Open Microscopy Environment

Hi,

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


This sounds very similar to an issue recently reported on the mailing lists:

See http://lists.openmicroscopy.org.uk/pipe ... 06886.html

The issue there was due to using the latest version of reportlab and was resolved by switching to reportlab 3.2.0. This issue is also fixed in a recent OMERO.figure release (also 3.2.0!) http://figure.openmicroscopy.org/2018/0 ... 3.2.0.html
Fix was in this PR: https://github.com/ome/omero-figure/pull/260

You say you've tried various versions of reportlab? Did that include 3.2.0?

This was due to the export of multi-page info PDF page. One quick test to see if this is the problem is to export a single-page figure as TIFF, which will not include the PDF info page.

Let us know if this is not the issue,

Regards,

Will.

Thanks,

I eventually tracked down the issue... Adding 8 or more images in figure caused the system to write to /var/lib/nginx/tmp and because the user Nginx was running under did not have write permission to this folder it subsequently failed.

I'm suspect that a recent Nginx/minor os update reverted permissions on /var/lib/nginx/tmp, hence why it had previously worked.

The fix for me was to revert the Nginx user to 'nginx' in /etc/nginx/nginx.conf and restart Nginx.

Regards,

Gareth