[yt-users] Pyx + Tex
John Wise
jwise at physics.gatech.edu
Mon Feb 15 23:05:04 PST 2016
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
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