Installing SBGrid Software
Using the SBGrid Environment
Support for Site Administrators
Hardware Support Notes
Support for Developers
SBGrid software is compatible with macOS 10.15 Catalina, macOS 11 Big Sur and macOS 12 Monterey with the exception of 32-bit software. Initial activation of an SBGrid installation requires a reboot after account activation to accomodate 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 to Catalina or later from an older version of macOS that did not require this, the /etc/synthetic.conf file can be created manually.. See below.
A reboot is required for /etc/synthetic.conf to take effect.
Once the activation process is completed and the system has been rebooted, the manager can be used normally.
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 lastest MacOS does not allow symlinks to be created in the root partition ( under / ), but provides the option to create links in the root partion via the /etc/synthetic.conf file.
This file has the following format:
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://sbgrid.org/wiki/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.
Apple has released ARM64 "apple silicon" macs with the "M1" class CPU. 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, RELION, Schrodinger).
In rare cases, it may be desirable to disable Apple's System Integrity Protection. For reference, we have included the process to do that here.
If SIP is disabled, it is possible to remount the filesystem as read/write. This is not required to use SBGrid, but can be useful in some circumstances. For reference we have included the instructions here.
sudo mount -uw /
It is possible to turn off the nagging pop ups.
sudo softwareupdate --ignore "macOS Catalina"
You will see :
Ignored updates: ( "macOS Catalina" )
You can reverse this later by running :
sudo softwareupdate --reset-ignored
This version of the page was edited by Jason Key at 2021-10-06 13:20:22. View the most recent version.