big-sur.md
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1
-## MacOS 11.0 Big Sur
2
-
3
-Apple has released MacOS 11.0 "Big Sur". This OS includes 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.
4
-
5
-<!-- TOC -->
6
-
7
-- [MacOS 11.0 Big Sur](#macos-110-big-sur)
8
- - [Apple M1 Silicon](#apple-m1-silicon)
9
- - [Installing SBGrid on Big Sur](#installing-sbgrid-on-big-sur)
10
- - [Known issues](#known-issues)
11
-
12
-<!-- /TOC -->
13
-
14
-### Apple M1 Silicon
15
-
16
-ARM64 compatibility
17
-
18
-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.
19
-
20
-### Installing SBGrid on Big Sur
21
-
22
-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 the [installation page for macOS Catalina for more info](catalina)
23
-
24
-### Known issues
25
-
26
-- Ilastik 1.3.3 and earlier are no supported. Support coming in 1.4.
27
-- No 32-bit support (dropped in Catalina) means no support for nmrDraw, other 32-bit applications.
28
-- Rosetta fails ( from Baker lab, not Apple Rosetta2 ). Needs to be recompiled with clang.
29
-- CCP-EM ( possibly fixed in latest nightly)
30
-- No GUI in FLTK applications (like RELION)
31
-- Xquartz window border takes a few seconds to appear. It does appear eventually. Possibly fixed in XQuartz 2.8 series.
big-sur.md
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+macos.md
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catalina.md
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1
-# Using SBGrid with MacOS 10.15 and later
2
-
3
-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.
4
-
5
-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.
6
-
7
-For users that have upgraded to Catalina or newer, [the _/etc/synthetic.conf_ file needs to be created manually.](#manual-creation-of-the-programs-path). See below.
8
-
9
-**A reboot is required for /etc/synthetic.conf to take effect.**
10
-
11
-For Activation instructions, see:
12
-[Command line : https://sbgrid.org/wiki/sbgrid-cli](https://sbgrid.org/wiki/sbgrid-cli)
13
-[Graphical : https://sbgrid.org/wiki/sbgrid-gui](https://sbgrid.org/wiki/sbgrid-gui)
14
-
15
-Once the activation process is completed and the system has been rebooted, the manager can be used normally.
16
-
17
-Notes on recent macOS changes :
18
- - [32-bit applications](https://docs.google.com/spreadsheets/d/e/2PACX-1vSZEEdZhYIdRq0BoY-Aq8XFO1QSR6idkO72N2UeACWSG8-84gLlPqE_v9NrFO9na66gZ3_6PCSDUXGI/pubhtml?gid=1974952972&single=true) are not supported on 10.15 Catalina and later.
19
- - 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](https://support.apple.com/en-us/HT208050)
20
-- 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/](https://www.xquartz.org/) for downloads and more info.
21
- - [More details about compatibility with the latest macOS and Apple hardware can be found here](big-sur)
22
-
23
-
24
-### Manual creation of the programs path ( after macOS upgrade )
25
-
26
-Users who have upgraded to Catalina or newer from a previous macOS release will need to create the _/etc/synthetic.conf_ file manually.
27
-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.
28
-This file has the following format:
29
-
30
-```
31
-programs /opt/sbgrid
32
-```
33
-
34
-Note that the whitespace MUST be a tab character. Spaces will not work.
35
-Here is a file for reference : [synthetic.conf](downloads/synthetic.conf).
36
-Thanks to Ron Rock at University of Chicago for pointing this out.
37
-
38
-You can download this file to the proper location on your machine with these two commands:
39
-
40
-```
41
-sudo /usr/bin/curl -k https://sbgrid.org/wiki/downloads/synthetic.conf -o /etc/synthetic.conf
42
-```
43
-
44
-Then you MUST REBOOT the computer for the changes to take effect.
45
-You should then see this in your root partition (/) :
46
-
47
-```
48
- $ ls -l /programs
49
-
50
-lrwxr-xr-x 1 root wheel 11 Jun 4 14:49 /programs -> /opt/sbgrid
51
-```
52
-
53
-From there, you can continue to install software with the installation manager, or use the [GUI](https://sbgrid.org/wiki/client_install).
54
-They are not mutually exclusive.
55
-
56
-### Disable SIP from Recovery mode (not recommended)
57
-
58
-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.
59
-
60
-- Restart your Mac.
61
-- 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.
62
-- From the Utilities menu, select Terminal.
63
-- At the prompt run the following and then press Return:
64
-
65
-```
66
-csrutil disable
67
-```
68
-
69
-- Terminal should display a message that SIP was disabled.
70
-- From the  menu, select Restart.
71
-
72
-### Remount root filesystem as read/write
73
-
74
-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.
75
-
76
-```
77
-sudo mount -uw /
78
-```
79
-
80
-### Re-enable SIP
81
-
82
-- Restart your Mac.
83
-- 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.
84
-- From the Utilities menu, select Terminal.
85
-- At the prompt, re-enbale SIP with :
86
-
87
-```
88
-csrutil enable
89
-```
90
-
91
-- Terminal should display a message that SIP was enabled.
92
-- From the apple menu, select Restart.
93
-
94
-### How to stop nagging macOS update alerts
95
-
96
-It is possible to turn off the nagging pop ups.
