<div dir="ltr">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.</div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jun 24, 2016 at 5:09 PM, Stephanie Tonnesen <span dir="ltr"><<a href="mailto:stonnes@gmail.com" target="_blank">stonnes@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div>Okay, sounds like a plan. Do I need to uninstall the current yt or delete it or something?<br><br></div>Thanks,<br></div>Stephanie<br></div><div class="gmail_extra"><span class=""><br clear="all"><div><div data-smartmail="gmail_signature"><div dir="ltr"><div><div><div><font face="garamond,serif">--<br>Dr. Stephanie Tonnesen<br></font></div><font face="garamond,serif">Alvin E. Nashman Postdoctoral Fellow<br></font></div><font face="garamond,serif">Carnegie Observatories, Pasadena, CA<br></font></div><font face="garamond,serif"><a href="mailto:stonnes@gmail.com" target="_blank">stonnes@gmail.com</a><br></font></div></div></div>
<br></span><div><div class="h5"><div class="gmail_quote">On Fri, Jun 24, 2016 at 2:33 PM, Nathan Goldbaum <span dir="ltr"><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">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.<div><br></div><div>It might be easiest just to try rerunning the install script at this point...<div><div><br><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jun 24, 2016 at 4:04 PM, Stephanie Tonnesen <span dir="ltr"><<a href="mailto:stonnes@gmail.com" target="_blank">stonnes@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div><div>Hi Nathan,<br><br></div>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:<span><br><br>Traceback (most recent call last):<br></span> File "yt_slicesonly_allouts.py", line 2, in <module><br> import numpy as np<br> File "/home/stonnes/yt-x86_64/lib/python2.7/site-packages/numpy/__init__.py", line 180, in <module><br> from . import add_newdocs<br> File "/home/stonnes/yt-x86_64/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13, in <module><br> from numpy.lib import add_newdoc<br> File "/home/stonnes/yt-x86_64/lib/python2.7/site-packages/numpy/lib/__init__.py", line 8, in <module><br> from .type_check import *<br> File "/home/stonnes/yt-x86_64/lib/python2.7/site-packages/numpy/lib/type_check.py", line 11, in <module><br> import numpy.core.numeric as _nx<br> File "/home/stonnes/yt-x86_64/lib/python2.7/site-packages/numpy/core/__init__.py", line 14, in <module><br> from . import multiarray<br>ImportError: libopenblas.so.0: cannot open shared object file: No such file or directory<br><br></div>If you think I need to reinstall yt at this point, I can just go ahead and do that.<br><br></div>Thanks!<span><font color="#888888"><br></font></span></div><span><font color="#888888">Stephanie<br></font></span></div><div class="gmail_extra"><span><br clear="all"><div><div data-smartmail="gmail_signature"><div dir="ltr"><div><div><div><font face="garamond,serif">--<br>Dr. Stephanie Tonnesen<br></font></div><font face="garamond,serif">Alvin E. Nashman Postdoctoral Fellow<br></font></div><font face="garamond,serif">Carnegie Observatories, Pasadena, CA<br></font></div><font face="garamond,serif"><a href="mailto:stonnes@gmail.com" target="_blank">stonnes@gmail.com</a><br></font></div></div></div>
<br></span><div><div><div class="gmail_quote">On Fri, Jun 24, 2016 at 1:33 PM, Nathan Goldbaum <span dir="ltr"><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">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.<div><br></div><div>Can you update pip itself?<div><br></div><div>$ pip install -U pip</div><div><br></div><div>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:</div><div><br></div><div><a href="http://bitbucket.org/yt_analysis/yt/raw/yt/doc/install_script.sh" target="_blank">http://bitbucket.org/yt_analysis/yt/raw/yt/doc/install_script.sh</a><span><font color="#888888"><br></font></span></div></div><span><font color="#888888"><div><br></div><div>-Nathan</div></font></span></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jun 24, 2016 at 3:10 PM, Stephanie Tonnesen <span dir="ltr"><<a href="mailto:stonnes@gmail.com" target="_blank">stonnes@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Hi Nathan,<br><br></div>So I tried to do that and now yt is totally broken. <br><br>Here is the printout after I typed in <br>$pip install -U matplotlib<div><br></div><br>Collecting matplotlib<br> Downloading matplotlib-1.5.1.tar.gz (54.0MB)<br> 100% |################################| 54.0MB 8.8kB/s <br>Collecting numpy>=1.6 (from matplotlib)<br> Downloading numpy-1.11.0.tar.gz (4.2MB)<br> 100% |################################| 4.2MB 105kB/s <br>Collecting python-dateutil (from matplotlib)<br> Downloading python_dateutil-2.5.3-py2.py3-none-any.whl (201kB)<br> 100% |################################| 204kB 1.2MB/s <br>Collecting pytz (from matplotlib)<br> Downloading pytz-2016.4-py2.py3-none-any.whl (480kB)<br> 100% |################################| 483kB 762kB/s <br>Collecting cycler (from matplotlib)<br> Downloading cycler-0.10.0-py2.py3-none-any.whl<br>Collecting pyparsing!