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

Tue Jun 20 04:31:45 PDT 2017

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-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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