[yt-users] Updated yt dev and now have strange plotting error

Stephanie Tonnesen stonnes at gmail.com
Fri Jun 24 14:04:09 PDT 2016


Hi Nathan,

It looked like that did it, after I did pip install -U pip then I could
install matplotlib, but I am still getting the same error message when my
code tries to import numpy:

Traceback (most recent call last):
  File "yt_slicesonly_allouts.py", line 2, in <module>
    import numpy as np
  File
"/home/stonnes/yt-x86_64/lib/python2.7/site-packages/numpy/__init__.py",
line 180, in <module>
    from . import add_newdocs
  File
"/home/stonnes/yt-x86_64/lib/python2.7/site-packages/numpy/add_newdocs.py",
line 13, in <module>
    from numpy.lib import add_newdoc
  File
"/home/stonnes/yt-x86_64/lib/python2.7/site-packages/numpy/lib/__init__.py",
line 8, in <module>
    from .type_check import *
  File
"/home/stonnes/yt-x86_64/lib/python2.7/site-packages/numpy/lib/type_check.py",
line 11, in <module>
    import numpy.core.numeric as _nx
  File
"/home/stonnes/yt-x86_64/lib/python2.7/site-packages/numpy/core/__init__.py",
line 14, in <module>
    from . import multiarray
ImportError: libopenblas.so.0: cannot open shared object file: No such file
or directory

If you think I need to reinstall yt at this point, I can just go ahead and
do that.

Thanks!
Stephanie

--
Dr. Stephanie Tonnesen
Alvin E. Nashman Postdoctoral Fellow
Carnegie Observatories, Pasadena, CA
stonnes at gmail.com

On Fri, Jun 24, 2016 at 1:33 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:

