[yt-users] Updated yt dev and now have strange plotting error
Nathan Goldbaum
nathan12343 at gmail.com
Fri Jun 24 15:15:34 PDT 2016
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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