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

Tue Jun 20 06:05:47 PDT 2017

I did delete the previous partial installations of yt before each attempt
at installation. I previously tried installing rockstar manually for a
conda-based environment, but I don't remember what went wrong, so I will
try that again and let you know. Either way, thank you for your insights.

Cheers,
Carla

2017-06-20 14:59 GMT+02:00 Nathan Goldbaum <nathan12343 at gmail.com>:

> 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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