Install Issue on Ubuntu

[Tyler Reddy]

Hi, 

Laura and I were trying to install MDAnalysis on an Ubuntu 14.04 machine with conda python and ran into quite a few issues. It seems that conda isn't behaving properly on her machine for some reason, so I've placed parts of the traces below in case there are suggestions:

when installing MDAnalysis 0.10 (or the most recent development branch)
python setup.py install


running install
Traceback (most recent call last):
  File "setup.py", line 321, in <module>
    zip_safe=False,  # as a zipped egg the *.so files are not found (at least in Ubuntu/Linux)
  File "/biggin/s23/lady4552/anaconda/lib/python2.7/distutils/core.py", line 151, in setup
    dist.run_commands()
  File "/biggin/s23/lady4552/anaconda/lib/python2.7/distutils/dist.py", line 953, in run_commands
    self.run_command(cmd)
  File "/biggin/s23/lady4552/anaconda/lib/python2.7/distutils/dist.py", line 972, in run_command
    cmd_obj.run()
  File "/usr/lib/python2.7/dist-packages/setuptools/command/install.py", line 73, in run
    self.do_egg_install()
  File "/usr/lib/python2.7/dist-packages/setuptools/command/install.py", line 82, in do_egg_install
    cmd.ensure_finalized()  # finalize before bdist_egg munges install cmd
  File "/biggin/s23/lady4552/anaconda/lib/python2.7/distutils/cmd.py", line 109, in ensure_finalized
    self.finalize_options()
  File "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", line 274, in finalize_options
    ('install_dir','install_dir')
  File "/biggin/s23/lady4552/anaconda/lib/python2.7/distutils/cmd.py", line 298, in set_undefined_options
    src_cmd_obj.ensure_finalized()
  File "/biggin/s23/lady4552/anaconda/lib/python2.7/distutils/cmd.py", line 109, in ensure_finalized
    self.finalize_options()
  File "/usr/lib/python2.7/dist-packages/setuptools/command/install_lib.py", line 13, in finalize_options
    self.set_undefined_options('install',('install_layout','install_layout'))
  File "/biggin/s23/lady4552/anaconda/lib/python2.7/distutils/cmd.py", line 302, in set_undefined_options
    getattr(src_cmd_obj, src_option))
  File "/biggin/s23/lady4552/anaconda/lib/python2.7/distutils/cmd.py", line 105, in __getattr__
    raise AttributeError, attr
AttributeError: install_layout



And this is the conda (just typing conda at the command line):

Traceback (most recent call last):
  File "/biggin/s23/lady4552/anaconda/bin/conda-server", line 4, in <module>
    from binstar_client.scripts.cli import main
  File "/biggin/s23/lady4552/anaconda/lib/python2.7/site-packages/binstar_client/__init__.py", line 11, in <module>
    from .requests_ext import stream_multipart
  File "/biggin/s23/lady4552/anaconda/lib/python2.7/site-packages/binstar_client/requests_ext.py", line 9, in <module>
    from requests.packages.urllib3.filepost import choose_boundary, iter_fields
ImportError: No module named packages.urllib3.filepost
failed: /biggin/s23/lady4552/anaconda/bin/conda-server --help
Error: could not import Crypto (required for "conda sign").
    Run the following command:

    $ conda install -n root pycrypto

failed: /biggin/s23/lady4552/anaconda/bin/conda-sign --help

[Tyler Reddy]

Also, worth mentioning that it seems that any and all attempts to update / install conda packages fail almost instantly with an error that Laura might be able to place in this thread. The /boot/ partition seemed extremely full of old images, some of which were cleared out, but there were a lot of errors, etc.

Tyler

[Tyler Reddy]

From Laura:

The error I get when trying to update conda packages is as follows:

The following packages will be UPDATED:

    conda-env:  2.2.3-py27_0  --> 2.3.0-py27_0
    pip:        7.0.3-py27_0  --> 7.1.0-py27_0
    setuptools: 17.1.1-py27_0 --> 18.0.1-py27_0

Proceed ([y]/n)? y

Fetching packages ...
Error: Could not open u'/biggin/s23/lady4552/anaconda/pkgs/conda-env-2.3.0-py27_0.tar.bz2.part' for writing (seek).                                                              | ETA:  --:--:--   0.00  B/s


Kind regards,

Laura

[Oliver Beckstein]

On 10 Jul, 2015, at 09:09, Tyler Reddy wrote:

> Fetching packages ...
> Error: Could not open u'/biggin/s23/lady4552/anaconda/pkgs/conda-env-2.3.0-py27_0.tar.bz2.part' for writing (seek). | ETA: --:--:-- 0.00 B/s

I'd fix this problem before anything else that comes later *might* be a consequence of this problem.

Maybe
- disk full or
- permission problems or
- disk dying or
- NFS throwing a hissy fit?


--
Oliver Beckstein, DPhil * oliver.b...@asu.edu
http://becksteinlab.physics.asu.edu/

Assistant Professor of Physics
Arizona State University
Center for Biological Physics and Department of Physics
Tempe, AZ 85287-1504
USA

Office: PSF 348
Phone: +1 (480) 727-9765
FAX: +1 (480) 965-4669

Department of Physics: https://physics.asu.edu/people/faculty/oliver-beckstein
Center for Biological Physics: http://biophysics.asu.edu/faculty/oliver-beckstein