUG:omeroweb.settings:WEBSTART_HOMEPAGE =
>>>'http://www.openmicroscopy.org' (source:default)
>>> DEBUG:omeroweb.settings:WEBSTART_HOST = 'localhost' (source:default)
>>> DEBUG:omeroweb.settings:WEBSTART_ICON =
>>>'webstart/img/icon-omero-insight.png' (source:default)
>>> DEBUG:omeroweb.settings:WEBSTART_JAR = 'omero.insight.jar'
>>>(source:default)
>>> DEBUG:omeroweb.settings:WEBSTART_PORT = '4064' (source:default)
>>> DEBUG:omeroweb.settings:WEBSTART_TITLE = 'OMERO.insight'
>>>(source:default)
>>> DEBUG:omeroweb.settings:WEBSTART_VENDOR = 'The Open Microscopy
>>>Environment' (source:default)
>>> DEBUG:omeroweb.settings:INSTALLED_APPS=[('django.contrib.staticfiles',
>>>'django.contrib.markup', 'django.contrib.auth',
>>>'django.contrib.contenttypes', 'django.contrib.sessions',
>>>'django.contrib.sites', 'omeroweb.feedback', 'omeroweb.webadmin',
>>>'omeroweb.webclient', 'omeroweb.webgateway', 'omeroweb.webtest',
>>>'omeroweb.webredirect', 'omeroweb.webstart')]
>>>
>>> 0 static files copied to
>>>'/opt/OMERO/OMERO.server-4.4.10-ice33-b112/lib/python/omeroweb/static'
>>>(810 unmodified).
>>> Starting OMERO.web... [OK]
>>>
>>> [root at lmu-omero2 ~]# ps -u omero
>>> PID TTY TIME CMD
>>> [root at lmu-omero2 ~]#
>>>
>>>
>>> Any idea what could cause this? Version 4.4.9 works fine, this is
>>>RedHat 5. Please let me know if you need more details about the
>>>installation.
>>>
>>> Best,
>>> Harri
>>>
>>> --
>>> __________________________________________________
>>> Harri Jäälinoja
>>> Light Microscopy Unit
>>> Institute of Biotechnology, University of Helsinki
>>> http://www.biocenter.helsinki.fi/bi/lmu/
>>> +358 9 191 59370 fax +358 9 191 59366
>>>
>>> _______________________________________________
>>> ome-devel mailing list
>>> ome-devel at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>>
>> The University of Dundee is a registered Scottish Charity, No: SC015096
>
>
>--
>__________________________________________________
>Harri Jäälinoja
>Light Microscopy Unit
>Institute of Biotechnology, University of Helsinki
>http://www.biocenter.helsinki.fi/bi/lmu/
>+358 9 191 59370 fax +358 9 191 59366
>
>_______________________________________________
>ome-devel mailing list
>ome-devel at lists.openmicroscopy.org.uk
>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
The University of Dundee is a registered Scottish Charity, No: SC015096
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