[yt-users] yt update and error

Nathan Goldbaum nathan12343 at gmail.com
Thu Aug 25 21:32:00 PDT 2016


It seems you have an old version of setuptools, do "pip install -U
setuptools" and "pip install -U pip", then try "python setup.py develop"
again. You might also need to update cython.

If this is getting too complicated, you can always re-run the latest
version of the install script from
https://bitbucket.org/yt_analysis/yt/src/yt/doc/install_script.sh in
e.g. /work/03858/thaque56/sw/yt-3.3
and use that yt installation instead.

On Thu, Aug 25, 2016 at 11:25 PM, tazkera haque <h.tazkera at gmail.com> wrote:

> and I did
>
> $ cd /work/03858/thaque56/sw/yt-3.1/yt-x86_64/src/yt-hg/
> $ hg --config extensions.purge= purge --all yt
> $ hg pull https://bitbucket.org/yt_analysis/yt
> $ hg update stable
> $ python setup.py develop
>
> On Fri, Aug 26, 2016 at 12:25 AM, tazkera haque <h.tazkera at gmail.com>
> wrote:
>
>> HI Nathan ,
>>
>> Thanks for your help but now it gives me a whole bunch of errors:
>>
>> (yt-x86_64)login2.stampede(6)$ python setup.py develop
>> Unable to find pgen, not compiling formal grammar.
>> Traceback (most recent call last):
>>   File "setup.py", line 391, in <module>
>>     ext_modules=cython_extensions + extensions,
>>   File "/work/03858/thaque56/sw/yt-3.1/yt-x86_64/lib/python2.7/distutils/core.py",
>> line 111, in setup
>>     _setup_distribution = dist = klass(attrs)
>>   File "build/bdist.linux-x86_64/egg/setuptools/dist.py", line 268, in
>> __init__
>>   File "build/bdist.linux-x86_64/egg/setuptools/dist.py", line 313, in
>> fetch_build_eggs
>>   File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line
>> 836, in resolve
>>
>>   File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line
>> 1081, in best_match
>>
>>   File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line
>> 1093, in obtain
>>
>>   File "build/bdist.linux-x86_64/egg/setuptools/dist.py", line 380, in
>> fetch_build_egg
>>   File "build/bdist.linux-x86_64/egg/setuptools/command/easy_install.py",
>> line 629, in easy_install
>>   File "build/bdist.linux-x86_64/egg/setuptools/command/easy_install.py",
>> line 659, in install_item
>>   File "build/bdist.linux-x86_64/egg/setuptools/command/easy_install.py",
>> line 842, in install_eggs
>>   File "build/bdist.linux-x86_64/egg/setuptools/command/easy_install.py",
>> line 1070, in build_and_install
>>   File "build/bdist.linux-x86_64/egg/setuptools/command/easy_install.py",
>> line 1056, in run_setup
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 240,
>> in run_setup
>>   File "/work/03858/thaque56/sw/yt-3.1/yt-x86_64/lib/python2.7/contextlib.py",
>> line 35, in __exit__
>>     self.gen.throw(type, value, traceback)
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 193,
>> in setup_context
>>   File "/work/03858/thaque56/sw/yt-3.1/yt-x86_64/lib/python2.7/contextlib.py",
>> line 35, in __exit__
>>     self.gen.throw(type, value, traceback)
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 152,
>> in save_modules
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 126,
>> in __exit__
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 110,
>> in dump
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 110,
>> in dump
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 110,
>> in dump
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 110,
>> in dump
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 110,
>> in dump
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 110,
>> in dump
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 110,
>> in dump
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 110,
>> in dump
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 110,
>> in dump
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 110,
>> in dump
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 110,
>> in dump
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 110,
>> in dump
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 110,
>> in dump
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 110,
>> in dump
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 110,
>> in dump
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 110,
>> in dump
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 110,
>> in dump
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 110,
>> in dump
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 110,
>> in dump
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 110,
>> in dump
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 110,
>> in dump
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 110,
>> in dump
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 110,
>> in dump
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 110,
>> in dump
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 110,
>> in dump
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 110,
>> in dump
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 110,
>> in dump
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 110,
>> in dump
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 110,
>> in dump
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 110,
>> in dump
>>   File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 110,
>> in dump
>> MemoryError
>>
>>
>> Tazkera
>>
>> On Thu, Aug 25, 2016 at 11:51 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>> wrote:
>>
>>>
>>>
>>> On Thu, Aug 25, 2016 at 9:49 PM, tazkera haque <h.tazkera at gmail.com>
>>> wrote:
>>>
>>>> Hi people,
>>>>
>>>> I would like to upgrade yt to the latest version, I tried typing *yt
>>>> update *in a folder on cluster /work/03858/thaque56/sw/yt-3.1 and it
>>>> gives me following error:
>>>>
>>>> Traceback (most recent call last):
>>>>   File "/work/03858/thaque56/sw/yt-3.1/yt-x86_64/bin/yt", line 9, in
>>>> <module>
>>>>     load_entry_point('yt==3.2.3', 'console_scripts', 'yt')()
>>>>   File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line
>>>> 558, in load_entry_point
>>>>
>>>>   File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line
>>>> 2682, in load_entry_point
>>>>
>>>>   File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line
>>>> 2355, in load
>>>>
>>>>   File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line
>>>> 2361, in resolve
>>>>
>>>>   File "/work/03858/thaque56/sw/yt-3.1/yt-x86_64/src/yt-hg/yt/__init__.py",
>>>> line 123, in <module>
>>>>     from yt.data_objects.api import \
>>>>   File "/work/03858/thaque56/sw/yt-3.1/yt-x86_64/src/yt-hg/yt/data_objects/api.py",
>>>> line 16, in <module>
>>>>     from .grid_patch import \
>>>>   File "/work/03858/thaque56/sw/yt-3.1/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py",
>>>> line 19, in <module>
>>>>     from yt.data_objects.data_containers import \
>>>>   File "/work/03858/thaque56/sw/yt-3.1/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>>>> line 55, in <module>
>>>>     from yt.utilities.parallel_tools.parallel_analysis_interface
>>>> import \
>>>>   File "/work/03858/thaque56/sw/yt-3.1/yt-x86_64/src/yt-hg/yt/utili
>>>> ties/parallel_tools/parallel_analysis_interface.py", line 33, in
>>>> <module>
>>>>     from yt.utilities.lib.quad_tree import \
>>>> ImportError: No module named quad_tree
>>>>
>>>>
>>> $ cd /work/03858/thaque56/sw/yt-3.1/yt-x86_64/src/yt-hg/
>>> $ hg --config extensions.purge= purge --all yt
>>> $ hg pull https://bitbucket.org/yt_analysis/yt
>>> $ hg update yt
>>> $ python setup.py develop
>>>
>>> This will put you on the latest in-development version of yt. If you'd
>>> instead like to be on the last stable release, do "hg update stable"
>>> instead of "hg update yt".
>>>
>>> "yt update" is supposed to automate this, but something seems to have
>>> gone wrong in your case. I'm not sure why.
>>>
>>>
>>>> and now I cannot excecute any of my python scripts there, please help
>>>> me upgrade and fix the problem. thanks
>>>>
>>>> Tazkera
>>>>
>>>> _______________________________________________
>>>> 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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