[yt-users] Greeting and questions.

Nathan Goldbaum nathan12343 at gmail.com
Tue Jul 12 10:16:59 PDT 2016


On Tue, Jul 12, 2016 at 12:14 PM, Martín Mestre <martinmestrec at gmail.com>
wrote:

> Hi Nathan,
> thank you for your email. I tried to install the development version of yt
> but I failed.
>
> Settings:
> INST_CONDA=1
> INST_YT_SOURCE=1
> INST_ROCKSTAR=1
> INST_SCIPY=1
> INST_H5PY=1
> INST_ASTROPY=0
> INST_NOSE=1
>
> The last lines of the log file are below.
> Thank you very much.
> Martín
>
> ------------------
> + mkdir /home/mmestre/ytProject/yt-conda/envs/_build/lib
> + cp librockstar.so /home/mmestre/ytProject/yt-conda/envs/_build/lib/
> Removing old build environment
> BUILD START: rockstar-1.0.0-0
> Package: rockstar-1.0.0-0
> source tree in: /home/mmestre/ytProject/yt-conda/conda-bld/work
> number of files: 1
> Fixing permissions
> patchelf: file:
> /home/mmestre/ytProject/yt-conda/envs/_build/lib/librockstar.so
>     setting rpath to: $ORIGIN/.
> Fixing permissions
> BUILD END: rockstar-1.0.0-0
> Nothing to test for: rockstar-1.0.0-0
> # If you want to upload this package to anaconda.org later, type:
> #
> # $ anaconda upload
> /home/mmestre/ytProject/yt-conda/conda-bld/linux-64/rockstar-1.0.0-0.tar.bz2
> #
> # To have conda build upload to anaconda.org automatically, use
> # $ conda config --set anaconda_upload yes
>
> EXECUTING:
>   conda install
> /home/mmestre/ytProject/yt-conda/conda-bld/linux-64/rockstar-1.0.0-0.tar.bz2
> An unexpected error has occurred, please consider sending the
> following traceback to the conda GitHub issue tracker at:
>
>     https://github.com/conda/conda/issues
>
> Include the output of the command 'conda info' in your report.
>
>
> Traceback (most recent call last):
>   File "/home/mmestre/ytProject/yt-conda/bin/conda", line 6, in <module>
>     sys.exit(main())
>   File
> "/home/mmestre/ytProject/yt-conda/lib/python2.7/site-packages/conda/cli/main.py",
> line 120, in main
>     exit_code = args_func(args, p)
>   File
> "/home/mmestre/ytProject/yt-conda/lib/python2.7/site-packages/conda/cli/main.py",
> line 130, in args_func
>     exit_code = args.func(args, p)
>   File
> "/home/mmestre/ytProject/yt-conda/lib/python2.7/site-packages/conda/cli/main_install.py",
> line 69, in execute
>     install(args, parser, 'install')
>   File
> "/home/mmestre/ytProject/yt-conda/lib/python2.7/site-packages/conda/cli/install.py",
> line 203, in install
>     explicit(args.packages, prefix, verbose=not args.quiet)
>   File
> "/home/mmestre/ytProject/yt-conda/lib/python2.7/site-packages/conda/misc.py",
> line 126, in explicit
>     index.update(get_index(**index_args))
>   File
> "/home/mmestre/ytProject/yt-conda/lib/python2.7/site-packages/conda/api.py",
> line 22, in get_index
>     channel_urls = normalize_urls(channel_urls, platform, offline)
>   File
> "/home/mmestre/ytProject/yt-conda/lib/python2.7/site-packages/conda/config.py",
> line 250, in normalize_urls
>     url = urls[0]
> KeyError: 0
> ---------------------------
>

Hmm, frustrating. This seems to be a bug in conda (outside of our control,
unfortuantely). Let me see if I can reproduce the issue or identify a
workaround...

