operatingsystems.md
... ...
@@ -10,15 +10,14 @@ We officially support the two most recent releases of Red Hat/CentOS/Scientific
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Currently Supported:
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* Red Hat Enterprise Linux 6.x and 7.x and the community supported versions: CentOS and Scientific Linux.
13
-* Fedora releases actively supported by the Fedora community. Check https://fedoraproject.org/wiki/Releases for the current list.
14
-* We are no longer building software for RHEL 5.x, but compatible applications will remain in the software tree. We will respond to support requests for these and we will resolve problems where possible. RHEL5 users may not receive the latest versions of software, but RHEL5 systems will continue to be functional and supported.
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+* We are no longer building software for RHEL 5.x, but compatible applications will remain in the software tree. We will respond to support requests for these and we will resolve problems where possible.
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## OS X Intel
17
-We build and test the programs under the most four most recent OS X releases.
16
+We build and test the programs under the most five most recent OS X releases.
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Currently Supported:
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21
-* OS X Intel 10.9 - 10.11
20
+* OS X Intel 10.9 - 10.12
22 21
* As above with earlier versions of linux, there are many software applications that are fully functional on earlier versions of MacOSX in the SBGrid tree. We work to maintain an environment compatible with these OS versions, though they may not receive the latest applications available.
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## OS X PowerPC
usage/_Sidebar.md
... ...
@@ -2,18 +2,18 @@
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3 3
Support for Users
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* [Getting Started with SBGrid](getting_started)
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-* [Software Help and Software Requests](help)
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+* [Software Help and Requests](help)
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* [Supported Operating Systems](operatingsystems)
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-* [Overriding Default Software Versions](versions)
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-* [Install The Software On Your Laptop](laptopinstall)
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-* [Using the SBGrid SHARP server](sharp)
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+* [Overriding Software Versions](versions)
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+* [Install SBGrid: MacOS GUI](client_install)
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+* [Install SBGrid: Command line tools](client_CLI_install)
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+* [SBGrid SHARP server](sharp)
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Support for Site Administrators
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* [Software Installation](installation_admin)
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* [Preparing Workstations to run the Software](workstation_setup)
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* [Managing your Installation](managing_install)
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* [Administrator Software Version Overrides](admin_overrides)
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-* [SBGrid CentOS/Fedora Mirrors](mirrors)
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* [Admins Mailing List](mailinglist)
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Support for Developers
usage/getting_started.md
... ...
@@ -2,6 +2,7 @@
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### Using the SBGrid software collection
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The SBGrid software collection can be found installed at **/programs**.
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+All software in the SBGrid collection is run from the the command line in a terminal. Do set up the shell environment the terminal to run the programs, you will need to initialize the SBGrid environment.
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Bash users should initialize the SBGrid environment using :
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... ...
@@ -15,7 +16,7 @@ On initialization, you should see the SBGrid welcome message
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![SBGrid](images/terminal1.png)
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-### Making the configuration automatic
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+### Making the shell configuration automatic
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To setup your terminal to automatically load the SBGrid environment, add the following to your configuration file:
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usage/laptopinstall.md
... ...
@@ -1,83 +1,36 @@
1
-## Copying the Software Installation
1
+## SBGrid Software Installation : Laptops and Desktops without shared network storage
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-If you run a machine that is frequently disconnected from the network, like a laptop, or don't want to set up an NFS-shared software installation, it is possible to install the software to the hard disk on your local machine.
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+If you would like to install SBGrid tools on a machine that is frequently disconnected from the network, like a laptop, or don't want to set up an NFS-shared software installation, it is possible to install the software to the hard disk on your local machine.
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-There are two scripts in the programs tree that can be used to create a copy of the software on your local hard disk. The ''sbgrid-laptop'' script allows you to select individual applications from the software distribution for installation on your laptop. By default only the latest version of the selected applications will be installed. The ''localsync'' script allows you to copy an entire operating system software branch to your local machine. This script can be used on laptops, but each branch is quite large in terms of disk space usage.
5
+We have a GUI-based installation client for MacOS that allows software to be selected, installed, and updated on demand from SBGrid servers. There is also a command-line client for MacOS and Linux that will allow installation and upgrade of individual titles from the command line.
