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

Tue Jun 20 07:49:07 PDT 2017

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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