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COSIMA / cosima-cookbook

Framework for indexing and querying ocean-sea ice model output.
https://cosima-recipes.readthedocs.io/en/latest/
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Matplotlib errors on rc('text', usetex=True) when loaded from jupyter-lab via gadi #162

Closed navidcy closed 4 years ago

navidcy commented 4 years ago

When loading jupyter labs on gadi via jupyter_gadi.sh script and call

import matplotlib
from matplotlib import rc
rc('text', usetex=True)

import matplotlib.pyplot as plt

plt.plot([1, 2], [1, 2])

I get

[<matplotlib.lines.Line2D at 0x1488fcad62b0>]
Error in callback <function install_repl_displayhook.<locals>.post_execute at 0x1488fec8b510> (for post_execute):
---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/pyplot.py in post_execute()
    147             def post_execute():
    148                 if matplotlib.is_interactive():
--> 149                     draw_all()
    150 
    151             # IPython >= 2

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/_pylab_helpers.py in draw_all(cls, force)
    134         for f_mgr in cls.get_all_fig_managers():
    135             if force or f_mgr.canvas.figure.stale:
--> 136                 f_mgr.canvas.draw_idle()
    137 
    138 atexit.register(Gcf.destroy_all)

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/backend_bases.py in draw_idle(self, *args, **kwargs)
   2053         if not self._is_idle_drawing:
   2054             with self._idle_draw_cntx():
-> 2055                 self.draw(*args, **kwargs)
   2056 
   2057     def draw_cursor(self, event):

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/backends/backend_agg.py in draw(self)
    435             # if toolbar:
    436             #     toolbar.set_cursor(cursors.WAIT)
--> 437             self.figure.draw(self.renderer)
    438             # A GUI class may be need to update a window using this draw, so
    439             # don't forget to call the superclass.

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs)
     53                 renderer.start_filter()
     54 
---> 55             return draw(artist, renderer, *args, **kwargs)
     56         finally:
     57             if artist.get_agg_filter() is not None:

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/figure.py in draw(self, renderer)
   1491 
   1492             mimage._draw_list_compositing_images(
-> 1493                 renderer, self, artists, self.suppressComposite)
   1494 
   1495             renderer.close_group('figure')

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/image.py in _draw_list_compositing_images(renderer, parent, artists, suppress_composite)
    139     if not_composite or not has_images:
    140         for a in artists:
--> 141             a.draw(renderer)
    142     else:
    143         # Composite any adjacent images together

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs)
     53                 renderer.start_filter()
     54 
---> 55             return draw(artist, renderer, *args, **kwargs)
     56         finally:
     57             if artist.get_agg_filter() is not None:

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/axes/_base.py in draw(self, renderer, inframe)
   2633             renderer.stop_rasterizing()
   2634 
-> 2635         mimage._draw_list_compositing_images(renderer, self, artists)
   2636 
   2637         renderer.close_group('axes')

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/image.py in _draw_list_compositing_images(renderer, parent, artists, suppress_composite)
    139     if not_composite or not has_images:
    140         for a in artists:
--> 141             a.draw(renderer)
    142     else:
    143         # Composite any adjacent images together

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs)
     53                 renderer.start_filter()
     54 
---> 55             return draw(artist, renderer, *args, **kwargs)
     56         finally:
     57             if artist.get_agg_filter() is not None:

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/axis.py in draw(self, renderer, *args, **kwargs)
   1193 
   1194         for tick in ticks_to_draw:
-> 1195             tick.draw(renderer)
   1196 
   1197         # scale up the axis label box to also find the neighbors, not

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs)
     53                 renderer.start_filter()
     54 
---> 55             return draw(artist, renderer, *args, **kwargs)
     56         finally:
     57             if artist.get_agg_filter() is not None:

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/axis.py in draw(self, renderer)
    302 
    303         if self.label1On:
--> 304             self.label1.draw(renderer)
    305         if self.label2On:
    306             self.label2.draw(renderer)

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs)
     53                 renderer.start_filter()
     54 
---> 55             return draw(artist, renderer, *args, **kwargs)
     56         finally:
     57             if artist.get_agg_filter() is not None:

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/text.py in draw(self, renderer)
    749                     textrenderer.draw_tex(gc, x, y, clean_line,
    750                                           textobj._fontproperties, angle,
--> 751                                           mtext=mtext)
    752                 else:
    753                     textrenderer.draw_text(gc, x, y, clean_line,

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/backends/backend_agg.py in draw_tex(self, gc, x, y, s, prop, angle, ismath, mtext)
    258         texmanager = self.get_texmanager()
    259 
--> 260         Z = texmanager.get_grey(s, size, self.dpi)
    261         Z = np.array(Z * 255.0, np.uint8)
    262 

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/texmanager.py in get_grey(self, tex, fontsize, dpi)
    455         alpha = self.grey_arrayd.get(key)
    456         if alpha is None:
--> 457             pngfile = self.make_png(tex, fontsize, dpi)
    458             X = read_png(os.path.join(self.texcache, pngfile))
    459             self.grey_arrayd[key] = alpha = X[:, :, -1]