> Hmm, this is annoying. Pip itself seems to be broken, or has broken itself
> in the process of updating matplotlib. I'm sorry that my advice put you
> into a situation that's hard to recover from.
>
> Can you update pip itself?
>
> $ pip install -U pip
>
> If you're not able to do that and pip itself is completely broken, you
> should be able to recreate a working python environment from scratch by
> re-running the install script:
>
> http://bitbucket.org/yt_analysis/yt/raw/yt/doc/install_script.sh
>
> -Nathan
>
> On Fri, Jun 24, 2016 at 3:10 PM, Stephanie Tonnesen <stonnes at gmail.com>
> wrote:
>
>> Hi Nathan,
>>
>> So I tried to do that and now yt is totally broken.
>>
>> Here is the printout after I typed in
>> $pip install -U matplotlib
>>
>>
>> Collecting matplotlib
>>   Downloading matplotlib-1.5.1.tar.gz (54.0MB)
>>     100% |################################| 54.0MB 8.8kB/s
>> Collecting numpy>=1.6 (from matplotlib)
>>   Downloading numpy-1.11.0.tar.gz (4.2MB)
>>     100% |################################| 4.2MB 105kB/s
>> Collecting python-dateutil (from matplotlib)
>>   Downloading python_dateutil-2.5.3-py2.py3-none-any.whl (201kB)
>>     100% |################################| 204kB 1.2MB/s
>> Collecting pytz (from matplotlib)
>>   Downloading pytz-2016.4-py2.py3-none-any.whl (480kB)
>>     100% |################################| 483kB 762kB/s
>> Collecting cycler (from matplotlib)
>>   Downloading cycler-0.10.0-py2.py3-none-any.whl
>> Collecting pyparsing!=2.0.4,>=1.5.6 (from matplotlib)
>>   Downloading pyparsing-2.1.5-py2.py3-none-any.whl (42kB)
>>     100% |################################| 45kB 8.7MB/s
>> Requirement already up-to-date: six>=1.5 in
>> ./yt-x86_64/lib/python2.7/site-packages/six-1.10.0-py2.7.egg (from
>> python-dateutil->matplotlib)
>> Building wheels for collected packages: matplotlib, numpy
>>   Running setup.py bdist_wheel for matplotlib
>>   Stored in directory:
>> /home/stonnes/.cache/pip/wheels/d8/38/3c/a388e11fd09f9b23f5e4cd74594197394d9fd65f91f64c4aa7
>>   Running setup.py bdist_wheel for numpy
>>   Stored in directory:
>> /home/stonnes/.cache/pip/wheels/d9/cc/5c/f60303cc48ac18e6bd359aa88e4fa50e8bd88fc7e9f001cfd8
>> Successfully built matplotlib numpy
>> Installing collected packages: numpy, python-dateutil, pytz, cycler,
>> pyparsing, matplotlib
>>   Found existing installation: numpy 1.9.2
>>     DEPRECATION: Uninstalling a distutils installed project (numpy) has
>> been deprecated and will be removed in a future version. This is due to the
>> fact that uninstalling a distutils project will only partially uninstall
>> the project.
>>     Uninstalling numpy-1.9.2:
>>       Successfully uninstalled numpy-1.9.2
>>   Found existing installation: python-dateutil 2.4.2
>>     Uninstalling python-dateutil-2.4.2:
>>       Successfully uninstalled python-dateutil-2.4.2
>>   Found existing installation: pytz 2015.7
>>     Uninstalling pytz-2015.7:
>>       Successfully uninstalled pytz-2015.7
>>   Found existing installation: pyparsing 2.0.7
>>     Uninstalling pyparsing-2.0.7:
>>       Successfully uninstalled pyparsing-2.0.7
>>   Found existing installation: matplotlib 1.4.3
>>     Uninstalling matplotlib-1.4.3:
>>       Successfully uninstalled matplotlib-1.4.3
>> Successfully installed cycler matplotlib numpy pyparsing python-dateutil
>> pytz
>> Traceback (most recent call last):
>>   File "/home/stonnes/yt-x86_64/bin/pip", line 11, in <module>
>>     sys.exit(main())
>>   File
>> "/home/stonnes/yt-x86_64/lib/python2.7/site-packages/pip/__init__.py", line
>> 217, in main
>>     return command.main(cmd_args)
>>   File
>> "/home/stonnes/yt-x86_64/lib/python2.7/site-packages/pip/basecommand.py",
>> line 248, in main
>>     pip_version_check(session)
>>   File
>> "/home/stonnes/yt-x86_64/lib/python2.7/site-packages/pip/utils/outdated.py",
>> line 102, in pip_version_check
>>     installed_version = get_installed_version("pip")
>>   File
>> "/home/stonnes/yt-x86_64/lib/python2.7/site-packages/pip/utils/__init__.py",
>> line 858, in get_installed_version
>>     working_set = pkg_resources.WorkingSet()
>>   File
>> "/home/stonnes/yt-x86_64/lib/python2.7/site-packages/pip/_vendor/pkg_resources/__init__.py",
>> line 629, in __init__
>>     self.add_entry(entry)
>>   File
>> "/home/stonnes/yt-x86_64/lib/python2.7/site-packages/pip/_vendor/pkg_resources/__init__.py",
>> line 685, in add_entry
>>     for dist in find_distributions(entry, True):
>>   File
>> "/home/stonnes/yt-x86_64/lib/python2.7/site-packages/pip/_vendor/pkg_resources/__init__.py",
>> line 2075, in find_eggs_in_zip
>>     if metadata.has_metadata('PKG-INFO'):
>>   File
>> "/home/stonnes/yt-x86_64/lib/python2.7/site-packages/pip/_vendor/pkg_resources/__init__.py",
>> line 1605, in has_metadata
>>     return self.egg_info and self._has(self._fn(self.egg_info, name))
>>   File
>> "/home/stonnes/yt-x86_64/lib/python2.7/site-packages/pip/_vendor/pkg_resources/__init__.py",
>> line 1963, in _has
>>     return zip_path in self.zipinfo or zip_path in self._index()
>>   File
