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

Tue Jun 20 05:59:56 PDT 2017

Are you running the install script from scratch in this situation? That
means removing the older partial installations before rerunning the install
script.

If that's not the problem I'm not sure what the issue is.

You could try setting up a python environment outside the install script
and set up rockstar manually following the instructions for conda-based
environments here:

http://yt-project.org/docs/dev/installing.html#installing-yt-using-anaconda

On Tue, Jun 20, 2017 at 6:31 AM Carla Bernhardt <carla.j.bernhardt at gmail.com>
wrote:

> Hi Nathan,
>
> Likely independent from the Cython discrepancy, when I try installing yt
> with rockstar enabled (from source only), I get this error: ValueError:
> HDF5 version string must be in X.Y.Z format (more of the error here
> <https://pastebin.com/ci3QMtRL>). So I tried installing with a different
> hdf5--same result. I tried disabling h5py, but then I get this error: ImportError:
> cannot import name 'print_line' (more of the error here
> <https://pastebin.com/61haGr3T>). I also tried installing yt with both
> INST_CONDA =1 and INST_YT_SOURCE=1 as listed in my previous email, but just
> for good measure, I retried with the new install script (same result
> <https://pastebin.com/xgXyzBQx>). Any suggestions?
>
> Cheers,
> Carla
>
> 2017-06-19 16:45 GMT+02:00 Nathan Goldbaum <nathan12343 at gmail.com>:
>
>> 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-packages/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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>>>>>>>
>>>>>>
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