change all to symlinks

-[SBGrid install client -- Usage info](client_usage)

-

-

-## SBGrid installation client - Usage

-SBGrid-Wiki.md

-SBGrid-Wiki.md

-## Welcome to the SBGrid Consortium Wiki

-

-

-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.

- **[SBGrid Wiki](Home)**

-

-Installing Software

-* [Installation: Overview](installation_overview)

-* [Supported Operating Systems](operatingsystems)

-* [Installation: 'Site' installation](installation_admin)

-* [Installation: MacOS GUI](client_install)

-* [Installation: Package Manager](client_CLI_install)

-

-Using the SBGrid Environment

-* [Getting Started with SBGrid](getting_started)

-* [Overriding Software Versions](versions)

-* [SBGrid environment: Capsules](capsules)

-* [SBGrid environment: Legacy](monolithic)

-* [SBGrid MacOS GUI : Usage](client_usage)

-* [SBGrid Package Manager : Usage](client_CLI_usage)

-

-Getting Help

-* [Software Help and Requests](help)

-

-Support for Site Administrators

-* [Preparing Workstations to run the Software](workstation_setup)

-* [Managing your Installation](managing_install)

-* [Administrator Software Version Overrides](admin_overrides)

-* [Admins Mailing List](mailinglist)

-

-Support for Developers

-* [Resources for Developers](developers)

-* [Build and Test Network](resources)

-

-Hardware Support Notes

-* [SBGrid Recommended Hardware](recommended)

-* [GPU computing](gpu)

-* [Setup Stereo 3D](stereo)

-

-Portals

-* [Data Processing After WSMR](wsmr-worked)

-* [SBGrid SHARP server](sharp)

-## Site Administrator Overrides

-

-SBGrid installations allow site-level software control for Administrators

-

-### Software Blacklist

-Site administrators can prevent the shell initialization files from configuring software on a host by creating an empty file at

-

- **/programs/local/conf/disabled-hosts/<hostname>**

-

-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.

-

-### Administrator Software Version Overrides

-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.

-

-There are two methods for site admins to configure version overrides using files placed in a **/programs/local/conf/** directory.

-

-- Site-wide Version Overrides

-A file named **site.conf** will be read when any SBGrid shell is initialized from the installation.

-

-- Per-host Version Overrides

-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.

-

-### Precedence

-There are three files that will be examined for version overrides during shell initialization. In order from lowest to highest precedence:

-

- * /programs/local/conf/site.conf

- * /programs/local/conf/<hostname.conf>

- * $HOME/.sbgrid.conf

-

-The overrides are reported during shell initialization:

-

-```

- Configuration options in effect for this shell:

- Variable Setting Configuration

- SPIDER_L 18.10 site

- CNS_L 1.21 machine

- CCP4_L 6.1.2 personal

-```

-## SBGrid package mangager installation client

-

-The SBGrid software stack can be installed using our CLI (command line interface) installation client for [Linux (CentOS/RHEL 6 or 7 recommended) or Apple OSX computers running MacOSX v10.9 - 10.12.](operatingsystems)

-

-Three software installers are available. Binary releases are available for MacOS and CentOS7/Ubuntu operating systems. A python release is also provided which is compatible with Mac and most Linux (CentOS6 and higher) operating systems.

-

-The SBGrid installation client requires an individual account. To get started, first, set up an account by registering here : [SBGrid registration](https://sbgrid.org/registration/register/)

-

-### Pre-installation requirements

-

-**Admin access required on your computer.**

- The SBGrid installation client will install the software tree to /opt/sbgrid and create a symlink from this directory to /programs. While admin privileges are not required to run the application, you will need admin privileges to create /opt/sbgrid and /programs .

-

-**Existing SBGrid installations must be renamed or removed.**

- If you have previously installed SBGrid software on your computer at /programs or at /opt/sbgrid, these directories should be removed or renamed. The client will create these on first run.

-

-**Hard Drive Space**

- Depending on what you install, ensure you have enough free hard drive space on your machine.

-

-**For large packages (Phenix, Rosetta, CCP4), a wired connection is recommended.**

- Some packages are quite large and can be slow to download, especially over WiFi.

-

-**pip**

- pip is a package management system used to install and manage software packages written in Python. The software installation client is installable by pip. This may not be on you machine by default, instructions for adding it are included here.

-

-### Binary releases : MacOS and Linux Installation

-

-There is minimal installation needed for these binaries. They can be run from any location. Untar the archive, make the file executable if necessary, and run from your preferred location.

-

-[Mac : 1.0.555, 2017-06-21](downloads/sbgrid-1.0.555-Darwin.tgz)

-

-[Linux : 1.0.555, 2017-06-21](downloads/sbgrid-1.0.555-Linux.tgz)

-

-```

-$ tar -zxf sbgrid-1.0.555-Darwin.tgz

-

-$ cd sbgrid-1.0.555-Darwin

-

-$ ./sbgrid

-usage:

-sbgrid <command> [<command_args>]

-

-Available commands are:

- activate activate new installation

- grids list available grids

- info print package metadata

- install install single package

- install-all install all packages from collection

- installed list installed packages

- list list available packages

- rebuild rebuild installation

- remove remove installed package

- resume resume interrupted installations

- update update package to latest release/version

- update-all update all packages to latest release/version

- updates list available updates for installed packages

- version print package version string

-sbgrid: error: too few arguments

-```

-

-### Install python wheel using **pip** - Mac Installation

-

- On mac, pip is available from [macports](https://www.macports.org/), [homebrew](http://brew.sh/), and [fink](http://finkproject.org/). It also can be added using **easy_install**. easy_install will install pip into your system python.

