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Kushalkr opened this issue Sep 30, 2018 · 4 comments
Closed

Too many levels of symbolic links #12354

Kushalkr opened this issue Sep 30, 2018 · 4 comments
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status: duplicate
Milestone
v3.0.1

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@Kushalkr
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Bug report

Bug summary

I get OSError: Too many levels of Symbolic links exception when I run the lorenz_attractor mplot3d example from the matplotlib gallery using matplotlib version 3.0.0 but the error disappears when I use version 2.2.3

Code for reproduction

#
#
# Plot of the Lorenz Attractor based on Edward Lorenz's 1963 "Deterministic
# Nonperiodic Flow" publication.
# http://journals.ametsoc.org/doi/abs/10.1175/1520-0469%281963%29020%3C0130%3ADNF%3E2.0.CO%3B2
#
# Note: Because this is a simple non-linear ODE, it would be more easily
#       done using SciPy's ode solver, but this approach depends only
#       upon NumPy.

import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D


def lorenz(x, y, z, s=10, r=28, b=2.667):
    x_dot = s*(y - x)
    y_dot = r*x - y - x*z
    z_dot = x*y - b*z
    return x_dot, y_dot, z_dot


dt = 0.01
stepCnt = 10000

# Need one more for the initial values
xs = np.empty((stepCnt + 1,))
ys = np.empty((stepCnt + 1,))
zs = np.empty((stepCnt + 1,))

# Setting initial values
xs[0], ys[0], zs[0] = (0., 1., 1.05)

# Stepping through "time".
for i in range(stepCnt):
    # Derivatives of the X, Y, Z state
    x_dot, y_dot, z_dot = lorenz(xs[i], ys[i], zs[i])
    xs[i + 1] = xs[i] + (x_dot * dt)
    ys[i + 1] = ys[i] + (y_dot * dt)
    zs[i + 1] = zs[i] + (z_dot * dt)

fig = plt.figure()
ax = fig.gca(projection='3d')

ax.plot(xs, ys, zs, lw=0.5)
ax.set_xlabel("X Axis")
ax.set_ylabel("Y Axis")
ax.set_zlabel("Z Axis")
ax.set_title("Lorenz Attractor")

plt.show()

Actual outcome

Traceback (most recent call last):
  File "/Users/kkeshava/Downloads/Analysis_tools/miniconda3/lib/python3.6/site-packages/matplotlib/font_manager.py", line 1353, in <module>
    fontManager = json_load(_fmcache)
  File "/Users/kkeshava/Downloads/Analysis_tools/miniconda3/lib/python3.6/site-packages/matplotlib/font_manager.py", line 888, in json_load
    with open(filename, 'r') as fh:
FileNotFoundError: [Errno 2] No such file or directory: '/Users/kkeshava/.matplotlib/fontlist-v300.json'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "lorenz_attractor.py", line 10, in <module>
    import matplotlib.pyplot as plt
  File "/Users/kkeshava/Downloads/Analysis_tools/miniconda3/lib/python3.6/site-packages/matplotlib/pyplot.py", line 32, in <module>
    import matplotlib.colorbar
  File "/Users/kkeshava/Downloads/Analysis_tools/miniconda3/lib/python3.6/site-packages/matplotlib/colorbar.py", line 32, in <module>
    import matplotlib.contour as contour
  File "/Users/kkeshava/Downloads/Analysis_tools/miniconda3/lib/python3.6/site-packages/matplotlib/contour.py", line 18, in <module>
    import matplotlib.font_manager as font_manager
  File "/Users/kkeshava/Downloads/Analysis_tools/miniconda3/lib/python3.6/site-packages/matplotlib/font_manager.py", line 1363, in <module>
    _rebuild()
  File "/Users/kkeshava/Downloads/Analysis_tools/miniconda3/lib/python3.6/site-packages/matplotlib/font_manager.py", line 1344, in _rebuild
    fontManager = FontManager()
  File "/Users/kkeshava/Downloads/Analysis_tools/miniconda3/lib/python3.6/site-packages/matplotlib/font_manager.py", line 978, in __init__
    ttffiles = findSystemFonts(paths) + findSystemFonts()
  File "/Users/kkeshava/Downloads/Analysis_tools/miniconda3/lib/python3.6/site-packages/matplotlib/font_manager.py", line 270, in findSystemFonts
    fontfiles.update(OSXInstalledFonts(fontext=fontext))
  File "/Users/kkeshava/Downloads/Analysis_tools/miniconda3/lib/python3.6/site-packages/matplotlib/font_manager.py", line 218, in OSXInstalledFonts
    for directory in directories
  File "/Users/kkeshava/Downloads/Analysis_tools/miniconda3/lib/python3.6/site-packages/matplotlib/font_manager.py", line 220, in <listcomp>
    for path in list_fonts(directory, ext)]
  File "/Users/kkeshava/Downloads/Analysis_tools/miniconda3/lib/python3.6/site-packages/matplotlib/font_manager.py", line 157, in list_fonts
    for path in filter(Path.is_file, Path(directory).glob("**/*.*"))
  File "/Users/kkeshava/Downloads/Analysis_tools/miniconda3/lib/python3.6/site-packages/matplotlib/font_manager.py", line 156, in <listcomp>
    return [str(path)
  File "/Users/kkeshava/Downloads/Analysis_tools/miniconda3/lib/python3.6/pathlib.py", line 1360, in is_file
    return S_ISREG(self.stat().st_mode)
  File "/Users/kkeshava/Downloads/Analysis_tools/miniconda3/lib/python3.6/pathlib.py", line 1156, in stat
    return self._accessor.stat(self)
  File "/Users/kkeshava/Downloads/Analysis_tools/miniconda3/lib/python3.6/pathlib.py", line 387, in wrapped
    return strfunc(str(pathobj), *args)
OSError: [Errno 62] Too many levels of symbolic links: 'Downloads/Analysis_tools/bin/grib2/jasper-1.900.1/jasper-1.900.1'

Expected outcome

Matplotlib version

  • Operating system: MacOS 10.13.6
  • Matplotlib version: 3.0.0
  • Matplotlib backend (print(matplotlib.get_backend())): Get the same error when I print the command
  • Python version: 3.6.6

Python was installed using miniconda 3 and all packages were installed from the from the conda-forge channel.
@ImportanceOfBeingErnest
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The first error is FileNotFoundError: [Errno 2] No such file or directory: '/Users/kkeshava/.matplotlib/fontlist-v300.json'. I would assume for the moment that the second one is a consequence of that. For the first error, this looks the same as #12291.

@ImportanceOfBeingErnest ImportanceOfBeingErnest added this to the v3.0.x milestone Sep 30, 2018
@QuLogic
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QuLogic commented Sep 30, 2018

You have an invalid (or at least recursive) symbolic link at Downloads/Analysis_tools/bin/grib2/jasper-1.900.1/ that points to itself.

This error is caused by #12176 and will be fixed in 3.0.1

@QuLogic QuLogic closed this as completed Sep 30, 2018
@QuLogic
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QuLogic commented Sep 30, 2018

As a workaround, you can import matplotlib while running python in an empty directory, and it should work fine after that.

@Kushalkr
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Kushalkr commented Oct 1, 2018 via email

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@QuLogic @Kushalkr @ImportanceOfBeingErnest