[yt-users] YT installation

Matthew Turk matthewturk at gmail.com
Fri Aug 3 18:01:54 PDT 2012 

Hi Sherwood,

On Fri, Aug 3, 2012 at 8:57 PM, Sherwood Richers <srichers at caltech.edu> wrote:
> Thanks for the response. The grid plotting works now

Glad to hear that, and thanks again for the bug report.

> The code I'm
> working with uses fixed mesh refinement AMR and multipatch (the AMR
> package is called Carpet and is a thorn for Cactus, if that is
> meaningful). We currently use Visit with a custom reader for
> visualizations. Thanks for the help.

We've been very interested in finding a contact in the Cactus
community!  Sam Skillman and I have done some investigation into
Cactus in the past, and I think a frontend for it within yt would be
very feasible.  Why don't we set up a time to chat in IRC or
Hangout/Skype, and we can hash out how things might proceed?  Let's
chat off-list to set up a time -- anyone else who wold be interested,
drop me a line as well.

-Matt

>
> On Fri, Aug 3, 2012 at 3:22 PM, Nathan Goldbaum <nathan12343 at gmail.com> wrote:
>> Hi Sherwood,
>>
>> Looks like there was a typo in the command line utilities.  If you're on the development version of yt you should be able to fix it by doing a 'yt update' on the command line.  We will be backporting this change to the stable version shortly.
>>
>> I'm not sure why you got an old version of the install script when you tried to download the install script for the stable version.  I just tried doing that myself and got the latest version of the install script corresponding to yt 2.4.  It must have been a hiccup due to the recent release.
>>
>> I can't speak to the difficulty of writing a custom reader, although I do know that answering your question in full would require a bit more detail.  Are you using a grid or SPH code?  If it's a grid code, is it AMR or uniform mesh?  If AMR, what sort of AMR algorithm does your code use?
>>
>> Cheers,
>>
>> Nathan Goldbaum
>>
>> On Aug 3, 2012, at 3:07 PM, Sherwood Richers wrote:
>>
>>> Thanks. The newer version installed successfully. (there are two links
>>> on the site and I chose the 'stable' version before)
>>>
>>> New problem: in running the test case, the final example
>>> (superimposing grids on the plots) spits out
>>> AttributeError: 'ProjectionPlot' object has no attribute 'draw_grids'
>>> The full output is below.
>>>
>>> Finally, how involved would writing a reader for a custom code be? We
>>> are simulating supernovae with a code that is not listed as being
>>> supported.
>>>
>>> Thanks!
>>> -Sherwood
>>>
>>> (yt-x86_64)sherwood at sherwood:~/yt-x86_64/src/yt-hg/tests/DD0010$ yt
>>> plot --show-grids -p moving7_0010
>>> yt : [INFO     ] 2012-08-03 14:56:14,998 Parameters: current_time
>>>        = 0.817513171191
>>> yt : [INFO     ] 2012-08-03 14:56:14,998 Parameters: domain_dimensions
>>>        = [16 16 16]
>>> yt : [INFO     ] 2012-08-03 14:56:14,999 Parameters: domain_left_edge
>>>        = [ 0.  0.  0.]
>>> yt : [INFO     ] 2012-08-03 14:56:14,999 Parameters: domain_right_edge
>>>        = [ 1.  1.  1.]
>>> yt : [INFO     ] 2012-08-03 14:56:15,000 Parameters:
>>> cosmological_simulation   = 1
>>> yt : [INFO     ] 2012-08-03 14:56:15,000 Parameters: current_redshift
>>>        = 9.99102779567
>>> yt : [INFO     ] 2012-08-03 14:56:15,000 Parameters: omega_lambda
>>>        = 0
>>> yt : [INFO     ] 2012-08-03 14:56:15,000 Parameters: omega_matter
>>>        = 1
>>> yt : [INFO     ] 2012-08-03 14:56:15,000 Parameters: hubble_constant
>>>        = 0.5
>>> yt : [INFO     ] 2012-08-03 14:56:15,001 Adding plot for axis 0
>>> yt : [INFO     ] 2012-08-03 14:56:15,007 Getting the binary hierarchy
>>> yt : [INFO     ] 2012-08-03 14:56:15,013 Finished with binary hierarchy reading
>>> yt : [INFO     ] 2012-08-03 14:56:15,462 Making a fixed resolution
>>> buffer of (Density) 800 by 800
>>> yt : [INFO     ] 2012-08-03 14:56:15,490 xlim = 0.000000 1.000000
>>> yt : [INFO     ] 2012-08-03 14:56:15,490 ylim = 0.000000 1.000000
>>> yt : [INFO     ] 2012-08-03 14:56:15,491 Making a fixed resolution
>>> buffer of (Density) 800 by 800
>>> yt : [INFO     ] 2012-08-03 14:56:15,519 Making a fixed resolution
>>> buffer of (Density) 800 by 800