-

- $ sudo easy_install pip

-

-### Install python wheel using **pip** - Linux Installation

-

- On CentOS6, you can install pip from the EPEL repository (yum -y install python-pip) or as [per these directions](https://pip.pypa.io/en/stable/installing/)

-

-## CLI client - Installation and activation

-**1. Download the latest SBGrid installation client from here.**

-

-[Latest build : 1.0.555, 2017-06-21](downloads/sbgrid-1.0.555-py2-none-any.whl)

-

-**2. Install / Upgrade with pip**

-

- $ sudo pip install SBGrid_Installer-1.0.461-py2-none-any.whl

-

- Which should produce output similar to :

-

-```

-Unpacking ./SBGrid_Installer-1.0.448-py2-none-any.whl

-Requirement already satisfied (use --upgrade to upgrade): pyasn1 in /nfs/programs-dev/i386-mac/python/2.7.5/lib/python2.7/site-packages (from SBGrid-Installer==1.0.488)

-Downloading/unpacking requests (from SBGrid-Installer==1.0b2.dev412)

- Downloading requests-2.11.1.tar.gz (485kB): 485kB downloaded

- Running setup.py egg_info for package requests

-

- warning: no files found matching 'test_requests.py'

-Installing collected packages: SBGrid-Installer, requests

- Running setup.py install for requests

-

- warning: no files found matching 'test_requests.py'

-Successfully installed SBGrid-Installer requests

-Cleaning up...

-```

-

-The *sbgrid* command will produce this usage info :

-

- $ sbgrid

-

-```

-usage:

-sbgrid <command> [<command_args>]

-

-Available commands are:

- activate Activate new installation

- list List available packages

- info Print package metadata

- install Install single package

- install-all Install all packages from collection

- installed List installed packages

- remove Remove installed package

- resume Resume interrupted installations

- upgrades List available upgrades for installed packages

- upgrade Upgrade package to latest version

- upgrade-all Upgrade all packages to latest version

- version Print package version string

-sbgrid: error: too few arguments

-

-```

-

-**4. Activate the installation**

-Enter your site and key which you should have received these by email.

-

- $ sbgrid activate <site name> <user name> <activation key>

-

-You may be prompted for your sudo password to create /programs and /opt/sbgrid.

-

-**5. On successful activation, list software titles.**

-

- $ sbgrid list

-

- If activation continues to fail, you may have an old SBGrid installation at /programs or /opt/sbgrid. These should be removed.

-

-You may also be blocked from accessing SBGrid servers on port 873 and port 8080 by your institution's firewall. You can check if you can access [port 873 here](http://portquiz.net:873) and [port 8080 here](http://portquiz.net:8080)

-

-For help, email *bugs@sbgrid.org.*

-

-### Installation on an external drive or USB key

-Currently the installer application installs the software tree in /opt/sbgrid and uses a symlink at /programs. This link is required for the software to work, but in principle the software can be located anywhere and linked to /opt/sbgrid. This functionality is not yet included in the SBGrid application, but can be set up manually with a symlink.

-

-An installation can be made on an external drive if you first do an install (into /opt/sbgrid), then move it and symlink to the new location.

-

-**Example:** 128Gb USB 'key' drives are available on Amazon for 30$ or less and are a nice way to supplement the SSDs that come in Mac laptops. To install on an external drive like this, mount it on your computer. For this example, the mount is */Volumes/sbgrid_client_install*. Then, using the SBGrid installer, do an initial installation on the hard drive. To make life easy, just do one application. Then close the installer application.

-

-Next move */opt/sbgrid* to the USB key at */Volumes/sbgrid_client_install*. You will likely need sudo for this.

-

- $ sudo mv /opt/sbgrid /Volumes/sbgrid_client_install/.

-

-Now we have */Volumes/sbgrid_client_install/sbgrid*. Create a symlink from */opt/sbgrid* to */Volumes/sbgrid_client_install/sbgrid*.

-

- $ sudo ln -s /Volumes/sbgrid_client_install/sbgrid /opt/sbgrid

-

-The symlink at */programs* still points to */opt/sbgrid*, and that is a link that points to the external location. Open the installer and add the desired applications. These will now install to the external drive.

-

-### Some known issues

-

-* **rsync required on 873 or 8080**. The application will fail if outbound port 873 and port 8080 are blocked by your institution or are otherwise not available.

-

-* **Activation Failed**. In some cases the Authorization dialog for admin privileges does not appear during activation. This causes the client activation to fail. This is usually due to a previously existing /programs directory or symlink from a prior installation. This must be removed for activation to be successful. Other users have reported successful activation after a restart.

-## SBGrid installation client - Usage

-

-**Instructions for installation of the SBGrid software installation client can be found here** --> [Installation Instructions](client_CLI_install).

-

-All SBGrid software is run from the the terminal.

-For information on how to run software from the SBGrid collection and configure your shell, check the [getting started page.](getting_started).

-

-### General

-The SBGrid software installation client is a command line-based installer for the SBGrid software collection. The application allows for selected applications to be installed in the familiar SBGrid environment.

