[yt-users] Cython discrepancy in yt install from source

Nathan Goldbaum nathan12343 at gmail.com
Mon Jun 19 07:45:29 PDT 2017


Done:

https://github.com/yt-project/yt/pull/1458/files

You should be able to get an updated install script by downloading it from
my fork:

$ wget
https://raw.githubusercontent.com/ngoldbaum/yt/27dafcdaf068829c78f34c4c7211f6dd56beea0d/doc/install_script.sh

-Nathan

On Mon, Jun 19, 2017 at 9:31 AM, Carla Bernhardt <
carla.j.bernhardt at gmail.com> wrote:

> Hi Nathan,
>
> I don't mind waiting, I think you will do a better job updating the
> script. I tried before, but the installation still failed. I am not using
> MacOS, I am on a server using Redhat.
>
> Cheers,
> Carla
>
> 2017-06-19 15:43 GMT+02:00 Nathan Goldbaum <nathan12343 at gmail.com>:
>
>> No, I haven't seen that error before.
>>
>> I'll be heading into the office shortly and will update the install
>> script when I get in. If you can't wait on me, you could try updating it
>> yourself to download the latest cython release from e.g. pypi.
>>
>> By the way, do you happen to be using the latest version of MacOS? In
>> that case building rockstar from source will not work:
>>
>> https://github.com/yt-project/yt/issues/1289
>>
>> Nathan
>>
>> On Mon, Jun 19, 2017 at 8:32 AM Carla Bernhardt <
>> carla.j.bernhardt at gmail.com> wrote:
>>
>>> Hi Nathan,
>>>
>>> I did try running with rockstar install enabled, INST_CONDA=1 and
>>> INST_YT_SOURCE=1 and I got this strange error
>>> <https://pastebin.com/EWXsbzCx> that I don't have the file
>>> "libisl.so.10". Any suggestions on that? I wasn't able to find anything
>>> helpful about this online. I just want to get a working version of yt going
>>> with rockstar enabled, it doesn't have to be from source.
>>>
>>> Cheers,
>>> Carla
>>>
>>> 2017-06-19 15:17 GMT+02:00 Nathan Goldbaum <nathan12343 at gmail.com>:
>>>
>>>> Hi Carla,
>>>>
>>>> I think we need to update the install script for the case with
>>>> INST_CONDA=0. For now you should be able to set INST_CONDA=1 and still get
>>>> rockstar setup, we made it so you can use rockstar with a conda-based
>>>> install a while back.
>>>>
>>>> Nathan
>>>>
>>>> On Mon, Jun 19, 2017 at 6:34 AM Carla Bernhardt <
>>>> carla.j.bernhardt at gmail.com> wrote:
>>>>
>>>>> Dear yt-users,
>>>>>
>>>>> I am trying to compile yt with rockstar enabled, so I am having yt
>>>>> install itself from source. The code downloads Cython 0.23.5, but later
>>>>> then requires Cython 0.24+. I tried downloading Cython-0.25.2, but this
>>>>> failed (I probably did it wrong). What do I need to change to make the
>>>>> install_script.sh work with Cython?
>>>>>
>>>>> Here is a piece of the failure report I got:
>>>>>
>>>>> Installing GitPython-2.1.3
>>>>> Installing sympy-1.0
>>>>> Building Rockstar
>>>>> Installing yt
>>>>> ********************************************
>>>>>         FAILURE REPORT:
>>>>> ********************************************
>>>>>
>>>>>   File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/site-packag
>>>>> es/setuptools-20.6.7-py3.5.egg/setuptools/command/sdist.py", line
>>>>> 132, in add_defaults
>>>>>   File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/distutils/cmd.py",
>>>>> line 299, in get_finalized_command
>>>>>     cmd_obj.ensure_finalized()
>>>>>   File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/distutils/cmd.py",
>>>>> line 107, in ensure_finalized
>>>>>     self.finalize_options()
>>>>>   File "setup.py", line 308, in finalize_options
>>>>>     cython.__version__)
>>>>> RuntimeError: Building yt from source requires Cython 0.24 or newer but
>>>>> Cython 0.23.5 is installed. Please update Cython using the appropriate
>>>>> package manager for your python environment.
>>>>>
>>>>> ********************************************
>>>>> ********************************************
>>>>>
>>>>> Cheers,
>>>>> Carla Bernhardt
>>>>> PhD Student
>>>>> ZAH Institut für Theoretische Astrophysik
>>>>> Universität Heidelberg
>>>>>
>>>>> _______________________________________________
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>>>>> yt-users at lists.spacepope.org
>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>
>>>>
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