[yt-users] Greeting and questions.

Martín Mestre martinmestrec at gmail.com
Tue Jul 12 10:25:19 PDT 2016


Hi Nathan,
I will complete that formulaire. Close to the end of the log file it says:
"Removing old build environment
BUILD START: rockstar-1.0.0-0"
Previus to installing I removed the whole directory of the stable version.
It talks about an "old" environment.
Thanks



2016-07-12 14:16 GMT-03:00 Nathan Goldbaum <nathan12343 at gmail.com>:

>
>
> 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 ?
>>>> ----------------------------------------------------------
>>>> ----------------------------------------------------------
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> .....
>>>>
>>>>
>>>>
>>>>
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>>>>
>>>>
>>>
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>>
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