-

-The client displays software 'Collections' as a list.

-

- $ sbgrid list

-

-```

-Crystallography

- 3dna

- adxv

- albula

- autoproc

- ...

-

-NMR

- aqua

- aria

- cara

- ccpnmr

- ccpnmr-chembuild

- ...

-

-Electron Microscopy

- 2dx

- ace2

- auto3dem

- bfactor

- bsoft

- burnham-brandeis-helical-package

- chimera

- ...

-

-Structure Visualization & Analysis

- 3dna

- anaconda

- apbs

- aqua

- bobscript

- caver

- caver-analyst

- ccp4mg

- chimera

- ...

-

-Computational Chemistry

- ambertools

- apbs

- appion

- autodock

- autodock-vina

- avogadro

- concoord

- dock

- gromacs

- ...

-

-Other

- a2ps

- abyss

- aline

- amigos-ii

- amps

- assemble2

- bamtools

- ...

-```

-

-Information about each title, including a description and links to documentation can be show with the *sbgrid info <title>* command.

-

-### Example : Installing Albula

-

- $ sbgrid info albula

-

-```

-Package: ALBULA

-Name slug: albula

-

-Available versions:

-* 3.2.0-2 (default)

-* 3.1.0-13

-* 3.0.0-14

-* 2.2.12

-

-Collection(s): Crystallography

-

-Description:

- consists of the standalone program ALBULA VIEWER, a fast and easy-to-

-use program that allows optimal visualization of PILATUS and EIGER data,

-and ALBULA API, a Python programming interface for displaying images and

-performing operations and calculations. The API enables you to easily

-integrate the viewer functionality into your beamline infrastructure or

-experimental setup.

-

-Links:

-* Website: https://www.dectris.com/Albula_Overview.html

-```

-

-To install:

-

- $ sbgrid install albula

-

-```

-Installing: albula

-Updating installation configuration...

-Installation was successfull!

-```

-

-To get started, load the SBGrid environment :

-

- $ source /programs/sbgrid.shrc

-

-```

- Software Support by SBGrid (www.sbgrid.org)

-********************************************************************************

-

-...

-

-SBGrid installation last updated: 2016-10-21

-Please submit bug reports and help requests to: <bugs@sbgrid.org> or

- <http://sbgrid.org/bugs>

-********************************************************************************

-```

-

-### Example : Removing Albula

-

- $ sbgrid remove albula

-

-results in :

-

-```

-Removing: albula

-Updating installation configuration...

-Package removed!

-```

-

-### Version selection

-

-Default versions are installed by default for each application, though individual versions can be selected for each title.

-

-To do so, include the version after the title followed the version. To see what versions are available, use the *sbgrid info <title>* command. Let;s us the title epmr as an example here:

-

- $ sbgrid info epmr

-

-```

-Package: EPMR

-Name slug: epmr

-

-Available versions:

-* 16.04 (default)

-* 16.01

-* 15.12

-* 15.04

-* 13.07

-* 11.02

-

-Collection(s): Crystallography

-

-Description:

- a program that finds crystallographic molecular replacement solutions

-using an evolutionary search algorithm. The program directly optimizes

-three rotational and three positional parameters for the search model with

-respect to the correlation coefficient between Fo and Fc.

-

-Links:

-* Website: http://www.epmr.info/

-* Manual: http://www.epmr.info/UsersGuide.html

-```

-

-To install version 11.02, add the version string like so:

-

- $ sbgrid install epmr 11.02

-

-which will produce :

-

-```

-Installing: epmr (11.02)

-Updating installation configuration...

-Installation was successfull!

-key@key-mbp [20161021-21:05:56] ~/Downloads

-```

-

-Check which versions are installed with the sbgrid info command again

-

- $ sbgrid info epmr

-

-```

-epPackage: EPMR

-Name slug: epmr

-

-Available versions:

-* 16.04 (default)

-* 16.01

-* 15.12

-* 15.04

-* 13.07

-* 11.02 (installed)

-

-...

-

-```

-

-Confirm with the *sbwhich* command

-

-

- $ sbwhich epmr

-```

-/programs/i386-mac/epmr/11.02/epmr

-```

-

-Reload the sbgrid shell to use the new version ( or set the environment variable EPMR_M=11.02 ).

-

-### Software Versions Management in the SBGrid environment

-If you have a single version of an application installed, explicit version selection in your environment is not needed.

-

-In the case of multiple installed versions, the *SBGrid Default* version will be the version available at the terminal when it is installed, unless configured otherwise in *~/.sbgrid.conf*.

-

-In the case of multiple non-default versions installed, the *latest release* will be version available in your shell. If you would like to have more than one version of a title installed, and prefer to use an older release or the non-default version when a default version is installed, you must set this explicitly in your *~/.sbgrid.conf* file. This is the same as in the standard SBGrid environment.

-

-**Version priority in the shell**

- 1. *~/.sbgrid.conf*

- 2. Installed single version

- 3. Installed Default version

- 4. Latest installed release

-

-There is more info on how to do that here --> [SBGrid version overrides](versions)

-

-### Running SBGrid software

-

-To use the software at the terminal in bash, open a new terminal and run

-

- $ source /programs/sbgrid.shrc

-

-or in tcsh

-

- $ source /programs/sbgrid.cshrc

-

-### Questions, Problems and Known Issues

-For questions or problems, the Help menu will direct to the SBGrid help page. Or just email *bugs@sbgrid.org*.

