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

Nathan Goldbaum nathan12343 at gmail.com
Tue Jun 20 08:43:02 PDT 2017


Hi Carla,

I think setuptools likely needs to be updated in the install script as
well. I've gone ahead and done that:

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

For the INST_CONDA=0 portion of the install script, keeping everything
up-to-date is a perpetually losing battle. I'd really like it if we could
just get rid of that option, since we don't really have the resources to
ensure it's always up-to-date and working on a variety of platforms.

Nathan

On Tue, Jun 20, 2017 at 9:49 AM Carla Bernhardt <carla.j.bernhardt at gmail.com>
wrote:

> I did forget to take off the modules (yes, that solves the h5py problem!),
> but I just tried again without any modules and I got the print_line error
> again (which I really don't understand): ImportError: cannot import name
> 'print_line' (more of the error here <https://pastebin.com/61haGr3T>).
>
> Cheers,
> Carla
>
> 2017-06-20 15:08 GMT+02:00 Nathan Goldbaum <nathan12343 at gmail.com>:
>
>> 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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