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macOS System Requirements

This page outlines the system requirements and configuration needed to run BioGrids software on macOS systems.

Supported macOS Versions

BioGrids supports the following macOS versions:

  • macOS 15.x (Sequoia)
  • macOS 14.x (Sonoma)
  • macOS 13.x (Ventura)
  • macOS 12.x (Monterey)
  • macOS 11.x (Big Sur)
  • macOS 10.15 (Catalina)
  • macOS 10.14 (Mojave)

Older versions may work but are not officially supported.

Hardware Requirements

Intel Macs

  • Processor: Intel x86_64 processor (Core i5 or better recommended)
  • Memory: 8GB RAM minimum (16GB+ recommended)
  • Storage: 100GB available disk space minimum
  • Graphics: Integrated or discrete graphics with OpenGL support

Apple Silicon Macs (M1/M2/M3/M4)

  • Processor: Apple M1, M2, M3, or M4 processor
  • Memory: 16GB unified memory minimum (32GB+ recommended for large analyses)
  • Storage: 100GB available disk space minimum (SSD standard)
  • Compatibility: Most BioGrids software runs via Rosetta 2 translation

Required Software

XQuartz (Essential)

XQuartz is required to provide X11 support for many bioinformatics applications:

  1. Download: Visit https://www.xquartz.org
  2. Install: Run the installer package
  3. Reboot: A system reboot is required after installation
  4. Verify: Open Terminal and run xquartz --version

Note: Some applications may have issues with newer XQuartz versions. If you experience problems, try XQuartz 2.7.11 or 2.7.8.

Command Line Tools

Install Xcode Command Line Tools for compilation support:

xcode-select --install

Install Homebrew for additional package management:

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

System Configuration

/programs Path and synthetic.conf

BioGrids is installed at /opt/biogrids by default and requires a symbolic link at /programs. On macOS Catalina and later, this requires creating an /etc/synthetic.conf file.

Automatic Configuration

The BioGrids Installation Manager (GUI) automatically creates the required /etc/synthetic.conf file. A reboot is required after initial account activation.

Manual Configuration

If you need to create the /programs path manually (e.g., after a macOS upgrade):

  1. Create the synthetic.conf file: 

    sudo tee /etc/synthetic.conf << EOF
programs /opt/biogrids
EOF
    Important: The whitespace must be a tab character, not spaces.

  2. Alternative method using curl: 

    sudo /usr/bin/curl -k https://docs.biogrids.org/downloads/synthetic.conf -o /etc/synthetic.conf

  3. Reboot your Mac for changes to take effect

  4. Verify the symlink exists: 

    ls -l /programs
# Should show: lrwxr-xr-x  1 root  wheel  12 /programs -> /opt/biogrids

File System Considerations

  • Case-sensitive filesystems are recommended for maximum compatibility
  • APFS (default on modern macOS) works well with BioGrids
  • Network storage (NFS, SMB) is supported for shared installations

Apple Silicon Compatibility

Rosetta 2 Translation

Most BioGrids software runs on Apple Silicon Macs using Rosetta 2:

  1. Install Rosetta 2 (if not already installed): 

    sudo softwareupdate --install-rosetta

  2. Performance: Most applications work seamlessly with good performance

  3. Compatible software: Standards like PyMOL, Chimera, R, and Python packages
  4. Exceptions: Some specialized tools may have compatibility issues

Native Apple Silicon Support

BioGrids is progressively adding native Apple Silicon support for key applications. Check the software catalog for current native ARM64 availability.

Network Configuration

Outbound Network Access

BioGrids requires internet access for: - Software downloads and installation - Automatic updates
- License verification

Required access: - HTTPS (443): Primary download protocol - HTTP (80): Fallback for some repositories - Git/SSH (22): For version control systems (optional)

Firewall Configuration

macOS firewall typically allows outbound connections by default. If using third-party firewall software, ensure BioGrids Installation Manager is permitted.

