usage/Home.md
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usage/README.md
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+SBGrid-Wiki.md
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usage/SBGrid-Wiki.md
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+## Welcome to the SBGrid Consortium Wiki
2
+![SBGrid](images/terminal.png)
3
+
4
+This site provides information on how to install, use, and get help with your SBGrid software collection. We also include some information about SBGrid services. Please let us know if you have questions.
usage/_Sidebar.md
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+![SBGrid](images/sbgrid_small_logo.gif) **[SBGrid Wiki](Home)**
2
+
3
+SBGrid Consortium Support for Users
4
+* [Software Help](help)
5
+* [New Software Requests](help)
6
+* [Supported Operating Systems](operatingsystems)
7
+* [Overriding Default Software Versions](usage/versions)
8
+* [Install The Software On Your Laptop](laptopinstall)
9
+* [Using the SBGrid SHARP server](sharp)
10
+
11
+SBGrid Consortium Support for Site Administrators
12
+* [Software Installation](installation_admin)
13
+* [Preparing Workstations to run the Software](workstation_setup)
14
+* [Managing your Installation](managing_install)
15
+* [Administrator Software Version Overrides](admin_overrides)
16
+* [SBGrid CentOS/Fedora Mirrors](mirrors)
17
+* [Admins Mailing List](mailinglist)
18
+
19
+SBGrid Consortium Support for Developers
20
+* [Resources for Developers](developers)
21
+* [Build and Test Network](resources)
22
+
23
+Hardware Support Notes
24
+* [SBGrid Recommended Hardware](recommended)
25
+* [Setup Stereo 3D](stereo)
usage/admin_overrides.md
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+## Site Administrator Overrides
2
+
3
+### Software Blacklist
4
+Site administrators can prevent the shell initialization files from configuring software on a host by creating an empty file at
5
+
6
+ **/programs/local/conf/disabled-hosts/<hostname>**
7
+
8
+where **<hostname>** is the output of the //hostname -s// command. This is useful for encouraging users not to run jobs on bastion hosts, file servers, etc.
9
+
10
+### Administrator Software Version Overrides
11
+Most of the software titles installed in the SBGrid Suite have several versions available. Typically, we try to provide at least three versions of each software package, although very old or very new applications may have fewer versions.
12
+
13
+There are two methods for site admins to configure version overrides using files placed in a **/programs/local/conf/** directory.
14
+
15
+- Site-wide Version Overrides
16
+A file named **site.conf** will be read when any SBGrid shell is initialized from the installation.
17
+
18
+- Per-host Version Overrides
19
+A file named **<hostname.conf>**, where **<hostname>** is the output of the //hostname -s// command, will be read after the site.conf on the host matching that hostname.
20
+
21
+### Precedence
22
+There are three files that will be examined for version overrides during shell initialization. In order from lowest to highest precedence:
23
+
24
+ * /programs/local/conf/site.conf
25
+ * /programs/local/conf/<hostname.conf>
26
+ * $HOME/.sbgrid.conf
27
+
28
+The overrides are reported during shell initialization:
29
+
30
+```
31
+ Configuration options in effect for this shell:
32
+ Variable Setting Configuration
33
+ SPIDER_L 18.10 site
34
+ CNS_L 1.21 machine
35
+ CCP4_L 6.1.2 personal
36
+```
usage/developers.md
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+## SBGrid Developer Support Program
2
+In an effort to show our appreciation for their hard work and to encourage the continuing development and support of cutting edge structural biology software, SBGrid offers a Developer Support Program featuring a wide array of benefits for structural biology software developers.
3
+
4
+### Developer Network
5
+We can provide access to a dedicated development and test network for software developers. As a developer of an SBGrid supported application, you can request an account on this network and use our infrastructure to build and test your application on a wide range of operating systems. Visit the [developer network page](resources) for more details.
6
+
7
+### Support Letters
8
+When applying for grants or financial support please let us know! We can provide support letters on behalf of members of SBGrid Consortium. Letters would include details about our membership, number of computers that can access your software, operating systems used by our community, etc. Please use the [contact form](http://sbgrid.org/contact.php|contact) on the SBGrid website.
9
+
10
+### Software Beta Testing
11
+You are welcome to use SBGrid laboratories to beta-test your software. Just let us know when the new beta is available, and we will install it for all participating laboratories or a limited subset that you choose.
12
+
13
+### SBGrid Consortium Membership
14
+If your application is under active maintenance or development, your development group is entitled to free membership in the consortium. Letting us maintain your general structural biology software environment leaves you with more time to concentrate on your unique software contribution to the community.
15
+
16
+### Annual Software Awards
17
+Members of SBGrid Consortium vote in an annual poll to select their favorite structural biology application. Paul Emsley was the winner of the first poll. He won a Macbook Air laptop for his application Coot.
18
+
19
+### Stretch Your Resources
20
+First level software support is provided by the SBGrid non-profit center at Harvard Medical School. All members of the consortium communicate with the service center for assistance with software installation, upgrades, and basic troubleshooting. For many of the mundane problems involving installation, operating system portability and environmental set up, SBGrid members will never need to contact you for support. Your expertise with the software be best utilized answering questions and working on problems that directly involve the science behind your application.
21
+
22
+### Broad Exposure for Your Software
23
+More than 140 structural biology laboratories from 50 institutions in 11 countries participate in the Consortium including the labs of 25 HHMI investigators and 2 Nobel Prize winners. Deployment of your application can be customized to include only non-profit labs or broadened to include industry labs as well. Please visit the Consortium website for the full list of participating groups that can benefit from rapid access to your software. Please note that most SBGrid Consortium laboratories standardize on hardware and operating systems, which simplifies the installation and support process.
24
+
25
+### Connect With Users
26
+Announcing a new version of your software? We can use webex to broadcast your presentation to all laboratories participating in our consortium. We can also disseminate information about your application to our community in our monthly newsletter. Visiting Boston? Please let us know because we'd love to schedule a seminar for members of our local structural biology community.
usage/help.md
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+## Software Help
2
+
3
+If you are having a problem with software included in the SBGrid suite or think you've discovered an application bug, please use the [SBGrid](http://sbgrid.org/bugs) web form to alert us to the problem. You can also email bugs@sbgrid.org with details on the problem, but the web form is the preferred method.
4
+
5
+If the problem with the software started after an update, you can configure your SBGrid environment to [use an older version of the software](overrides).
6
+
7
+### New Software and Software Updates
8
+To request a new software package or an update to an existing package, please use the [Software](http://sbgrid.org/req) Update/Installation Request form]].
9
+
10
+We try to accommodate most requests for new software, but we do occasionally run into difficulties. Despite most of our software being free for academics, some developers insist that each lab download and install their own software. We are happy to provide developers with the list of SBGrid members that have access to their software, but that doesn't always satisfy their requirements.
11
+
12
+Even when things go smoothly, license requests and working out licensing details with developers can take some time, so please don't wait until the last minute before requesting software you anticipate you may need for your project.
13
+
14
+### Newsletter
15
+SBGrid sends a monthly newsletter with information concerning software updates, upcoming webinars, talks and other items of interest to our community. The archive of previous newsletters is available online at the [SBGrid Newsletter Archive](https://sbgrid.org/newsletters/).
usage/installation_admin.md
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+##Managing Your Software Installation
2
+
3
+### *sbgrid-admin* Utility
4
+The *sbgrid-admin* utility used to install the software has a few other uses. There is a download link in the initial site set up email, and it is included in the installation itself at */programs/share/sbgrid/bin/sbgrid-admin*. It includes built-in help:
5
+
6
+```
7
+ $ sbgrid-admin -h
8
+sbgrid-admin: a tool for administering an SBGrid Software suite installation
9
+
10
+Usage: sbgrid-admin [-chirstu]
11
+
12
+ -c Cron mode. Used for automated updates of the software suite.
13
+ -h Help message.
14
+ -i Install the software suite on this machine.
15
+ -p Print a launchd plist for updating the software on OS X machines.
16
+ -r Regenerate sh/csh shell configuration files.
17
+ -s Install the software branch for SGI IRIX.
18
+ -t Test the configuration file.
19
+ -u Force manual update of an existing installation.
20
+```
21
+
22
+The most commonly used option is *sbgrid-admin -u* to force a manual update. This will synchronize your local installation with the SBGrid master installation hosted at Harvard Medical School.
23
+
24
+The SBGrid software configuration files use both static and dynamically generated files. The main shell initialization files, **/programs/sbgrid.cshrc** and **/programs/sbgrid.shrc** are static files, but the operating-system specific configurations are dynamically generated and customized for the packages available at your site. *sbgrid-admin -r* will regenerate the branch-specific configuration files should you accidentally delete or alter them.
25
+
26
+ Configuration Options
27
+The *sbgrid-admin* script has some additional configuration options to accommodate the installation requirements at different sites.
28
+
29
+The ~sbgrid/.sbgridrc configuration file for the *sbgrid-admin* script must contain a sitename and site key. All other configurations are optional.
30
+
31
+Options take the form of *OPTION_NAME="setting"*.
32
+
33
+| **Option** |** Example** | **Description** |
34
+|:------------- |:-------------:| :---------------|
35
+| SB_SITENAME | sbgrid-bene | The site name for your installation provided by SBGrid |
36
+| SB_SITEKEY | xyxyxyxyxyxyxy | The installation key for your site provided by SBGrid |
37
+| INSTALL_TARGET| /nfs/programs | The installation directory for the software |
38
+| RSYNC_ARGS | "%%--%%port 8080"| Advanced arguments to rsync. Can be used to workaround blocked rsync ports. |
39
+| HTTP_PROXY | host.name:port | Proxy hostname and port for use by rsync and curl |
40
+| POST_UPDATE_SCRIPT | /absolute/path/to/script|Optional script to be run after a successful software update |
41
+| CRON_SCHEDULE | 5 1 * * * | Set a custom cron schedule |
42
+
43
+
44
+ Rsync Transaction Logging
45
+If you want a date-stamped log of all rsync downloads, deletions and updates, you can add a line like this to the ~sbgrid/.sbgridrc file:
46
+
47
+```
48
+RSYNC_ARGS="--log-file=$HOME/logs/sbgrid-admin-`date +%Y%m%d`.log"
49
+```
50
+
51
+This will create a date-stamped log file any time an actual change to the software tree happens. In general this should not be necessary, but for troubleshooting purposes it can be useful.
usage/laptopinstall.md
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1
+## Copying the Software Installation
2
+
3
+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.
4
+
5
+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.
6
+
7
+### Laptop installation
8
+
9
+We have two options for installation of selected applications from the SBGrid software tree.
10
+
11
+ * *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.
14
+
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.
19
+
20
+### sbgrid-sync
21
+
22
+This script can be found in the programs installation at */programs/share/bin/sbgrid-sync*.
23
+
24
+```
25
+sbgrid-sync: install or update the SBGrid Consortium software
26
+ collection on your laptop or workstation.
27
+
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.
31
+
32
+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.
35
+
36
+Usage: sbgrid-sync [-iesudt]
37
+
38
+Install/Configure Options:
39
+
40
+ -i Initial set up and installation of the SBGrid software.
41
+ -e Edit the software download list.
42
+
43
+Update Options:
44
+
45
+ -u Update an existing installation using the current
46
+ configuration.
47
+
48
+Troubleshooting Options:
49
+
50
+ -d Debug mode creates a log file for troubleshooting purposes.
51
+ -t Test your current configuration.
52
+
53
+```
54
+
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.
56
+
57
+![sync software list ](sbgrid-sync_software_list.png "sbgrid-sync software list")
58
+
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
+```
64
+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
+```
70
+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
77
+
78
+ source /programs/sbgrid.shrc
79
+
80
+to get started.
81
+
82
+
83
+### laptop-sync
84
+You can create a customized local installation of the software using the ''sbgrid-laptop'' script located at ''/programs/share/bin/sbgrid-laptop''. This script requires you to have an SSH login to a computer that has access to an SBGrid software installation and will let you specify which packages you want to install.
85
+
86
+```
87
+ sbgrid-laptop: a tool for creating a local installation of the
88
+ SBGrid software on a laptop.
89
+
90
+ Usage: sbgrid-laptop [-ituv] [-e list|config]
91
+
92
+ -d Debug mode creates a log file for troubleshooting purposes.
93
+ -e [list|config]
94
+ Edit the software download list.
95
+ -i Initial set up and installation of the SBGrid software.
96
+ -s Re-run SSH key set up process.
97
+ -t Test your current configuration.
98
+ -u Update an existing installation using the current
99
+ configuration.
100
+ -v Verbose option for the file transfer.
101
+```
102
+
103
+ You need an SSH login to a machine with the SBGrid software installed
104
+ to use this script. The script will create an SSH key and run an SSH
105
+ agent process to handle authentication for the file transfers.
106
+
107
+
108
+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.
109
+
110
+### Sync Script
111
+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.
112
+
113
+Copy /programs/share/bin/localsync from the machine that has the software to your home directory on the standalone machine:
114
+
115
+
116
+ scp your.server.name:/programs/share/bin/localsync ~/
117
+
118
+
119
+Then run the script like this:
120
+
121
+ chmod 755 ~/localsync
122
+ ~/localsync yourusername@your.server.name
123
+
124
+
125
+The script will prompt you for your sudo (admin) password in order to create the programs directory, and then it will prompt you for your login password to the server that hosts your programs installation.
126
+
127
+Here is an example run on my workstation:
128
+
129
+```
130
+ $ ./localsync bene@developer.sbgrid.org
131
+ Running 'sudo mkdir /programs && sudo chown bene /programs'
132
+ [sudo] password for bene:
133
+ Copying the software from the i386-mac branch on your server to your local
134
+ hard disk. Enter your ssh login password below for bene@developer.sbgrid.org:
135
+
136
+ receiving file list ...
137
+```
138
+
139
+This will copy the entire branch for your architecture to your local hard drive. For the OS X branch, this will use approximately 100 GB of disk space.
140
+
141
+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.
142
+
143
+# Sharing a Software Installation without NFS
144
+
145
+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.
146
+
147
+On each client machine, you'll need an 'sbgrid' user. That user will have a passphraseless ssh key that lets it log into the machine that hosts your primary installation. Each client machine will have a cron job for that sbgrid user that runs at 2 AM that will sync the programs from the master installation to the client machine.
148
+
149
+Here is a basic command run down. 'server1' holds the programs installation and 'client1' is what will be connecting to it.
150
+
151
+ * Login as root/administrator on client1
152
+ * Create the 'sbgrid' user on client1
153
+ * Check the free space on /.
154
+ * If there's enough free space, set up the programs directory:
155
+
156
+
157
+ mkdir /programs
158
+ chown -R sbgrid:sbgrid /programs
159
+
160
+ * If there is not enough free space on the root volume, you'll need to find space on a local volume.
161
+
162
+ * Login as 'sbgrid' on client1.
163
+ * Create the passphraseless ssh key:
164
+
165
+
166
+ ssh-keygen -d
167
+
168
+
169
+(hit enter to confirm default file location, no passphrase, etc)
170
+
171
+ * Copy the ssh key to server1:
172
+
173
+
174
+ cat ~/.ssh/id_dsa.pub | ssh server1 'cat - >> ~/.ssh/authorized_keys'
175
+
176
+ * Copy the localsync script from server1 to client1. From client1:
177
+
178
+
179
+ scp sbgrid@server1:/programs/share/bin/localsync .
180
+
181
+
182
+(May prompt to accept the host key. If you can't login without a password, the ssh key stuff above has failed, and you'll need to troubleshoot that.)
183
+
184
+ chmod 755 localsync
185
+ ./localsync sbgrid@server1
186
+
187
+(This will take a while depending on the speed of the machines/network.)
188
+
189
+ * Test the installation:
190
+
191
+
192
+tcsh
193
+
194
+ source /programs/sbgrid.cshrc
195
+
196
+or
197
+bash
198
+
199
+ source /programs/sbgrid.shrc
200
+
201
+
202
+(You should get a message like this: )
203
+```
204
+ Welcome to SBGrid!
205
+
206
+********************************************************************************
207
+ Your use of the applications contained in the /programs directory constitutes
208
+ acceptance of the terms of the SBGrid License Agreement included in the file
209
+ /programs/share/LICENSE. The applications distributed by SBGrid are licensed
210
+ exclusively to member laboratories of the SBGrid Consortium.
211
+
212
+ To hush this license message, run 'touch ~/.agree2sbgrid'.
213
+
214
+********************************************************************************
215
+ Please submit bug reports and help requests to: `<bugs@sbgrid.org>` or
216
+ `<http://sbgrid.org/bugs>`
217
+ This installation last updated: 20110411
218
+
219
+********************************************************************************
220
+ Total time to initialize: 1 second(s)
221
+```
222
+
223
+ * Add a cronjob for the updates. As the 'sbgrid' user on client1:
224
+
225
+
226
+ echo "0 2 * * * ~/localsync sbgrid@server1" | crontab
227
+
228
+ * Check the cronjob:
229
+
230
+
231
+ crontab -l
232
+
233
+
234
+You're done!
usage/mailinglist.md
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1
+## Mailing List for Site Administrators
2
+
3
+We have a small mailing list for technical users and site administrators.
4
+
5
+Visit the [SBGrid-tech mailing list](https///cmcd.hms.harvard.edu/sympa/info/sbgrid-tech) page to sign up.
usage/managing_install.md
... ...
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1
+# HOWTOs: SBGrid Installation Notes
2
+
3
+## Site Configuration
4
+
5
+The SBGrid Software Suite is designed to be installed on a single computer at your site, which will then share that installation with all the workstations on your network via NFS.
6
+We refer to this computer as the site "master" server.
7
+
8
+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.
9
+
10
+![NFS-based installation](images/site_diagram.png "NFS-based installation")
11
+
12
+## Pre-Installation
13
+```
14
+ | Installation Requirements | |
15
+ | ------------------------- | ----------------------------------------------------|
16
+ | Hard Drive Space | 250 GB required |
17
+ | Operating System | Linux, OS X and other UNIX |
18
+ | Privileges | Root account (Linux) or Administrator account (Mac) |
19
+```
20
+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:
21
+
22
+ * Lab Name
23
+ * Types of computers on site: Linux, OS X Intel, OS X PowerPC, IRIX
24
+ * The names and email addresses of lab members that will use the software. One user may be designated to receive the majority of our correspondence if you would prefer not to hear from us too often.
25
+
26
+Once the email has been received and your information has been entered into our system, we will email you a script you will run that will begin the remote installation process. Instructions for running the script will be included in that email, and are reproduced below for reference.
27
+
28
+## Installation
29
+
30
+ 1. Create an 'sbgrid' user on the machine that will host your software installation. This should be a normal, unprivileged user account.
31
+ 2. Log in as this 'sbgrid' user.
32
+ 3. Download the installation script from the URL provided in the account creation email.
33
+ 4. Make it executable: `chmod +x sbgrid-admin`
34
+ 5. Run the script: `./sbgrid-admin -i`
35
+ 6. The script will walk you through configuring your installation, downloading the software and installing a cron job that will keep the software updated at your site. You will need the **site name** and **install key** provided in the account creation email. The installation may take anywhere from several hours to a day, depending on your network and the number of applications available to your site.
36
+
37
+## Post-Installation Steps
38
+
39
+ 1. Add a symlink in the root directory of each machine that wants to use the software. The installation script will print the suggested syntax for the command.`ln -s /path/to/sbgrid/installation /programs`
40
+ 2. Any user that wishes to use the software needs to configure their shell to initialize the SBGrid shell environment. For bash and other sh-compliant shells, add the following line to your ~/.bash_profile or ~/.bashrc: `. /programs/sbgrid.shrc` For csh and tcsh, add the following line to your ~/.cshrc: `source /programs/sbgrid.cshrc`
41
+ 3. For some linux distributions, the shipped version of tcsh does not support shell variables longer than 4096 characters. Since the current PATH in our default shell initialization is larger than that, you will need to update tcsh. RPMs for Red Hat 4/5 and CentOS 4/5 are provided at /programs/i386-linux/system/RPMS.
42
+
43
+
44
+## SGI IRIX Software Branch
45
+
46
+Since the IRIX software branch is frozen and no longer receiving updates, it is not installed and updated in the same manner as the active software branches. In order to install the IRIX software branch, please run: `./sbgrid-admin -s`
47
+
48
+Note that the IRIX branch is only compatible with *tcsh*; there is no sh-compatible configuration for this branch.
usage/mirrors.md
... ...
@@ -0,0 +1,3 @@
1
+# SBGrid Mirrors
2
+
3
+For the benefit of the local SBGrid community, we recommend the following to access frequently-used open source software. If you would like for us to add a mirror, please [contact us](help@sbgrid.org).
usage/operatingsystems.md
... ...
@@ -0,0 +1,32 @@
1
+## Supported Operating Systems
2
+
3
+The SBGrid Software Suite can run on Linux, OS X and IRIX machines.
4
+
5
+### Linux
6
+We build and test software under 64-bit Red Hat 6. The majority of our Linux users are using the Red Hat/CentOS/Scientific Linux or Fedora distributions, but 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, and we will work to resolve problems reported by users of these Linux distributions.
7
+
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.
9
+
10
+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.
14
+
15
+## OS X Intel
16
+We build and test the programs under the most four most recent OS X releases.
17
+
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.
21
+
22
+## OS X PowerPC
23
+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
+Currently Supported:
26
+ * OS X PowerPC 10.4 - 10.5
27
+
28
+## IRIX
29
+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
+
31
+Currently Supported:
32
+ * IRIX 6.5.26 + bugfix releases
usage/overrides.md
... ...
@@ -0,0 +1,71 @@
1
+# Overriding Software Versions
2
+
3
+Most of the software titles installed in the SBGrid software collection have several versions available. We try to provide at least three versions of each software package, although very old or very new applications may have fewer versions.
4
+
5
+## Display Available Versions
6
+
7
+To list the available versions of a software title, you can use the *sbgrid* utility. Running *sbgrid -l* will list the versions for your current platform. From a Linux machine, a search for CCP4 versions looks like this:
8
+
9
+
10
+ $ sbgrid -l ccp4
11
+ Version information for: /programs/x86_64-linux/ccp4
12
+
13
+ Default version: 7.0
14
+ In-use version: 6.5
15
+ Other available versions: 6.4.0 6.3.0
16
+ Overrides use this shell variable: CCP4_X
17
+
18
+
19
+Running *sbgrid -L* will print the available versions for the three current platforms (OS X PowerPC and Intel, Linux).
20
+
21
+
22
+ $ sbgrid -L gnuplot
23
+ Version information for: /programs/x86_64-linux/gnuplot
24
+
25
+ Default version: 4.6.4
26
+ In-use version: 4.6.4
27
+ Other available versions: 4.6.0 4.4.3 4.2.6
28
+ Overrides use this shell variable: GNUPLOT_X
29
+
30
+ Version information for: /programs/i386-linux/gnuplot
31
+
32
+ Default version: 4.6.0
33
+ Other available versions: 4.4.3 4.2.6
34
+ Overrides use this shell variable: GNUPLOT_L
35
+
36
+ Version information for: /programs/i386-mac/gnuplot
37
+
38
+ Default version: 4.6.4
39
+ Other available versions: 4.4.3 4.2.6 4.6.0
40
+ Overrides use this shell variable: GNUPLOT_M
41
+
42
+
43
+## Overriding Default Versions
44
+
45
+To override the default version of a software title, you need to create an override file. The shell configuration scripts will read this file and override the default version.
46
+
47
+The override file is named .sbgrid.conf and should be placed in your $HOME directory. The syntax for overrides is a simple key=value pair. E.g. it should look like this:
48
+
49
+`APPLICATION_X=1.2`
50
+
51
+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:
52
+
53
+ | Software Directory | Shorthand Initial |
54
+ | :----------------- | :---------------- |
55
+ | i386-linux | _L |
56
+ | x86_64-linux | _X |
57
+ | i386-mac | _M |
58
+
59
+To quickly open the overrides file in your default $EDITOR, you can run *sbgrid-overrides -e*.
60
+
61
+When you open a new shell, you will see a message about the overridden version. Note that a site administrator can create sitewide or machine-specific overrides as well.
62
+
63
+The example output below shows CCP4 on linux being changed from the default version:
64
+
65
+ Configuration options in effect for this shell:
66
+ Variable Setting Configuration
67
+ CCP4_M 6.3.0 personal
68
+
69
+
70
+## Disabling a Software Package
71
+To disable a specific software package, set its version to "disable" in your ~/.sbgrid.conf file.
usage/recommended.md
... ...
@@ -0,0 +1,7 @@
1
+# Recommended Hardware
2
+
3
+## Linux Workstations
4
+SBGrid's preferred hardware vendor is [ThinkMate](http://thinkmate.com) and we have some [recommended configurations](http://www.thinkmate.com/sbgrid) for structural biology computing. Please feel free to contact us at help@sbgrid.org regarding upcoming hardware purchases if you have questions - we'd be happy to advise.
5
+
6
+## Apple Workstations
7
+Any Apple machine can be a capable computer for structural biology. The basic Apple educational discount is available through their online web store, and your institution may have negotiated an even better deal with their Apple representative. SBGrid has several labs that run exclusively on Macs and OS X.
usage/resources.md
... ...
@@ -0,0 +1,86 @@
1
+# Development Network
2
+
3
+The basic account is a UNIX shell account accessible via SSH. This network account will let you access designated machines in the developer network. Along with the shell account you also get up to 10 GB of data storage, access to high performance compilers, basic development tools like version control systems (svn, git, etc) and shell text editors.
4
+
5
+Once you have an account, you can access the developer network by connecting via SSH to:
6
+
7
+ *developer.sbgrid.org*
8
+
9
+ developer runs Scientific Linux 6 x86_64
10
+
11
+This machine (internally named sbgrid-dev-architect) is the only external facing host on the network, and it hosts your home directory and acts as the SSH bastion host for the network. From this machine you can SSH to any of the build and test hosts via their hostname in the table below in order to compile software, run tests, etc.
12
+
13
+The following are the always-on operating system/hardware combinations. They are generally kept at the latest point release:
14
+
15
+```
16
+ Hostname Operating System Architecture Notes
17
+ ------------------|-----------------|-------------|------------------------------------
18
+ sbgrid-c5b CentOS 5 x86 base SBGrid 32-bit Linux build VM
19
+ sbgrid-c5b-64 CentOS 5 x86_64 base SBGrid 64-bit Linux build VM
20
+ sbgrid-c5t-64 CentOS 5 x86_64 minimal install for portability testing
21
+ sbgrid-c6b CentOS 6 x86 base SBGrid 32-bit Linux build VM
22
+ sbgrid-c6b-64 CentOS 6 x86_64 base SBGrid 64-bit Linux build VM
23
+ sbgrid-c6t-64 CentOS 6 x86_64 minimal install for portability testing
24
+ sbgrid-dev-vm-07 Debian 5 x86
25
+ sbgrid-dev-vm-08 Debian 5 x86_64
26
+ sbgrid-dev-vm-16 Debian 6 x86
27
+ sbgrid-dev-vm-17 Debian 6 x86_64
28
+ sbgrid-dev-vm-03 Ubuntu 10.10 x86
29
+ sbgrid-dev-vm-04 Ubuntu 10.10 x86_64
30
+ sbgrid-dev-vm-14 OpenSuSE 11.3 x86
31
+ sbgrid-dev-vm-15 OpenSuSE 11.3 x86_64
32
+ sbgrid-m106 OS X 10.6 x86/x86_64 Base SBGrid OS X Intel build machine
33
+ sbgrid-m107 OS X 10.7 x86/x86_64
34
+ sbgrid-m108 OS X 10.8 x86/x86_64
35
+ sbgrid-m109 OS X 10.9 x86/x86_64
36
+ sbgrid-m1010 OS X 10.10 x86/x86_64
37
+ sbgrid-dev-flange OS X 10.5 PowerPC
38
+```
39
+
40
+We have the Intel, Portland and Absoft (PPC) compilers:
41
+
42
+* Intel 12.0, 11.1, 10.1 (ifc, ifort) - any linux host, OS X Intel hosts
43
+* Portland 14.4, 12.6, 10.9, 10.2, 9.0-1 (pgcc, pgf77/90/95) - sbgrid-dev-architect, sbgrid-dev-moose
44
+
45
+There is a configuration file for sh-compatible shells that will enable the compilers and their environmental settings:
46
+
47
+ $ . /build/conf/buildenv.sh
48
+
49
+Then you can use the 'build' function to control your compiler settings:
50
+
51
+ $ build help
52
+ build: a shell function for controlling compilers
53
+
54
+ Usage: build (help3264list)
55
+
56
+ help This help message
57
+ 32 Configure 32-bit compilers
58
+ 64 Configure 64-bit compilers
59
+ list List available compilers
60
+
61
+Additionally, there are other operating systems available as virtual machines that can be enabled (OpenSuSE, Ubuntu, Fedora, etc), and some additional hardware that can be made available (Sun SPARC, IRIX MIPS, etc) on request.
62
+
63
+Graphical access to the machines may be available through Apple Remote Desktop, VNC or the NoMachine desktop sharing client. Other tools could be made available if necessary as well. The whole thing's a bit of an experiment, really, so email us at `<bugs@sbgrid.org>`, and we'll see what we can work out.
64
+
65
+# Request an Account
66
+
67
+Thanks for your interest in participating in the SBGrid Developer Network.
68
+
69
+In order to be eligible for an account, you must have software in the SBGrid software suite or be planning to make your software available through SBGrid. This requirement limits accounts to developers of scientific software used in structural biology and related disciplines.
70
+
71
+That's the only requirement for new accounts. In return for access to these resources, you must agree to not abuse the resources for:
72
+
73
+* sending spam
74
+* cracking our computers or other peoples' computers
75
+* other activity which is illegal in the USA or your country
76
+
77
+And you agree to take reasonable precautions to maintain the security of your password and account by not sharing this information with other people.
78
+On our end, we will:
79
+
80
+* take reasonable precautions to maintain the security of the network, accounts and data
81
+* make occasional backups of account data (but don't count on it!)
82
+* attempt to maintain a high availability of the developer resources
83
+
84
+We reserve the right to close accounts at any time for any reason.
85
+
86
+Still interested? Great! We want to work with you, so please email `<bugs@sbgrid.org>` with your account request, and we'll get back to you as soon as possible.
usage/sharp.md
... ...
@@ -0,0 +1,8 @@
1
+## SBGrid Sharp server
2
+
3
+SBGrid maintains a server for Global Phasing's application [Sharp/AutoSharp](https://sharp.sbgrid.org:8080) for use by consortium members.
4
+To use the sharp server, email accounts@sbgrid.org for account credentials.
5
+
6
+Documentation for using Sharp can be found [here](http://www.globalphasing.com/sharp/manual/)
7
+
8
+
usage/stereo.md
... ...
@@ -0,0 +1,83 @@
1
+## General
2
+
3
+### 3D Stereo on RHEL/CentOS 6 systems
4
+
5
+Nvidia 3d stereo on RHEL 6 is reasonably straight-forward.
6
+Take a look [here](xorg_conf) for an example xorg.conf file. This configuration if for a Quadro 4000 card and a 1920x1080 display. Your settings may vary depending on your hardware.
7
+
8
+### 3D Stereo on RHEL/CentOS 7 systems with Gnome 3
9
+
10
+Nvidia 3D stereo typically requires disabling the Composite extension in X.org. Unfortunately, this extension is required to run Gnome 3 and the gdm login mangager supplied as the default desktop in CentOS and many other linux distributions.
11
+
12
+As of version 337.19 of the nvidia driver, some Quadro configurations can operate with the composite extension enabled, but stereo functionality depends on a stereo-aware composite manager. The Composite manager in CentOS7 Gnome3 is not stereo aware and 3D stereo does not work by default.
13
+
14
+In order to use 3D stereo on Gnome3 systems, you can switch from Gnome3/gdm to MATE/lightdm.
15
+The MATE Desktop Environment is the continuation of GNOME 2 which is the default desktop in CentOS 5 and 6.
16
+
17
+To change to MATE on CentOS7 systems, first, install the Extra Packages for Enterprise Linux (EPEL) repo:
18
+
19
+
20
+ yum install epel-release
21
+
22
+
23
+Then install the nvidia drivers from epel
24
+
25
+
26
+ yum install kmod-nvidia
27
+
28
+
29
+You may find you need these packages as well
30
+
31
+
32
+ yum install mesa-libGLU-9.0.0-4.el7.x86_64 libXScrnSaver-1.2.2-6.1.el7.x86_64
33
+
34
+
35
+Next, install lightdm which doesn't require the composite extension.
36
+
37
+
38
+ yum install lightdm
39
+
40
+
41
+From there we do a couple of groupinstalls
42
+You may have these rpms installed already, but just for good measure
43
+
44
+
45
+ yum group install "X Window System"
46
+
47
+
48
+then
49
+
50
+
51
+ yum groupinstall "MATE Desktop"
52
+
53
+
54
+Toggle from gdm to lightdm in systemd using systemctl.
55
+To see what you are using as a 'display manager', check this link
56
+
57
+
58
+ ls -l /etc/systemd/system/display-manager.service
59
+
60
+
61
+This is likely pointing to gdm and should be changed to point to lightdm.
62
+You can change that with systemctl.
63
+
64
+
65
+ systemctl disable gdm
66
+ systemctl enable lightdm
67
+
68
+
69
+And then this will reload you changes, similar to changing runlevels with sysinitV
70
+
71
+
72
+ systemctl isolate graphical.target
73
+
74
+
75
+Make sure to select MATE from the drop menu as your graphical before you login.
76
+## Mac OS X
77
+
78
+* Prior to OS X 10.8, the stock X11 has better compatibility than the Xquartz development version available from MacOSForge. With the OS X 10.8 release, X11 is no longer included by Apple, and you'll need to install the latest Xquartz version offered on the MacOSForge site to run X11-based applications.
79
+
80
+## Laptops
81
+
82
+* You can create a local installation to take along with you.
83
+http://www.sbgrid.org/wiki/laptopinstall
usage/workstation_setup.md
... ...
@@ -0,0 +1,35 @@
1
+## General
2
+
3
+* You should use a network installation for workstations and servers if at all possible. NFS, SMB and AFP all work for sharing a single installation among multiple machines. The decreased admin overhead, bandwidth and disk savings of sharing a single installation is a significant benefit.
4
+
5
+## Linux
6
+Information on configuring 3D stereo can be found [here](stereo)
7
+
8
+* All Linux machines need installations of a recent version (6.17+) of csh/tcsh. Red Hat Enterprise Linux 6 and other recent distributions usually have an up to date version. There are RPMs for Red Hat/CentOS/Scientific Linux 5.x in the software tree in the architecture specific directories:
9
+
10
+ /programs/i386-linux/system/RPMs
11
+ /programs/x86_64-linux/system/RPMs
12
+
13
+* SELinux must be disabled.
14
+
15
+* 64-bit machines need a number of 32-bit compatibility packages installed **even when using the 64-bit software branch**. This is due to a number of binary-only and legacy packages that are only available as 32-bit applications. Additional fonts for Tcl/Tk, Motif and Xview applications are also encouraged.
16
+
17
+Packages for RHEL 6, and 7 and compatible machines:
18
+
19
+ yum install glibc.i686 libgcc.i686 libX11.i686 libXaw.i686 libXext.i686 ncurses.i686 \
20
+ redhat-lsb.i686 xorg-x11-fonts-75dpi xorg-x11-fonts-100dpi xorg-x11-fonts-ISO8859-1-75dpi \
21
+ xorg-x11-fonts-ISO8859-1-100dpi xorg-x11-fonts-misc libXScrnSaver
22
+
23
+
24
+* The same 32-bit requirement applies for 64-bit Debian and Ubuntu machines. This is supported via the [Multiarch](https///wiki.debian.org/Multiarch/HOWTO) system. You'll need at least the following packages to run most of the software. Please email us if you discover we have left some out.
25
+`apt-get install libc6-i386 lsb tcsh gawk libjpeg62 curl libx11-6:i386 libxext6:i386`
26
+
27
+## Mac OS X
28
+Information on configuring 3D stereo can be found [here](stereo)
29
+
30
+* Prior to OS X 10.8, the stock X11 has better compatibility than the Xquartz development version available from MacOSForge. With the OS X 10.8 release, X11 is no longer included by Apple, and you'll need to install the latest Xquartz version offered on the MacOSForge site to run X11-based applications.
31
+
32
+## Laptops
33
+
34
+* You can create a local installation to take along with you.
35
+http://www.sbgrid.org/wiki/laptopinstall
usage/xorg_conf.md
... ...
@@ -0,0 +1,77 @@
1
+## Example xorg.conf for Nvidia 3D
2
+
3
+### This configuration is for an ASUS VG278HE display and a Nvidia Quadro 4000
4
+
5
+```
6
+# SBGrid
7
+# nvidia version 319.32
8
+
9
+Section "ServerLayout"
10
+ Identifier "Layout0"
11
+ Screen 0 "Screen0" 0 0
12
+ InputDevice "Keyboard0" "CoreKeyboard"
13
+ InputDevice "Mouse0" "CorePointer"
14
+ Option "Xinerama" "0"
15
+EndSection
16
+
17
+Section "Files"
18
+ ModulePath "/usr/lib64/xorg/modules/extensions/nvidia"
19
+ ModulePath "/usr/lib64/xorg/modules"
20
+ FontPath "/usr/share/fonts/default/Type1"
21
+EndSection
22
+
23
+Section "InputDevice"
24
+
25
+ # generated from default
26
+ Identifier "Mouse0"
27
+ Driver "mouse"
28
+ Option "Protocol" "auto"
29
+ Option "Device" "/dev/psaux"
30
+ Option "Emulate3Buttons" "no"
31
+ Option "ZAxisMapping" "4 5"
32
+EndSection
33
+
34
+Section "InputDevice"
35
+
36
+ # generated from data in "/etc/sysconfig/keyboard"
37
+ Identifier "Keyboard0"
38
+ Driver "kbd"
39
+ Option "XkbLayout" "us"
40
+ Option "XkbModel" "pc105"
41
+EndSection
42
+
43
+Section "Monitor"
44
+ Identifier "Monitor0"
45
+ VendorName "Unknown"
46
+ ModelName "Ancor Communications Inc ASUS VG278HE"
47
+ HorizSync 24.0 - 162.0
48
+ VertRefresh 50.0 - 148.0
49
+ Option "DPMS"
50
+EndSection
51
+
52
+Section "Device"
53
+ Identifier "Device0"
54
+ Driver "nvidia"
55
+ VendorName "NVIDIA Corporation"
56
+ BoardName "Quadro 4000"
57
+EndSection
58
+
59
+Section "Screen"
60
+ Identifier "Screen0"
61
+ Device "Device0"
62
+ Monitor "Monitor0"
63
+ DefaultDepth 24
64
+ Option "AllowDFPStereo" "1"
65
+ Option "UBB" "1"
66
+ Option "Stereo" "10"
67
+ Option "metamodes" "DFP-0: nvidia-auto-select +1920+0, DFP-2: nvidia-auto-select +0+0"
68
+ SubSection "Display"
69
+ Depth 24
70
+ EndSubSection
71
+EndSection
72
+
73
+Section "Extensions"
74
+ Option "Composite" "Disable"
75
+EndSection
76
+
77
+```
versions.md
... ...
@@ -0,0 +1,71 @@
1
+# Overriding Software Versions
2
+
3
+Most of the software titles installed in the SBGrid software collection have several versions available. We try to provide at least three versions of each software package, although very old or very new applications may have fewer versions.
4
+
5
+## Display Available Versions
6
+
7
+To list the available versions of a software title, you can use the *sbgrid* utility. Running *sbgrid -l* will list the versions for your current platform. From a Linux machine, a search for CCP4 versions looks like this:
8
+
9
+
10
+ $ sbgrid -l ccp4
11
+ Version information for: /programs/x86_64-linux/ccp4
12
+
13
+ Default version: 7.0
14
+ In-use version: 6.5
15
+ Other available versions: 6.4.0 6.3.0
16
+ Overrides use this shell variable: CCP4_X
17
+
18
+
19
+Running *sbgrid -L* will print the available versions for the three current platforms (OS X PowerPC and Intel, Linux).
20
+
21
+
22
+ $ sbgrid -L gnuplot
23
+ Version information for: /programs/x86_64-linux/gnuplot
24
+
25
+ Default version: 4.6.4
26
+ In-use version: 4.6.4
27
+ Other available versions: 4.6.0 4.4.3 4.2.6
28
+ Overrides use this shell variable: GNUPLOT_X
29
+
30
+ Version information for: /programs/i386-linux/gnuplot
31
+
32
+ Default version: 4.6.0
33
+ Other available versions: 4.4.3 4.2.6
34
+ Overrides use this shell variable: GNUPLOT_L
35
+
36
+ Version information for: /programs/i386-mac/gnuplot
37
+
38
+ Default version: 4.6.4
39
+ Other available versions: 4.4.3 4.2.6 4.6.0
40
+ Overrides use this shell variable: GNUPLOT_M
41
+
42
+
43
+## Overriding Default Versions
44
+
45
+To override the default version of a software title, you need to create an override file. The shell configuration scripts will read this file and override the default version.
46
+
47
+The override file is named .sbgrid.conf and should be placed in your $HOME directory. The syntax for overrides is a simple key=value pair. E.g. it should look like this:
48
+
49
+`APPLICATION_X=1.2`
50
+
51
+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:
52
+
53
+ | Software Directory | Shorthand Initial |
54
+ | :----------------- | :---------------- |
55
+ | i386-linux | _L |
56
+ | x86_64-linux | _X |
57
+ | i386-mac | _M |
58
+
59
+To quickly open the overrides file in your default $EDITOR, you can run *sbgrid-overrides -e*.
60
+
61
+When you open a new shell, you will see a message about the overridden version. Note that a site administrator can create sitewide or machine-specific overrides as well.
62
+
63
+The example output below shows CCP4 on linux being changed from the default version:
64
+
65
+ Configuration options in effect for this shell:
66
+ Variable Setting Configuration
67
+ CCP4_M 6.3.0 personal
68
+
69
+
70
+## Disabling a Software Package
71
+To disable a specific software package, set its version to "disable" in your ~/.sbgrid.conf file.