5baf44d09de5c2b352d616c46599eea65bf58c9c
_Sidebar.md
| ... | ... | @@ -3,36 +3,26 @@ |
| 3 | 3 | Installing Software |
| 4 | 4 | |
| 5 | 5 | - [Overview](installation_overview) |
| 6 | -- [Site installation](managing_install) |
|
| 7 | -- [Graphical installation manager](client_install) |
|
| 6 | +- [Site installation](site_installation) |
|
| 7 | +- [Graphical installation manager](sbgrid-gui) |
|
| 8 | 8 | - [Command line installation manager](sbgrid-cli) |
| 9 | -- [Installation on macOS 10.15+ (Catalina, Big Sur)](catalina) |
|
| 10 | -- [Apple Silicon Support](big_sur) |
|
| 9 | +- [Installation on macOS (10.15+ Catalina, Big Sur)](catalina) |
|
| 10 | +- [Apple M1 Silicon Support](apple_silicon) |
|
| 11 | 11 | |
| 12 | 12 | Using the SBGrid Environment |
| 13 | 13 | |
| 14 | 14 | - [Getting Started with SBGrid](getting_started) |
| 15 | -- [Managing Software Versions](versions) |
|
| 16 | 15 | - [SBGrid Capsules Environment](capsules) |
| 17 | -- [SBGrid Legacy Environment](monolithic) |
|
| 16 | +- [Managing Software Versions](versions) |
|
| 18 | 17 | - [Modulefiles for SBGrid](modulefiles) |
| 19 | 18 | |
| 20 | -Getting Help |
|
| 21 | - |
|
| 22 | -- [Software Help and Requests](help) |
|
| 23 | -- [Software Usage Examples](examples) |
|
| 24 | - |
|
| 25 | 19 | Support for Site Administrators |
| 26 | 20 | |
| 27 | -- [Preparing Workstations to run the Software](workstation_setup) |
|
| 21 | +- [Required packages to run the Software](workstation_setup) |
|
| 28 | 22 | - [Managing your Installation](managing_install) |
| 29 | 23 | - [Administrator Software Version Overrides](admin_overrides) |
| 30 | 24 | - [Admins Mailing List](mailinglist) |
| 31 | 25 | |
| 32 | -Support for Developers |
|
| 33 | - |
|
| 34 | -- [Resources for Developers](developers) |
|
| 35 | - |
|
| 36 | 26 | Hardware Support Notes |
| 37 | 27 | |
| 38 | 28 | - [Recommended Hardware](recommended) |
| ... | ... | @@ -40,6 +30,15 @@ Hardware Support Notes |
| 40 | 30 | - [Setup Stereo 3D](stereo) |
| 41 | 31 | - [SBGrid on AWS EC2](AWS) |
| 42 | 32 | |
| 33 | +Getting Help |
|
| 34 | + |
|
| 35 | +- [Software Help and Requests](help) |
|
| 36 | +- [Software Usage Examples](examples) |
|
| 37 | + |
|
| 38 | +Support for Developers |
|
| 39 | + |
|
| 40 | +- [Resources for Developers](developers) |
|
| 41 | + |
|
| 43 | 42 | Portals |
| 44 | 43 | |
| 45 | 44 | - [Data Processing After WSMR](wsmr-worked) |
apple_silicon.md
| ... | ... | @@ -0,0 +1 @@ |
| 1 | +big_sur.md |
|
| ... | ... | \ No newline at end of file |
capsules.md
| ... | ... | @@ -1,6 +1,6 @@ |
| 1 | 1 | # SBGrid software environment |
| 2 | 2 | |
| 3 | -SBGrid Capsules is a new software environment which is significantly faster than the older 'monolithic' shell environment. This environment includes added features for users to manage their software. Older features (such as version selection) are still present but improved. Old scripts should run unaltered and no new commands are required. |
|
| 3 | +The SBGrid Capsule software environment which is significantly faster than the older 'monolithic' shell environment. This environment includes added features for users to manage software versions and duplicate executables. Older features (such as version selection) are still present but improved. Old scripts should run unaltered and no new commands are required. |
|
| 4 | 4 | |
| 5 | 5 | - [SBGrid software environment](#sbgrid-software-environment) |
