catalina

Using SBGrid with MacOS 10.15 and later (Catalina, Big Sur and Monterey)

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 filesystem controls in the root partition (/) of the apple filesystem.

This additional reboot step is only needed after the initial account activation and is handled by our installation manager in most cases. The latest versions for the SBGrid Installation manager (GUI and CLI) will handle the creation of the required /etc/synthetic.conf file automatically.

For users that have upgraded to Catalina or newer from an older version of macOS that did not require this, 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.

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.

SBGrid on Apple M1 Silicon

ARM64 compatibility

Apple released the first of its new ARM64 "apple silicon" macs with the "M1" CPU. We are testing the SBGrid software stack on the M1 chip and, so far, compatibility and performance look very good. Most of the SBGrid applications work on the new M1 CPU with macOS 11 and Apple's Rosetta compatibility environment. Standards like COOT, PyMOL, Chimera, CCP4, and PHENIX work seamlessly, but there are exceptions (CCPEM, RELION). We expect to support most titles on BigSur with the new M1 hardware early in 2021.

SBGrid on macOS 11 "Big Sur"

Apple has released MacOS 11.0 "Big Sur" which provides compatibilty for Apple's new 'Apple Silicon' ARM-based computers as well as numerous changes and security enhancements. Because this is a major update, we reccommend waiting to upgrade any system required for scientific data processing. MacOS 10.14 "Mojave" or 10.15 "Catalina" are currently supported by SBGrid.

Installation of SBGrid on Big Sur is basically the same as on Catalina. Due to Apple's filesystem protections and our current requirement of a symlink at /programs, a /etc/synthetic.conf file is necessary. See above for more info.

SBGrid on macOS 12 "Monterey"

We are not aware of any issues specific to macOS 12 at this time. The "Monterey" beta release appears to be very similar to Big Sur, SBGrid installation managers work, PyMOL and COOT are known to work. This appears to be a safe upgrade from macOS 11, at least in the macOS 12 beta.

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 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