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@gmail.com On Fri, Jun 24, 2016 at 12:56 PM, Nathan Goldbaum 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-wi...

-Nathan

On Fri, Jun 24, 2016 at 2:39 PM, Stephanie Tonnesen 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

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

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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@gmail.com On Fri, Jun 24, 2016 at 1:33 PM, Nathan Goldbaum 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 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@gmail.com

On Fri, Jun 24, 2016 at 12:56 PM, Nathan Goldbaum 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-wi...

-Nathan

On Fri, Jun 24, 2016 at 2:39 PM, Stephanie Tonnesen 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

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

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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@gmail.com On Fri, Jun 24, 2016 at 2:33 PM, Nathan Goldbaum 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 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@gmail.com

On Fri, Jun 24, 2016 at 1:33 PM, Nathan Goldbaum 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 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@gmail.com

On Fri, Jun 24, 2016 at 12:56 PM, Nathan Goldbaum < nathan12343@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-wi...

-Nathan

On Fri, Jun 24, 2016 at 2:39 PM, Stephanie Tonnesen

...

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

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

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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@gmail.com On Fri, Jun 24, 2016 at 3:15 PM, Nathan Goldbaum 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 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@gmail.com

On Fri, Jun 24, 2016 at 2:33 PM, Nathan Goldbaum 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 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@gmail.com

On Fri, Jun 24, 2016 at 1:33 PM, Nathan Goldbaum

...

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

...

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@gmail.com

On Fri, Jun 24, 2016 at 12:56 PM, Nathan Goldbaum < nathan12343@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-wi... > > -Nathan > > On Fri, Jun 24, 2016 at 2:39 PM, Stephanie Tonnesen < > stonnes@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> 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@gmail.com >> >> _______________________________________________ >> yt-users mailing list >> yt-users@lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >

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