-If relevant, please include a screenshot of the GUI if possible (command + shift + 4) and please include the ~/Library/Application Support/SBGrid/sbgrid.log file with your report.

-

-**Known issues**

-

-* The application will fail if outbound port 873 and port 8080 are blocked by your institution or are otherwise not available.

-

-* In some cases the prompt for admin credentials fails to appear on activation. Be sure there is no prior SBGrid install on your machine at /programs or /opt/sbgrid.

-## SBGrid installation client - Usage

-

-**Instructions for installing the SBGrid software installation client can be found here** --> [Installation Instructions](client_install)

-

-### General

-The SBGrid software installation client is a GUI-based installer for the SBGrid software collection. The application allows for selected applications to be installed in the familiar SBGrid environment.

-

- 

-

-The client GUI is displays software 'Collections' on the right panel with folder icons under the 'Packages' heading. These Collections control the list of titles displayed in the center 'main' panel.

-

-The first of two of these 'Collections' are shortcut meta-collections of the local machine. The first is the currently installed titles. The second icon, Updates, shows updates available from SBGrid. 'Pending' is a collection of pending installs and removals. Below these shortcuts are packages are grouped by primary scientific uses. Installation status is also indicated in theses collections.

-

-Information about each title, including a description and links to documentation are shown in the upper right panel when that title is selected in the main pane.

-

-Once packages have been configured for installation and/or removal by selecting their checkbox, clicking the 'Apply Changes' button will perform update the titles, adding pending installations and removing pending deletions.

-

-### Example : Installing Albula

-Check the box to select Albula, then click the 'Apply Changes' button.

-Notice the text turns green for pending installations. Pending updates are Orange.

-

-

-### Example : Removing Albula

-Uncheck the box for Albula. Removals are shown in red text.

-

-

-Click apply changes. Albula will be removed.

-

-

-### Version selection

-

-Default versions are installed by default for each application, though individual versions can be selected for each title. To do so, show the version pane by selecting **"Show all package versions"** from the **"View"** menu. Then, in the bottom right, select a desired version with the check boxes. Multiple versions of a given title can be installed and are indicated in the main panel.

-

-Enable version panel

-

-

-Check old/non-default versions

-

-

-

-### Versions and the SBGrid environment

-If you have a single version of an application installed, explicitly version selection in your environment will not be needed. In the case of multiple installed versions, the *SBGrid Default* version will be the version available at the terminal when installed, unless configured otherwise in *~/.sbgrid.conf*.

-

-If you have multiple non-default versions installed, the *latest release* will be version available in your shell. If you would like to have more than one version of a title installed, and prefer to use either an older release or the non-default version when a default version is installed, you must set this explicitly in your *~/.sbgrid.conf* file as in the standard SBGrid environment.

-

-**Version priority in the shell**

- 1. *~/.sbgrid.conf*

- 2. Installed Default version

- 3. Latest installed release

-

-You can do open the configuration file by selecting the *"Edit Configuration File"* from the *"SBGrid Installer"* menu.

-

-

-

-This will open a text editor with a sample configuration file, or your *~/.sbgrid.conf* file if you have one already.

-

-

-

-There is more info on how to do that here --> [SBGrid version overrides](versions)

-

-

-### Running the software

-

-To run the software, you can click the "SBGrid Shell" button for an initialized bash shell.

-

-You may also run the software from another terminal on your machine.

-To use the software at the terminal in bash, open a new terminal and run

-

- source /programs/sbgrid.shrc

-

-or in tcsh

-

- source /programs/sbgrid.cshrc

-

-### Questions, Problems and Known Issues

-For questions or problems, the Help menu will direct to the SBGrid help page. Or just email *bugs@sbgrid.org*.

-If relevant, please include a screenshot of the GUI if possible (command + shift + 4) and please include the ~/Library/Application Support/SBGrid/sbgrid.log file with your report.

-

-**Known issues**

-

-* The application will fail if outbound port 873 and port 8080 are blocked by your institution or are otherwise not available.

-

-* In some cases the prompt for admin credentials fails to appear on activation. Be sure there is no prior SBGrid install on your machine at /programs or /opt/sbgrid.

-## SBGrid Developer Support Program

-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.

-

-### Developer Network

-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.

-

-### Support Letters

-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.

-

-### Software Beta Testing

-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.

-

-### SBGrid Consortium Membership

-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.

-

-### Annual Software Awards

-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.

-

-### Stretch Your Resources

-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.

-

-### Broad Exposure for Your Software

-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.

-

-### Connect With Users

-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.

-## Getting Started

-

-### Using the SBGrid software collection

-The SBGrid software collection can be found installed at **/programs**.

-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.

-

-Bash users should initialize the SBGrid environment using :

-

- source /programs/sbgrid.shrc

-

-Tcsh users should initialize the SBGrid environment with :

-

- source /programs/sbgrid.cshrc

-

-On initialization, you should see the SBGrid welcome message

-

-

-

-### Making the shell configuration automatic

-

-To setup your terminal to automatically load the SBGrid environment, add the following to your configuration file:

-

-For Bash, in **~/.bashrc**, add :

-

- if [ -f /programs/sbgrid.shrc ] ; then

- source /programs/sbgrid.shrc

- fi

-

-For tcsh, in **~/.tcshrc** or **~/.cshrc**, add :

-

- if ( -e /programs/sbgrid.cshrc ) then

- source /programs/sbgrid.cshrc

- endif

-

-### Setting an alias

-

-If you would prefer to load the SBGrid environment on demand and not have to type the command above, you can set an alias to a shorter command of your choosing.