In the meantime, can you open an issue to track this?

https://bitbucket.org/yt_analysis/yt/issues/new


>
> 2016-07-11 12:07 GMT-03:00 Nathan Goldbaum <nathan12343 at gmail.com>:
>
>> Hi Martín,
>>
>> Someone else should be able to help you with your halo catalog-specific
>> questions, but I can help you out with some of these issues.
>>
>> On Mon, Jul 11, 2016 at 9:45 AM, Martín Mestre <martinmestrec at gmail.com>
>> wrote:
>>
>>> Dear yt community,
>>>
>>> a week ago I knew about this project and after reading a small part of
>>> the manual, the mission statement and the code of conduct I got encouraged
>>> to try to learn yt (and python). I would be very glad if I could use yt to
>>> study the structure of some disrupted satellites that I evolved with
>>> Gadget-2 (dark matter only).
>>>
>>> I have installed yt and made a simple halo catalog but I am not sure if
>>> I have proceeded correctly. I have written some questions below. Thank you
>>> very much in advance for any answer or suggestion.
>>>
>>> Best regards from La Plata, Argentina,
>>>
>>> Martín Mestre
>>>
>>>
>>> ----------------
>>> INSTALLATION
>>>
>>> The Host information is: Linux seminare 2.6.37.1-mosix #2 SMP Tue Apr 19
>>> 12:57:51 ART 2011 x86_64 GNU/Linux.
>>> I installed yt 3.2.3 as a simple cluster user in my home directory with
>>> the installation script. I have run the script a second time setting the
>>> option: INST_ROCKSTAR=1.
>>>
>>> The installation log is too large for the pastebin. I have only pasted
>>> the lines with the words "error" and "Error" respectively in the links:
>>> http://paste.yt-project.org/show/6657/ and
>>> http://paste.yt-project.org/show/6658/ .
>>>
>>> The first/last 400 lines of the log are here:
>>> http://paste.yt-project.org/show/6659/ and
>>> http://paste.yt-project.org/show/6660/ .
>>>
>>> How could I proceed to eliminate these errors ?
>>>
>>
>> We're getting ready to release yt 3.3, along with it a new version of the
>> install script that is more robust. Can you delete your old yt installation
>> and try re-running the version of the install script from yt's development
>> branch:
>>
>> http://bitbucket.org/yt_analysis/yt/raw/yt/doc/install_script.sh
>>
>> By default this will still install yt 3.2.3, but you can set
>> INST_YT_SOURCE=1 to get the latest development version of yt. You will need
>> to do this if you also want to install rockstar.
>>
>>
>>>
>>>
>>> -----------------------------------------------------------
>>> LOADING GADGET-2 SNAPSHOT IN BINARY FORMAT
>>> AND COMPUTATION OF HALO CATALOG
>>>
>>> I have run the following scritp:
>>> http://paste.yt-project.org/show/6661/
>>> and the log files was:
>>> http://paste.yt-project.org/show/6662/
>>> I would like to know if everything looks right in the log file.
>>>
>>> I wasn't able to upload the image file (36KB), saying:
>>> ERROR HTTP Error 404: Not Found
>>>
>>
>> Yes, imgur changed their APIs, this issue will be fixed in yt 3.3.
>>
>>
>>>
>>> I will be willing to send it by email because I have
>>> a question to do about the use of the halo finder.
>>> It found 8 halos, one of them many orders of magnitude more
>>>  massive than the rest. This was expected because it identifies
>>> the stream progenitor. The location of this halo is much closer
>>> to the centre of mass of the whole ensemble than to the point
>>> of maximum density (which I had previusly found through the
>>> method of the "shrinking spheres").
>>> Is there any scale parameter of the halo finder that allows me
>>> to identify halo centres as the points of local maxima of the
>>> volumetric density ?
>>> ----------------------------------------------------------
>>> ----------------------------------------------------------
>>>
>>>
>>>
>>>
>>>
>>> .....
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> 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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