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-### Laptop installation
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+ - [Information on installation of our MacOS GUI.](client_install)
8 8
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-We have two options for installation of selected applications from the SBGrid software tree.
9
+ - [Information on installation of our command-line tools for MacOS and Linux](client_CLI_install).
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- * *sbgrid-sync*
12
- - This script installs software from SBGrid's servers.
13
- - an account on SBGrid's server is required. To request one, email accounts@sbgrid.org.
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-
15
-
16
- * *laptop-sync*
17
- - This script installs software from your own local installation.
18
- - This script requires an account on a local machine with access to the SBGrid softare collection.
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-
20
-### sbgrid-sync
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-
22
-This script can be found in the programs installation at */programs/share/bin/sbgrid-sync*.
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-
24
-```
25
-sbgrid-sync: install or update the SBGrid Consortium software
26
- collection on your laptop or workstation.
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-
28
-You will need a Consortium UNIX account to install and update your
29
-installation. If you don't have an account or don't remember your password,
30
-please email <accounts@sbgrid.org> for assistance.
11
+### Script-based installation tools
31 12
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-This script will create an SSH key and run an SSH agent process to handle
33
-authentication for the file transfers. Unless otherwise configured only the
34
-default version of the software titles will be installed.
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-
36
-Usage: sbgrid-sync [-iesudt]
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-
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-Install/Configure Options:
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-
40
- -i Initial set up and installation of the SBGrid software.
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- -e Edit the software download list.
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-
43
-Update Options:
13
+While we recommend the software tools above, if you would like to install your software from a local source, there are script-based tools in the SBGrid programs tree that will create a copy of the software on your local hard disk.
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- -u Update an existing installation using the current
46
- configuration.
15
+The 'sbgrid-laptop' script allows you to select individual applications from the software distribution for installation on your laptop. By default only the latest version of the selected applications will be installed. The 'localsync' script allows you to copy an entire operating system software branch to your local machine. This script can be used on laptops, but each branch is quite large in terms of disk space usage. Finally, the 'sbgrid-sync' script will allow you to install software from SBGrid servers. This script is deprecated in favor of the better CLI tools above and its use is discouraged.
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-Troubleshooting Options:
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- -d Debug mode creates a log file for troubleshooting purposes.
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- -t Test your current configuration.
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-
53
-```
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-
55
-Once an account has be created at SBGrid, the software can be installed with for a username (at SBGrid) and a path for the software installation. the -i flag. The user will be prompted with a list of software to add.
18
+ * *laptop-sync*
19
+ - This script installs software from your own **local** installation.
20
+ - This script requires an account on a local machine with access to the SBGrid softare collection.
21
+ - Only latest versions will be installed.
56 22
57
-![sync software list ](images/sbgrid-sync_software_list.png "sbgrid-sync software list")
58 23
59
-```
60
-| We need to create a list of software you want included in the local
61
-| installation. We will start with a list of all the software titles.
62
-| Remove the leading hash mark (#) to _include_ a software title.
63
-```
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-Any titles NOT preceded with a '#' character will be installed.
65
-```
66
-| Save and _QUIT_ the text editor after making your changes. If you are
67
-| using TextEdit on a Mac, you must completely quit (Apple-Q) the
68
-| application to continue.
69
-```
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-Once the editor has quit, software installation will start.
71
-
72
-```
73
-| Creating an rsync include list to download files.
74
-| Running rsync to download the latest software.
75
-```
76
-Once installation is completed, open a new terminal and
24
+ * *localsync*
25
+ - This script installs software from your own **local** installation.
26
+ - This script requires an account on a local machine with access to the SBGrid softare collection.
27
+ - All versions of the software will be installed.
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78
- source /programs/sbgrid.shrc
79 29
80
-to get started.
30
+ * *sbgrid-sync (deprecated)*
31
+ - This script installs software from SBGrid's servers.
32
+ - an account on SBGrid's server is required.
33
+ - THIS INSTALL METHOD WILL NO LONGER BE SUPPORTED IN A FUTURE RELEASE.
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### laptop-sync
... ...
