Installing SBGrid Software
Using the SBGrid Environment
Support for Site Administrators
Hardware Support Notes
Getting Help
Support for Developers
SBGrid software is compatible with the following versions of macOS:
Note that hanges to application signing verification in recent versions of macOS may require a work-around for chimerax and possibly other signed app bundles. We are working on a remedy for this.
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 a admin privleges and 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 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.
For Activation instructions, see:
Command line : https://sbgrid.org/wiki/sbgrid-cli
Graphical : https://sbgrid.org/wiki/sbgrid-gui
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:
programs /opt/sbgridNote 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/sbgridFrom 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. 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).