ee13fa398b4d235eed497c81a89f7b2ac5aba5cc
catalina.md
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| 1 | -# Using SBGrid with MacOS 10.15+ 'Catalina', 'Big Sur' |
|
| 1 | +# 1. Using SBGrid with MacOS 10.15+ 'Catalina', 'Big Sur' |
|
| 2 | + |
|
| 2 | 3 | SBGrid software is largely compatible with MacOS Catalina and later, but the installation process requires a work-around to handle new filesystem controls. These controls impact the 'activation' process of our installation manager and also the ability to install the software. |
| 3 | 4 | |
| 4 | -Once the activation process is completed following the procedure below, the manager can be used normally. The SBGrid software is then functional, though [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. |
|
| 5 | +<!-- TOC --> |
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| 6 | + |
|
| 7 | +- [1. Using SBGrid with MacOS 10.15+ 'Catalina', 'Big Sur'](#1-using-sbgrid-with-macos-1015-catalina-big-sur) |
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| 8 | + - [1.1. Activation changes](#11-activation-changes) |
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| 9 | + - [1.2. Installation : the easy way with the latest command line application sbgrid-cli.](#12-installation--the-easy-way-with-the-latest-command-line-application-sbgrid-cli) |
|
| 10 | + - [1.2.1. Download the installation manager, sbgrid-cli :](#121-download-the-installation-manager-sbgrid-cli-) |
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| 11 | + - [1.2.2. Activate your installation :](#122-activate-your-installation-) |
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| 12 | + - [1.2.3. Create link at /programs :](#123-create-link-at-programs-) |
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| 13 | + - [3.1. Reboot](#31-reboot) |
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| 14 | + - [1.2. Method 2, SBGrid graphical installation manager, activate by disabling SIP. Requires a few reboots.](#12-method-2-sbgrid-graphical-installation-manager-activate-by-disabling-sip-requires-a-few-reboots) |
|
| 15 | + - [1.2.1. Disable SIP from Recovery mode](#121-disable-sip-from-recovery-mode) |
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| 16 | + - [1.2.2. Remount root filesystem as read/write to create /programs](#122-remount-root-filesystem-as-readwrite-to-create-programs) |
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| 17 | + - [1.2.3. Re-enable SIP (optional)](#123-re-enable-sip-optional) |
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| 18 | + - [1.2. How to stop nagging macOS update alerts](#12-how-to-stop-nagging-macos-update-alerts) |
|
| 19 | + - [1.3. How to ignore macOS Catalina update on your mac](#13-how-to-ignore-macos-catalina-update-on-your-mac) |
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| 20 | + |
|
| 21 | +<!-- /TOC --> |
|
| 22 | + |
|
| 23 | +## 1.1. Activation changes |
|
| 24 | + |
|
| 25 | +Once the activation process is completed following the procedure below, the manager can be used normally. The SBGrid software is then functional, though [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. |
|
| 5 | 26 | |
| 6 | -Note that macOS now uses the z-shell (zsh) by default. |
|
| 7 | -This shell is also supported in SBGrid using the standard sbgrid.shrc file. |
|
| 8 | -More info regarding managing your shell on macOS [can be found here](https://support.apple.com/en-us/HT208050) |
|
| 27 | +Note that 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) |
|
| 9 | 28 | |
| 10 | -Also note the XQuartz is required for many applications. |
|
| 11 | -If you have upgraded to Catalina from an 10.14 or earlier, you will need to reinstall XQuartz. |
|
