[yt-users] yt on Pleiades

Desika Narayanan dnarayan at haverford.edu
Mon Oct 19 13:56:20 PDT 2015


does pip come with miniconda?  you might need to install that separately.
 i think it comes with the full anaconda.  (fwiw, i installed yt on
pleiades by using full anaconda, doing the pip install -U cython, then the
hg clone yt etc. that you do).



On Mon, Oct 19, 2015 at 4:42 PM, Mateusz Ruszkowski <mateuszr at umich.edu>
wrote:

>
>
>    Hi Nathan,
>
> Thanks for your help. I think also this almost works ...  I downloaded the
> latest miniconda and followed this procedure:
>
>
> bash Miniconda3-latest-Linux-x86_64.sh
> miniconda3/bin/conda build conda-recipes/yt
> hg clone https://bitbucket.org/yt_analysis/yt
> cd yt/
> hy up yt
> python setup.py develop
>
> This resulted in:
>
> 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 I am not able to install via "pip install -U Cython." So this is
> essentially the same error message I got when I attempted to install yt
> using the method described in my previous e-mail. Any idea what may still
> be wrong?
>
>
>    Thanks,
>       Mateusz
>
>
>
>
> On Oct 19, 2015, at 2:26 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
> Hi Mateusz
>
> Rather than using the python module on pleiades, I'd suggest setting up
> your python stack on your own in your home folder.
>
> By far the quickest way to do this is to install miniconda and then
> install yt into the miniconda environment using "conda install yt". You
> could also use the yt install script, although you might have issues with
> that if Pleiades has an older (insecure) version of OpenSSL installed,
> which is sadly quite common on supercomputers these days...
>
> Personally, I set up my python environment on Pleiades using miniconda.
>
> -Nathan
>
> On Mon, Oct 19, 2015 at 11:23 AM, Mateusz Ruszkowski <mateuszr at umich.edu>
> wrote:
>
>>
>>   Hi,
>>
>> I am trying to install yt on Pleiades. I was able to complete a number
>> installation steps but I eventually got an error message related to Cython
>> (Cython seems to be installed though). The error message is attached below.
>> Does anybody have an idea what needs to be done to complete this
>> installation?
>>
>>     Thanks,
>>        Mateusz
>>
>> ------------------------------------------------
>> Dr. Mateusz Ruszkowski
>> Associate Professor
>>
>> University of Michigan
>> Department of Astronomy
>> 301C West Hall
>> 1085 South University Ave.
>> Ann Arbor, MI 48109-1107, USA
>>
>> e-mail: mateuszr at umich.edu
>>
>>
>> ————————————————————————
>>
>> % module load pkgsrc/2014Q3
>> % module load python/2.7.9
>> % hg clone https://bitbucket.org/yt_analysis/yt
>> warning: bitbucket.org certificate with fingerprint
>> 46:de:34:e7:9b:18:cd:7f:ae:fd:8b:e3:bc:f4:1a:5e:38:d7:ac:24 not verified
>> (check hostfingerprints or web.cacerts config setting)
>> destination directory: yt
>> requesting all changes
>> adding changesets
>> adding manifests
>> adding file changes
>> added 17568 changesets with 36510 changes to 3053 files (+3 heads)
>> updating to bookmark @ on branch stable
>> 1209 files updated, 0 files merged, 0 files removed, 0 files unresolved
>> % cd yt
>> % hg update yt
>> 317 files updated, 0 files merged, 148 files removed, 0 files unresolved
>> (leaving bookmark @)
>> % python setup.py install --user --prefix=/nobackupnfs2/mruszkow
>> 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
>> % pip install -U Cython
>> Downloading/unpacking Cython from
>> https://pypi.python.org/packages/source/C/Cython/Cython-0.23.4.tar.gz#md5=157df1f69bcec6b56fd97e0f2e057f6e
>>   Downloading Cython-0.23.4.tar.gz (1.6MB): 1.6MB downloaded
>>   Running setup.py (path:/tmp/pip_build_mruszkow/Cython/setup.py)
>> egg_info for package Cython
>>     Unable to find pgen, not compiling formal grammar.
>>
>>     warning: no files found matching '*.pyx' under directory
>> 'Cython/Debugger/Tests'
>>     warning: no files found matching '*.pxd' under directory
>> 'Cython/Debugger/Tests'
>>     warning: no files found matching '*.h' under directory
>> 'Cython/Debugger/Tests'
>>     warning: no files found matching '*.pxd' under directory
>> 'Cython/Utility'
>> Installing collected packages: Cython
>>   Found existing installation: Cython 0.21.1
>>     Uninstalling Cython:
>> Cleaning up...
>> Exception:
>> Traceback (most recent call last):
>>   File
>> "/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/pip/basecommand.py", line
>> 122, in main
>>     status = self.run(options, args)
>>   File
>> "/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/pip/commands/install.py",
>> line 283, in run
>>     requirement_set.install(install_options, global_options,
>> root=options.root_path)
>>   File "/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/pip/req.py", line
>> 1431, in install
>>     requirement.uninstall(auto_confirm=True)
>>   File "/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/pip/req.py", line
>> 598, in uninstall
>>     paths_to_remove.remove(auto_confirm)
>>   File "/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/pip/req.py", line
>> 1836, in remove
>>     renames(path, new_path)
>>   File "/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/pip/util.py",
>> line 295, in renames
>>     shutil.move(old, new)
>>   File "/nasa/pkgsrc/2014Q4/lib/python2.7/shutil.py", line 300, in move
>>     rmtree(src)
>>   File "/nasa/pkgsrc/2014Q4/lib/python2.7/shutil.py", line 247, in rmtree
>>     rmtree(fullname, ignore_errors, onerror)
>>   File "/nasa/pkgsrc/2014Q4/lib/python2.7/shutil.py", line 252, in rmtree
>>     onerror(os.remove, fullname, sys.exc_info())
>>   File "/nasa/pkgsrc/2014Q4/lib/python2.7/shutil.py", line 250, in rmtree
>>     os.remove(fullname)
>> OSError: [Errno 30] Read-only file system:
>> '/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/Cython/Build/BuildExecutable.py'
>>
>> Storing debug log for failure in /u/mruszkow/.pip/pip.log
>> %
>>
>>
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>>
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