Proxy Configuration

For corporate networks with proxy servers:

# Set proxy environment variables
export http_proxy=http://proxy.company.com:8080
export https_proxy=http://proxy.company.com:8080

# Add to shell profile for persistence
echo 'export http_proxy=http://proxy.company.com:8080' >> ~/.zshrc
echo 'export https_proxy=http://proxy.company.com:8080' >> ~/.zshrc

User Account Requirements

Administrator Privileges

  • Initial setup: Admin privileges required for:
  • Creating /etc/synthetic.conf
  • Installing XQuartz

  • System-level dependencies

  • Daily use: Standard user privileges sufficient for personal installations

Multi-User Systems

For shared Mac systems: - Create a dedicated biogrids user account - Configure appropriate file permissions - Use the Admin tools for user management

Storage Planning

Disk Space Requirements

Installation Type Storage Needed
Basic personal 50-100 GB
Standard personal 200-300 GB
Comprehensive 500+ GB
Site installation 1-2 TB

Performance Considerations

  • SSD storage: Standard on modern Macs, provides optimal performance
  • External storage: Thunderbolt/USB-C external drives supported
  • Network storage: AFP, SMB, NFS supported for shared installations

Known Issues and Limitations

macOS Version Specific

macOS Catalina and Later

  • No 32-bit support: Legacy 32-bit applications will not run
  • Notarization requirements: Some software may show security warnings
  • Gatekeeper: May need to allow apps in Security & Privacy preferences

Apple Silicon Specific

  • Rosetta 2 dependency: Required for Intel-compiled software
  • Memory architecture: Unified memory may affect large-memory applications
  • Virtualization: Docker/VMs may have different performance characteristics

X11 and Graphics Issues

Remote X11 forwarding: Can be problematic with newer XQuartz versions 

# For remote connections, use trusted X11 forwarding
ssh -Y username@remote-host

Graphics performance: Some OpenGL applications may have reduced performance on integrated graphics

Application-Specific Issues

  • Java applications: May require specific Java versions
  • Python packages: Some scientific packages may need native compilation
  • Commercial software: License servers may need macOS-specific configuration

Performance Optimization

Memory Management

# Check memory usage
vm_stat

# Monitor memory pressure
memory_pressure

CPU Optimization

  • Enable all CPU cores for parallel processing
  • Activity Monitor helps identify resource usage
  • Energy Saver settings should allow high performance for compute tasks

Network Optimization

# Test network performance
networkQuality

# Check DNS resolution
dscacheutil -q host -a name biogrids.org

Development Environment

Python Configuration

BioGrids includes Python environments, but system Python setup helps:

# Install Python via Homebrew (recommended)
brew install python

# Verify Python installation
python3 --version
pip3 --version

R Configuration

For R-based bioinformatics:

# Install R via Homebrew
brew install r

# Or download from CRAN: https://cran.r-project.org/bin/macosx/

Conda/Mamba Integration

BioGrids works alongside conda environments:

# Install miniforge for Apple Silicon
curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
bash Miniforge3-$(uname)-$(uname -m).sh

Troubleshooting

Common Installation Issues

"Cannot verify developer" errors: 

# Temporarily disable Gatekeeper for specific app
sudo spctl --master-disable
# Re-enable after installation
sudo spctl --master-enable

Permission denied errors: 

# Check directory permissions
ls -la /opt/biogrids
# Fix permissions if needed
sudo chown -R $(whoami) /opt/biogrids

X11/Graphics Issues

XQuartz not launching: 1. Completely quit XQuartz 2. Restart with: open -a XQuartz 3. Test with: xeyes or xclock

Remote display issues: 

# Set display variable
export DISPLAY=:0
# Or for remote connections
export DISPLAY=localhost:10.0

Apple Silicon Specific

Rosetta 2 not working: 

# Check if Rosetta 2 is installed
pgrep oahd

# Reinstall if needed
sudo softwareupdate --install-rosetta --agree-to-license

Architecture conflicts: 

# Check binary architecture
file /path/to/binary

# Force Intel mode for specific applications
arch -x86_64 /path/to/application

Getting Help

For macOS-specific issues:

  • Email: help@biogrids.org
  • Include in support requests:
  • macOS version: sw_vers
  • Hardware info: system_profiler SPHardwareDataType
  • Installation logs from ~/Library/BioGrids/logs/
  • XQuartz version: xquartz --version

Useful Diagnostic Commands

# System information
sw_vers
system_profiler SPHardwareDataType | head -20
uname -m

# BioGrids environment
echo $BIOGRIDS_ROOT
ls -la /programs
source ~/.biogrids/biogrids.shrc && biogrids-cli --version

# X11 testing
echo $DISPLAY
xset q