| 12 | -See [https://www.xquartz.org/](https://www.xquartz.org/) for downloads and more info. |
|
| 29 | +Also note the 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. |
|
| 30 | + |
|
| 31 | +## 1.2. Installation : the easy way with the latest command line application sbgrid-cli. |
|
| 13 | 32 | |
| 14 | -## Installation : the easy way with the latest command line application sbgrid-cli. |
|
| 15 | 33 | Activation with our latest command-line installation manager is possible in 3 steps, but a reboot is required to add the '/programs' path. |
| 16 | 34 | |
| 17 | -### 1. Download the installation manager, sbgrid-cli : |
|
| 35 | +### 1.2.1. Download the installation manager, sbgrid-cli : |
|
| 36 | + |
|
| 18 | 37 | First, download the latest installation manager from here |
| 19 | 38 | |
| 20 | 39 | [sbgrid-cli version 2.2.9](downloads/sbgrid-cli_2.2.9_macos.tar.gz) |
| 21 | 40 | |
| 22 | -You can use *curl* to download the tarball directly in your terminal. |
|
| 23 | -This approach has the added benefit of not triggering the macOS "unidentified developer" Gatekeeper response which requires the *xattr* step below. |
|
| 41 | +You can use _curl_ to download the tarball directly in your terminal. |
|
| 42 | +This approach has the added benefit of not triggering the macOS "unidentified developer" Gatekeeper response which requires the _xattr_ step below. |
|
| 24 | 43 | |
| 25 | 44 | ``` |
| 26 | 45 | curl -k -LO https://sbgrid.org/wiki/downloads/sbgrid-cli_2.2.9_macos.tar.gz |
| 27 | 46 | ``` |
| 28 | 47 | |
| 29 | - |
|
| 30 | 48 | Untar and run the application to test. |
| 31 | 49 | Untar : |
| 32 | 50 | |
| ... | ... | @@ -34,7 +52,7 @@ Untar : |
| 34 | 52 | tar -zxf sbgrid-cli_2.2.9_macos.tar.gz |
| 35 | 53 | ``` |
| 36 | 54 | |
| 37 | -then run : |
|
| 55 | +then run : |
|
| 38 | 56 | |
| 39 | 57 | ``` |
| 40 | 58 | ./sbgrid-cli |
| ... | ... | @@ -42,31 +60,35 @@ then run : |
| 42 | 60 | |
| 43 | 61 | You should see the application usage info. |
| 44 | 62 | |
| 45 | -If you see a pop-up warning about "unidentified developer", you likely need to strip apple's quartine extended attribute. |
|
| 63 | +If you see a pop-up warning about "unidentified developer", you likely need to strip apple's quartine extended attribute. |
|
| 46 | 64 | Cancel the dialog and then run this in your terminal: |
| 65 | + |
|
| 47 | 66 | ``` |
| 48 | 67 | xattr -d com.apple.quarantine sbgrid-cli |
| 49 | 68 | ``` |
| 50 | 69 | |
| 51 | -You should then be able to run the application normally. |
|
| 70 | +You should then be able to run the application normally. |
|
| 71 | + |
|
| 72 | +### 1.2.2. Activate your installation : |
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| 52 | 73 | |
| 53 | -### 2. Activate your installation : |
|
| 54 | 74 | To activate, use the credentials provided by email after [registration](https://sbgrid.org/registration/register/). |
| 75 | + |
|
| 55 | 76 | ``` |
| 56 | 77 | ./sbgrid-cli activate <your site> <your username> <your key> |
| 57 | 78 | ``` |
| 58 | 79 | |
| 59 | -### 3. Create link at /programs : |
|
| 60 | -The lastest MacOS provides the option to create links in the root partion via the */etc/synthetic.conf* file. |
|
| 80 | +### 1.2.3. Create link at /programs : |
|
| 81 | + |
|
| 82 | +The lastest MacOS provides the option to create links in the root partion via the _/etc/synthetic.conf_ file. |
|
| 61 | 83 | This file has the following format: |
| 84 | + |
|
| 62 | 85 | ``` |
| 63 | -#link target |
|
| 64 | 86 | programs /opt/sbgrid |
| 65 | 87 | ``` |
| 66 | - |
|
| 67 | -Note that the whitespace MUST be a tab character. Spaces will not work. |
|
| 88 | + |
|
| 89 | +Note that the whitespace MUST be a tab character. Spaces will not work. |
|
