Using SBGrid with MacOS 10.15 and later

SBGrid software is compatible with macOS 10.15 Catalina and macOS 11 Big Sur, with the exception of 32-bit software. Initial activation of an SBGrid installation requires a reboot after account activation to accomodate macOS filesystem controls in the / partition. This step is only needed after the initial account activation.

The latest versions for the SBGrid Installation manager (GUI and CLI) will handle the creation of the required /etc/synthetic.conf file automatically on activation.

For users that have upgraded to Catalina or newer, the /etc/synthetic.conf file needs to be created manually.. 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.

Notes on recent macOS changes :

• 32-bit applications are not supported on 10.15 Catalina and later.
• macOS now uses the z-shell (zsh) by default. This shell is also supported in SBGrid using the standard sbgrid.shrc file. More info regarding managing your shell on macOS can be found here
  • XQuartz is required for many applications. If you have upgraded to Catalina from an 10.14 or earlier, you will need to reinstall XQuartz. See https://www.xquartz.org/ for downloads and more info.
• More details about compatibility with the latest macOS and Apple hardware can be found here

Manual creation of the programs path ( after macOS upgrade )

Users who have upgraded to Catalina or newer from a previous macOS release will need to create the /etc/synthetic.conf file manually. SBGrid requires the /programs path to run software. 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/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://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.

Disable SIP from Recovery mode

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.

• Restart your Mac.
• Before macOS starts up, hold down Command-R and keep it held down until you see an Apple icon and a progress bar. Release. This boots you into Recovery.
• From the Utilities menu, select Terminal.
• At the prompt run the following and then press Return:

csrutil disable

• Terminal should display a message that SIP was disabled.
• From the  menu, select Restart.

Remount root filesystem as read/write

If SIP is disabled, it is possible to remount the filesystem as read/write. This is not required to use SBGrid, but for reference we have included the instructions here.

sudo mount -uw /

Re-enable SIP

• Restart your Mac.
• Before macOS starts up, hold down Command-R and keep it held down until you see an Apple icon and a progress bar. Release. This boots you into Recovery.
• From the Utilities menu, select Terminal.
• At the prompt, re-enbale SIP with :

csrutil enable

• Terminal should display a message that SIP was enabled.
• From the apple menu, select Restart.

How to stop nagging macOS update alerts

It is possible to turn off the nagging pop ups.

• Open System Preferences.
• Click on Software Update.
• Deselect Automatically keep my Mac up to date

How to ignore macOS Catalina update on your mac

  sudo softwareupdate --ignore "macOS Catalina"

You will see :

Ignored updates:
(
    "macOS Catalina"
)

You can reverse this later by running :

  sudo softwareupdate --reset-ignored