I've been spending a lot of time organizing my code for the cross correlation project to run more efficiently. Part of this is setting up my code so that it can process/run a lot of different runs simultaneously. It's been a lot of fun learning all the cool tricks I can do with python to help with this. I should blog about some of these tricks.... but not right now....
This blog is about an error I was getting when I tried to run my newly optimized code on riemann. I use qsub/PBS to submit jobs, and I was getting the following errors in my qsub.out file:
File "/clusterfs/riemann/software/matplotlib/1.0.0/lib64/python2.7/site-packages/matplotlib/pyplot.py", line 270, in figure **kwargs)
File "/clusterfs/riemann/software/matplotlib/1.0.0/lib64/python2.7/site-packages/matplotlib/backends/backend_tkagg.py", line 83, in new_figure_manager
window = Tk.Tk() File "/clusterfs/riemann/software/Python/2.7.1/lib/python2.7/lib-tk/Tkinter.py", line 1685, in __init__
self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)
_tkinter.TclError: no display name and no $DISPLAY environment variable
I know that when I run jobs on other riemann nodes using qsub, that the X11 forwarding doesn't work properly. Or in other words, I can't view any of the plots I make when I am running an interactive PBS session. However, for this code, I simply wanted to save plots to .pdf files. However, for some reason there isn't a simple command (that I can find) to plot something in python directly to a file. If anyone out there knows how to do this, please help me!
But I did come across the following from matplotlib's faq page:
How To Generate Python/Matplotlib Images Without Having A Window Appear
The easiest way to do this is use a non-interactive backend such as Agg (for PNGs), PDF, SVG or PS. In your figure-generating script, just call the matplotlib.use() directive before importing pylab or pyplot:
import matplotlib.pyplot as plt
You need to make sure to call matplotlib.use() before pyplot or you will get the following error
UserWarning: This call to matplotlib.use() has no effect because the the backend has already been chosen;
matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
if warn: warnings.warn(_use_error_msg)
I actually had an alias set up so that I call pyplot when I open up python, so I was getting this error until I changed that.
So now, I don't the the "$DISPLAY environment variable" error, because python knows to use the non-interactive backend Agg instead of trying to display to the screen. Yippee!