Advanced rsync Workflows

Last updated on 2026-08-24 | Edit this page

Overview

Questions

  • How do I exclude certain files from rsync transfers?
  • How do I safely delete remote files not present locally?
  • How can I use rsync in SLURM job scripts?

Objectives

After completing this episode, participants will be able to: - Use exclude patterns to skip unwanted files - Preview operations with dry-run before executing - Safely use the –delete flag with proper safeguards - Integrate rsync into SLURM job scripts

Exclude Patterns

Skip files you do not want to transfer:

BASH 

rsync -avhPr --exclude='.git' --exclude='*.pyc' --exclude='__pycache__' \
  ~/myproject/ <myusername>@sagehen.hpc.pomona.edu:/rhome/<myusername>/myproject/

Common exclusions:

BASH 

--exclude='*.pyc'        # Python compiled files
--exclude='__pycache__'  # Python cache directories
--exclude='.git'         # Git history
--exclude='.DS_Store'    # macOS metadata files
--exclude='*.tmp'        # Temporary files
--exclude='.venv'        # Virtual environments

Include Only Specific Files

Transfer only matching file types by combining include and exclude:

BASH 

rsync -avhPr --include='*.txt' --exclude='*' \
  ~/myproject/ <myusername>@sagehen.hpc.pomona.edu:/rhome/<myusername>/myproject/

Dry Run (Preview)

See what rsync would do without actually transferring anything:

BASH 

rsync -avhPr --dry-run ~/myproject/ <myusername>@sagehen.hpc.pomona.edu:/rhome/<myusername>/myproject/

Output includes (DRY RUN) and shows files that would transfer. Always use this before any destructive operation.

Deleting Remote Files

The --delete flag removes files from the destination that do not exist in the source:

BASH 

# DANGEROUS: Always dry-run first!
rsync -avhPr --delete --dry-run ~/myproject/ <myusername>@sagehen.hpc.pomona.edu:/rhome/<myusername>/myproject/

# If the dry-run output looks correct, run without --dry-run
rsync -avhPr --delete ~/myproject/ <myusername>@sagehen.hpc.pomona.edu:/rhome/<myusername>/myproject/
Callout

Warning: –delete Can Destroy Data

Running --delete with an empty source directory will delete everything on the remote side. Always preview with --dry-run first.

Compression

For slow connections, compress data during transfer:

BASH 

rsync -avhPrz ~/myproject/ <myusername>@sagehen.hpc.pomona.edu:/rhome/<myusername>/myproject/

Compression helps for text-heavy files but provides no benefit for already-compressed formats (images, videos, archives).

Bandwidth Limiting

Avoid saturating your network by limiting transfer speed:

BASH 

rsync -avhPr --bwlimit=10m ~/myproject/ <myusername>@sagehen.hpc.pomona.edu:/rhome/<myusername>/myproject/

Units: k = kilobytes/s, m = megabytes/s.

Rsync in Job Scripts

Use rsync to stage data into fast temporary storage during SLURM jobs:

BASH 

#!/bin/bash
#SBATCH --job-name=data_process
#SBATCH --time=04:00:00

# Copy input to fast scratch
rsync -avhP /rhome/<myusername>/input.dat /scratch/$SLURM_JOB_USER/$SLURM_JOB_ID/

# Run computation on scratch
cd /scratch/$SLURM_JOB_USER/$SLURM_JOB_ID/
./myanalysis input.dat

# Copy results back to permanent storage
rsync -avhP output.dat /rhome/<myusername>/results/

Common Mistakes

  1. Wrong trailing slash: rsync ~/myproject host:/dest/ creates /dest/myproject/, while rsync ~/myproject/ host:/dest/ puts contents directly in /dest/
  2. Forgetting -P: Without -P, large interrupted transfers cannot resume
  3. Using –delete carelessly: Always dry-run first
  4. Forgetting -r for directories: Without -r, subdirectories are not transferred (though -a implies -r)
Challenge

Challenge: Selective Sync with Dry Run

  1. Create a local project with mixed files:

    BASH 

    mkdir -p ~/testproject/data ~/testproject/scripts
echo "data" > ~/testproject/data/data.txt
echo "print('hello')" > ~/testproject/scripts/main.py
echo "cache" > ~/testproject/scripts/main.pyc

  2. Dry-run an rsync excluding .pyc files:

    BASH 

    rsync -avhPr --exclude='*.pyc' --dry-run ~/testproject/ <myusername>@sagehen.hpc.pomona.edu:/rhome/<myusername>/testproject/

  3. Verify that main.pyc is not listed in the dry-run output

  4. Run without --dry-run to actually transfer

The dry-run should show data/data.txt and scripts/main.py but not scripts/main.pyc. The (DRY RUN) tag confirms no files were actually transferred. Running without --dry-run completes the transfer of only the non-excluded files.

Key Points
  • Use --exclude patterns to skip unwanted files like .git, .pyc, and caches
  • Always use --dry-run before --delete to prevent accidental data loss
  • Compression (-z) helps on slow networks but not for already-compressed files
  • rsync integrates well into SLURM job scripts for staging data to fast storage