Hi Juan,
This looks like a problem with Anaconda's matplotlib TkAgg backend. Here
is where it's described in Google Groups:
https://groups.google.com/a/continuum.io/forum/#!topic/anaconda/xssOnleIPFw
I saw the same behavior on my Anaconda distribution. I was able to fix it
by running the command:
conda upgrade -n py35 --all
In this case, replace "py35" with the name of your conda environment (which
you can find as the environment with the * next to it when you run the
command "conda env list").
HTH,
Jason
On Mon, Oct 31, 2016 at 8:09 AM, Eiros Zamora, Juan <
j.eiros-zamora14.imperial.ac.uk> wrote:
> Dear Amberists,
>
> I’m using mdout_analyzer.py to read an mdout file, and I see some warnings
> and errors and I was hoping you could help me figure out what’s wrong.
> First, when I call the program, I get the following warnings (but the GUI
> opens just fine):
>
> /Users/je714/anaconda3/lib/python3.5/site-packages/matplotlib/__init__.py:461:
> UserWarning: matplotlibrc ps.usedistiller can not be set to xpdf unless
> xpdf-3.0 or later is installed on your system
> 'your system') % pdftops_req)
> objc[17603]: Class TKApplication is implemented in both
> /System/Library/Frameworks/Tk.framework/Versions/8.5/Tk and
> /Users/je714/anaconda3/lib/libtk8.5.dylib. One of the two will be used.
> Which one is undefined.
> objc[17603]: Class TKMenu is implemented in both
> /System/Library/Frameworks/Tk.framework/Versions/8.5/Tk and
> /Users/je714/anaconda3/lib/libtk8.5.dylib. One of the two will be used.
> Which one is undefined.
> objc[17603]: Class TKContentView is implemented in both
> /System/Library/Frameworks/Tk.framework/Versions/8.5/Tk and
> /Users/je714/anaconda3/lib/libtk8.5.dylib. One of the two will be used.
> Which one is undefined.
> objc[17603]: Class TKWindow is implemented in both
> /System/Library/Frameworks/Tk.framework/Versions/8.5/Tk and
> /Users/je714/anaconda3/lib/libtk8.5.dylib. One of the two will be used.
> Which one is undefined.
>
> I can chose any item in the ‘Select Data to Analyze’ list and click on
> 'Show Statistics’ or ’Save to File', for example. But when I try to plot
> them with the ‘Graph Them!’, ‘Histogram Data’ or ‘Autocorrelation’,
> ‘Running Average’ or ‘Cumulative Running Average' buttons, I first get this
> error:
>
> Exception in Tkinter callback
> Traceback (most recent call last):
> File "/Users/je714/anaconda3/lib/python3.5/site-packages/matplotlib/backends/tkagg.py",
> line 22, in blit
> id(data), colormode, id(bbox_array))
> _tkinter.TclError: invalid command name "PyAggImagePhoto"
>
> During handling of the above exception, another exception occurred:
>
> Traceback (most recent call last):
> File "/Users/je714/anaconda3/lib/python3.5/tkinter/__init__.py", line
> 1550, in __call__
> return self.func(*args)
> File "/usr/local/amber16/lib/python3.5/site-packages/mdoutanalyzer/widgets.py",
> line 91, in new_fcn
> return fcn(self)
> File "/usr/local/amber16/lib/python3.5/site-packages/mdoutanalyzer/widgets.py",
> line 63, in new_fcn
> if fcn(self, newfig, ax, self.graph_props.nexcl()) == 1:
> File "/usr/local/amber16/lib/python3.5/site-packages/mdoutanalyzer/widgets.py",
> line 469, in execute
> fig.show()
> File "/Users/je714/anaconda3/lib/python3.5/site-packages/
> matplotlib/backends/backend_tkagg.py", line 355, in draw
> tkagg.blit(self._tkphoto, self.renderer._renderer, colormode=2)
> File "/Users/je714/anaconda3/lib/python3.5/site-packages/matplotlib/backends/tkagg.py",
> line 30, in blit
> id(data), colormode, id(bbox_array))
> _tkinter.TclError
>
> Then an empty window titled ‘Mdout Analyzer’ pops up. I can then close it,
> and re-click any of the buttons, followed by a close down of the program
> with the following error:
>
> python(17641,0x7fff79860000) malloc: *** error for object 0x100c21cd0:
> pointer being freed was not allocated
> *** set a breakpoint in malloc_error_break to debug
> Abort trap: 6
>
>
> I’m not familiar with the tkinter module so I’m not too sure what’s going
> wrong.
>
> My Mac is running on OS X El Capitan Version 10.11.6, my Python is Python
> 3.5.2 :: Anaconda 4.0.0 (x86_64), here (http://lpaste.net/raw/
> 5192122385733517312) is the result of conda list command (I’m running
> mdout_analyzer.py on my root environment), result of uname -a command is:
> Darwin ch-knuth.ch.ic.ac.uk<http://ch-knuth.ch.ic.ac.uk> 15.6.0 Darwin
> Kernel Version 15.6.0: Mon Aug 29 20:21:34 PDT 2016;
> root:xnu-3248.60.11~1/RELEASE_X86_64 x86_64.
>
> Please let me know if you need more information to replicate this error,
>
> Thanks for any comments,
>
> Juan Eiros
>
>
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
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Received on Mon Oct 31 2016 - 12:00:03 PDT
