[yt-users] Greeting and questions.

Nathan Goldbaum nathan12343 at gmail.com
Tue Jul 12 10:32:32 PDT 2016


OK, in the mean time, you might have success by removing the old, broken
installation (rm -r yt-conda) and trying again, but this time with
INST_CONDA=0. This will build yt from source (which might cause other
issues) but should work around the issue you're having.

On Tue, Jul 12, 2016 at 12:25 PM, Martín Mestre <martinmestrec at gmail.com>
wrote:

> 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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>>>>> yt-users at lists.spacepope.org
>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>
>>>>>
>>>>
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