>>> Traceback (most recent call last):
>>>  File "/home/sherwood/yt-x86_64/bin/yt", line 9, in <module>
>>>    load_entry_point('yt==2.4', 'console_scripts', 'yt')()
>>>  File "/home/sherwood/yt-x86_64/src/yt-hg/yt/utilities/command_line.py",
>>> line 1540, in run_main
>>>    args.func(args)
>>>  File "/home/sherwood/yt-x86_64/src/yt-hg/yt/utilities/command_line.py",
>>> line 97, in run
>>>    self(args)
>>>  File "/home/sherwood/yt-x86_64/src/yt-hg/yt/utilities/command_line.py",
>>> line 1239, in __call__
>>>    plt.draw_grids()
>>> AttributeError: 'ProjectionPlot' object has no attribute 'draw_grids'
>>>
>>>
>>>
>>>
>>> On Fri, Aug 3, 2012 at 3:20 AM, Matthew Turk <matthewturk at gmail.com> wrote:
>>>> Hi Sherwood,
>>>>
>>>> On Fri, Aug 3, 2012 at 2:34 AM, Sherwood Richers <srichers at caltech.edu> wrote:
>>>>> Hello,
>>>>>
>>>>> I tried installing YT on my (Ubuntu 12.04 x86_64) laptop and got the
>>>>> following error messages when the install script tried updating. I
>>>>> also tried starting python and executing "import hashlib" and got the
>>>>> same messages. Does anybody know the cause of this or what I can do to
>>>>> fix the errors? (I don't know if it's of any relevance, but there were
>>>>> also a bunch of warnings in the attached install log).
>>>>
>>>> Reading over the install log, it looks like you've diagnosed the issue
>>>> -- a bunch of the Python modules failed to compile.  I also run on
>>>> Ubuntu 12.04 and these packages are required to install yt:
>>>>
>>>>  * libssl-dev
>>>>  * build-essential
>>>>  * libncurses5
>>>>  * libncurses5-dev
>>>>  * zip
>>>>
>>>> Can you make sure they are installed by running:
>>>>
>>>> $ sudo apt-get install libssl-dev build-essential libncurses5
>>>> libncurses5-dev zip
>>>>
>>>> Unfortunately you'll then have to rm -rf yt-x86_64 and re-run the
>>>> install script from scratch.
>>>>
>>>> Thanks, and let us know how it goes,
>>>>
>>>> Matt
>>>>
>>>>>
>>>>> Thanks a ton.
>>>>> -Sherwood
>>>>>
>>>>> Installing Forthon-0.8.5 (arguments: 'Forthon-0.8.5')
>>>>> Doing yt update, wiping local changes and updating to branch stable
>>>>> ERROR:root:code for hash sha224 was not found.
>>>>> Traceback (most recent call last):
>>>>>  File "/home/sherwood/yt-x86_64/lib/python2.7/hashlib.py", line 139,
>>>>> in <module>
>>>>>    globals()[__func_name] = __get_hash(__func_name)
>>>>>  File "/home/sherwood/yt-x86_64/lib/python2.7/hashlib.py", line 91,
>>>>> in __get_builtin_constructor
>>>>>    raise ValueError('unsupported hash type %s' % name)
>>>>> ValueError: unsupported hash type sha224
>>>>> ERROR:root:code for hash sha256 was not found.
>>>>> Traceback (most recent call last):
>>>>>  File "/home/sherwood/yt-x86_64/lib/python2.7/hashlib.py", line 139,
>>>>> in <module>
>>>>>    globals()[__func_name] = __get_hash(__func_name)
>>>>>  File "/home/sherwood/yt-x86_64/lib/python2.7/hashlib.py", line 91,
>>>>> in __get_builtin_constructor
>>>>>    raise ValueError('unsupported hash type %s' % name)
>>>>> ValueError: unsupported hash type sha256
>>>>> ERROR:root:code for hash sha384 was not found.
>>>>> Traceback (most recent call last):
>>>>>  File "/home/sherwood/yt-x86_64/lib/python2.7/hashlib.py", line 139,
>>>>> in <module>
>>>>>    globals()[__func_name] = __get_hash(__func_name)
>>>>>  File "/home/sherwood/yt-x86_64/lib/python2.7/hashlib.py", line 91,
>>>>> in __get_builtin_constructor
>>>>>    raise ValueError('unsupported hash type %s' % name)
>>>>> ValueError: unsupported hash type sha384
>>>>> ERROR:root:code for hash sha512 was not found.
>>>>> Traceback (most recent call last):
>>>>>  File "/home/sherwood/yt-x86_64/lib/python2.7/hashlib.py", line 139,
>>>>> in <module>
>>>>>    globals()[__func_name] = __get_hash(__func_name)
>>>>>  File "/home/sherwood/yt-x86_64/lib/python2.7/hashlib.py", line 91,
>>>>> in __get_builtin_constructor
>>>>>    raise ValueError('unsupported hash type %s' % name)
>>>>> ValueError: unsupported hash type sha512
>>>>> Installing yt
>>>>> Failure.  Check /home/sherwood/yt-x86_64/yt_install.log.
>>>>>
>>>>> _______________________________________________
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>>>>>
>>>>
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