| 68 | 90 | Here is a file for reference : [synthetic.conf](downloads/synthetic.conf). |
| 69 | -Thanks to Ron Rock at University of Chicago for pointing this out. |
|
| 91 | +Thanks to Ron Rock at University of Chicago for pointing this out. |
|
| 70 | 92 | |
| 71 | 93 | You can download this file to the proper location on your machine with these two commands: |
| 72 | 94 | |
| ... | ... | @@ -76,11 +98,11 @@ cd /etc |
| 76 | 98 | sudo /usr/bin/curl -k https://sbgrid.org/wiki/downloads/synthetic.conf -o synthetic.conf |
| 77 | 99 | ``` |
| 78 | 100 | |
| 79 | -Then you MUST REBOOT the computer for the changes to take effect. |
|
| 101 | +Then you MUST REBOOT the computer for the changes to take effect. |
|
| 80 | 102 | |
| 81 | -### 4. Reboot |
|
| 103 | +### 3.1. Reboot |
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| 82 | 104 | |
| 83 | -You should then see this in your root partition (/) : |
|
| 105 | +You should then see this in your root partition (/) : |
|
| 84 | 106 | |
| 85 | 107 | ``` |
| 86 | 108 | $ ls -l /programs |
| ... | ... | @@ -88,20 +110,22 @@ You should then see this in your root partition (/) : |
| 88 | 110 | lrwxr-xr-x 1 root wheel 11 Jun 4 14:49 /programs -> /opt/sbgrid |
| 89 | 111 | ``` |
| 90 | 112 | |
| 91 | -From there, you can continue to install software with the installation manager, or use the [GUI](https://sbgrid.org/wiki/client_install). |
|
| 113 | +From there, you can continue to install software with the installation manager, or use the [GUI](https://sbgrid.org/wiki/client_install). |
|
| 92 | 114 | They are not mutually exclusive. |
| 93 | 115 | |
| 94 | -## Method 2, SBGrid graphical installation manager, activate by disabling SIP. Requires a few reboots. |
|
| 95 | -Activation with our graphical installation manager is not compatible with MacOS 10.15 "Catalina" without temporarily disabling System Integrity Protection (SIP). While the approach above is easier and recommended, it is possible to activate with the GUI by following the process below. |
|
| 116 | +## 1.2. Method 2, SBGrid graphical installation manager, activate by disabling SIP. Requires a few reboots. |
|
| 117 | + |
|
| 118 | +Activation with our graphical installation manager is not compatible with MacOS 10.15 "Catalina" without temporarily disabling System Integrity Protection (SIP). While the approach above is easier and recommended, it is possible to activate with the GUI by following the process below. |
|
| 96 | 119 | |
| 97 | -To create the /programs symlink in Catalina without using the /etc/synthetic.conf file, the system filesystem must be remounted as read/write. |
|
| 98 | -To do that in Catalina, system integrity protection (SIP) must be disabled. |
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| 120 | +To create the /programs symlink in Catalina without using the /etc/synthetic.conf file, the system filesystem must be remounted as read/write. |
|
| 121 | +To do that in Catalina, system integrity protection (SIP) must be disabled. |
|
| 122 | + |
|
| 123 | +### 1.2.1. Disable SIP from Recovery mode |
|
| 99 | 124 | |
| 100 | -### 1. Disable SIP from Recovery mode |
|
| 101 | 125 | - Restart your Mac. |
| 102 | 126 | - 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. |
| 103 | 127 | - From the Utilities menu, select Terminal. |
| 104 | -- At the prompt run the following and then press Return: |
|
| 128 | +- At the prompt run the following and then press Return: |
|
| 105 | 129 | |
| 106 | 130 | ``` |
| 107 | 131 | csrutil disable |
| ... | ... | @@ -110,26 +134,28 @@ csrutil disable |
| 110 | 134 | - Terminal should display a message that SIP was disabled. |
| 111 | 135 | - From the menu, select Restart. |
| 112 | 136 | |
| 113 | -### 2. Remount root filesystem as read/write to create /programs |
