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

Nathan Goldbaum nathan12343 at gmail.com
Tue Jun 20 06:08:09 PDT 2017


Also if this is a cluster, make sure you have any modules unloaded. I think
your HDF5 issue might be because h5py is picking up a system HDF5
installation.

On Tue, Jun 20, 2017 at 8:05 AM Carla Bernhardt <carla.j.bernhardt at gmail.com>
wrote:

> 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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