-

-For example, for bash in ~/.bashrc :

-

- alias sbg='source /programs/sbgrid.shrc'

-

-For tcsh in ~/.tcshrc, this would be

-

- alias sbg 'source /programs/sbgrid.cshrc'

-

-Questions or problems? Please email **bugs@sbgrid.org**

-## Software Help

-

-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.

-

-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).

-

-### New Software and Software Updates

-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]].

-

-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.

-

-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.

-

-### Newsletter

-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/).

-##Managing Your Software Installation

-

-### *sbgrid-admin* Utility

-The *sbgrid-admin* utility used to install the complete software collection. A download link is provided in the initial site set up email, and the script is included in the installation itself at */programs/share/sbgrid/bin/sbgrid-admin*. It includes built-in help:

-

-```

- $ sbgrid-admin -h

-sbgrid-admin: a tool for administering an SBGrid Software suite installation

-

-Usage: sbgrid-admin [-chirstu]

-

- -c Cron mode. Used for automated updates of the software suite.

- -h Help message.

- -i Install the software suite on this machine.

- -p Print a launchd plist for updating the software on OS X machines.

- -r Regenerate sh/csh shell configuration files.

- -s Install the software branch for SGI IRIX.

- -t Test the configuration file.

- -u Force manual update of an existing installation.

-```

-

-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.

-

-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.

-

- Configuration Options

-The *sbgrid-admin* script has some additional configuration options to accommodate the installation requirements at different sites.

-

-The ~sbgrid/.sbgridrc configuration file for the *sbgrid-admin* script must contain a sitename and site key. All other configurations are optional.

-

-Options take the form of *OPTION_NAME="setting"*.

-

-| **Option** |** Example** | **Description** |

-|:------------- |:-------------:| :---------------|

-| SB_SITENAME | sbgrid-bene | The site name for your installation provided by SBGrid |

-| SB_SITEKEY | xyxyxyxyxyxyxy | The installation key for your site provided by SBGrid |

-| INSTALL_TARGET| /nfs/programs | The installation directory for the software |

-| RSYNC_ARGS | "--port 8080"| Advanced arguments to rsync. Can be used to workaround blocked rsync ports. |

-| HTTP_PROXY | host.name:port | Proxy hostname and port for use by rsync and curl |

-| POST_UPDATE_SCRIPT | /absolute/path/to/script|Optional script to be run after a successful software update |

-| CRON_SCHEDULE | 5 1 * * * | Set a custom cron schedule |

-

-

- Rsync Transaction Logging

-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:

-

-```

-RSYNC_ARGS="--log-file=$HOME/logs/sbgrid-admin-`date +%Y%m%d`.log"

-```

-

-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.

-## SBGrid Software Installation : Laptops and Desktops without shared network storage

-

-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.

-

-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.

-

- - [Information on installation of our MacOS GUI.](client_install)

-

- - [Information on installation of our command-line tools for MacOS and Linux](client_CLI_install).

-

-### Script-based installation tools

-

-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.

-

-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.

-

-

- * *laptop-sync*

- - This script installs software from your own **local** installation.

- - This script requires an account on a local machine with access to the SBGrid softare collection.

- - Only latest versions will be installed.

-

-

- * *localsync*

- - This script installs software from your own **local** installation.

- - This script requires an account on a local machine with access to the SBGrid softare collection.

- - All versions of the software will be installed.

-

-

- * *sbgrid-sync (deprecated)*

- - This script installs software from SBGrid's servers.

- - an account on SBGrid's server is required.

- - THIS INSTALL METHOD WILL NO LONGER BE SUPPORTED IN A FUTURE RELEASE.

-

-

-### laptop-sync

-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.

-

-```

- sbgrid-laptop: a tool for creating a local installation of the

- SBGrid software on a laptop.

-

- Usage: sbgrid-laptop [-ituv] [-e list|config]

-

- -d Debug mode creates a log file for troubleshooting purposes.

- -e [list|config]

- Edit the software download list.

- -i Initial set up and installation of the SBGrid software.

- -s Re-run SSH key set up process.

- -t Test your current configuration.

- -u Update an existing installation using the current

- configuration.

- -v Verbose option for the file transfer.

-```

-

- You need an SSH login to a machine with the SBGrid software installed

- to use this script. The script will create an SSH key and run an SSH

- agent process to handle authentication for the file transfers.

-

-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.

-

-

-### localsync Sync Script

-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.

-

-Copy /programs/share/bin/localsync from the machine that has the software to your home directory on the standalone machine:

-

-

- scp your.server.name:/programs/share/bin/localsync ~/

-

-

-Then run the script like this:

-

- chmod 755 ~/localsync

- ~/localsync yourusername@your.server.name

-

-

-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.

-

-Here is an example run on my workstation:

-

-```

- $ ./localsync bene@developer.sbgrid.org

- Running 'sudo mkdir /programs && sudo chown bene /programs'

- [sudo] password for bene:

- Copying the software from the i386-mac branch on your server to your local

- hard disk. Enter your ssh login password below for bene@developer.sbgrid.org:

-

- receiving file list ...

