On Mon, Oct 19, 2015 at 1:42 PM, Mateusz Ruszkowski <mateuszr@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

Here you want to do "conda install yt" to get all of yt's dependencies.  From there you can install the development version of yt. You can "conda install" must python packages.

As desika mentioned, you can also install pip with "conda install pip".

I'd caution against using the full anaconda distribution since anaconda's MPI will shadow the system MPI installation unless you explicitly remove it.
 
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@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@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



———————————————————————— 

% 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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