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/texmanager.py in make_png(self, tex, fontsize, dpi)
    420             self._run_checked_subprocess(
    421                 ["dvipng", "-bg", "Transparent", "-D", str(dpi),
--> 422                  "-T", "tight", "-o", pngfile, dvifile], tex)
    423         return pngfile
    424 

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/texmanager.py in _run_checked_subprocess(self, command, tex)
    333             report = subprocess.check_output(command,
    334                                              cwd=self.texcache,
--> 335                                              stderr=subprocess.STDOUT)
    336         except subprocess.CalledProcessError as exc:
    337             raise RuntimeError(

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/subprocess.py in check_output(timeout, *popenargs, **kwargs)
    334 
    335     return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
--> 336                **kwargs).stdout
    337 
    338 

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/subprocess.py in run(input, timeout, check, *popenargs, **kwargs)
    401         kwargs['stdin'] = PIPE
    402 
--> 403     with Popen(*popenargs, **kwargs) as process:
    404         try:
    405             stdout, stderr = process.communicate(input, timeout=timeout)

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/subprocess.py in __init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, encoding, errors)
    707                                 c2pread, c2pwrite,
    708                                 errread, errwrite,
--> 709                                 restore_signals, start_new_session)
    710         except:
    711             # Cleanup if the child failed starting.

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/subprocess.py in _execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, restore_signals, start_new_session)
   1342                         if errno_num == errno.ENOENT:
   1343                             err_msg += ': ' + repr(err_filename)
-> 1344                     raise child_exception_type(errno_num, err_msg, err_filename)
   1345                 raise child_exception_type(err_msg)
   1346 

FileNotFoundError: [Errno 2] No such file or directory: 'dvipng': 'dvipng'
---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/IPython/core/formatters.py in __call__(self, obj)
    339                 pass
    340             else:
--> 341                 return printer(obj)
    342             # Finally look for special method names
    343             method = get_real_method(obj, self.print_method)

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/IPython/core/pylabtools.py in <lambda>(fig)
    242 
    243     if 'png' in formats:
--> 244         png_formatter.for_type(Figure, lambda fig: print_figure(fig, 'png', **kwargs))
    245     if 'retina' in formats or 'png2x' in formats:
    246         png_formatter.for_type(Figure, lambda fig: retina_figure(fig, **kwargs))

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/IPython/core/pylabtools.py in print_figure(fig, fmt, bbox_inches, **kwargs)
    126 
    127     bytes_io = BytesIO()
--> 128     fig.canvas.print_figure(bytes_io, **kw)
    129     data = bytes_io.getvalue()
    130     if fmt == 'svg':

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/backend_bases.py in print_figure(self, filename, dpi, facecolor, edgecolor, orientation, format, **kwargs)
   2210                     orientation=orientation,
   2211                     dryrun=True,
-> 2212                     **kwargs)
   2213                 renderer = self.figure._cachedRenderer
   2214                 bbox_inches = self.figure.get_tightbbox(renderer)

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/backends/backend_agg.py in print_png(self, filename_or_obj, *args, **kwargs)
    515 
    516     def print_png(self, filename_or_obj, *args, **kwargs):
--> 517         FigureCanvasAgg.draw(self)
    518         renderer = self.get_renderer()
    519         original_dpi = renderer.dpi

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/backends/backend_agg.py in draw(self)
    435             # if toolbar:
    436             #     toolbar.set_cursor(cursors.WAIT)
--> 437             self.figure.draw(self.renderer)
    438             # A GUI class may be need to update a window using this draw, so
    439             # don't forget to call the superclass.

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs)
     53                 renderer.start_filter()
     54 
---> 55             return draw(artist, renderer, *args, **kwargs)
     56         finally:
     57             if artist.get_agg_filter() is not None:

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/figure.py in draw(self, renderer)
   1491 
   1492             mimage._draw_list_compositing_images(
-> 1493                 renderer, self, artists, self.suppressComposite)
   1494 
   1495             renderer.close_group('figure')

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/image.py in _draw_list_compositing_images(renderer, parent, artists, suppress_composite)
    139     if not_composite or not has_images:
    140         for a in artists:
--> 141             a.draw(renderer)
    142     else:
    143         # Composite any adjacent images together

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs)
     53                 renderer.start_filter()
     54 
---> 55             return draw(artist, renderer, *args, **kwargs)
     56         finally:
     57             if artist.get_agg_filter() is not None:

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/axes/_base.py in draw(self, renderer, inframe)
   2633             renderer.stop_rasterizing()
   2634 
-> 2635         mimage._draw_list_compositing_images(renderer, self, artists)
   2636 
   2637         renderer.close_group('axes')

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/image.py in _draw_list_compositing_images(renderer, parent, artists, suppress_composite)
    139     if not_composite or not has_images:
    140         for a in artists:
--> 141             a.draw(renderer)
    142     else:
    143         # Composite any adjacent images together

