This page introduces several terminal-based working environments available on UCR’s HPCC/Biocluster that are useful for a variety of computer languages.
To work efficiently on remote systems like a computer cluster, it is essential
to learn how to work in a pure command-line interface. GUI environments like
RStudio and similar coding environments are not suitable for this. In addition,
there is a lot of value of knowing how to work in an environment that is not
restricted to a specific programming language. Therefore, for working on remote
systems like HPCC Cluster, this site focuses on Nvim and Tmux. Both are useful
for many programming languages. Combinded with the
nvim-r plugin they also
provide a powerful command-line working environment for R. Users of Emacs may
want to consider using ESS instead. The following
provides a brief introduction to the Nvim-R-Tmux environment.
The following opens a file (here
myfile) with nvim (or vim)
nvim myfile.txt # for neovim (or 'vim myfile.txt' for vim)
Once you are in Nvim, there are three main modes: normal, insert and command mode. The most important commands for switching between the three modes are:
ikey brings you from the normal mode to the insert mode. The latter is used for typing.
Esckey brings you from the insert mode back to the normal mode.
:key starts the command mode at the bottom of the screen.
Use the arrow keys to move your cursor in the text. Using
Fn Up/Down key allows to page through
the text quicker. In the following command overview, all commands starting with
: need to be typed in the command mode.
All other commands are typed in the normal mode after pushing the
Important modifier keys to control vim/nvim
:w: save changes to file. If you are in editing mode you have to hit
:q: quit file that has not been changed
:wq: save and quit file
:!q: quit file without saving any changes
Useful resources for learning vim/nvim
For R: nvim-R
Tmux is a terminal multiplexer that allows to split terminal windows and to detach/reattach to
existing terminal sessions. Combinded with the
nvim-r plugin it provides a powerful command-line working
environment for R where users can send code from a script to the R console or command-line.
Both tmux and the
nvim-r plugin need to be installed on a system. On HPCC Cluster both are configured
in each user account. If this is not the case then follow the quick configuration instructions given in the following subsection.
Quick configuration in user accounts
Skip these steps if Nvim-R-Tmux is already configured in your account. Or follow the detailed instructions to install Nvim-R-Tmux from scratch on your own system.
- Log in to your user account on HPCC and execute
install_nvimRtmux. Alternatively, follow these step-by-step install commands.
- To enable the nvim-R-tmux environment, log out and in again.
- Follow usage instructions of next section.
Basic usage of Nvim-R-Tmux
The official and much more detailed user manual for
Nvim-R is available here.
The following gives a short introduction into the basic usage of Nvim-R-Tmux:
1. Start tmux session (optional)
Note, running Nvim from within a tmux session is optional. Skip this step if tmux functionality is not required (e.g. reattaching to sessions on remote systems).
tmux # starts a new tmux session tmux a # attaches to an existing session
2. Open nvim-connected R session
*.Rmd file with
nvim and intialize a connected R session with
\rf. This command can be remapped to other key combinations, e.g. uncommenting lines 10-12 in
.config/nvim/init.vim will remap it to the
F2 key. Note, the resulting split window among Nvim and R behaves like a split viewport in
vim meaning the usage of
Ctrl-w w followed by
Esc is important for navigation.
nvim myscript.R # or *.Rmd file
3. Send R code from nvim to the R pane
Single lines of code can be sent from nvim to the R console by pressing the space bar. To send
several lines at once, one can select them in nvim’s visual mode and then hit the space bar.
Please note, the default command for sending code lines in the nvim-r-plugin is
\l. This key
binding has been remapped in the provided
.config/nvim/init.vim file to the space bar. Most other key bindings (shortcuts) still start with the
\ as LocalLeader, e.g.
\rh opens the help for a function/object where the curser is located in nvim. More details on this are given below.
Important keybindings for nvim
The main advantages of Neovim compared to Vim are its better performance and its built-in terminal emulator facilitating the communication among Neovim and interactive programming environments such as R. Since the Vim and Neovim environments are managed independently, one can run them in parallel on the same system without interfering with each other. The usage of Neovim is almost identical to Vim.
\rf: opens vim-connected R session. If you do this the first time in your user account, you might be asked to create an
~/. If so approve this action by pressing
spacebar: sends code from vim to R; here remapped in
:vsplit: splits viewport (similar to pane split in tmux)
gz: maximizes size of viewport in normal mode (similar to Tmux’s
Ctrl-a zzoom utility)
Ctrl-w w: jumps cursor to R viewport and back; toggle between insert (
i) and command (
Esc) mode is required for navigation and controlling the environment.
Ctrl-w r: swaps viewports
Ctrl-w =: resizes splits to equal size
:resize <+5 or -5>: resizes height by specified value
:vertical resize <+5 or -5>: resizes width by specified value
Ctrl-w K: toggles between horizontal/vertical splits
Ctrl-spacebar: omni completion for R objects/functions when nvim is in insert mode. Note, this has been remapped in
init.vimfrom difficult to type default
:h nvim-R: opens nvim-R’s user manual; navigation works the same as for any Vim/Nvim help document
:Rhelp fct_name: opens help for a function from nvim’s command mode with text completion support
Ctrl-s and Ctrl-x: freezes/unfreezes vim (some systems)
Important keybindings for tmux
Ctrl-a %: splits pane vertically
Ctrl-a ": splits pane horizontally
Ctrl-a o: jumps cursor to next pane
Ctrl-a Ctrl-o: swaps panes
Ctrl-a <space bar>: rotates pane arrangement
Ctrl-a Alt <left or right>: resizes to left or right
Ctrl-a Esc <up or down>: resizes to left or right
Ctrl-a n: switches to next tmux window
Ctrl-a Ctrl-a: switches to previous tmux window
Ctrl-a c: creates a new tmux window
Ctrl-a 1: switches to specific tmux window selected by number
Ctrl-a d: detaches from current session
Ctrl-a s: switch between available tmux sesssions
$ tmux new -s <name>: starts new session with a specific name
$ tmux ls: lists available tmux session(s)
$ tmux attach -t <id>: attaches to specific tmux session
$ tmux attach: reattaches to session
$ tmux kill-session -t <id>: kills a specific tmux session
Ctrl-a : kill-session: kills a session from tmux command mode that can be initiated with
For Bash, Python and other languages
To install it, one needs to copy from the
vimcmdline resository the directories
syntax and their files to
user accounts of UCR’s HPCC, the above install script
install_nvimRtmux includes the
vimcmdline (since 09-Jun-18).
The usage of
vimcmdline is very similar to
nvim-R. To start a connected terminal session, one
opens with nvim a code file with the extension of a given language (e.g.
*.sh for Bash or
*.py for Python),
while the corresponding interactive interpreter session is initiated
by pressing the key sequence
\s (corresponds to
nvim-R). Subsequently, code lines can be sent
with the space bar. More details are available here.