[yt-users] Greeting and questions.

Martín Mestre martinmestrec at gmail.com
Tue Jul 12 10:14:39 PDT 2016


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
---------------------------

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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