Re: [Matplotlib-users] Error when running multiple jobs utilizing the Tex utilities in matplotlib

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Hi Darren,

Thanks for helping with this problem.

I have investigated further this issue and here is what I have found out:

I have traced the errors themselves back to two functions in texmanager.py
(matplotlib.texmanager), make_dvi and make_png. Most of the errors seem to
mention 'Stale NFS file handles' and crop up at a variety of different
places throughout these functions. I guess this is because on our clusters
/home/[username] is not a local directory, we have seen issues before with
other code if a lot of nodes try to access the same directory on the NFS
file system simultaneously. I tried altering the __init__.py to force the
code to put the .matplotlib directory on filesystems local to each node.
Moving the .matplotlib directory to a local drive solves almost all of these
errors.
One error that remained was the one about file opening
fh = file(outfile)
I added a 'w' to this and this seemed to solve this problem, I also
commented out some of the verbose generating commands (specifically
fh.read() was causing a problem (probably expected with 'w')) within these
functions and the errors go away. I guess 'a' would be better but the
commands only seem to be called if the file doesn't exist?

As we have a lot of users running this code a solution like this is
unworkable (as a lot of our users are unfamiliar with python/Linux and want
to run a simple command). Do you have any ideas of how we could solve this
issue?

Thanks again for your help

Ian Harry

2008/7/10 Darren Dale <dsd...@gm...>:

> On Thursday 10 July 2008 10:48:01 am you wrote:
> > Hi Darren,
> >
> > I have tried rerunning our code with the change you suggested in the
> > make_dvi and make_png functions. I am still noticing failures however. I
> > put these at the bottom of this message. Strangely enough, these errors
> > don't seem to occur when there are a lot of files in my tex.cache
> > directory. For example, I ran the code (consisting of ~40 codes all
> making
> > ~10-20 plots each), successfully 3 times (the OSError wasn't raised at
> all,
> > I used a print statement to check). I realised after this that a lot of
> > temp files were in my tex.cache directory, so I emptied it and then I
> > noticed that a lot of failures occured when I ran the code the next time
> > (the OSError I showed previously was raised as well as the error messages
> > shown below). It seems weird that it should run fine when a lot of files
> > are left in my temp directory and not when it is empty?
>
> Most of those files are not temporary files, but cached files. The error
> you
> reported only occurs when a required file does not already exist in the
> cache, and like you said, it appears to be the case that two jobs are
> trying
> to add the same file to the cache at the same time, and one job is failing
> because the other deletes a temporary file that is being used by both. I
> guess.
>
> > Here are the error messages that are occuring now:
> >
> > Traceback (most recent call last):
> >   File
> >
> "/home/spxiwh/ihope/852450000-852700000/nsbhinj_summary_plots/../executable
> >s/plotinspmissed", line 625, in ?
> >     savePlot( opts, filename, titleText)
> >   File
> >
> "/home/spxiwh/ihope/852450000-852700000/nsbhinj_summary_plots/../executable
> >s/plotinspmissed", line 108, in savePlot
> >     dpi_thumb=opts.figure_resolution)
> >   File
> >
> "/home/spxiwh/lscsoft/executables/cbc_s5_1yr_20070129/pylal//lib64/python2.
> >4/site-packages/pylal/InspiralUtils.py", line 54, in savefig_pylal
> >     fig.savefig(filename, dpi=dpi)
> >   File "/home/spxiwh/test/matplotlib/figure.py", line 682, in savefig
> >     self.canvas.print_figure(*args, **kwargs)
> >   File "/home/spxiwh/test/matplotlib/backends/backend_agg.py", line 456,
> in
> > print_figure
> >     self.draw()
> >   File "/home/spxiwh/test/matplotlib/backends/backend_agg.py", line 392,
> in
> > draw
> >     self.figure.draw(renderer)
> >   File "/home/spxiwh/test/matplotlib/figure.py", line 544, in draw
> >     for a in self.axes: a.draw(renderer)
> >   File "/home/spxiwh/test/matplotlib/axes.py", line 1063, in draw
> >     a.draw(renderer)
> >   File "/home/spxiwh/test/matplotlib/axis.py", line 595, in draw
> >     self.label.draw(renderer)
> >   File "/home/spxiwh/test/matplotlib/text.py", line 340, in draw
> >     bbox, info = self._get_layout(renderer)
> >   File "/home/spxiwh/test/matplotlib/text.py", line 187, in _get_layout
> >     w,h = renderer.get_text_width_height(
> >   File "/home/spxiwh/test/matplotlib/backends/backend_agg.py", line 240,
> in
> > get_text_width_height
> >     Z = texmanager.get_rgba(s, size, self.dpi.get(), rgb)
> >   File "/home/spxiwh/test/matplotlib/texmanager.py", line 334, in
> get_rgba
> >     pngfile = self.make_png(tex, fontsize, dpi, force=False)
> >   File "/home/spxiwh/test/matplotlib/texmanager.py", line 255, in
> make_png
> >     fh = file(outfile)
> > IOError: [Errno 2] No such file or directory:
> >
> '/home/spxiwh/.matplotlib/tex.cache/fb2014e54961855bd04020b61190867c.output
> >'
>
> That doesnt make any sense to me. file defaults to open a file in append
> mode,
> it doesnt matter if a file exists or not. Maybe you could try to figure out
> why that fails and report back.
>
> > And once I noticed:
> >
> > Traceback (most recent call last):
> >   File
> >
> "/home/spxiwh/ihope/852450000-852700000/allinj_summary_plots/../executables
> >/plotinspmissed", line 661, in ?
> >     dpi_thumb=opts.figure_resolution)
> >   File
> >
> "/home/spxiwh/lscsoft/executables/cbc_s5_1yr_20070129/pylal//lib64/python2.
> >4/site-packages/pylal/InspiralUtils.py", line 54, in savefig_pylal
> >     fig.savefig(filename, dpi=dpi)
> >   File "/usr/lib64/python2.4/site-packages/matplotlib/figure.py", line
> 682,
> > in savefig
> >     self.canvas.print_figure(*args, **kwargs)
> >   File
> > "/usr/lib64/python2.4/site-packages/matplotlib/backends/backend_agg.py",
> > line 456, in print_figure
> >     self.draw()
> >   File
> > "/usr/lib64/python2.4/site-packages/matplotlib/backends/backend_agg.py",
> > line 392, in draw
> >     self.figure.draw(renderer)
> >   File "/usr/lib64/python2.4/site-packages/matplotlib/figure.py", line
> 544,
> > in draw
> >     for a in self.axes: a.draw(renderer)
> >   File "/usr/lib64/python2.4/site-packages/matplotlib/axes.py", line
> 1063,
> > in draw
> >     a.draw(renderer)
> >   File "/usr/lib64/python2.4/site-packages/matplotlib/text.py", line 340,
> > in draw
> >     bbox, info = self._get_layout(renderer)
> >   File "/usr/lib64/python2.4/site-packages/matplotlib/text.py", line 187,
> > in _get_layout
> >     w,h = renderer.get_text_width_height(
> >   File
> > "/usr/lib64/python2.4/site-packages/matplotlib/backends/backend_agg.py",
> > line 240, in get_text_width_height
> >     Z = texmanager.get_rgba(s, size, self.dpi.get(), rgb)
> >   File "/usr/lib64/python2.4/site-packages/matplotlib/texmanager.py",
> line
> > 330, in get_rgba
> >     X = readpng(os.path.join(self.texcache, pngfile))
> > RuntimeError: _image_module::readpng: file not recognized as a PNG file
>
> No idea, sorry.
>
> Darren
>
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Ian Harry
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