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Using SBGrid with MacOS

/programs and synthetic.conf

SBGrid is installed at /opt/sbgrid by default and requires a link at /programs to create the proper path. Initial activation of an SBGrid installation requires admin privileges and a reboot after account activation to accommodate macOS controls in the root partition (/) of the Apple filesystem. This additional reboot is only needed after the initial account activation and creation of the /etc/synthetic.conf configuration file. The latest versions for the SBGrid Installation manager (GUI) will handle the creation of the required /etc/synthetic.conf file automatically.

For users that have upgraded macOS, the /etc/synthetic.conf file can be created manually. This file can be removed during the upgrade process. See below.

A reboot is required for /etc/synthetic.conf to take effect.

Manual creation of the programs path (after macOS upgrade)

SBGrid requires the /programs path to run software. Users who have upgraded to Catalina or newer from a previous macOS release will need to create the /etc/synthetic.conf file manually. The latest macOS does not allow symlinks to be created in the root partition (under /), but provides the option to create links in the root partition via the /etc/synthetic.conf file.

This file has the following format:

programs /opt/sbgrid

Note that the whitespace MUST be a tab character. Spaces will not work. Here is a file for reference: synthetic.conf. Thanks to Ron Rock at University of Chicago for pointing this out.

You can download this file to the proper location on your machine with these two commands:

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

Then you MUST REBOOT the computer for the changes to take effect. You should then see this in your root partition (/):

$ ls -l /programs

lrwxr-xr-x  1 root  wheel  11 Jun  4 14:49 /programs -> /opt/sbgrid

From there, you can continue to install software with the installation manager, or use the GUI. They are not mutually exclusive.

SBGrid on Apple M1 Silicon ARM64

Apple has released ARM64 "Apple Silicon" Macs. Compatibility and performance of the SBGrid software collection looks good and most applications work with Apple's "Rosetta" compatibility environment. Standards like COOT, PyMOL, Chimera, CCP4, and PHENIX work seamlessly, but there are exceptions (CCPEM, Schrodinger).

Known macOS issues

  • On macOS 26, coot versions 0.9x and earlier do not function properly; newer coot versions should work.
  • No 32-bit support (dropped in Catalina) means no support for nmrDraw, other 32-bit applications.
  • X11 forwarding from Linux is sketchy with XQuartz 2.8 and later. We have had best results by downgrading to either XQuartz 2.7.11 or 2.7.8.

XQuartz

  • XQuartz is required to provide X11 support on macOS. The latest Xquartz version can be downloaded from the MacOSForge site here: https://www.xquartz.org.