-```

-

-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.

-

-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.

-

-### Sharing a 'localsync' Software Installation without NFS

-

-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.

-

-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.

-

-Here is a basic command run down. 'server1' holds the programs installation and 'client1' is what will be connecting to it.

-

- * Login as root/administrator on client1

- * Create the 'sbgrid' user on client1

- * Check the free space on /.

- * If there's enough free space, set up the programs directory:

-

-

- mkdir /programs

- chown -R sbgrid:sbgrid /programs

-

- * If there is not enough free space on the root volume, you'll need to find space on a local volume.

-

- * Login as 'sbgrid' on client1.

- * Create the passphraseless ssh key:

-

-

- ssh-keygen -d

-

-

-(hit enter to confirm default file location, no passphrase, etc)

-

- * Copy the ssh key to server1:

-

-

- cat ~/.ssh/id_dsa.pub | ssh server1 'cat - >> ~/.ssh/authorized_keys'

-

- * Copy the localsync script from server1 to client1. From client1:

-

-

- scp sbgrid@server1:/programs/share/bin/localsync .

-

-

-(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.)

-

- chmod 755 localsync

- ./localsync sbgrid@server1

-

-(This will take a while depending on the speed of the machines/network.)

-

- * Test the installation:

-

-

-tcsh

-

- source /programs/sbgrid.cshrc

-

-or

-bash

-

- source /programs/sbgrid.shrc

-

-

-(You should get a message like this: )

-```

- Welcome to SBGrid!

-

-********************************************************************************

- Your use of the applications contained in the /programs directory constitutes

- acceptance of the terms of the SBGrid License Agreement included in the file

- /programs/share/LICENSE. The applications distributed by SBGrid are licensed

- exclusively to member laboratories of the SBGrid Consortium.

-

- To hush this license message, run 'touch ~/.agree2sbgrid'.

-

-********************************************************************************

- Please submit bug reports and help requests to: `<bugs@sbgrid.org>` or

- `<http://sbgrid.org/bugs>`

- This installation last updated: 20110411

-

-********************************************************************************

- Total time to initialize: 1 second(s)

-```

-

- * Add a cronjob for the updates. As the 'sbgrid' user on client1:

-

-

- echo "0 2 * * * ~/localsync sbgrid@server1" | crontab

-

- * Check the cronjob:

-

-

- crontab -l

-

-You're done!

-

-

-### sbgrid-sync (DEPRECATED)

-

-This script can be found in the programs installation at */programs/share/bin/sbgrid-sync*.

-

-```

-sbgrid-sync: install or update the SBGrid Consortium software

- collection on your laptop or workstation.

-

-You will need a Consortium UNIX account to install and update your

-installation. If you don't have an account or don't remember your password,

-please email <accounts@sbgrid.org> for assistance.

-

-This script will create an SSH key and run an SSH agent process to handle

-authentication for the file transfers. Unless otherwise configured only the

-default version of the software titles will be installed.

-

-Usage: sbgrid-sync [-iesudt]

-

-Install/Configure Options:

-

- -i Initial set up and installation of the SBGrid software.

- -e Edit the software download list.

-

-Update Options:

-

- -u Update an existing installation using the current

- configuration.

-

-Troubleshooting Options:

-

- -d Debug mode creates a log file for troubleshooting purposes.

- -t Test your current configuration.

-

-```

-

-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.

-

-

-

-```

-| We need to create a list of software you want included in the local

-| installation. We will start with a list of all the software titles.

-| Remove the leading hash mark (#) to _include_ a software title.

-```

-Any titles NOT preceded with a '#' character will be installed.

-```

-| Save and _QUIT_ the text editor after making your changes. If you are

-| using TextEdit on a Mac, you must completely quit (Apple-Q) the

-| application to continue.

-```

-Once the editor has quit, software installation will start.

-

-```

-| Creating an rsync include list to download files.

-| Running rsync to download the latest software.

-```

-Once installation is completed, open a new terminal and

-

- source /programs/sbgrid.shrc

-

-to get started.

-## Mailing List for Site Administrators

-

-We have a small mailing list for technical users and site administrators.

-

-Visit the [SBGrid-tech mailing list](https///cmcd.hms.harvard.edu/sympa/info/sbgrid-tech) page to sign up.

-# HOWTOs: SBGrid Installation Notes

-

-## Site Configuration

-

-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.

-We refer to this computer as the site "master" server.

-

-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.

-

-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.

-

-

-

-## Pre-Installation

-

-| Installation Requirements | |

-| ------------------------- | ----------------------------------------------------|

-| Hard Drive Space | ~400 GB required |

-| Operating System | Linux, OS X and other UNIX |

-| Privileges | Root account (Linux) or Administrator account (Mac) |

-| network | Outbound http, rsync (ports 80 and 873, 8080) |

-

-

-### Approximate size per Branch

-| Branch | size |

-| ------------ | ------ |

-| i386-mac | 175Gb |

-| x86_64-linux | 210Gb |

-| shared files | 18Gb |

-

-[Size breakdown of titles in a typical installation](size_graph)

-

-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:

-

- * Lab Name

- * Types of computers on site: Linux, OS X Intel, OS X PowerPC, IRIX

- * 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.

-

-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.

-

-## Installation

-

- 1. Create an 'sbgrid' user on the machine that will host your software installation. This should be a normal, unprivileged user account.

