[ome-devel] omero web problem with 4.4.10
Harri Jäälinoja
harri.jaalinoja at helsinki.fi
Tue Jan 28 14:04:26 GMT 2014
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/clients/icommands/bin:/opt/iRODS/current/clients/fuse/bin:/home/omero/bin:/opt/OMERO/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
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