[yt-dev] adventures in trying to install yt_dev

Nathan Goldbaum nathan12343 at gmail.com
Fri Jul 31 10:23:12 PDT 2015


On Fri, Jul 31, 2015 at 12:19 PM, Molly Peeples <molly at stsci.edu> wrote:

> Hey Nathan,
>
> My setup / compilers / etc. are a software bundle maintained by STScI for
> the staff here (that's the ssb thing you can see in my paths). They do run
> as a virtual machine. I do not use Xcode.
>

Unfortunately we only test the install script (and yt itself on OSX) on
compilers provided by Xcode. It's extremely difficult to test against all
possible compiler combinations.


> Both machines are on OSX 10.9.5. Any ideas as to what's wrong with the
> build environment?
>

The install script is failing to build hdf5 because gcc can't find zlib. We
build our own version of zlib in the installs script, I'm not sure why yt's
zlib isn't compiling or being found.


> I'd really not like to have to install and maintain everything
> independently, especially since the build I have "just works" for every
> other application I have. If I can get the HDF5 problem diagnosed well then
> there's a chance they will be able to fix it here.
>
> Re. cython:
> molly% cython -V
> Cython version 0.22.1
> And __file__ does confirm that it is installed as part of the virtual env
> ('/usr/stsci/ssb/python/lib/python2.7/site-packages/Cython-0.21.1-py2.7-macosx-10.6-x86_64.egg/cython.py')
>

So it looks like you *do* have cython 0.22 installed (the cython executable
points to it), but python is finding cython 0.21.1

Unfortunately a recent change in yt *requires* cython 0.22 or newer, so the
version of cython in your virtualenv won't work. Is there any chance you
can work with a tech at stsci to update cython in the stsci environment?


>
> --Molly
>
>
> On Fri, Jul 31, 2015 at 11:29 AM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
>>
>>
>> On Friday, July 31, 2015, Molly Peeples <molly at stsci.edu> wrote:
>>
>>> Hi folks,
>>>
>>> I'm trying to install the dev branch of yt and I'm hitting some
>>> stumbling blocks. (For those of you who I talked to about this in May, the
>>> short version is that I've managed to recreate the same issues I had on my
>>> laptop but now on my desktop.)
>>>
>>> The first thing I tried was the
>>> http://bitbucket.org/yt_analysis/yt/raw/yt/doc/install_script.sh
>>> script, which fails at installing HDF5 (http://pastebin.com/QSnKqHtW).
>>> The same thing happens for the stable branch install script, and when I try
>>> this on a different machine (laptop vs desktop, but similar setups and
>>> python installations).
>>>
>>
>> There is something wrong with your build environment. How did you set up
>> your compilers? Using the Xcode command line tools or did you get your
>> compilers from a third-party source?
>>
>>
>>>
>>> I can install the stable branch no problem just doing pip install yt.
>>> But I'd still like the dev branch and / or source code. When I do hg clone
>>> https://bitbucket.org/yt_analysis/yt and then python setup.py develop,
>>> I get a:
>>> [oak:~/yt] molly% python setup.py develop
>>> Cython is a build-time requirement for the source tree of yt.
>>> Please either install yt from a provided, release tarball,
>>> or install Cython (version 0.22 or higher).
>>> You may be able to accomplish this by typing:
>>>      pip install -U Cython
>>> Which, naturally, I did, and it says it's successfully installed, but I
>>> get the same error when I then rerun the setup.py. (I think this is the
>>> same line we went through when trying to get it working on my laptop which
>>> is why we eventually used conda to get the stable version + source on my
>>> laptop.) FWIW, I seem to not be able to uninstall cython, though it's
>>> somewhat unclear on why:
>>> [oak:~/yt] molly% pip uninstall cython
>>> Not uninstalling Cython at
>>> /usr/stsci/ssb/python/lib/python2.7/site-packages/Cython-0.21.1-py2.7-macosx-10.6-x86_64.egg,
>>> outside environment /Users/molly/ssbvirt/ssb-OS X
>>>
>>>
>>>
>>>
>>> Soo...suggestions? It looks like I can get the binary no problem but if
>>> I want the source + dev branch, there are issues.
>>>
>>
>>
>>
>>
>> Does cython import successfully? If so, what's the output of
>> cython.__file__? cython.__version?
>>
>> I think this message about not uninstalling cython is related to
>> virtualenvs. Do you use virtualenvs?
>>
>> How did you set up your Python environment? You mentioned anaconda
>> Python, what happens if you install cython using conda?
>>
>> Finally, OSX 10.6 is getting a bit long in the tooth (for example, conda
>> no longer supports it), maybe that's part of the issue?
>>
>>
>>
>>
>>
>>
>>>
>>> --Molly
>>>
>>
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>>
>>
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