| 6 | 6 | - [Notable features of Capsules](#notable-features-of-capsules) |
| ... | ... | @@ -12,18 +12,13 @@ SBGrid Capsules is a new software environment which is significantly faster than |
| 12 | 12 | - [Managing Duplicate with userpath](#managing-duplicate-with-userpath) |
| 13 | 13 | - [EXAMPLES:](#examples) |
| 14 | 14 | |
| 15 | -<a name="overview"></a> |
|
| 16 | - |
|
| 17 | 15 | ### Notable features of Capsules |
| 18 | 16 | |
| 19 | 17 | - Specify software version on the fly by setting single environment variable |
| 20 | -- Single path entry, minimal environment |
|
| 18 | +- Single path entry, minimal environment required |
|
| 21 | 19 | - Compatile with existing software stacks, modules |
| 22 | 20 | |
| 23 | 21 | **Check out Carol Herre's [presentation on Capsules on SBGrid TV](https://www.youtube.com/watch?v=baexe9R128A)** |
| 24 | - |
|
| 25 | -<a name="getting-started"></a> |
|
| 26 | - |
|
| 27 | 22 | ## Getting started |
| 28 | 23 | |
| 29 | 24 | You can switch from the legacy SBGrid environment to the new with the _sbcap_ command. _sbcap on_ will enable the capsule environment. |
| ... | ... | @@ -31,8 +26,6 @@ You can always return to the legacy configuration with the _sbcap off_ command a |
| 31 | 26 | |
| 32 | 27 | The sbcap setting is persistent across shells - You don't need to do this for every shell. |
| 33 | 28 | |
| 34 | -<a name="getting-started_sbcap-example"></a> |
|
| 35 | - |
|
| 36 | 29 | ### sbcap - Example |
| 37 | 30 | |
| 38 | 31 | ``` |
| ... | ... | @@ -62,8 +55,6 @@ $ sbcap status |
| 62 | 55 | Active |
| 63 | 56 | ``` |
| 64 | 57 | |
| 65 | -<a name="usage-capsule-environment-for-sbgrid"></a> |
|
| 66 | - |
|
| 67 | 58 | ## Usage - Capsule Environment for SBGrid |
| 68 | 59 | |
| 69 | 60 | ``` |
| ... | ... | @@ -84,8 +75,6 @@ Usage: sbgrid-exectable [ --sbwhich | --sbenv | --sbman | --sbapp:[adlshrH] | - |
| 84 | 75 | sbhelp this message |
| 85 | 76 | ``` |
| 86 | 77 | |
| 87 | -<a name="usage-capsule-environment-for-sbgrid_overrides-managing-versions"></a> |
|
| 88 | - |
|
| 89 | 78 | ### Overrides - managing versions : |
| 90 | 79 | |
| 91 | 80 | Version overrides may be defined in the ~/.sbgrid.conf file, which will be used each time the sbgrid.[sh|csh] file are sourced. A version override can also be instantiated by simply defining the APP_M prior to capsule execution. |
| ... | ... | @@ -108,8 +97,6 @@ We can change this by setting the variable BUSTER_X to 20151214 and calling sbwh |
| 108 | 97 | |
| 109 | 98 | This can also be accomplished by simply setting BUSTER_X=20151214 in the shell or adding the line BUSTER_X=20151214 to your ~/.sbgrid.conf file as [described here](overrides). Note that case is important for the variable names. All SBGrid variable names are ALL CAPS. |
| 110 | 99 | |
| 111 | -<a name="usage-capsule-environment-for-sbgrid_managing-duplicate-executables"></a> |
|
| 112 | - |
|
| 113 | 100 | ### Managing Duplicate Executables |
| 114 | 101 | |
| 115 | 102 | In some cases an executable may exist in multiple applications, i.e. the program _fft_ exists in CCP4 **and** Tigris. A default application is already defined based on what executable would be used in the legacy environment, but the user can choose to override this selectively or permanently. |
| ... | ... | @@ -126,8 +113,6 @@ You can override the default in 4 ways. They are |
| 126 | 113 | |
| 127 | 114 | 4. A localsite file in _${SB_BASE}/local/capsule/${SB_ARCH}/defaults/execname_ |
| 128 | 115 | |