@@ -104,10 +57,10 @@ You can create a customized local installation of the software using the ''sbgri
104 57
to use this script. The script will create an SSH key and run an SSH
105 58
agent process to handle authentication for the file transfers.
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107
-
108 60
Copy the script the machine you want to install the software on, and then run it in install mode: ''./sbgrid-laptop -i''. Follow the prompts on the screen to create your configuration file, your software installation list and to enable logins using an SSH key for authentication.
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-### Sync Script
62
+
63
+### localsync Sync Script
111 64
There is a script in the programs tree that can be used to copy the appropriate branch from a shared installation to your laptop or workstation.
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Copy /programs/share/bin/localsync from the machine that has the software to your home directory on the standalone machine:
... ...
@@ -140,7 +93,7 @@ This will copy the entire branch for your architecture to your local hard drive.
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You should use a network cable for the initial download, since the download is fairly large. Subsequent runs of the 'localsync' script are differential; they will only copy new or changed files, so they can be run over a wireless connection. The script can be run at any time to make your local installation match the installation on your local server.
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-# Sharing a Software Installation without NFS
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+### Sharing a 'localsync' Software Installation without NFS
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While we recommend that sites export their software installation via NFS to their workstations, it is possible to use rsync to copy the master installation to each workstation. This method has the drawback that it requires manual intervention on the part of the local sysadmin, and updates will not be instantaneous or simultaneous for all machines.
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... ...
@@ -230,5 +183,67 @@ bash
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crontab -l
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-
234 186
You're done!
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+
188
+
189
+### sbgrid-sync (DEPRECATED)
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+
191
+This script can be found in the programs installation at */programs/share/bin/sbgrid-sync*.
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+
193
+```
194
+sbgrid-sync: install or update the SBGrid Consortium software
195
+ collection on your laptop or workstation.
196
+
197
+You will need a Consortium UNIX account to install and update your
198
+installation. If you don't have an account or don't remember your password,
199
+please email <accounts@sbgrid.org> for assistance.
200
+
201
+This script will create an SSH key and run an SSH agent process to handle
202
+authentication for the file transfers. Unless otherwise configured only the
203
+default version of the software titles will be installed.
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+
205
+Usage: sbgrid-sync [-iesudt]
206
+
207
+Install/Configure Options:
208
+
209
+ -i Initial set up and installation of the SBGrid software.
210
+ -e Edit the software download list.
211
+
212
+Update Options:
213
+
214
+ -u Update an existing installation using the current
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+ configuration.
216
+
217
+Troubleshooting Options:
218
+
219
+ -d Debug mode creates a log file for troubleshooting purposes.
220
+ -t Test your current configuration.
221
+
222
+```
223
+
224
+Once an account has be created at SBGrid, the software can be installed with for a username (at SBGrid) and a path for the software installation. the -i flag. The user will be prompted with a list of software to add.
225
+
226
+![sync software list ](images/sbgrid-sync_software_list.png "sbgrid-sync software list")
227
+
228
+```
229
+| We need to create a list of software you want included in the local
230
+| installation. We will start with a list of all the software titles.
231
+| Remove the leading hash mark (#) to _include_ a software title.
232
+```
233
+Any titles NOT preceded with a '#' character will be installed.
234
+```
235
+| Save and _QUIT_ the text editor after making your changes. If you are
236
+| using TextEdit on a Mac, you must completely quit (Apple-Q) the
237
+| application to continue.
238
+```
239
+Once the editor has quit, software installation will start.
240
+
241
+```
242
+| Creating an rsync include list to download files.
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+| Running rsync to download the latest software.
244
+```
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+Once installation is completed, open a new terminal and
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+
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+ source /programs/sbgrid.shrc
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+
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+to get started.
usage/managing_install.md
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@@ -7,6 +7,8 @@ We refer to this computer as the site "master" server.
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The master server will require at least 250 GB of free disk space on a case-sensitive file system and must run some variety of UNIX. The installation script will download the software branches you select, and then install a cron job that will run regularly to check for updates.
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+Software installation and update are initiated from your local server at your site and downloaded from our servers. http is used to query our servers to check for update, and rsync is used to download the updates. Outbound HTTP, and RSYNC is necessary.
