[yt-users] yt on Pleiades

[Nathan Goldbaum]

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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