| 129 | -<a name="usage-capsule-environment-for-sbgrid_managing-duplicate-userpath"></a> |
|
| 130 | - |
|
| 131 | 116 | ### Managing Duplicate with userpath |
| 132 | 117 | |
| 133 | 118 | Sometimes a duplicate occurs with an executable that is outside of the SBGrid or BioGrids software tree. For example xterm on x86_64-linux is provided by sbgrid and usually provided by the operating system. A user may use the "userpath" directive to select the one that is accessible from the PATH prior to sourcing the SBGrid/BioGrids environment. |
| ... | ... | @@ -141,8 +126,6 @@ Sometimes a duplicate occurs with an executable that is outside of the SBGrid or |
| 141 | 126 | |
| 142 | 127 | 4. A localsite file in _${SB_BASE}/local/capsule/${SB_ARCH}/defaults/execname_ |
| 143 | 128 | |
| 144 | -<a name="usage-capsule-environment-for-sbgrid_examples"></a> |
|
| 145 | - |
|
| 146 | 129 | ### EXAMPLES: |
| 147 | 130 | |
| 148 | 131 | Which executable am I using? |
catalina.md
| ... | ... | @@ -1,83 +1,23 @@ |
| 1 | 1 | # Using SBGrid with MacOS 10.15+ 'Catalina', 'Big Sur' |
| 2 | 2 | |
| 3 | -SBGrid software is largely compatible with MacOS *Catalina* and *Big Sur*, 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. [More details about compatibility with the latest macOS and Apple hardware can be found here](big-sur.md) |
|
| 3 | +SBGrid software is largely compatible with macOS 10.15 *Catalina* and macOS 11 *Big Sur*, but the installation process requires a reboot after account activation to accomodate new filesystem controls.This is only needed after the initial account activation. |
|
| 4 | 4 | |
| 5 | -<!-- TOC --> |
|
| 5 | +**The latest versions for the SBGrid Installation manager (GUI and CLI) will handle the creation of the required '/etc/synthetic.conf' file automatically. A reboot is required after the activation step, but no other action should be required.** SBGrid software will be available after reboot. |
|
| 6 | 6 | |
| 7 | -- [Using SBGrid with MacOS 10.15+ 'Catalina', 'Big Sur'](#using-sbgrid-with-macos-1015-catalina-big-sur) |
|
| 8 | - - [Activation changes](#activation-changes) |
|
| 9 | - - [Installation : the easy way with the latest command line application sbgrid-cli.](#installation--the-easy-way-with-the-latest-command-line-application-sbgrid-cli) |
|
| 10 | - - [Download the installation manager, sbgrid-cli :](#download-the-installation-manager-sbgrid-cli-) |
|
| 11 | - - [Activate your installation :](#activate-your-installation-) |
|
| 12 | - - [Create link at /programs :](#create-link-at-programs-) |
|
| 13 | - - [Reboot](#reboot) |
|
| 14 | - - [Method 2, SBGrid graphical installation manager, activate by disabling SIP. Requires a few reboots.](#method-2-sbgrid-graphical-installation-manager-activate-by-disabling-sip-requires-a-few-reboots) |
|
| 15 | - - [Disable SIP from Recovery mode](#disable-sip-from-recovery-mode) |
|
| 16 | - - [Remount root filesystem as read/write to create /programs](#remount-root-filesystem-as-readwrite-to-create-programs) |
|
| 17 | - - [Re-enable SIP (optional)](#re-enable-sip-optional) |
|
| 18 | - - [How to stop nagging macOS update alerts](#how-to-stop-nagging-macos-update-alerts) |
|
| 19 | - - [How to ignore macOS Catalina update on your mac](#how-to-ignore-macos-catalina-update-on-your-mac) |
|
| 7 | +Activation instructions: |
|
| 8 | +[Command line : https://sbgrid.org/sbgrid-cli.md](https://sbgrid.org/sbgrid-cli.md) |
|
| 9 | +[Graphical : https://sbgrid.org/sbgrid-gui.md](https://sbgrid.org/sbgrid-gui.md) |