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+
10 12
![NFS-based installation](images/site_diagram.png "NFS-based installation")
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## Pre-Installation
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@@ -16,6 +18,15 @@ The master server will require at least 250 GB of free disk space on a case-sens
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| Hard Drive Space | 250 GB required |
17 19
| Operating System | Linux, OS X and other UNIX |
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| Privileges | Root account (Linux) or Administrator account (Mac) |
21
+| network | Outbound http, rsync (ports 80 and 873, 8080) |
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+
23
+
24
+### Approximate size per Branch
25
+| Branch | size |
26
+| ------------ | ------ |
27
+| i386-mac | 86Gb |
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+| x86_64-linux | 105Gb |
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+| shared files | 12Gb |
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Email [accounts@sbgrid.org](accounts@sbgrid.org) to request the installation script for the software. Be sure to include the following information in your email:
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usage/operatingsystems.md
... ...
@@ -8,25 +8,28 @@ We build and test software under 64-bit Red Hat 6. The majority of our Linux us
8 8
We officially support the two most recent releases of Red Hat/CentOS/Scientific Linux (currently 6 and 7) and the two most recent releases of Fedora Linux. At this time, only 64-bit versions of linux are fully supported. As of January 2015, we are no longer updating the 32-bit software branch, though we will work to resolve reported problems.
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Currently Supported:
11
- * Red Hat Enterprise Linux 6.x and 7.x and the community supported versions: CentOS and Scientific Linux.
12
- * Fedora releases actively supported by the Fedora community. Check https://fedoraproject.org/wiki/Releases for the current list.
13
- * We are no longer building software for RHEL 5.x, but compatible applications will remain in the software tree. We will respond to support requests for these and we will resolve problems where possible. RHEL5 users may not receive the latest versions of software, but RHEL5 systems will continue to be functional and supported.
11
+
12
+* Red Hat Enterprise Linux 6.x and 7.x and the community supported versions: CentOS and Scientific Linux.
13
+* We are no longer building software for RHEL 5.x, but compatible applications will remain in the software tree. We will respond to support requests for these and we will resolve problems where possible.
14 14
15 15
## OS X Intel
16
-We build and test the programs under the most four most recent OS X releases.
16
+We build and test the programs under the most five most recent OS X releases.
17 17
18 18
Currently Supported:
19
- * OS X Intel 10.9 - 10.11
20
- * As above with earlier versions of linux, there are many software applications that are fully functional on earlier versions of MacOSX in the SBGrid tree. We work to maintain an environment compatible with these OS versions, though they may not receive the latest applications available.
19
+
20
+* OS X Intel 10.9 - 10.12
21
+* As above with earlier versions of linux, there are many software applications that are fully functional on earlier versions of MacOSX in the SBGrid tree. We work to maintain an environment compatible with these OS versions, though they may not receive the latest applications available.
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## OS X PowerPC
23 24
The OS X PowerPC branch is currently frozen. The applications are stable and work well on our PowerPC hardware, but they are not being updated.
24 25
25 26
Currently Supported:
26
- * OS X PowerPC 10.4 - 10.5
27
+
28
+* OS X PowerPC 10.4 - 10.5
27 29
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## IRIX
29 31
The IRIX programs branch is currently frozen. The applications are stable and work well on our SGI hardware, but they are not being updated.
30 32
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Currently Supported:
32
- * IRIX 6.5.26 + bugfix releases
34
+
35
+* IRIX 6.5.26 + bugfix releases
usage/versions.md
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@@ -50,11 +50,11 @@ The override file is named .sbgrid.conf and should be placed in your $HOME direc
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APPLICATION_X is the name of the application followed by an underscore and the shorthand initial for the architecture. The last field on the line is the software version number you want to use. The initials for each software branch are:
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- | Software Directory | Shorthand Initial |
54
- | :----------------- | :---------------- |
55
- | i386-linux | _L |
56
- | x86_64-linux | _X |
57
- | i386-mac | _M |
53
+| Software Directory | Shorthand Initial |
54
+| ------------------ | ----------------- |
55
+| i386-linux | _L |
56
+| x86_64-linux | _X |
57
+| i386-mac | _M |
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To quickly open the overrides file in your default $EDITOR, you can run *sbgrid-overrides -e*.
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