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installation troubleshooting

Oliver Beckstein edited this page Nov 8, 2018 · 1 revision

Installing a complex scientific computing environment or a diverse set of laptops is very challenging. Even though our instructions work for most students, there are many ways in which something can not quite work the way as expected.

This page collects notes and recipes on trouble shooting (or "debugging" as we say) the installation process.

For additional help see also SoftwareCarpentry's Configuration Problems and Solutions.

Windows 10

pip or python are not found in git-bash

description

You opened git-bash and try to run the command

pip install vpython

or

python --version

but you get an error such as bash: pip: command not found.

solution

We are adding additional information to your bash shell startup file so that Anaconda will be found.

This solution assumes that you installed Anaconda3 in the default location — if you changed the location in the installation process then you will have to change the content of the MYCONDA variable below to use your custom location.

  1. open git-bash

  2. type

    cd
    echo $HOME

    (always hit RETURN after typing a command)

    You should see output such as /c/Users/YOUR-USERNAME (where "YOUR-USERNAME" stands for your user name, e.g., "alice", "bob", or "dvader")

  3. type exactly

    cat >> $HOME/.bash_profile << 'EOF'
    # PHY494 bash startup for local Anaconda
    # see https://github.com/ASU-CompMethodsPhysics-PHY494/PHY494-resources/wiki/installation-troubleshooting
    MYCONDA="$HOME/Anaconda3"
    export PATH="$MYCONDA:$MYCONDA/Scripts:$MYCONDA/Library/bin:$PATH"
    unset MYCONDA
    EOF
  4. close git-bash

  5. open a new git-bash (this is important so that the changes take effect)

  6. type

    which conda

    Should print something like /c/Users/YOUR-USERNAME/Anaconda3/Scripts/conda.

Then try out again to run pip or python.

explanation

Newer versions of Anaconda do not add themselves to the Windows PATH anymore. The installer for Anaconda3 now recommends users by default to NOT add anaconda path to Windows PATH environment variable and thus our installation instructions for windows lead to an installation with Anaconda3 not immediately accessible from the command line.

VPython: notebook stays blank, no box shown

The box in VPython is not visible, only a blank square. (Note: initially you look at the box side on so it looks like a gray square on black background.)

Try opening the notebook in the Chrome web browser instead of Explorer/Edge: Just type http://localhost:8888 in Chrome's URL bar.

git-bash hangs on start-up

It is possible that the startup files for the bash shell got corrupted. Try finding any of the following files in your home directory (typically C:\Users\USERNAME) and rename them (which inactivates them). Not all files might be present:

  • .bashrc --> X.bashrc
  • .bash_profile --> X.bash_profile
  • .profile --> X.profile

Then try re-opening git-bash.

If it works you can then look at your X. files to see if there was anything in there that might have been responsible for the problems or show them to your instructor.

macOS

Error 49 when running jupyter notebook

On macOS, if you get the error OSError: [Errno 49] Can't assign requested address you might need to use

jupyter notebook --ip=127.0.0.1

Linux

General

The following problems can occur independent of the operating system

Wrong conda is used

Wrong conda is used. Check

which conda

in the terminal: it should show a path in your home directory. E.g., for user "physics":

  • Windows: /c/Users/Physics/Anaconda3/conda
  • macOS: /Users/physics/Anaconda3/conda
  • Linux: /home/physics/Anaconda3/conda

Try exiting the terminal and open a new terminal (or git bash) and try again. Changes to PATH only take effect when a new shell is opened.

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