=2.0.4,>=1.5.6 (from matplotlib)<br> Downloading pyparsing-2.1.5-py2.py3-none-any.whl (42kB)<br> 100% |################################| 45kB 8.7MB/s <br>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)<br>Building wheels for collected packages: matplotlib, numpy<br> Running setup.py bdist_wheel for matplotlib<br> Stored in directory: /home/stonnes/.cache/pip/wheels/d8/38/3c/a388e11fd09f9b23f5e4cd74594197394d9fd65f91f64c4aa7<br> Running setup.py bdist_wheel for numpy<br> Stored in directory: /home/stonnes/.cache/pip/wheels/d9/cc/5c/f60303cc48ac18e6bd359aa88e4fa50e8bd88fc7e9f001cfd8<br>Successfully built matplotlib numpy<br>Installing collected packages: numpy, python-dateutil, pytz, cycler, pyparsing, matplotlib<br> Found existing installation: numpy 1.9.2<br> 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.<br> Uninstalling numpy-1.9.2:<br> Successfully uninstalled numpy-1.9.2<br> Found existing installation: python-dateutil 2.4.2<br> Uninstalling python-dateutil-2.4.2:<br> Successfully uninstalled python-dateutil-2.4.2<br> Found existing installation: pytz 2015.7<br> Uninstalling pytz-2015.7:<br> Successfully uninstalled pytz-2015.7<br> Found existing installation: pyparsing 2.0.7<br> Uninstalling pyparsing-2.0.7:<br> Successfully uninstalled pyparsing-2.0.7<br> Found existing installation: matplotlib 1.4.3<br> Uninstalling matplotlib-1.4.3:<br> Successfully uninstalled matplotlib-1.4.3<br>Successfully installed cycler matplotlib numpy pyparsing python-dateutil pytz<span><br>Traceback (most recent call last):<br></span> File "/home/stonnes/yt-x86_64/bin/pip", line 11, in <module><br> sys.exit(main())<br> File "/home/stonnes/yt-x86_64/lib/python2.7/site-packages/pip/__init__.py", line 217, in main<br> return command.main(cmd_args)<br> File "/home/stonnes/yt-x86_64/lib/python2.7/site-packages/pip/basecommand.py", line 248, in main<br> pip_version_check(session)<br> File "/home/stonnes/yt-x86_64/lib/python2.7/site-packages/pip/utils/outdated.py", line 102, in pip_version_check<br> installed_version = get_installed_version("pip")<br> File "/home/stonnes/yt-x86_64/lib/python2.7/site-packages/pip/utils/__init__.py", line 858, in get_installed_version<br> working_set = pkg_resources.WorkingSet()<br> File "/home/stonnes/yt-x86_64/lib/python2.7/site-packages/pip/_vendor/pkg_resources/__init__.py", line 629, in __init__<br> self.add_entry(entry)<br> File "/home/stonnes/yt-x86_64/lib/python2.7/site-packages/pip/_vendor/pkg_resources/__init__.py", line 685, in add_entry<br> for dist in find_distributions(entry, True):<br> File "/home/stonnes/yt-x86_64/lib/python2.7/site-packages/pip/_vendor/pkg_resources/__init__.py", line 2075, in find_eggs_in_zip<br> if metadata.has_metadata('PKG-INFO'):<br> File "/home/stonnes/yt-x86_64/lib/python2.7/site-packages/pip/_vendor/pkg_resources/__init__.py", line 1605, in has_metadata<br> return self.egg_info and self._has(self._fn(self.egg_info, name))<br> File "/home/stonnes/yt-x86_64/lib/python2.7/site-packages/pip/_vendor/pkg_resources/__init__.py", line 1963, in _has<br> return zip_path in self.zipinfo or zip_path in self._index()<br> File "/home/stonnes/yt-x86_64/lib/python2.7/site-packages/pip/_vendor/pkg_resources/__init__.py", line 1843, in zipinfo<br> return self._zip_manifests.load(self.loader.archive)<br> File "/home/stonnes/yt-x86_64/lib/python2.7/site-packages/pip/_vendor/pkg_resources/__init__.py", line 1783, in load<br> mtime = os.stat(path).st_mtime<br>OSError: [Errno 2] No such file or directory: '/home/stonnes/yt-x86_64/lib/python2.7/site-packages/pytz-2015.7-py2.7.egg'<br><br></div><div class="gmail_extra"><span><br clear="all"><div><div data-smartmail="gmail_signature"><div dir="ltr"><div><div><div><font face="garamond,serif">--<br>Dr. Stephanie Tonnesen<br></font></div><font face="garamond,serif">Alvin E. Nashman Postdoctoral Fellow<br></font></div><font face="garamond,serif">Carnegie Observatories, Pasadena, CA<br></font></div><font face="garamond,serif"><a href="mailto:stonnes@gmail.com" target="_blank">stonnes@gmail.com</a><br></font></div></div></div>
