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CLOSED: piechart (disk space) - could not open display

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CLOSED: piechart (disk space) - could not open display

Postby carandraug » Thu Sep 30, 2010 3:47 pm

Hi

when trying to see diskspace with Webadmin, I get the message "Piechart could not be displayed. Please check log file to solve the problem.". I looked into the log messages, searched in the forum and installation troubleshooting guide but my problem seems to be none of the previously reported.

Here's the error and traceback that I find in the log:
Code: Select all
Thu, 30 Sep 2010 16:26:57 views-admin  ERROR    Traceback (most recent call last):
  File "/home/omero/OMERO.server-Beta-4.2.0/lib/python/omeroweb/webadmin/views.py", line 1013, in piechart
    import matplotlib.pyplot as plt
  File "/usr/lib64/python2.4/site-packages/matplotlib/pyplot.py", line 78, in ?
    new_figure_manager, draw_if_interactive, show = pylab_setup()
  File "/usr/lib64/python2.4/site-packages/matplotlib/backends/__init__.py", line 25, in pylab_setup
    globals(),locals(),[backend_name])
  File "/usr/lib64/python2.4/site-packages/matplotlib/backends/backend_gtkagg.py", line 10, in ?
    from matplotlib.backends.backend_gtk import gtk, FigureManagerGTK, FigureCanvasGTK,\
  File "/usr/lib64/python2.4/site-packages/matplotlib/backends/backend_gtk.py", line 8, in ?
    import gtk; gdk = gtk.gdk
  File "/usr/lib64/python2.4/site-packages/gtk-2.0/gtk/__init__.py", line 76, in ?
    _init()
  File "/usr/lib64/python2.4/site-packages/gtk-2.0/gtk/__init__.py", line 64, in _init
    _gtk.init_check()
RuntimeError: could not open display

Thu, 30 Sep 2010 16:26:57 views-feedback ERROR    handler500: Server error
Thu, 30 Sep 2010 16:26:57 views-feedback ERROR    Traceback (most recent call last):

  File "/home/omero/OMERO.server-Beta-4.2.0/lib/python/django/core/handlers/base.py", line 92, in get_response
    response = callback(request, *callback_args, **callback_kwargs)

  File "/home/omero/OMERO.server-Beta-4.2.0/lib/python/omeroweb/webadmin/views.py", line 204, in wrapped
    return f(request, *args, **kwargs)

  File "/home/omero/OMERO.server-Beta-4.2.0/lib/python/omeroweb/webadmin/views.py", line 1017, in piechart
    rv = "Error: %s" % x.message

AttributeError: RuntimeError instance has no attribute 'message'


The "could not open display" may be related to the fact that there's no display, it's a remote virtual machine.

I'm running OMERO.server Beta 4.2.o on CentOS 5.5. Here's the output of diagnostic
Code: Select all
================================================================================
OMERO Diagnostics Beta-4.2.0-r7571-b29
================================================================================
       
Commands:   java -version                  1.6.0     (/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                 8.4.4     (/usr/bin/psql)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 19174, enabled)
Server:     DropBox                        inactive (disabled)
Server:     FileServer                     active (pid = 19199, enabled)
Server:     Indexer-0                      active (pid = 19185, enabled)
Server:     MonitorServer                  inactive (disabled)
Server:     OMERO.Glacier2                 active (pid = 19188, enabled)
Server:     OMERO.IceStorm                 active (pid = 19192, enabled)
Server:     Processor-0                    active (pid = 19194, enabled)
Server:     Repository-1                   error: node `repo' couldn't be reached:
the node is not active
Server:     Tables-0                       inactive (disabled)
Server:     TestDropBox                    inactive (enabled)

Log dir:    /home/omero/OMERO.server-Beta-4.2.0/var/log exists

Log files:  Blitz-0.log                    3.0 MB        errors=0    warnings=28 
Log files:  DropBox.log                    0.0 KB        errors=2    warnings=0   
Log files:  FileServer.log                 0.0 KB       
Log files:  Indexer-0.log                  154.0 KB      errors=0    warnings=10 
Log files:  MonitorServer.log              0.0 KB        errors=1    warnings=0   
Log files:  OMEROweb.log                   43.0 KB       errors=88   warnings=2   
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       
Log files:  master.out                     0.0 KB       
Log files:  Total size                     3.40 MB

Parsing Blitz-0.log:[line:69] => Server restarted <=

Environment:OMERO_HOME=(unset)             
Environment:OMERO_NODE=(unset)             
Environment:OMERO_MASTER=(unset)           
Environment:PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/omero/bin
Environment:ICE_HOME=(unset)               
Environment:LD_LIBRARY_PATH=(unset)       
Environment:DYLD_LIBRARY_PATH=(unset)     


EDIT: I looked into the matplotlib documentation and found this
matplotlib documentation on http://matplotlib.sourceforge.net/faq/h ... ion-server wrote:Many users report initial problems trying to use maptlotlib in web application servers, because by default matplotlib ships configured to work with a graphical user interface which may require an X11 connection. Since many barebones application servers do not have X11 enabled, you may get errors if you don’t configure matplotlib for use in these environments. Most importantly, you need to decide what kinds of images you want to generate (PNG, PDF, SVG) and configure the appropriate default backend. For 99% of users, this will be the Agg backend, which uses the C++ antigrain rendering engine to make nice PNGs. The Agg backend is also configured to recognize requests to generate other output formats (PDF, PS, EPS, SVG). The easiest way to configure matplotlib to use Agg is to call:
Code: Select all
# do this before importing pylab or pyplot
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt



I don't know python but I looked into ''lib/python/omeroweb/webadmin/views.py'' and found something that already said ''agg''.
Code: Select all
        from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas
        import numpy as np
        import matplotlib.pyplot as plt
        from pylab import *
carandraug
 
Posts: 15
Joined: Mon Sep 06, 2010 8:50 pm

Re: piechart (disk space) - could not open display

Postby atarkowska » Mon Oct 11, 2010 10:49 am

Hi, could you please check if your configuration (file: matplotlibrc) includes:

Code: Select all
backend      : Agg


and mod_python includes:

Code: Select all
SetEnv MPLCONFIGDIR /home/omero/weblog/matplotlib
atarkowska
 
Posts: 327
Joined: Mon May 18, 2009 12:44 pm

Re: piechart (disk space) - could not open display

Postby carandraug » Mon Oct 11, 2010 1:02 pm

atarkowska wrote:Hi, could you please check if your configuration (file: matplotlibrc) includes:

Code: Select all
backend      : Agg



The file matplotlibrc had GTKAgg set as the default backend. I changed it to Agg and it works now. Thank you very much

A few notes to users that may come across the same problem:

    In CentOS, the file is located at /usr/lib64/python2.4/site-packages/matplotlib/mpl-data/matplotlibrc
    The changes only enter in effect after restarting WebAdmin
carandraug
 
Posts: 15
Joined: Mon Sep 06, 2010 8:50 pm


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