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Useful HPC Bash Aliases

This document provides a collection of useful bash aliases for working in HPC environments, particularly those using SLURM. These aliases include PBS/SGE-style command mappings for SLURM, safer file operations, and various utility functions.

Quick Setup

Copy the following block into your ~/.bashrc file:

# SLURM Job Management (PBS/SGE style)
alias qstat="squeue -u \$USER"
alias qw="watch -n 2 squeue -u \$USER"
alias qsub=sbatch
alias qdel=scancel
alias sq='squeue -u $USER -o "%.18i %.9P %.8j %.8u %.2t %.10M %.6D %R"'
alias usage='sreport cluster AccountUtilizationByUser start=0101 format=Login,Proper,Account,Used'

# Listing and File Information
alias la="ls -la"
alias lh="ls -lh"
alias ll="ls -l"
alias lt="ls -ltr"
alias df='df -h'
alias duh="du -h --max-depth=1"

# Directory Navigation
alias cdd='cd -'
alias ..="cd .."
alias ...="cd ../.."
alias path='echo $PATH | tr ":" "\n"'
alias pwdcp='pwd | tr -d "\n" | xclip'

# Safe File Operations
alias rm="rm -i"
alias cp='cp -i'
alias mv='mv -i'
alias mkdir='mkdir -p'
alias wget='wget -c'

# Process Management
alias psg='ps aux | grep'
alias topme='top -u $USER'

# Search and Find
alias findh='find . -name'
alias greph='grep -r --color'

After adding these aliases, run:

source ~/.bashrc

Detailed Explanation

SLURM Job Management

These aliases make SLURM commands more familiar to users coming from PBS or SGE systems:

  • qstat: Shows your current jobs in the queue (equivalent to squeue -u $USER)
  • qw: Watch your queue status, updating every 2 seconds
  • qsub: Submit a job (equivalent to sbatch)
  • qdel: Delete a job (equivalent to scancel)
  • sq: Enhanced queue display with formatted output
  • usage: Show your cluster usage statistics

Listing and File Information

Enhanced versions of common listing commands:

  • la: Long listing including hidden files
  • lh: Long listing with human-readable sizes
  • ll: Long listing
  • lt: List files sorted by modification time (newest last)
  • df: Disk usage in human-readable format
  • duh: Directory sizes in human-readable format

Directory Navigation

Shortcuts for navigating directories:

  • cdd: Return to previous directory
  • ..: Go up one directory
  • ...: Go up two directories
  • path: Display PATH environment variable, one entry per line
  • pwdcp: Copy current directory path to clipboard

Safe File Operations

Safer versions of common file operations that prompt before overwriting:

  • rm: Prompt before removal
  • cp: Prompt before overwriting
  • mv: Prompt before overwriting
  • mkdir: Create parent directories if needed
  • wget: Resume interrupted downloads

Process Management

Tools for managing processes:

  • psg: Search for a process
  • topme: Show only your processes in top

Search and Find

Enhanced search commands:

  • findh: Quick find by name in current directory
  • greph: Recursive grep with color highlighting

Notes

  • These aliases are particularly useful in HPC environments but can be used in any bash shell
  • The prompting behavior of the safe file operations can be overridden by adding the -f flag
  • Some aliases (like pwdcp) may require additional software installation
  • Customize the aliases based on your specific needs and workflow

Usage Tips

  1. Always source your .bashrc after making changes: source ~/.bashrc
  2. Test new aliases in a safe environment before using them with important data
  3. Consider adding your own custom aliases for frequently used commands