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-- Jason M. Swails > On Nov 1, 2016, at 8:59 AM, Eiros Zamora, Juan <j.eiros-zamora14.imperial.ac.uk> wrote: > > 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 > > > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org<mailto:AMBER.ambermd.org> > http://lists.ambermd.org/mailman/listinfo/amber > > > > > -- > Jason M. Swails > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org<mailto:AMBER.ambermd.org> > http://lists.ambermd.org/mailman/listinfo/amber > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Nov 01 2016 - 06:30:04 PDT