97
-
98
-- Open System Preferences.
99
-- Click on Software Update.
100
-- Deselect Automatically keep my Mac up to date
101
-
102
-## How to ignore macOS Catalina update on your mac
103
-
104
-```
105
- sudo softwareupdate --ignore "macOS Catalina"
106
-```
107
-
108
-You will see :
109
-
110
-```
111
-Ignored updates:
112
-(
113
- "macOS Catalina"
114
-)
115
-```
116
-
117
-You can reverse this later by running :
118
-
119
-```
120
- sudo softwareupdate --reset-ignored
121
-```
catalina.md
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macos.md
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1
+## Using SBGrid with MacOS 10.15 and later (Catalina, Big Sur and Monterey)
2
+
3
+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.
4
+
5
+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.
6
+
7
+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.](#manual-creation-of-the-programs-path). See below.
8
+
9
+**A reboot is required for /etc/synthetic.conf to take effect.**
10
+
11
+For Activation instructions, see:
12
+[Command line : https://sbgrid.org/wiki/sbgrid-cli](https://sbgrid.org/wiki/sbgrid-cli)
13
+[Graphical : https://sbgrid.org/wiki/sbgrid-gui](https://sbgrid.org/wiki/sbgrid-gui)
14
+
15
+Once the activation process is completed and the system has been rebooted, the manager can be used normally.
16
+
17
+### Manual creation of the programs path ( after macOS upgrade )
18
+
19
+Users who have upgraded to Catalina or newer from a previous macOS release will need to create the _/etc/synthetic.conf_ file manually.
20
+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.
21
+This file has the following format:
22
+
23
+```
24
+programs /opt/sbgrid
25
+```
26
+
27
+Note that the whitespace MUST be a tab character. Spaces will not work.
28
+Here is a file for reference : [synthetic.conf](downloads/synthetic.conf).
29
+Thanks to Ron Rock at University of Chicago for pointing this out.
30
+
31
+You can download this file to the proper location on your machine with these two commands:
32
+
33
+```
34
+sudo /usr/bin/curl -k https://sbgrid.org/wiki/downloads/synthetic.conf -o /etc/synthetic.conf
35
+```
36
+
37
+Then you MUST REBOOT the computer for the changes to take effect.
38
+You should then see this in your root partition (/) :
39
+
40
+```
41
+ $ ls -l /programs
42
+
43
+lrwxr-xr-x 1 root wheel 11 Jun 4 14:49 /programs -> /opt/sbgrid
44
+```
45
+
46
+From there, you can continue to install software with the installation manager, or use the [GUI](https://sbgrid.org/wiki/client_install).
47
+They are not mutually exclusive.
48
+
49
+## SBGrid on Apple M1 Silicon
50
+
51
+ARM64 compatibility
52
+
53
+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.
54
+
55
+## SBGrid on macOS 11 "Big Sur"
56
+
57
+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.
58
+
59
+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.
60
+
61
+## SBGrid on macOS 12 "Monterey"
62
+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.
63
+
64
+## Known macOS issues
65
+
66
+- Ilastik 1.3.3 and earlier are no supported. Support coming in 1.4.
67
+- No 32-bit support (dropped in Catalina) means no support for nmrDraw, other 32-bit applications.
68
+- Rosetta fails ( from Baker lab, not Apple Rosetta2 ). Needs to be recompiled with clang.
69
+- 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](https://www.xquartz.org/releases/XQuartz-2.7.11.html) or [2.7.8](https://www.xquartz.org/releases/XQuartz-2.7.8.html).
70
+
71
+## Misc tips for macOS
72
+### Disable SIP from Recovery mode (not recommended)
73
+
74
+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.
75
+
76
+- Restart your Mac.
77
+- 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.
78
+- From the Utilities menu, select Terminal.
79
+- At the prompt run the following and then press Return:
80
+
81
+```
82
+csrutil disable
83
+```
84
+
85
+- Terminal should display a message that SIP was disabled.
86
+- From the apple menu, select Restart.
87
+
88
+### Remount root filesystem as read/write
89
+
90
+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.
91
+
92
+```
93
+sudo mount -uw /
94
+```
95
+
96
+### Re-enable SIP
97
+
98
+- Restart your Mac.
99
+- 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.
100
+- From the Utilities menu, select Terminal.
101
+- At the prompt, re-enbale SIP with :
102
+
103
+```
104
+csrutil enable
105
+```
106
+
107
+- Terminal should display a message that SIP was enabled.
108
+- From the apple menu, select Restart.
109
+
110
+### How to stop nagging macOS update alerts
111
+
112
+It is possible to turn off the nagging pop ups.
113
+
114
+- Open System Preferences.
115
+- Click on Software Update.
116
+- Deselect Automatically keep my Mac up to date
117
+
118
+### How to ignore macOS Catalina update on your mac
119
+
120
+```
121
+ sudo softwareupdate --ignore "macOS Catalina"
122
+```
123
+
124
+You will see :
125
+
126
+```
127
+Ignored updates:
128
+(
129
+ "macOS Catalina"
130
+)
131
+```
132
+
133
+You can reverse this later by running :
134
+
135
+```
136
+ sudo softwareupdate --reset-ignored
137
+```
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