>> "/home/stonnes/yt-x86_64/lib/python2.7/site-packages/pip/_vendor/pkg_resources/__init__.py",
>> line 1843, in zipinfo
>>     return self._zip_manifests.load(self.loader.archive)
>>   File
>> "/home/stonnes/yt-x86_64/lib/python2.7/site-packages/pip/_vendor/pkg_resources/__init__.py",
>> line 1783, in load
>>     mtime = os.stat(path).st_mtime
>> OSError: [Errno 2] No such file or directory:
>> '/home/stonnes/yt-x86_64/lib/python2.7/site-packages/pytz-2015.7-py2.7.egg'
>>
>>
>> --
>> Dr. Stephanie Tonnesen
>> Alvin E. Nashman Postdoctoral Fellow
>> Carnegie Observatories, Pasadena, CA
>> stonnes at gmail.com
>>
>> On Fri, Jun 24, 2016 at 12:56 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>> wrote:
>>
>>> Hi Stephanie,
>>>
>>> The quick fix is to update your matplotlib installation:
>>>
>>> $ pip install -U matplotlib
>>>
>>> There's an open pull request that fixes your issue, it should be merged
>>> soon:
>>>
>>>
>>> https://bitbucket.org/yt_analysis/yt/pull-requests/2234/fix-compatibility-with-matplotlib-143-and/diff
>>>
>>> -Nathan
>>>
>>> On Fri, Jun 24, 2016 at 2:39 PM, Stephanie Tonnesen <stonnes at gmail.com>
>>> wrote:
>>>
>>>> Hi yt-users,
>>>>
>>>> I just updated my yt dev and suddenly my plotting scripts don't work.
>>>> When I actually try and save my plot, I am told that I don't have "classic"
>>>> style available.  I am not sure where this problem is coming from, does
>>>> anyone have some advice for me?
>>>>
>>>> The code commands:
>>>>
>>>> ds =
>>>> yt.load("/data001/stonnes/MWtype_BPtest/DD"+loop[i]+"/DDMWtestf"+loop[i])
>>>> ds.add_field(('gas','tracer'),function=tfrac)
>>>> logs = {('index','cylindrical_r'):False}
>>>> logs = {('gas','velocity_z'):False}
>>>> logs = {('gas','velocity_x'):False}
>>>> logs = {('gas','velocity_y'):False}
>>>> logs = {('gas','tracer'):False}
>>>>
>>>> ds.index
>>>> ds.field_info['gas','velocity_z'].take_log = False
>>>> ds.field_info['gas','velocity_x'].take_log = False
>>>>
>>>> plot6p = yt.ProjectionPlot(ds,"z","density")
>>>> plot6p.save()
>>>>
>>>> The error message:
>>>>
>>>> yt : [INFO     ] 2016-06-24 12:25:04,736 Parameters:
>>>> current_time              = 0
>>>> yt : [INFO     ] 2016-06-24 12:25:04,736 Parameters:
>>>> domain_dimensions         = [256 256 256]
>>>> yt : [INFO     ] 2016-06-24 12:25:04,736 Parameters:
>>>> domain_left_edge          = [ 0.  0.  0.]
>>>> yt : [INFO     ] 2016-06-24 12:25:04,737 Parameters:
>>>> domain_right_edge         = [ 1.  1.  1.]
>>>> yt : [INFO     ] 2016-06-24 12:25:04,737 Parameters:
>>>> cosmological_simulation   = 0.0
>>>>
>>>> Parsing Hierarchy :   0%|          | 0/2503 [00:00<?, ?it/s]
>>>> Parsing Hierarchy : 100%|##########| 2503/2503 [00:00<00:00,
>>>> 33786.39it/s]
>>>> yt : [INFO     ] 2016-06-24 12:25:04,952 Gathering a field list (this
>>>> may take a moment.)
>>>> yt : [INFO     ] 2016-06-24 12:25:50,114 Projection completed
>>>> yt : [INFO     ] 2016-06-24 12:25:50,328 xlim = 0.000000 1.000000
>>>> yt : [INFO     ] 2016-06-24 12:25:50,328 ylim = 0.000000 1.000000
>>>> yt : [INFO     ] 2016-06-24 12:25:50,329 xlim = 0.000000 1.000000
>>>> yt : [INFO     ] 2016-06-24 12:25:50,329 ylim = 0.000000 1.000000
>>>> yt : [INFO     ] 2016-06-24 12:25:50,336 Making a fixed resolution
>>>> buffer of (('gas', 'density')) 800 by 800
>>>> yt : [INFO     ] 2016-06-24 12:25:51,408 Saving plot
>>>> DDMWtestf0000_Projection_z_density.png
>>>> Traceback (most recent call last):
>>>>   File "yt_slicesonly_allouts.py", line 29, in <module>
>>>>     plot6p.save()
>>>>   File
>>>> "/home/stonnes/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py",
>>>> line 79, in newfunc
>>>>     rv = f(*args, **kwargs)
>>>>   File
>>>> "/home/stonnes/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py",
>>>> line 575, in save
>>>>     names.append(v.save(n, mpl_kwargs))
>>>>   File
>>>> "/home/stonnes/yt-x86_64/src/yt-hg/yt/visualization/base_plot_types.py",
>>>> line 104, in save
>>>>     with matplotlib_style_context():
>>>>   File "/home/stonnes/yt-x86_64/lib/python2.7/contextlib.py", line 17,
>>>> in __enter__
>>>>     return self.gen.next()
>>>>   File
>>>> "/home/stonnes/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.4.3-py2.7-linux-x86_64.egg/matplotlib/style/core.py",
>>>> line 86, in context
>>>>     use(name)
>>>>   File
>>>> "/home/stonnes/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.4.3-py2.7-linux-x86_64.egg/matplotlib/style/core.py",
>>>> line 66, in use
>>>>     raise ValueError(msg % style)
>>>> ValueError: 'classic' not found in the style library and input is not a
>>>> valid URL or path. See `style.available` for list of available styles.
>>>>
>>>> Thanks!
>>>> Stephanie
>>>> --
>>>> Dr. Stephanie Tonnesen
>>>> Alvin E. Nashman Postdoctoral Fellow
>>>> Carnegie Observatories, Pasadena, CA
>>>> stonnes at gmail.com
>>>>
>>>> _______________________________________________
>>>> yt-users mailing list
>>>> yt-users at lists.spacepope.org
>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>
>>>>
>>>
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