[yt-users] Updated yt dev and now have strange plotting error
Stephanie Tonnesen
stonnes at gmail.com
Fri Jun 24 15:24:21 PDT 2016
Hi Nathan,
That did not work. Any chance I can email you off the list? I feel like
this is turning into spam for anyone who doesn't have my problem.
Thanks,
Stephanie
--
Dr. Stephanie Tonnesen
Alvin E. Nashman Postdoctoral Fellow
Carnegie Observatories, Pasadena, CA
stonnes at gmail.com
On Fri, Jun 24, 2016 at 3:15 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:
> It'll install into its own directory isolated directory (yt-conda instead
> of yt-x86_64, by default), so you should be able to install it alongside
> the old installation and then delete the old installation once the new one
> is working.
>
> On Fri, Jun 24, 2016 at 5:09 PM, Stephanie Tonnesen <stonnes at gmail.com>
> wrote:
>
>> Okay, sounds like a plan. Do I need to uninstall the current yt or
>> delete it or something?
>>
>> Thanks,
>> Stephanie
>>
>> --
>> Dr. Stephanie Tonnesen
>> Alvin E. Nashman Postdoctoral Fellow
>> Carnegie Observatories, Pasadena, CA
>> stonnes at gmail.com
>>
>> On Fri, Jun 24, 2016 at 2:33 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>> wrote:
>>
>>> Hmm, it looks like numpy linked against openblas at build time, but
>>> can't find the library at runtime. Not sure what's causing this, as it
>>> depends on how you installed openblas (yt's install script doesn't do
>>> that). I'd need to know more about your system to figure out what's
>>> happening here.
>>>
>>> It might be easiest just to try rerunning the install script at this
>>> point...
>>>
>>>
>>> On Fri, Jun 24, 2016 at 4:04 PM, Stephanie Tonnesen <stonnes at gmail.com>
>>> wrote:
>>>
>>>> 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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>>>>>>
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>>>>>
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