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

Carla Bernhardt carla.j.bernhardt at gmail.com
Tue Jun 20 08:52:49 PDT 2017


Hi Nathan,

I finally got yt installed successfully with rockstar using INST_CONDA=1
and INST_YT_SOURCE=1. Thanks for your help. I must have just not disabled
the modules before.

Cheers,
Carla

2017-06-20 17:43 GMT+02:00 Nathan Goldbaum <nathan12343 at gmail.com>:

> 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/27dafcda
>>>>>>> f068829c78f34c4c7211f6dd56beea0d/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-x8
>>>>>>>>>>>> 6_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-x8
>>>>>>>>>>>> 6_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-x8
>>>>>>>>>>>> 6_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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