bodhi-docs/bashrc.example at main · rnabioco/bodhi-docs · GitHub

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# Example ~/.bashrc for the Bodhi cluster (Slurm)
# Anonymized — replace <username>, hostnames, and account/queue names for your
# own account. Secrets (API tokens, etc.) intentionally omitted: keep those in
# ~/.bashrc.local (sourced at the end) and never commit them.

export TERM=xterm-256color

# Accept a working directory pushed over SSH (e.g. from an editor remote)
if [ -n "$SSH_PWD" ] && [ -d "$SSH_PWD" ]; then
   cd "$SSH_PWD"
   unset SSH_PWD
fi

### Functions ---------------------------------------------------------------

# ls after every cd
cd() {
  builtin cd "$@"
  ls -F --color=auto
}

histgrep() {
    grep "$@" ~/.history/*
    history | grep "$@"
}

today() {
    date "+%Y-%m-%d"
}

### Aliases -----------------------------------------------------------------

alias q='exit'
alias df='df -h'
alias la='ls -F -a --color=auto'
alias ls='ls -F --color=auto'
alias ll='ls -hF -l --color=auto'
alias lll='ls -hF -la --color=auto'
alias lr='ls -hF -lagFqt --color=auto | head'
alias rm='rm -i'
alias gzcat='zcat'

# SSH shortcuts — replace hostnames/usernames with your own
alias bodhi='ssh <cluster-head-node>'
# alias alpine="ssh <username>@<other-cluster-login>"

### Environment modules -----------------------------------------------------

if ! [ -z "$MODULESHOME" ]; then
    module load modules-init
    # module load gcc/10.1.0
fi

### PATH --------------------------------------------------------------------

PATH=${HOME}/bin:${HOME}/.local/bin:${PATH}
export HDF5_PLUGIN_PATH=$HOME/.local/hdf5/lib/plugin

# Rust / cargo
[ -f "$HOME/.cargo/env" ] && . "$HOME/.cargo/env"

# pixi
export PATH="${HOME}/.pixi/bin:$PATH"
export PIXI_CACHE_DIR=/tmp/pixi-cache-${USER}

### Slurm -------------------------------------------------------------------

export PATH="/cluster/slurm-25.11.2/bin:/cluster/slurm-25.11.2/sbin:$PATH"
export SBATCH_ACCOUNT="<account>"
export SBATCH_PARTITION="<partition>"

# my jobs
alias sq='squeue -u $USER -o "%.10i %.9P %.30j %.8u %.2t %.10M %.10L %.4C %.8m %R"'
# my jobs, live-refreshing (needs hwatch)
alias wsq='hwatch -n 5 "squeue -u \$USER -o \"%.10i %.9P %.50k %.8T %.10M %.10L %.6D %.4C %.8m %R %.10Q\""'
# another user's jobs, live-refreshing:  wsqu <username>
wsqu() {
    local user="${1:?Usage: wsqu <username>}"
    hwatch -n 5 "squeue -u $user -o \"%.10i %.9P %.50k %.8T %.10M %.10L %.6D %.4C %.8m %R %.10Q\""
}

### Node / direnv / prompt --------------------------------------------------

export NVM_DIR="$HOME/.nvm"
[ -s "$NVM_DIR/nvm.sh" ] && \. "$NVM_DIR/nvm.sh"
[ -s "$NVM_DIR/bash_completion" ] && \. "$NVM_DIR/bash_completion"

command -v direnv   >/dev/null && eval "$(direnv hook bash)"
command -v starship >/dev/null && eval "$(starship init bash)"

### Local secrets (not committed) -------------------------------------------
# Put tokens/keys here, e.g. export NETLIFY_AUTH_TOKEN=...
[ -f "$HOME/.bashrc.local" ] && . "$HOME/.bashrc.local"