PDF backend errors out; PNG works fine

"John Kerenyi" <johnk@...2697...> writes:

  File
"/soft/python/lib/python2.6/site-packages/matplotlib/backends/backend_pd
f.py", line 44, in <module>
    from matplotlib import ttconv
ImportError:
/soft/python/lib/python2.6/site-packages/matplotlib/ttconv.so: undefined
symbol: _ZTVSt19basic_ostringstreamIcSt11char_traitsIcESaIcEE

Sounds like a mismatch between C++ libraries on the system where
matplotlib was built and where it is being used. You mentioned a
cluster; perhaps your sysadmin compiled matplotlib on a special node
that has more libraries installed than the computation nodes. I don't
know how to fix this, but as a first step you could try compiling
matplotlib on a computation node (submit something like "python setup.py
build" as a job the same way you would submit another task on the
cluster) and seeing if that gives more clues about what is missing.

···

--
Jouni K. Sepp�nen
http://www.iki.fi/jks

Thank you for your response. Your response made me wonder how the script would operate in a non-graphic environment--I had tested it on a login node but not on a computing node. It appears that even though I have no need for any graphic display, the modules I am loading expect to have it nonetheless. I invoke matplotlib using the standard "import matplotlib.pyplot as plt" line. Here is the output when run on a compute node:

···

-------------------------

[ac.jkerenyi@...2700... pygraph]$ ./run_pygraph.py png
Creating Top 100 V/C ratios graph...
Traceback (most recent call last):
  File "./run_pygraph.py", line 566, in <module>
    GraphTop100VC (Top100VCFilename)
  File "./run_pygraph.py", line 326, in GraphTop100VC
    fig=plt.figure()
  File "/soft/python/lib/python2.6/site-packages/matplotlib/pyplot.py", line 251, in figure
    **kwargs)
  File "/soft/python/lib/python2.6/site-packages/matplotlib/backends/backend_tkagg.py", line 90, in new_figure_manager
    window = Tk.Tk()
  File "/soft/python/lib/python2.6/lib-tk/Tkinter.py", line 1643, in __init__
    self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)
_tkinter.TclError: no display name and no $DISPLAY environment variable

---------------------

Can anyone advise if there another way to invoke matplotlib that does not require graphic support?

With respect to your suggestion that I run python setup.py build, I don't seem to have the necessary permissions but the sysadmin is very helpful and once I have a little more information on the new problem I'll get his help again.

Thanks again,

John Kerenyi

-----Original Message-----
From: Jouni K. Seppänen [mailto:jks@…397…]
Sent: Wednesday, July 22, 2009 9:38 AM
To: matplotlib-users@lists.sourceforge.net
Subject: Re: [Matplotlib-users] PDF backend errors out; PNG works fine

"John Kerenyi" <johnk@...2697...> writes:

  File
"/soft/python/lib/python2.6/site-packages/matplotlib/backends/backend_
pd
f.py", line 44, in <module>
    from matplotlib import ttconv
ImportError:
/soft/python/lib/python2.6/site-packages/matplotlib/ttconv.so:
undefined
symbol: _ZTVSt19basic_ostringstreamIcSt11char_traitsIcESaIcEE

Sounds like a mismatch between C++ libraries on the system where matplotlib was built and where it is being used. You mentioned a cluster; perhaps your sysadmin compiled matplotlib on a special node that has more libraries installed than the computation nodes. I don't know how to fix this, but as a first step you could try compiling matplotlib on a computation node (submit something like "python setup.py build" as a job the same way you would submit another task on the
cluster) and seeing if that gives more clues about what is missing.

--
Jouni K. Seppänen
http://www.iki.fi/jks

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You can use the "Agg" or "PDF" backends to run matplotlib without display support:

import matplotlib
matplotlib.use("PDF")

Cheers,
Mike

John Kerenyi wrote:

···

Thank you for your response. Your response made me wonder how the script would operate in a non-graphic environment--I had tested it on a login node but not on a computing node. It appears that even though I have no need for any graphic display, the modules I am loading expect to have it nonetheless. I invoke matplotlib using the standard "import matplotlib.pyplot as plt" line. Here is the output when run on a compute node:

-------------------------

[ac.jkerenyi@...2700... pygraph]$ ./run_pygraph.py png
Creating Top 100 V/C ratios graph...
Traceback (most recent call last):
  File "./run_pygraph.py", line 566, in <module>
    GraphTop100VC (Top100VCFilename)
  File "./run_pygraph.py", line 326, in GraphTop100VC
    fig=plt.figure()
  File "/soft/python/lib/python2.6/site-packages/matplotlib/pyplot.py", line 251, in figure
    **kwargs)
  File "/soft/python/lib/python2.6/site-packages/matplotlib/backends/backend_tkagg.py", line 90, in new_figure_manager
    window = Tk.Tk()
  File "/soft/python/lib/python2.6/lib-tk/Tkinter.py", line 1643, in __init__
    self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)
_tkinter.TclError: no display name and no $DISPLAY environment variable

---------------------

Can anyone advise if there another way to invoke matplotlib that does not require graphic support?

With respect to your suggestion that I run python setup.py build, I don't seem to have the necessary permissions but the sysadmin is very helpful and once I have a little more information on the new problem I'll get his help again.

Thanks again,

John Kerenyi

-----Original Message-----
From: Jouni K. Sepp�nen [mailto:jks@…397…] Sent: Wednesday, July 22, 2009 9:38 AM
To: matplotlib-users@lists.sourceforge.net
Subject: Re: [Matplotlib-users] PDF backend errors out; PNG works fine

"John Kerenyi" <johnk@...2697...> writes:

  File
"/soft/python/lib/python2.6/site-packages/matplotlib/backends/backend_
pd
f.py", line 44, in <module>
    from matplotlib import ttconv
ImportError:
/soft/python/lib/python2.6/site-packages/matplotlib/ttconv.so: undefined
symbol: _ZTVSt19basic_ostringstreamIcSt11char_traitsIcESaIcEE
    
Sounds like a mismatch between C++ libraries on the system where matplotlib was built and where it is being used. You mentioned a cluster; perhaps your sysadmin compiled matplotlib on a special node that has more libraries installed than the computation nodes. I don't know how to fix this, but as a first step you could try compiling matplotlib on a computation node (submit something like "python setup.py build" as a job the same way you would submit another task on the
cluster) and seeing if that gives more clues about what is missing.

--
Jouni K. Sepp�nen
http://www.iki.fi/jks

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--
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA