AWS.md
... ...
@@ -24,16 +24,15 @@ It is not provided on linux by default but is required by several SBGrid titles.
24 24
Download the SBGrid CLI installation manager.
25 25
26 26
```
27
-curl -LO https://sbgrid.org/wiki/downloads/sbgrid-1.0.694-Linux.tgz
28
-tar -zxvf sbgrid-1.0.694-Linux.tgz
29
-cd sbgrid-1.0.694-Linux
27
+curl -LO https://sbgrid.org/wiki/downloads/sbgrid-cli_2.1.1_linux.tar.gz
28
+tar -zxvf sbgrid-cli_2.1.1_linux.tar.gz
30 29
```
31 30
32 31
### Activate your installation
33 32
If you don't have a username and key, register here : [https://sbgrid.org/registration/register/](https://sbgrid.org/registration/register/)
34 33
35 34
```
36
-./sbgrid activate <site> <user> <key>
35
+./sbgrid-cli activate <site> <user> <key>
37 36
```
38 37
39 38
### Install programs
... ...
@@ -41,7 +40,7 @@ If you don't have a username and key, register here : [https://sbgrid.org/regist
41 40
EPMR as an example here -
42 41
43 42
```
44
-./sbgrid install epmr
43
+./sbgrid-cli install epmr
45 44
```
46 45
47 46
### Run your software
... ...
@@ -51,7 +50,6 @@ Initialize the environment, and the instance is ready to go.
51 50
source /programs/sbgrid.shrc
52 51
```
53 52
54
-
55 53
```
56 54
[ec2-user@ip-172-31-62-107 sbgrid-1.0.694-Linux]$ source /programs/sbgrid.shrc
57 55
********************************************************************************
SBGrid-Wiki.md
... ...
@@ -1,10 +1,19 @@
1
+```
2
+ _______ _____ _ __
3
+ / __/ _ )/ ___/___(_)__/ /
4
+ _\ \/ _ / (_ / __/ / _ /
5
+ /___/____/\___/_/ /_/\_,_/
6
+ C o n s o r t i u m
7
+```
1 8
## Welcome to the SBGrid Consortium Wiki
2 9
3 10
This site provides information on how to install, use, and get help with your SBGrid software installation. Here you can also find information about SBGrid services. Please let us know if you have questions.
4 11
5 12
### Recent Posts
6 13
7
-[2020.12.01 - Notes on MacOS 11 "Big Sur" compatibility](big-sur)
14
+[2021.01.06 - new sbgrid-cli version, 2.1.1](cli_v2.md)
15
+
16
+[2020.12.01 - MacOS 11 "Big Sur" compatibility](big-sur)
8 17
9 18
[2020.10.27 - Examples on changing COOT verions](coot)
10 19
admin_overrides.md
... ...
@@ -2,10 +2,10 @@
2 2
## Site Administrator Overrides
3 3
SBGrid installations allow site-level software control for Administrators
4 4
5
-- [Software Blacklist](#site-administrator-overrides_software-blacklist)
6
-- [Administrator Software Version Overrides](#site-administrator-overrides_administrator-software-version-overrides)
7
-- [Precedence](#site-administrator-overrides_precedence)
8
-
5
+- [Site Administrator Overrides](#site-administrator-overrides)
6
+ - [Software Blacklist](#software-blacklist)
7
+ - [Administrator Software Version Overrides](#administrator-software-version-overrides)
8
+ - [Precedence](#precedence)
9 9
10 10
### Software Blacklist
11 11
Site administrators can prevent the shell initialization files from configuring software on a host by creating an empty file at
... ...
@@ -37,7 +37,7 @@ The overrides are reported during shell initialization:
37 37
```
38 38
Configuration options in effect for this shell:
39 39
Variable Setting Configuration
40
- SPIDER_L 18.10 site
41
- CNS_L 1.21 machine
42
- CCP4_L 6.1.2 personal
40
+ SPIDER_X 18.10 site
41
+ CNS_X 1.21 machine
42
+ CCP4_X 6.1.2 personal
43 43
```
big-sur.md
... ...
@@ -7,9 +7,14 @@ ARM64 compatibility
7 7
8 8
Apple released the first of its new ARM64 "apple silicon" macs this month. 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.
9 9
10
+## Installing SBGrid on Big Sur
11
+
12
+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)
13
+
10 14
### Known issues
11
- - Rosetta ( Baker lab, not Apple) fails
15
+ - No 32-bit support (dropped in Catalina) means no support for nmrDraw, other 32-bit applications.
16
+ - Rosetta ( from Baker lab, not Apple Rosetta2 ) fails
12 17
- CCP-EM ( possibly fixed in latest nightly)
13
- - No compatible release of Schrodinger
18
+ - No compatible release of Schrodinger is currently available
14 19
- No GUI in FLTK applications (like RELION)
15 20
- Xquartz window border takes a few seconds to appear. It does appear eventually.
capsules.md
... ...
@@ -1,13 +1,15 @@
1 1
# SBGrid software environment
2 2
3
-- [Overview](#overview)
4
-- [Getting started](#getting-started)
5
- - [sbcap - Example](#getting-started_sbcap-example)
6
-- [Usage - Capsule Environment for SBGrid](#usage-capsule-environment-for-sbgrid)
7
- - [Overrides - managing versions :](#usage-capsule-environment-for-sbgrid_overrides-managing-versions)
8
- - [Managing Duplicate executables](#usage-capsule-environment-for-sbgrid_managing-duplicate-executables)
9
- - [Managing Duplicate with userpath](#usage-capsule-environment-for-sbgrid_managing-duplicate-userpath)
10
- - [EXAMPLES:](#usage-capsule-environment-for-sbgrid_examples)
3
+- [SBGrid software environment](#sbgrid-software-environment)
4
+ - [Overview](#overview)
5
+ - [Notable features of Capsules](#notable-features-of-capsules)
6
+ - [Getting started](#getting-started)
7
+ - [sbcap - Example](#sbcap---example)
8
+ - [Usage - Capsule Environment for SBGrid](#usage---capsule-environment-for-sbgrid)
9
+ - [Overrides - managing versions :](#overrides---managing-versions-)
10
+ - [Managing Duplicate Executables](#managing-duplicate-executables)
11
+ - [Managing Duplicate with userpath](#managing-duplicate-with-userpath)
12
+ - [EXAMPLES:](#examples)
11 13
12 14
<a name="overview"></a>
13 15
## Overview
... ...
@@ -17,6 +19,12 @@ This environment includes added features for users to manage their software.
17 19
Older features (such as version selection) are still present but improved.
18 20
Old scripts should run unaltered and no new commands are required.
19 21
22
+### Notable features of Capsules
23
+
24
+ - Specify software version on the fly by setting single environment variable
25
+ - Single path entry, minimal environment
26
+ - Compatile with existing software stacks, modules
27
+
20 28
**Check out Carol Herre's [presentation on Capsules on SBGrid TV](https://www.youtube.com/watch?v=baexe9R128A)**
21 29
22 30
<a name="getting-started"></a>
client_downloads.md
... ...
@@ -13,6 +13,15 @@ To install, first mount the .dmg disk image on your Mac. Copy the 'SBGrid instal
13 13
14 14
You may be prompted that the appication is from an "Unidentified Developer". On MacOS, if you try to open an app that is not signed by an Apple-registered developer, you will be prompted by a warning dialog. This doesn’t necessarily mean that something’s wrong with the app. Some apps were written by developers who are not members of the Apple developers program.
15 15
16
+### Command line manager for MacOS and Linux, v2.1.1
17
+
18
+[macOS : 2.1.1, 2020-05-31](downloads/sbgrid-cli_2.1.1_macos.tar.gz)
19
+
20
+[Linux : 2.1.1, 2020-05-31](downloads/sbgrid-cli_2.1.1_linux.tar.gz)
21
+
22
+This is the new command line application with advanced features.
23
+See [this page](cli_v2) for usage info.
24
+
16 25
### Command line manager for MacOS and Linux, v1.0.695
17 26
18 27
[macOS : 1.0.695, 2020-05-31](downloads/sbgrid-1.0.695-Darwin.tgz)
... ...
@@ -25,17 +34,8 @@ This is the original SBGrid CLI install manager.
25 34
Minimal installation required for these binaries and they can be run from any location with no dependencies.
26 35
Untar the archive, make the file executable if necessary and run from your preferred location.
27 36
28
-### Command line manager for MacOS and Linux, v2.1.1
29
-
30
-[macOS : 2.1.1, 2020-05-31](downloads/sbgrid-cli_2.1.1_macos.tar.gz)
31
-
32
-[Linux : 2.1.1, 2020-05-31](downloads/sbgrid-cli_2.1.1_linux.tar.gz)
33
-
34
-New command line application with advanced features.
35
-See [this page](cli_v2) for usage info.
36
-
37 37
### GUI manager 2.0 for MacOS and Linux
38 38
39
-Coming 6/2020!
39
+Coming in 2021!
40 40
Interested in beta testing? Email bugs@sbgrid.org
41 41
![SBGrid](images/new_client_thumb.png)
client_install.md
... ...
@@ -42,8 +42,12 @@ A command line version is also available for mac and linux - installation instru
42 42
**5. For large packages (Phenix, Rosetta, CCP4), a wired connection is recommended.**
43 43
Some packages are quite large and can be slow to download, especially over WiFi.
44 44
45
+
45 46
### Download, Installation and activation
46 47
48
+For macOS Catalina (10.15 and later), a work-around is required for installation. Please see [this page for more info](catalina).
49
+For 10.14 "Mojave" and earlier, this step is not required.
50
+
47 51
**1. Download the latest SBGrid installation manager from here.**
48 52
49 53
[Latest build : 1.0.695, 2020-05-31](downloads/SBGrid_Installer-1.0.695.dmg)
installation_overview.md
... ...
@@ -31,22 +31,23 @@ The SBGrid CLI tool allows users to choose the titles they wish to install using
31 31
Member labs may use any/all of the installation types above for as many Computers as they require. 
32 32
33 33
## Supported Operating Systems
34
-The SBGrid Software Suite can run on Linux, OS X and IRIX machines.
34
+The SBGrid Software Suite can run on Linux and macOS/OS X machines.
35 35
36 36
### Linux
37
-We build and test software under 64-bit CentOS 6. The majority of our Linux users are using the Red Hat / CentOS / Scientific Linux / Fedora distributions. We also have labs using the software with Ubuntu, Debian and OpenSuSE. We don't explicitly test the software on these distributions, but it is known to work. We will work to resolve problems reported by users of these Linux distributions.
37
+We build and test software under 64-bit CentOS 7. The majority of our Linux users are using the Red Hat / CentOS / Scientific Linux / Fedora distributions. We also have labs using the software with Ubuntu, Debian and OpenSuSE. We don't explicitly test the software on these distributions, but it is known to work. We will work to resolve problems reported by users of these Linux distributions.
38 38
39
-We officially support the two most recent releases of Red Hat/CentOS/Scientific Linux (currently 7 and 8, with additional support for 6) 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.
39
+We officially support the two most recent releases of Red Hat/CentOS/Scientific Linux (currently 7 and 8). Only 64-bit versions of linux are supported (though 32-bit software is included in the collection). As of January 2015, we are no longer updating the 32-bit software branch, though we will work to resolve reported problems. We also have a library of IRIX and PowerPC software. If those titles are needed, make a request at bugs@sbgrid.org.
40 40
41 41
Currently Supported:
42 42
43
-* Red Hat Enterprise Linux 6.x, 7.x 8.x and the community supported versions: CentOS and Scientific Linux.
44
-* 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.
43
+* Red Hat Enterprise Linux 7.x and 8.x and the community supported versions: CentOS and Scientific Linux.
44
+* We are no longer building software for RHEL 5.x or 6.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.
45 45
46
-### OS X Intel
46
+### OS X Intel
47 47
We build and test the programs under the most five most recent OS X releases.
48 48
49 49
Currently Supported:
50 50
51 51
* OS X Intel 10.11 - 10.15
52 52
* 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.
53
+* "Apple Silicon" macs can run most of the software in the collection on macOS 11 "Big Sur. Few native applications are currently available, but most software works in our early testing.
... ...
\ No newline at end of file
laptopinstall.md
... ...
@@ -8,3 +8,4 @@ We have a GUI-based installation client for MacOS that allows software to be sel
8 8
9 9
- [Information on installation of our command-line tools for MacOS and Linux](client_CLI_install).
10 10
11
+Our sbgrid-laptop installation shell-script is no longer supported.
operatingsystems.md
... ...
@@ -1,16 +1,16 @@
1 1
## Supported Operating Systems
2 2
3
-The SBGrid Software Suite can run on Linux, OS X and IRIX machines.
3
+The SBGrid Software Suite can run on Linux and macOS/OS X.
4 4
5 5
### Linux
6
-We build and test software under 64-bit CentOS 6 and test on CentOS 6 and 7. The majority of our Linux users are using Red Hat or CentOS distributions, but we also have labs using the software with Ubuntu, Debian and OpenSuSE. We don't explicitly test the software on distributions other than CentOS, but the software is known to work, and we will work to resolve problems reported by users of these Linux distributions.
6
+We build and test software under 64-bit CentOS 7 and 8. The majority of our Linux users are using Red Hat or CentOS distributions, but we also have labs using the software with Ubuntu, Debian and OpenSuSE. We don't explicitly test the software on distributions other than CentOS, but the software is known to work, and we will work to resolve problems reported by users of these Linux distributions.
7 7
8
-We officially support the two most recent releases of Red Hat/CentOS/Scientific Linux (currently 7 and 8, with additonal support for 6). Only 64-bit versions of linux are supported. As of January 2015, we are no longer updating the 32-bit software branch.
8
+We officially support the two most recent releases of Red Hat/CentOS/Scientific Linux (currently 7 and 8). Only 64-bit versions of linux are supported. As of January 2015, we are no longer updating the 32-bit software branch.
9 9
10 10
Currently Supported:
11 11
12
-* Red Hat Enterprise Linux 6.x, 7.x and 8.x and the community supported versions: CentOS and Scientific Linux.
13
-* We are no longer building software for RHEL 5.x.
12
+* Red Hat Enterprise Linux 7.x and 8.x and the community supported versions: CentOS and Scientific Linux.
13
+* We are no longer building software for RHEL 5.x or 6.x.
14 14
15 15
## OS X Intel
16 16
We build and test the programs under the most five most recent OS X releases.
versions.md
... ...
@@ -52,7 +52,6 @@ APPLICATION_X is the name of the application followed by an underscore and the s
52 52
53 53
| Software Directory | Shorthand Initial |
54 54
| ------------------ | ----------------- |
55
-| i386-linux | _L |
56 55
| x86_64-linux | _X |
57 56
| i386-mac | _M |
58 57
... ...
@@ -66,6 +65,5 @@ The example output below shows CCP4 on linux being changed from the default vers
66 65
Variable Setting Configuration
67 66
CCP4_M 6.3.0 personal
68 67
69
-
70 68
## Disabling a Software Package
71 69
To disable a specific software package, set its version to "disable" in your ~/.sbgrid.conf file.
workstation_setup.md
... ...
@@ -11,7 +11,7 @@ Information on configuring 3D stereo can be found [here](stereo)
11 11
12 12
* 64-bit machines need a number of 32-bit compatibility packages due to a number of legacy packages that are only available as 32-bit applications. Additional fonts for Tcl/Tk, Motif and Xview applications are also encouraged.
13 13
14
-Packages for RHEL 6, and 7 and compatible machines:
14
+Packages for RHEL 7, and 8 and compatible machines:
15 15
16 16
yum install glibc.i686 gnome-terminal libgcc.i686 libX11.i686 libXaw.i686 libXext.i686 \
17 17
ncurses.i686 redhat-lsb.i686 xorg-x11-fonts-75dpi xorg-x11-fonts-100dpi xorg-x11-fonts-ISO8859-1-75dpi \