[yt-users] Pyx + Tex

John Regan johnanthonyregan at gmail.com
Wed Feb 24 04:25:22 PST 2016


Hi John and DK,

Sorry I only saw this late. For me the problem was also the texlive
installation which I did eventually track down. The problem for me was not
an older version however, simply that texlive wasn't installed on the
compute nodes of the cluster I was using - it was however installed on the
login nodes which I didn't cotton on to at first. This is likely to be a
common problem with Pyx though when running (at least initially) on a new
machine which won't usually have latex installed on the compute nodes.
Something to be mindful of I think.

On Tue, Feb 16, 2016 at 7:05 AM, John Wise <jwise at physics.gatech.edu> wrote:

> Hi everyone,
>
> I just wanted to follow-up on this problem.  I found that the latex
> version is very old (from 2007) on Comet.  I installed my own version,
> using basic scheme with the TeX Live install script
>
> http://mirror.ctan.org/systems/texlive/tlnet/install-tl-unx.tar.gz
>
> and PyX works perfectly now without any errors or warnings.
>
> Thanks,
> John
>
>
> On 02/15/2016 01:51 PM, John Wise wrote:
>
>> Hi DK,
>>
>> I didn't have the chance to look into this issue.  John R, did you
>> manage to figure out a solution?
>>
>> Thanks,
>> John
>>
>> On 02/14/2016 07:54 PM, Koh, Daegene wrote:
>>
>>> Hi John,
>>>
>>> Were you ever able to resolve this issue? I’m having the same problem
>>> on Comet.
>>>
>>> Cheers,
>>> DK
>>>
>>> On Nov 25, 2015, at 10:06 AM, John Regan <johnanthonyregan at gmail.com>
>>>> wrote:
>>>>
>>>> Hi All,
>>>>
>>>> I recently moved to working on a new machine and I've run into
>>>> problems with eps_writer and pyx and tex. It seems pyx and tex are
>>>> not talking to one another. I know pyx can sometimes have an iffy
>>>> relationship with tex but does anyone know how to make them like each
>>>> other?
>>>>
>>>> This is the output I get.
>>>>
>>>> yt : [INFO     ] 2015-11-25 14:51:23,198 xlim = 0.456408 0.541884
>>>> yt : [INFO     ] 2015-11-25 14:51:23,198 ylim = 0.482775 0.568251
>>>> yt : [INFO     ] 2015-11-25 14:51:23,200 Making a fixed resolution
>>>> buffer of (('gas', 'H_number_density')) 800 by 800
>>>> Create Multiplot....
>>>> yt : [WARNING  ] 2015-11-25 14:51:24,085 No field specified.
>>>> Choosing first field (('gas', 'H2_fraction'))
>>>> yt : [WARNING  ] 2015-11-25 14:51:24,955 No field specified.
>>>> Choosing first field (('gas', 'H_number_density'))
>>>> still waiting for tex after 5 (of 60) seconds...
>>>> still waiting for tex after 10 (of 60) seconds...
>>>> still waiting for tex after 15 (of 60) seconds...
>>>> still waiting for tex after 20 (of 60) seconds...
>>>> still waiting for tex after 25 (of 60) seconds...
>>>> still waiting for tex after 30 (of 60) seconds...
>>>> still waiting for tex after 35 (of 60) seconds...
>>>> still waiting for tex after 40 (of 60) seconds...
>>>> still waiting for tex after 45 (of 60) seconds...
>>>> still waiting for tex after 50 (of 60) seconds...
>>>> still waiting for tex after 55 (of 60) seconds...
>>>> the timeout of 60 seconds expired and tex did not respond.
>>>> We try to finish the dvi due to an unhandled tex error
>>>> still waiting for tex after 5 (of 60) seconds...
>>>> still waiting for tex after 10 (of 60) seconds...
>>>> still waiting for tex after 15 (of 60) seconds...
>>>> still waiting for tex after 20 (of 60) seconds...
>>>> still waiting for tex after 25 (of 60) seconds...
>>>> still waiting for tex after 30 (of 60) seconds...
>>>> still waiting for tex after 35 (of 60) seconds...
