NewLinuxBox.md

New Cluster Account

1. Install dotfiles:

    cd ~ && git clone --recursive https://github.com/dwhswenson/dotfiles.git
    cd dotfiles && ./install
   

2. Install conda:

    MINICONDA_ROOT=$HOME  # or other
    CONDA_PY=3.7
    source miniconda_install.sh
    conda init
    conda config --add channels omnia
    conda config --add channels conda-forge
   

3. Add a few packages to the base conda env:

    conda install glances
    pip install thefuck
   

4. Set up miscellaneous things:

    sh -c "$(curl -fsSL https://raw.github.com/robbyrussell/oh-my-zsh/master/tools/install.sh)"
    mv ~/.zshrc.pre-oh-my-zsh ~/.zshrc # RESPECT MY ZSHRC, OMZ!
    # Vundle plugins
    vim "+PluginInstall" "+q" "+q"
   

5. Set up computer-specific bashrc

• set up computer specific bashrc (add conda to $PATH)

5. Set up SSH keys for the new machine

6. Compile YouCompleteMe

    cd ~/.vim/bundle/YouCompleteMe
    ./install.py --clang-completer
   

7. Make ssh keys and copy them over

    # in .ssh/ directory on local machine
    ssh-keygen -t rsa
    ssh-copy-id -i ~/.ssh/mykey user@host
   

8. Copy .ssh over.

9. Copy private GPG key over (for signing commits)

10. Install dev version of OPS from my fork, with other forks as remotes

     mkdir src
     pushd src
     git clone git@github.com:dwhswenson/openpathsampling.git
     cd openpathsampling
     git remote add upstream https://github.com/openpathsampling/openpathsampling.git
     git remote add jhp https://github.com/jhprinz/openpathsampling.git
     python devtools/install_recipe_requirements.py devtools/conda-recipe/meta.yaml
     pip install -e .
    

11. Install dev versions of other software

Directory structure

$HOME/
  dotfiles/
  installed/
    (source packages for installed things; e.g. GSL)
  src/
    openpathsampling/
    openmmtools/
    ipynb-test/
    ...
  projects/

with subdirectories of projects/ often having symlinks to the main directory