Hi Jason,
I upgraded the environment as suggested (here’s the complete log
http://lpaste.net/2338255014272696320) , but I’m afraid this has somehow screwed up matplotlib even further. Now mdout_analyzer.py won’t load, with the following Traceback:
Traceback (most recent call last):
File "/usr/local/amber16/bin/mdout_analyzer.py", line 9, in <module>
from mdoutanalyzer.graphproperties import GraphControlWindow
File "/usr/local/amber16/lib/python3.5/site-packages/mdoutanalyzer/graphproperties.py", line 6, in <module>
from mdoutanalyzer.widgets import LabeledEntry
File "/usr/local/amber16/lib/python3.5/site-packages/mdoutanalyzer/widgets.py", line 7, in <module>
import matplotlib.pyplot as plt
File "/Users/je714/anaconda3/lib/python3.5/site-packages/matplotlib/pyplot.py", line 29, in <module>
import matplotlib.colorbar
File "/Users/je714/anaconda3/lib/python3.5/site-packages/matplotlib/colorbar.py", line 34, in <module>
import matplotlib.collections as collections
File "/Users/je714/anaconda3/lib/python3.5/site-packages/matplotlib/collections.py", line 27, in <module>
import matplotlib.backend_bases as backend_bases
File "/Users/je714/anaconda3/lib/python3.5/site-packages/matplotlib/backend_bases.py", line 62, in <module>
import matplotlib.textpath as textpath
File "/Users/je714/anaconda3/lib/python3.5/site-packages/matplotlib/textpath.py", line 18, in <module>
from matplotlib.mathtext import MathTextParser
File "/Users/je714/anaconda3/lib/python3.5/site-packages/matplotlib/mathtext.py", line 60, in <module>
import matplotlib._png as _png
ImportError: dlopen(/Users/je714/anaconda3/lib/python3.5/site-packages/matplotlib/_png.so, 2): Library not loaded: @rpath/libpng16.16.dylib
Referenced from: /Users/je714/anaconda3/lib/python3.5/site-packages/matplotlib/_png.so
Reason: Incompatible library version: _png.so requires version 39.0.0 or later, but libpng16.16.dylib provides version 34.0.0
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/amber16/bin/mdout_analyzer.py", line 18, in <module>
(amberhome, amberhome))
ImportError: Could not import Amber Python modules. Please make sure you have sourced /usr/local/amber16/amber.sh (if you are using sh/ksh/bash/zsh) or /usr/local/amber16/amber.csh (if you are using csh/tcsh)
I do have sourced $AMBERHOME/amber.sh previously.
I’ve googled the libpng16.16.dylib error, and followed suggestions like this
https://github.com/pyskell/slouchy/issues/11 or this
https://codedump.io/share/5ap8ZmVDafxz/1
Seems to me that the error is with some of the stuff I have in my root environment is crashing with libraries installed with brew, as not only mdout_analyzer.py is crashing now.
I also get the same Traceback if I open a Python shell and run `import seaborn` or try to use %pylab inline in a Jupyter notebook.
My next step is going to be erasing my Anaconda distribution and start one from fresh, as apparently something’s gone pretty wrong. But I just wanted to ask you in case you have any suggestion :)
Best
Juan
On 31 Oct 2016, at 18:48, Jason Swails <jason.swails.gmail.com<mailto:jason.swails.gmail.com>> wrote:
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<mailto:
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/><
http://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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Jason M. Swails
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Received on Tue Nov 01 2016 - 06:30:02 PDT
