macos

SBGrid SBGrid Wiki

Installing SBGrid Software

Using the SBGrid Environment

Support for Site Administrators

Hardware Support Notes

Getting Help

Support for Developers

Using SBGrid with MacOS 11-14

SBGrid software is compatible with macOS macOS 11 Big Sur, macOS 12 Monterey, macOS 13 Ventura and macOS 14 Sonoma. Changes 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.

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 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.

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 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.

SBGrid on Apple M1 Silicon ARM64

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).

Known macOS issues

  • Ilastik 1.3.3 and earlier are no supported. Support coming in 1.4.
  • No 32-bit support (dropped in Catalina) means no support for nmrDraw, other 32-bit applications.
  • Rosetta fails ( from Baker lab, not Apple Rosetta2 ). Needs to be recompiled with clang.
  • X11 forwarding from Linux is sketchy with XQuartz 2.8 and later. We have had best results by downgrading to either XQuartzx 2.7.11 or 2.7.8.

Misc tips for macOS

Disable SIP from Recovery mode (not recommended)

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 apple 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 can be useful in some circumstances. 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 Sonoma update on your mac

  sudo softwareupdate --ignore "macOS Sonoma"

You will see :

Ignored updates:
(
    "macOS Sonoma"
)

You can reverse this later by running :

  sudo softwareupdate --reset-ignored