>>>> still waiting for tex after 40 (of 60) seconds...
>>>> still waiting for tex after 45 (of 60) seconds...
>>>> still waiting for tex after 50 (of 60) seconds...
>>>> still waiting for tex after 55 (of 60) seconds...
>>>> the timeout of 60 seconds expired and tex did not respond.
>>>> Traceback (most recent call last):
>>>>    File "OnAxisMultiPlot_TimeSeries.py", line 173, in <module>
>>>>      figsize=(8,4), shrink_cb=1.8)
>>>>    File
>>>>
>>>> "/cosma/home/jregan/YT/yt-x86_64/src/yt-hg/yt/visualization/eps_writer.py",
>>>> line 1164, in multiplot
>>>>      bbox = (100.0 * d.canvas.bbox().left().t,
>>>>    File
>>>>
>>>> "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/canvas.py",
>>>> line 156, in bbox
>>>>      obbox += cmd.bbox()
>>>>    File
>>>>
>>>> "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/graph.py",
>>>> line 181, in bbox
>>>>      self.finish()
>>>>    File
>>>>
>>>> "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/graph.py",
>>>> line 311, in finish
>>>>      self.doaxes()
>>>>    File
>>>>
>>>> "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/graph.py",
>>>> line 588, in doaxes
>>>>      self.dolayout()
>>>>    File
>>>>
>>>> "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/graph.py",
>>>> line 572, in dolayout
>>>>      self.doaxiscreate(axisname)
>>>>    File
>>>>
>>>> "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/graph.py",
>>>> line 248, in doaxiscreate
>>>>      self.axes[axisname].create()
>>>>    File
>>>>
>>>> "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/axis/axis.py",
>>>> line 586, in create
>>>>      self.canvas = self.axis.create(self.data, self.positioner,
>>>> self.graphtexrunner, self.errorname)
>>>>    File
>>>>
>>>> "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/axis/axis.py",
>>>> line 245, in create
>>>>      return _regularaxis._create(self, data, positioner,
>>>> graphtexrunner, self.parter, self.rater, errorname)
>>>>    File
>>>>
>>>> "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/axis/axis.py",
>>>> line 146, in _create
>>>>      return layout(data)
>>>>    File
>>>>
>>>> "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/axis/axis.py",
>>>> line 141, in layout
>>>>      self.painter.paint(canvas, data, self, positioner)
>>>>    File
>>>>
>>>> "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/axis/painter.py",
>>>> line 258, in paint
>>>>      _title.paint(self, canvas, data, axis, axispos)
>>>>    File
>>>>
>>>> "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/axis/painter.py",
>>>> line 109, in paint
>>>>      title = canvas.layer("title").text_pt(x, y, axis.title, titleattrs)
>>>>    File
>>>>
>>>> "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/canvas.py",
>>>> line 334, in text_pt
>>>>      return self.insert(self.texrunner.text_pt(x, y, atext, *args))
>>>>    File
>>>>
>>>> "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/text.py",
>>>> line 1223, in text_pt
>>>>      return self.text(x * unit.t_pt, y * unit.t_pt, expr, *args,
>>>> **kwargs)
>>>>    File
>>>>
>>>> "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/text.py",
>>>> line 1201, in text
>>>>      raise e
>>>> pyx.text.TexResultError: TeX didn't respond as expected within the
>>>> timeout period (60 seconds).
>>>> The expression passed to TeX was:
>>>>    \scrollmode
>>>>    \raiseerror%
>>>>    \def\PyX{P\kern-.3em\lower.5ex\hbox{Y}\kern-.18em X}%
>>>>    \gdef\PyXBoxHAlign{0}%
>>>>    \newbox\PyXBox%
>>>>    \newbox\PyXBoxHAligned%
>>>>    \newdimen\PyXDimenHAlignLT%
