[yt-users] Updated yt dev and now have strange plotting error
Stephanie Tonnesen
stonnes at gmail.com
Fri Jun 24 15:09:45 PDT 2016
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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