When you see the combination of these errors:

bash: rsync: command not found
rsync: connection unexpectedly closed (0 bytes received so far) [sender]
rsync error: error in rsync protocol data stream (code 12) at io.c(600) [sender=3.0.6]

You're facing a classic case of SSH-based rsync misconfiguration. The "command not found" error suggests the remote server can't locate rsync in its PATH, while the protocol error indicates the communication handshake failed.

The primary suspects in this scenario are:

• Missing rsync installation on the remote host
• PATH environment variable corruption during SSH connection
• SSH forced command configurations interfering with rsync
• Firewall or network restrictions blocking rsync protocol traffic

Solution 1: Verify Remote Rsync Installation

First, check if rsync exists on the remote machine:

ssh myuser@999.999.99.9 "which rsync || echo 'Rsync not found'"

If missing, install it:

# For Debian/Ubuntu:
ssh myuser@999.999.99.9 "sudo apt-get install rsync -y"

# For RHEL/CentOS:
ssh myuser@999.999.99.9 "sudo yum install rsync -y"

Solution 2: Explicit Rsync Path Specification

When the PATH is corrupted, specify the full path:

sudo rsync -av -e 'ssh' /var/www/html/somedir/ \
myuser@999.999.99.9:/usr/bin/rsync Users/myuser/Desktop/ec2backup

Solution 3: Rsync Over SSH Debug Mode

Enable verbose output to identify the exact failure point:

rsync -avvv --progress -e 'ssh -v' /source/ user@host:/destination/

Since you mentioned recent VirtualBox/Vagrant installations, check for:

# Network interface conflicts
ifconfig | grep -i virtualbox

# SSH config changes
diff ~/.ssh/config ~/.ssh/config.bak

VirtualBox often creates NAT networks that might conflict with your existing network configuration. Reset your network stack:

sudo service networking restart  # Linux
sudo ifconfig en0 down && sudo ifconfig en0 up  # macOS

For persistent issues, try these advanced methods:

# Force rsync protocol version
rsync --protocol=30 -av /source/ user@host:/destination/

# Test with minimal options
rsync -rlptD --rsync-path='/usr/bin/rsync' /source/ user@host:/destination/

# Check for SELinux/AppArmor restrictions
ssh user@host "sudo ausearch -m avc -ts recent"

Remember that rsync protocol errors often mask deeper system configuration issues. The solution typically involves methodically eliminating potential causes until you isolate the root problem.

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I recently hit a wall with my regular rsync over SSH operations. The exact command that worked flawlessly for months suddenly started throwing this error:

bash: rsync: command not found
rsync: connection unexpectedly closed (0 bytes received so far) [sender]
rsync error: error in rsync protocol data stream (code 12) at io.c(600) [sender=3.0.6]

Before diving deep, I performed several validation tests:

• Remote sync between other servers - same error
• Local rsync operations - worked perfectly
• Direct SSH connection to target - successful

The timeline points to VirtualBox/Vagrant installation as the likely culprit. These virtualization tools can:

1. Modify network interfaces (creating new virtual adapters)
2. Alter SSH configurations
3. Change system PATH variables

Here's how I systematically diagnosed the problem:

# First verify remote rsync availability
ssh myuser@999.999.99.9 "which rsync"

# Check PATH environment variable
ssh myuser@999.999.99.9 "echo \$PATH"

# Test basic SSH connection
ssh -v myuser@999.999.99.9

The key discovery was that VirtualBox had modified the default SSH configuration. The PATH environment variable on the remote server wasn't including the directory containing rsync when accessed via SSH (but worked fine with direct login).

Here are the steps that ultimately fixed the issue:

# On the remote server, edit the SSH environment
sudo nano /etc/ssh/sshd_config

# Add or modify these lines:
AcceptEnv LANG LC_*
PermitUserEnvironment yes

# Then create environment file for the user
mkdir -p ~/.ssh
echo "PATH=/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin" > ~/.ssh/environment

# Restart SSH service
sudo service ssh restart

If the above doesn't work, consider these options:

# Specify full rsync path in command
sudo rsync -av -e "ssh" /var/www/html/somedir/ \
myuser@999.999.99.9:/usr/bin/rsync Users/myuser/Desktop/ec2backup

# Or install rsync in a standard location
ssh myuser@999.999.99.9 "sudo ln -s $(which rsync) /usr/bin/rsync"

To avoid similar issues in the future:

• Document all PATH modifications from new software installs
• Create system-wide rsync symlinks
• Set up SSH environment variables proactively