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs)
     53                 renderer.start_filter()
     54 
---> 55             return draw(artist, renderer, *args, **kwargs)
     56         finally:
     57             if artist.get_agg_filter() is not None:

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/axis.py in draw(self, renderer, *args, **kwargs)
   1193 
   1194         for tick in ticks_to_draw:
-> 1195             tick.draw(renderer)
   1196 
   1197         # scale up the axis label box to also find the neighbors, not

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs)
     53                 renderer.start_filter()
     54 
---> 55             return draw(artist, renderer, *args, **kwargs)
     56         finally:
     57             if artist.get_agg_filter() is not None:

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/axis.py in draw(self, renderer)
    302 
    303         if self.label1On:
--> 304             self.label1.draw(renderer)
    305         if self.label2On:
    306             self.label2.draw(renderer)

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs)
     53                 renderer.start_filter()
     54 
---> 55             return draw(artist, renderer, *args, **kwargs)
     56         finally:
     57             if artist.get_agg_filter() is not None:

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/text.py in draw(self, renderer)
    749                     textrenderer.draw_tex(gc, x, y, clean_line,
    750                                           textobj._fontproperties, angle,
--> 751                                           mtext=mtext)
    752                 else:
    753                     textrenderer.draw_text(gc, x, y, clean_line,

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/backends/backend_agg.py in draw_tex(self, gc, x, y, s, prop, angle, ismath, mtext)
    258         texmanager = self.get_texmanager()
    259 
--> 260         Z = texmanager.get_grey(s, size, self.dpi)
    261         Z = np.array(Z * 255.0, np.uint8)
    262 

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/texmanager.py in get_grey(self, tex, fontsize, dpi)
    455         alpha = self.grey_arrayd.get(key)
    456         if alpha is None:
--> 457             pngfile = self.make_png(tex, fontsize, dpi)
    458             X = read_png(os.path.join(self.texcache, pngfile))
    459             self.grey_arrayd[key] = alpha = X[:, :, -1]

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/texmanager.py in make_png(self, tex, fontsize, dpi)
    420             self._run_checked_subprocess(
    421                 ["dvipng", "-bg", "Transparent", "-D", str(dpi),
--> 422                  "-T", "tight", "-o", pngfile, dvifile], tex)
    423         return pngfile
    424 

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/site-packages/matplotlib/texmanager.py in _run_checked_subprocess(self, command, tex)
    333             report = subprocess.check_output(command,
    334                                              cwd=self.texcache,
--> 335                                              stderr=subprocess.STDOUT)
    336         except subprocess.CalledProcessError as exc:
    337             raise RuntimeError(

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/subprocess.py in check_output(timeout, *popenargs, **kwargs)
    334 
    335     return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
--> 336                **kwargs).stdout
    337 
    338 

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/subprocess.py in run(input, timeout, check, *popenargs, **kwargs)
    401         kwargs['stdin'] = PIPE
    402 
--> 403     with Popen(*popenargs, **kwargs) as process:
    404         try:
    405             stdout, stderr = process.communicate(input, timeout=timeout)

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/subprocess.py in __init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, encoding, errors)
    707                                 c2pread, c2pwrite,
    708                                 errread, errwrite,
--> 709                                 restore_signals, start_new_session)
    710         except:
    711             # Cleanup if the child failed starting.

/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.10/lib/python3.6/subprocess.py in _execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, restore_signals, start_new_session)
   1342                         if errno_num == errno.ENOENT:
   1343                             err_msg += ': ' + repr(err_filename)
-> 1344                     raise child_exception_type(errno_num, err_msg, err_filename)
   1345                 raise child_exception_type(err_msg)
   1346 

FileNotFoundError: [Errno 2] No such file or directory: 'dvipng': 'dvipng'
<Figure size 432x288 with 1 Axes>

On the other hand, if I suppress line 

rc('text', usetex=True)

then the plot comes up just fine.

Why is that?

aekiss commented 4 years ago

dvi makes me think it's latex-related.... Could it be something to do with latex being at /usr/bin/latex on raijin but /bin/latex on gadi....? Wild stab in the dark...

angus-g commented 4 years ago

I think it's exactly as the error suggests: dvipng is an executable on raijin, but not on gadi. I guess different latex installations between the systems

navidcy commented 4 years ago

OK, how do we fix this? Or does this deserves an email to NCI helpdesk?

aidanheerdegen commented 4 years ago

Send an email to cws_help as it is the conda distro

janjaapmeijer commented 2 years ago

OK, how do we fix this? Or does this deserves an email to NCI helpdesk?

@navidcy , were you able to fix this, it worked for me before, but now in the OOD environment it start issuing the 'dvipng' error

navidcy commented 2 years ago

that was 3 years ago! I don't remember anything tbh :)

navidcy commented 2 years ago

@janjaapmeijer feel free to reopen the issue tho!