We have an issue with the omero-figure plugin specifically when trying to export a figure with more than 8-12 images on a page. Figures containing less than 8 images usually export fine.
When you click "Export PDF" the button changes to "Exporting figure..." and stops there with a spinning icon. At this point there doesn't appear to be anything in the Blitz log and it does not to get as far as running "Figure_To_Pdf.py"
I've tried various combinations of Pillow/markdown/reportlab installed via pip, but no difference. The server has 16Gb RAM and is running Scientific Linux (REHL7/Centos) 7.4. It was working at some point over the past year and the only change I can think of is an upgrade from 7.3 to 7.4. Upgrading the omero/figure plugin to the latest version did not resolve the problem.
Any ideas on how I can go about debugging/pinpointing the source of the problem? Do you think it's a memory problem?
Many thanks,
Gareth
School of Biological Sciences, University of Edinburgh
- Code: Select all
$ bin/omero config get
omero.db.poolsize=50
omero.jvmcfg.percent.blitz=40
omero.jvmcfg.percent.pixeldata=10
omero.throttling.method_time.error=60000
omero.web.application_server=wsgi-tcp
omero.web.apps=["omero_figure"]
omero.web.open_with=[["Image viewer", "webgateway", {"supported_objects": ["image"], "script_url": "webclient/javascript/ome.openwith_viewer.js"}], ["omero_figure", "new_figure", {"supported_objects": ["images"], "target": "_blank", "label": "OMERO.figure"}]]
omero.web.ui.top_links=[["Data", "webindex", {"title": "Browse Data via Projects, Tags etc"}], ["History", "history", {"title": "History"}], ["Help", "http://help.openmicroscopy.org/", {"target": "new", "title": "Open OMERO user guide in a new tab"}], ["Figure", "figure_index", {"target": "_blank", "title": "Open Figure in new tab"}]]
$ bin/omero admin diagnostics
================================================================================
OMERO Diagnostics (admin) 5.4.3-ice36-b77
================================================================================
Commands: java -version 1.8.0 (/bin/java)
Commands: python -V 2.7.5 (/bin/python)
Commands: icegridnode --version 3.6.4 (/bin/icegridnode)
Commands: icegridadmin --version 3.6.4 (/bin/icegridadmin)
Commands: psql --version 9.2.23 (/bin/psql)
Server: icegridnode running
Server: Blitz-0 active (pid = 4393, enabled)
Server: DropBox active (pid = 4410, enabled)
Server: FileServer active (pid = 4414, enabled)
Server: Indexer-0 active (pid = 4424, enabled)
Server: MonitorServer active (pid = 4464, enabled)
Server: OMERO.Glacier2 active (pid = 4421, enabled)
Server: OMERO.IceStorm active (pid = 4418, enabled)
Server: PixelData-0 active (pid = 4441, enabled)
Server: Processor-0 active (pid = 4449, enabled)
Server: Tables-0 active (pid = 4454, enabled)
Server: TestDropBox inactive (enabled)
Log dir: /opt/OMERO/OMERO.server-5.4.3-ice36-b77/var/log exists
Log files: Blitz-0.log 239.0 MB errors=25 warnings=421
Log files: DropBox.log 9.0 KB errors=0 warnings=3
Log files: FileServer.log 1.0 KB
Log files: Indexer-0.log 194.0 KB errors=0 warnings=44
Log files: MonitorServer.log 5.0 KB
Log files: OMEROweb.lock 0.0 KB
Log files: OMEROweb.log 4.0 MB errors=16 warnings=588
Log files: PixelData-0.log 51.0 KB
Log files: Processor-0.log 2.0 MB errors=1 warnings=17
Log files: Tables-0.log 6.0 KB
Log files: TestDropBox.log n/a
Log files: master.err 13.0 KB errors=3 warnings=7
Log files: master.out 0.0 KB
Log files: Total size 246.61 MB
Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_USERDIR=(unset)
Environment:OMERO_TMPDIR=(unset)
Environment:PATH=/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin
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:'/mnt/sbsomero/OMERO.data' Exists? True Is writable? True
OMERO temp dir:'/localdisk/home/user/user/tmp' Exists? True Is writable? True (Size: 68308)
JVM settings: Blitz-${index} -Xmx6729m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index} -Xmx1682m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index} -Xmx1682m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index} -Xmx1682m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