>>>>    \newdimen\PyXDimenHAlignRT%
>>>>    \gdef\PyXFlushHAlign{0}%
>>>>    \def\PyXragged{%
>>>>    \leftskip=0pt plus \PyXFlushHAlign fil%
>>>>    \rightskip=0pt plus 1fil%
>>>>    \advance\rightskip0pt plus -\PyXFlushHAlign fil%
>>>>    \parfillskip=0pt%
>>>>    \pretolerance=9999%
>>>>    \tolerance=9999%
>>>>    \parindent=0pt%
>>>>    \hyphenpenalty=9999%
>>>>    \exhyphenpenalty=9999}%
>>>>    \newbox\PyXBoxVBox%
>>>>    \newdimen\PyXDimenVBox%
>>>>    \newbox\PyXBoxVAlign%
>>>>    \newdimen\PyXDimenVAlign%
>>>>    \newdimen\PyXDimenVShift%
>>>>    \long\def\ProcessPyXBox#1#2{%
>>>>    \setbox\PyXBox=\hbox{{#1}}%
>>>>    \PyXDimenHAlignLT=\PyXBoxHAlign\wd\PyXBox%
>>>>    \PyXDimenHAlignRT=\wd\PyXBox%
>>>>    \advance\PyXDimenHAlignRT by -\PyXDimenHAlignLT%
>>>>    \gdef\PyXBoxHAlign{0}%
>>>>
>>>>
>>>> \immediate\write16{PyXBox:page=#2,lt=\the\PyXDimenHAlignLT,rt=\the\PyXDimenHAlignRT,ht=\the\ht\PyXBox,dp=\the\dp\PyXBox:}%
>>>>
>>>>    \setbox\PyXBoxHAligned=\hbox{\kern-\PyXDimenHAlignLT\box\PyXBox}%
>>>>    \ht\PyXBoxHAligned0pt%
>>>>
>>>> {\count0=80\count1=121\count2=88\count3=#2\shipout\box\PyXBoxHAligned}}%
>>>>    \def\PyXInput#1{\immediate\write16{PyXInputMarker:executeid=#1:}}%
>>>>    \def\PyXMarker#1{\hskip0pt\special{PyX:marker #1}}%%
>>>>    \PyXInput{1}%
>>>> After parsing the return message from TeX, the following was left:
>>>>    This is TeX, Version 3.14159265 (TeX Live 2015) (preloaded
>>>> format=tex)
>>>> Error in atexit._run_exitfuncs:
>>>> Traceback (most recent call last):
>>>>    File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/atexit.py",
>>>> line 24, in _run_exitfuncs
>>>>      func(*targs, **kargs)
>>>>    File
>>>>
>>>> "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/text.py",
>>>> line 744, in _cleantmp
>>>>      texrunner.expectqueue.put_nowait(None)              # do not
>>>> expect any output anymore
>>>>    File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/Queue.py",
>>>> line 148, in put_nowait
>>>>      return self.put(item, False)
>>>>    File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/Queue.py",
>>>> line 123, in put
>>>>      raise Full
>>>> Full
>>>> Error in sys.exitfunc:
>>>> Traceback (most recent call last):
>>>>    File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/atexit.py",
>>>> line 24, in _run_exitfuncs
>>>>      func(*targs, **kargs)
>>>>    File
>>>>
>>>> "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/text.py",
>>>> line 744, in _cleantmp
>>>>      texrunner.expectqueue.put_nowait(None)              # do not
>>>> expect any output anymore
>>>>    File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/Queue.py",
>>>> line 148, in put_nowait
>>>>      return self.put(item, False)
>>>>    File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/Queue.py",
>>>> line 123, in put
>>>>      raise Full
>>>> Queue.Full
>>>>
>>>>
>>>>
>>>> The call I make is:
>>>>
>>>> multi = eps.multiplot(NCOLS, NROWS, projections,
>>>> bare_axes=True,cb_labels=colorbar_label, figsize=(8,4), shrink_cb=1.8)
>>>>
>>>> Cheers,
>>>> John
>>>>
>>>>
>>>>
>>>> _______________________________________________
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>>>>
>>>
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>>>
>>
> --
> John Wise
> Assistant Professor of Physics
> Center for Relativistic Astrophysics, Georgia Tech
> http://cosmo.gatech.edu
> _______________________________________________
> yt-users mailing list
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>
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