|
| 114 | - To remount the disk as read/write, run : |
|
| 137 | +### 1.2.2. Remount root filesystem as read/write to create /programs |
|
| 138 | + |
|
| 139 | +To remount the disk as read/write, run : |
|
| 115 | 140 | |
| 116 | 141 | ``` |
| 117 | -sudo mount -uw / |
|
| 142 | +sudo mount -uw / |
|
| 118 | 143 | ``` |
| 119 | 144 | |
| 120 | -To create the SBGrid /programs link, run : |
|
| 145 | +To create the SBGrid /programs link, run : |
|
| 121 | 146 | |
| 122 | 147 | ``` |
| 123 | 148 | sudo ln -s /opt/sbgrid /programs |
| 124 | 149 | ``` |
| 125 | 150 | |
| 126 | -To install the software, you can use the installation manager normally. It will create the required paths and install the software. After the initial installation, you can use the installation manager as in previous MacOS releases, even after the steps below. |
|
| 151 | +To install the software, you can use the installation manager normally. It will create the required paths and install the software. After the initial installation, you can use the installation manager as in previous MacOS releases, even after the steps below. |
|
| 152 | + |
|
| 153 | +### 1.2.3. Re-enable SIP (optional) |
|
| 127 | 154 | |
| 128 | -### 3. Re-enable SIP (optional) |
|
| 129 | 155 | - Restart your Mac. |
| 130 | 156 | - 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. |
| 131 | 157 | - From the Utilities menu, select Terminal. |
| 132 | -- At the prompt, re-enbale SIP with : |
|
| 158 | +- At the prompt, re-enbale SIP with : |
|
| 133 | 159 | |
| 134 | 160 | ``` |
| 135 | 161 | csrutil enable |
| ... | ... | @@ -138,19 +164,21 @@ csrutil enable |
| 138 | 164 | - Terminal should display a message that SIP was enabled. |
| 139 | 165 | - From the menu, select Restart. |
| 140 | 166 | |
| 141 | -## How to stop nagging macOS update alerts |
|
| 142 | -It is possible to turn off the nagging pop ups. |
|
| 167 | +## 1.2. How to stop nagging macOS update alerts |
|
| 168 | + |
|
| 169 | +It is possible to turn off the nagging pop ups. |
|
| 143 | 170 | |
| 144 | 171 | - Open System Preferences. |
| 145 | 172 | - Click on Software Update. |
| 146 | 173 | - Deselect Automatically keep my Mac up to date |
| 147 | 174 | |
| 148 | -## How to ignore macOS Catalina update on your mac |
|
| 175 | +## 1.3. How to ignore macOS Catalina update on your mac |
|
| 176 | + |
|
| 149 | 177 | ``` |
| 150 | 178 | sudo softwareupdate --ignore "macOS Catalina" |
| 151 | 179 | ``` |
| 152 | 180 | |
| 153 | -You will see : |
|
| 181 | +You will see : |
|
| 154 | 182 | |
| 155 | 183 | ``` |
| 156 | 184 | Ignored updates: |
downloads/sbgrid-cli_2.1.5_linux.tar.gz
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downloads/sbgrid-cli_2.1.5_macos.tar.gz
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downloads/sbgrid-cli_2.2.11_linux.tar.gz
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downloads/sbgrid-cli_2.2.11_macos.tar.gz
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downloads/sbgrid-cli_2.2.1_linux.tar.gz
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downloads/sbgrid-cli_2.2.1_macos.tar.gz
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downloads/sbgrid-cli_2.2.2_linux.tar.gz
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downloads/sbgrid-cli_2.2.2_macos.tar.gz
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downloads/sbgrid-cli_2.2.5_linux.tar.gz
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downloads/sbgrid-cli_2.2.5_macos.tar.gz
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downloads/sbgrid-cli_2.2.8_linux.tar.gz
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downloads/sbgrid-cli_2.2.8_macos.tar.gz
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