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macOS dependencies and requirements

SBGrid on macOS has three primary requirements: the /programs path (via synthetic.conf), Rosetta 2 (on Apple Silicon), and XQuartz.

/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 this command:

sudo /usr/bin/curl 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.

Rosetta 2

Apple Silicon (ARM64) Macs need Apple's Rosetta 2 compatibility environment to run titles that aren't yet compiled natively for ARM64. Install it with:

/usr/sbin/softwareupdate --install-rosetta

Compatibility and performance of the SBGrid software collection under Rosetta 2 is good — COOT, PyMOL, Chimera, CCP4, and PHENIX work seamlessly — but there are exceptions (CCPEM, Schrodinger, and some older Rosetta and RELION versions compiled with Intel compilers).

XQuartz

XQuartz is required to provide X11 support on macOS. The latest version can be downloaded from https://www.xquartz.org.

Known macOS issues

  • No 32-bit support (dropped in Catalina) means no support for nmrDraw, other 32-bit applications.