|
| 20 | 10 | |
| 21 | -<!-- /TOC --> |
|
| 11 | +Once the activation process is completed and the system has been rebooted, the manager can be used normally. |
|
| 22 | 12 | |
| 23 | -## Activation changes |
|
| 13 | + - The SBGrid software is then functional, but [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. |
|
| 14 | + - 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) |
|
| 15 | +- 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. |
|
| 16 | + - [More details about compatibility with the latest macOS and Apple hardware can be found here](big-sur.md) |
|
| 24 | 17 | |
| 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. |
|
| 18 | +### Manual creation of the programs path |
|
| 26 | 19 | |
| 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) |
|
| 28 | - |
|
| 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 | -## Installation : the easy way with the latest command line application sbgrid-cli. |
|
| 32 | - |
|
| 33 | -Activation with our latest command-line installation manager is possible in 3 steps, but a reboot is required to add the '/programs' path. |
|
| 34 | - |
|
| 35 | -### Download the installation manager, sbgrid-cli : |
|
| 36 | - |
|
| 37 | -First, download the latest installation manager from here |
|
| 38 | - |
|
| 39 | -[sbgrid-cli version 2.2.18](downloads/sbgrid-cli_2.2.18_macos.tar.gz) |
|
| 40 | - |
|
| 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. |
|
| 43 | - |
|
| 44 | -``` |
|
| 45 | -curl -k -LO https://sbgrid.org/wiki/downloads/sbgrid-cli_2.2.18_macos.tar.gz |
|
| 46 | -``` |
|
| 47 | - |
|
| 48 | -Untar and run the application to test. |
|
| 49 | -Untar : |
|
| 50 | - |
|
| 51 | -``` |
|
| 52 | -tar -zxf sbgrid-cli_2.2.18_macos.tar.gz |
|
| 53 | -``` |
|
| 54 | - |
|
| 55 | -then run : |
|
| 56 | - |
|
| 57 | -``` |
|
| 58 | -./sbgrid-cli |
|
| 59 | -``` |
|
| 60 | - |
|
| 61 | -You should see the application usage info. |
|
| 62 | - |
|
| 63 | -If you see a pop-up warning about "unidentified developer", you likely need to strip apple's quartine extended attribute. |
|
| 64 | -Cancel the dialog and then run this in your terminal: |
|
| 65 | - |
|
| 66 | -``` |
|
| 67 | -xattr -d com.apple.quarantine sbgrid-cli |
|
| 68 | -``` |
|
| 69 | - |
|
| 70 | -You should then be able to run the application normally. |
|
| 71 | - |
|
| 72 | -### Activate your installation : |
|
| 73 | - |
|
| 74 | -To activate, use the credentials provided by email after [registration](https://sbgrid.org/registration/register/). |
|
| 75 | - |
|
| 76 | -``` |
|
| 77 | -./sbgrid-cli activate <your site> <your username> <your key> |
|
| 78 | -``` |
|
| 79 | - |
|
| 80 | -### Create link at /programs : |
|
| 20 | +This process is not typically required with the latest versions of the SBGrid Installation manager, but we have provided the instructions here for reference. |
|
| 81 | 21 | |
| 82 | 22 | The lastest MacOS provides the option to create links in the root partion via the _/etc/synthetic.conf_ file. |
| 83 | 23 | This file has the following format: |
| ... | ... | @@ -98,8 +38,6 @@ sudo /usr/bin/curl -k https://sbgrid.org/wiki/downloads/synthetic.conf -o /etc/s |
| 98 | 38 | |
| 99 | 39 | Then you MUST REBOOT the computer for the changes to take effect. |
| 100 | 40 | |
| 101 | -### Reboot |
|
| 102 | - |
|
| 103 | 41 | You should then see this in your root partition (/) : |
| 104 | 42 | |
| 105 | 43 | ``` |