<br></span><div><div><div class="gmail_quote">On Fri, Jun 24, 2016 at 12:56 PM, Nathan Goldbaum <span dir="ltr"><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Stephanie,<div><br></div><div>The quick fix is to update your matplotlib installation:</div><div><br></div><div>$ pip install -U matplotlib</div><div><br></div><div>There's an open pull request that fixes your issue, it should be merged soon:</div><div><br></div><div><a href="https://bitbucket.org/yt_analysis/yt/pull-requests/2234/fix-compatibility-with-matplotlib-143-and/diff" target="_blank">https://bitbucket.org/yt_analysis/yt/pull-requests/2234/fix-compatibility-with-matplotlib-143-and/diff</a><br></div><div><br></div><div>-Nathan</div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div>On Fri, Jun 24, 2016 at 2:39 PM, Stephanie Tonnesen <span dir="ltr"><<a href="mailto:stonnes@gmail.com" target="_blank">stonnes@gmail.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div dir="ltr"><div><div><div><div><div>Hi yt-users,<br><br></div>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?<br><br></div>The code commands:<br><br>ds = yt.load("/data001/stonnes/MWtype_BPtest/DD"+loop[i]+"/DDMWtestf"+loop[i])<br>ds.add_field(('gas','tracer'),function=tfrac)<br>logs = {('index','cylindrical_r'):False}<br>logs = {('gas','velocity_z'):False}<br>logs = {('gas','velocity_x'):False}<br>logs = {('gas','velocity_y'):False}<br>logs = {('gas','tracer'):False}<br><br>ds.index<br>ds.field_info['gas','velocity_z'].take_log = False<br>ds.field_info['gas','velocity_x'].take_log = False<br> <br>plot6p = yt.ProjectionPlot(ds,"z","density")<br>plot6p.save()<br> <br></div>The error message:<br><br>yt : [INFO ] 2016-06-24 12:25:04,736 Parameters: current_time = 0<br>yt : [INFO ] 2016-06-24 12:25:04,736 Parameters: domain_dimensions = [256 256 256]<br>yt : [INFO ] 2016-06-24 12:25:04,736 Parameters: domain_left_edge = [ 0. 0. 0.]<br>yt : [INFO ] 2016-06-24 12:25:04,737 Parameters: domain_right_edge = [ 1. 1. 1.]<br>yt : [INFO ] 2016-06-24 12:25:04,737 Parameters: cosmological_simulation = 0.0<br><br>Parsing Hierarchy : 0%| | 0/2503 [00:00<?, ?it/s]<br>Parsing Hierarchy : 100%|##########| 2503/2503 [00:00<00:00, 33786.39it/s]<br>yt : [INFO ] 2016-06-24 12:25:04,952 Gathering a field list (this may take a moment.)<br>yt : [INFO ] 2016-06-24 12:25:50,114 Projection completed<br>yt : [INFO ] 2016-06-24 12:25:50,328 xlim = 0.000000 1.000000<br>yt : [INFO ] 2016-06-24 12:25:50,328 ylim = 0.000000 1.000000<br>yt : [INFO ] 2016-06-24 12:25:50,329 xlim = 0.000000 1.000000<br>yt : [INFO ] 2016-06-24 12:25:50,329 ylim = 0.000000 1.000000<br>yt : [INFO ] 2016-06-24 12:25:50,336 Making a fixed resolution buffer of (('gas', 'density')) 800 by 800<br>yt : [INFO ] 2016-06-24 12:25:51,408 Saving plot DDMWtestf0000_Projection_z_density.png<br>Traceback (most recent call last):<br> File "yt_slicesonly_allouts.py", line 29, in <module><br> plot6p.save()<br> File "/home/stonnes/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py", line 79, in newfunc<br> rv = f(*args, **kwargs)<br> File "/home/stonnes/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py", line 575, in save<br> names.append(v.save(n, mpl_kwargs))<br> File "/home/stonnes/yt-x86_64/src/yt-hg/yt/visualization/base_plot_types.py", line 104, in save<br> with matplotlib_style_context():<br> File "/home/stonnes/yt-x86_64/lib/python2.7/contextlib.py", line 17, in __enter__<br> return self.gen.next()<br> 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<br> use(name)<br> 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<br> raise ValueError(msg % style)<br>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.<br><br></div>Thanks!<br></div>Stephanie<br clear="all"><div><div><div><div><div><div><div><div data-smartmail="gmail_signature"><div dir="ltr"><div><div><div><font face="garamond,serif">--<br>Dr. Stephanie Tonnesen<br></font></div><font face="garamond,serif">Alvin E. Nashman Postdoctoral Fellow<br></font></div><font face="garamond,serif">Carnegie Observatories, Pasadena, CA<br></font></div><font face="garamond,serif"><a href="mailto:stonnes@gmail.com" target="_blank">stonnes@gmail.com</a><br></font></div></div></div>
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