| ... | ... | @@ -111,15 +49,10 @@ lrwxr-xr-x 1 root wheel 11 Jun 4 14:49 /programs -> /opt/sbgrid |
| 111 | 49 | From there, you can continue to install software with the installation manager, or use the [GUI](https://sbgrid.org/wiki/client_install). |
| 112 | 50 | They are not mutually exclusive. |
| 113 | 51 | |
| 114 | -## Method 2, SBGrid graphical installation manager, activate by disabling SIP. Requires a few reboots. |
|
| 115 | - |
|
| 116 | -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. |
|
| 117 | - |
|
| 118 | -To create the /programs symlink in Catalina without using the /etc/synthetic.conf file, the system filesystem must be remounted as read/write. |
|
| 119 | -To do that in Catalina, system integrity protection (SIP) must be disabled. |
|
| 120 | - |
|
| 121 | 52 | ### Disable SIP from Recovery mode |
| 122 | 53 | |
| 54 | +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. |
|
| 55 | + |
|
| 123 | 56 | - Restart your Mac. |
| 124 | 57 | - 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. |
| 125 | 58 | - From the Utilities menu, select Terminal. |
| ... | ... | @@ -132,23 +65,15 @@ csrutil disable |
| 132 | 65 | - Terminal should display a message that SIP was disabled. |
| 133 | 66 | - From the menu, select Restart. |
| 134 | 67 | |
| 135 | -### Remount root filesystem as read/write to create /programs |
|
| 68 | +### Remount root filesystem as read/write |
|
| 136 | 69 | |
| 137 | -To remount the disk as read/write, run : |
|
| 70 | +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. |
|
| 138 | 71 | |
| 139 | 72 | ``` |
| 140 | 73 | sudo mount -uw / |
| 141 | 74 | ``` |
| 142 | 75 | |
| 143 | -To create the SBGrid /programs link, run : |
|
| 144 | - |
|
| 145 | -``` |
|
| 146 | -sudo ln -s /opt/sbgrid /programs |
|
| 147 | -``` |
|
| 148 | - |
|
| 149 | -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. |
|
| 150 | - |
|
| 151 | -### Re-enable SIP (optional) |
|
| 76 | +### Re-enable SIP |
|
| 152 | 77 | |
| 153 | 78 | - Restart your Mac. |
| 154 | 79 | - 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. |
| ... | ... | @@ -162,7 +87,7 @@ csrutil enable |
| 162 | 87 | - Terminal should display a message that SIP was enabled. |
| 163 | 88 | - From the menu, select Restart. |
| 164 | 89 | |
| 165 | -## How to stop nagging macOS update alerts |
|
| 90 | +### How to stop nagging macOS update alerts |
|
| 166 | 91 | |
| 167 | 92 | It is possible to turn off the nagging pop ups. |
| 168 | 93 |
sbgrid-cli.md
| ... | ... | @@ -70,9 +70,16 @@ First, cancel the dialog and then run this in your terminal: |
| 70 | 70 | xattr -d com.apple.quarantine sbgrid-cli |
| 71 | 71 | ``` |
| 72 | 72 | |
| 73 | -You should then be able to run the application normally without warnings. |
|
| 73 | +You should then be able to run the application normally without warnings) |
|
| 74 | 74 | |
| 75 | ---- |
|
| 75 | +You can use _curl_ to download the tarball directly in your terminal. |
|
| 76 | +This approach has the added benefit of not triggering the macOS "unidentified developer" Gatekeeper response which requires the _xattr_ step below. |
|
| 77 | + |
|
| 78 | +``` |
|
| 79 | +curl -k -LO https://sbgrid.org/wiki/downloads/sbgrid-cli_2.2.18_macos.tar.gz |
|
| 80 | +``` |
|
| 81 | + |
|
| 82 | +Untar and run the application to test. |
|
| 76 | 83 | |
| 77 | 84 | ## General Usage |
| 78 | 85 |
site_installation.md
| ... | ... | @@ -0,0 +1 @@ |
| 1 | +managing_install.md |
|
| ... | ... | \ No newline at end of file |