- 2. Log in as this 'sbgrid' user.

- 3. Download the installation script from the URL provided in the account creation email.

- 4. Make it executable: `chmod +x sbgrid-admin`

- 5. Run the script: `./sbgrid-admin -i`

- 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.

-

-## Post-Installation Steps

-

- 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`

- 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`

- 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.

-

-

-## SGI IRIX Software Branch

-

-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`

-

-Note that the IRIX branch is only compatible with *tcsh*; there is no sh-compatible configuration for this branch.

-# SBGrid Mirrors

-

-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).

-## Supported Operating Systems

-

-The SBGrid Software Suite can run on Linux, OS X and IRIX machines.

-

-### Linux

-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.

-

-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.

-

-Currently Supported:

-

-* Red Hat Enterprise Linux 6.x and 7.x and the community supported versions: CentOS and Scientific Linux.

-* 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.

-

-## OS X Intel

-We build and test the programs under the most five most recent OS X releases.

-

-Currently Supported:

-

-* OS X Intel 10.9 - 10.12

-* 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.

-

-## OS X PowerPC

-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.

-

-Currently Supported:

-

-* OS X PowerPC 10.4 - 10.5

-

-## IRIX

-The IRIX programs branch is currently frozen. The applications are stable and work well on our SGI hardware, but they are not being updated.

-

-Currently Supported:

-

-* IRIX 6.5.26 + bugfix releases

-# Overriding Software Versions

-

-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.

-

-## Display Available Versions

-

-To list the available versions of a software title, you can use the *sbgrid-info* utility. Running *sbgrid-info -l* will list the versions for your current platform. From a Linux machine, a search for CCP4 versions looks like this:

-

-

- $ sbgrid-info -l ccp4

- Version information for: /programs/x86_64-linux/ccp4

-

- Default version: 7.0

- In-use version: 6.5

- Other available versions: 6.4.0 6.3.0

- Overrides use this shell variable: CCP4_X

-

-

-Running *sbgrid-info -L* will print the available versions for the three current platforms (OS X PowerPC and Intel, Linux).

-

-

- $ sbgrid-info -L gnuplot

- Version information for: /programs/x86_64-linux/gnuplot

-

- Default version: 4.6.4

- In-use version: 4.6.4

- Other available versions: 4.6.0 4.4.3 4.2.6

- Overrides use this shell variable: GNUPLOT_X

-

- Version information for: /programs/i386-linux/gnuplot

-

- Default version: 4.6.0

- Other available versions: 4.4.3 4.2.6

- Overrides use this shell variable: GNUPLOT_L

-

- Version information for: /programs/i386-mac/gnuplot

-

- Default version: 4.6.4

- Other available versions: 4.4.3 4.2.6 4.6.0

- Overrides use this shell variable: GNUPLOT_M

-

-

-## Overriding Default Versions

-

-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.

-

-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:

-

-`APPLICATION_X=1.2`

-

-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:

-

-| Software Directory | Shorthand Initial |

-| ------------------ | ----------------- |

-| i386-linux | _L |

-| x86_64-linux | _X |

-| i386-mac | _M |

-

-To quickly open the overrides file in your default $EDITOR, you can run *sbgrid-overrides -e*.

-

-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.

-

-The example output below shows CCP4 on linux being changed from the default version:

-

- Configuration options in effect for this shell:

- Variable Setting Configuration

- CCP4_M 6.3.0 personal

-

-

-## Disabling a Software Package

-To disable a specific software package, set its version to "disable" in your ~/.sbgrid.conf file.

-# Recommended Hardware

-

-## Linux Workstations

-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.

-

-## Apple Workstations

-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.

-# Development Network

-

-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.

-

-Once you have an account, you can access the developer network by connecting via SSH to:

-

- *developer.sbgrid.org*

-

- developer runs Scientific Linux 6 x86_64

-

-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.

-

-The following are the always-on operating system/hardware combinations. They are generally kept at the latest point release:

-

-| Hostname | Operating System | Architecture | Notes |

-| ------------------ | --------------- | ----------- | ----------------------------------------- |

-| sbgrid-c5b | CentOS 5 | x86 | base SBGrid 32-bit Linux build VM |

-| sbgrid-c5b-64 | CentOS 5 | x86_64 | base SBGrid 64-bit Linux build VM |

-| sbgrid-c5t-64 | CentOS 5 | x86_64 | minimal install for portability testing |

-| sbgrid-c6b | CentOS 6 | x86 | base SBGrid 32-bit Linux build VM |

-| sbgrid-c6b-64 | CentOS 6 | x86_64 | base SBGrid 64-bit Linux build VM |

-| sbgrid-c6t-64 | CentOS 6 | x86_64 | minimal install for portability testing |

-| sbgrid-dev-vm-07 | Debian 5 | x86 | |

-| sbgrid-dev-vm-08 | Debian 5 | x86_64 | |

-| sbgrid-dev-vm-16 | Debian 6 | x86 | |

-| sbgrid-dev-vm-17 | Debian 6 | x86_64 | |

-| sbgrid-dev-vm-03 | Ubuntu 10.10 | x86 | |

-| sbgrid-dev-vm-04 | Ubuntu 10.10 | x86_64 | |

-| sbgrid-dev-vm-14 | OpenSuSE 11.3 | x86 | |

-| sbgrid-dev-vm-15 | OpenSuSE 11.3 | x86_64 | |

-| sbgrid-m106 | OS X 10.6 | x86/x86_64 | Base SBGrid OS X Intel build machine |

-| sbgrid-m107 | OS X 10.7 | x86/x86_64 | |

-| sbgrid-m108 | OS X 10.8 | x86/x86_64 | |

-| sbgrid-m109 | OS X 10.9 | x86/x86_64 | |

-| sbgrid-m1010 | OS X 10.10 | x86/x86_64 | |

-| sbgrid-dev-flange | OS X 10.5 | PowerPC | |

-

-

-We have the Intel, Portland and Absoft (PPC) compilers:

-

-* Intel 12.0, 11.1, 10.1 (ifc, ifort) - any linux host, OS X Intel hosts

-* Portland 14.4, 12.6, 10.9, 10.2, 9.0-1 (pgcc, pgf77/90/95) - sbgrid-dev-architect, sbgrid-dev-moose

-

-There is a configuration file for sh-compatible shells that will enable the compilers and their environmental settings:

-

- $ . /build/conf/buildenv.sh

-

-Then you can use the 'build' function to control your compiler settings:

-

- $ build help

- build: a shell function for controlling compilers

-

- Usage: build (help3264list)

-

- help This help message

- 32 Configure 32-bit compilers

- 64 Configure 64-bit compilers

- list List available compilers

-

-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.

-

-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.

-

-# Request an Account

-

-Thanks for your interest in participating in the SBGrid Developer Network.

-

-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.

-

-That's the only requirement for new accounts. In return for access to these resources, you must agree to not abuse the resources for:

-

-* sending spam

-* cracking our computers or other peoples' computers

-* other activity which is illegal in the USA or your country

-

-And you agree to take reasonable precautions to maintain the security of your password and account by not sharing this information with other people.

-On our end, we will:

-

-* take reasonable precautions to maintain the security of the network, accounts and data

-* make occasional backups of account data (but don't count on it!)

-* attempt to maintain a high availability of the developer resources

-

-We reserve the right to close accounts at any time for any reason.

-

-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.

-## SBGrid Sharp server

-

-SBGrid maintains a server for Global Phasing's application [Sharp/AutoSharp](https://sharp.sbgrid.org:8080) for use by consortium members.

-To use the sharp server, email accounts@sbgrid.org for account credentials.

-

-Documentation for using Sharp can be found [here](http://www.globalphasing.com/sharp/manual/)

-

-

-## General

-

-### 3D Stereo on RHEL/CentOS 6 systems

-

-Nvidia 3d stereo on RHEL 6 is reasonably straight-forward.

-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.

-

-### 3D Stereo on RHEL/CentOS 7 systems with Gnome 3

-

-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.

-

-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.

-

-In order to use 3D stereo on Gnome3 systems, you can switch from Gnome3/gdm to MATE/lightdm.

-The MATE Desktop Environment is the continuation of GNOME 2 which is the default desktop in CentOS 5 and 6.

-

-To change to MATE on CentOS7 systems, first, install the Extra Packages for Enterprise Linux (EPEL) repo:

-

-

- yum install epel-release

-

-

-Then install the nvidia drivers from epel

-

-

- yum install kmod-nvidia

-

-

-You may find you need these packages as well

-

-

- yum install mesa-libGLU-9.0.0-4.el7.x86_64 libXScrnSaver-1.2.2-6.1.el7.x86_64

-

-

-Next, install lightdm which doesn't require the composite extension.

-

-

- yum install lightdm

-

-

-From there we do a couple of groupinstalls

-You may have these rpms installed already, but just for good measure

-

-

- yum group install "X Window System"

-

-

-then

-

-

- yum groupinstall "MATE Desktop"

-

-

-Toggle from gdm to lightdm in systemd using systemctl.

-To see what you are using as a 'display manager', check this link

-

-

- ls -l /etc/systemd/system/display-manager.service

-

-

-This is likely pointing to gdm and should be changed to point to lightdm.

-You can change that with systemctl.

-

-

- systemctl disable gdm

- systemctl enable lightdm

-

-

-And then this will reload you changes, similar to changing runlevels with sysinitV

-

-

- systemctl isolate graphical.target

-

-

-Make sure to select MATE from the drop menu as your graphical before you login.

-## Mac OS X

-

-* 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.

-

-## Laptops

-

-* You can create a local installation to take along with you.

-http://www.sbgrid.org/wiki/laptopinstall

-# Overriding Software Versions

-

-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.

-

-## Display Available Versions

-

-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:

-

-

- $ sbgrid-info -l ccp4

- Version information for: /programs/x86_64-linux/ccp4

-

- Default version: 7.0

- In-use version: 6.5

- Other available versions: 6.4.0 6.3.0

- Overrides use this shell variable: CCP4_X

-

-

-Running *sbgrid-info -L* will print the available versions for the three current platforms (OS X PowerPC and Intel, Linux).

-

-

- $ sbgrid-info -L gnuplot

- Version information for: /programs/x86_64-linux/gnuplot

-

- Default version: 4.6.4

- In-use version: 4.6.4

- Other available versions: 4.6.0 4.4.3 4.2.6

- Overrides use this shell variable: GNUPLOT_X

-

- Version information for: /programs/i386-linux/gnuplot

-

- Default version: 4.6.0

- Other available versions: 4.4.3 4.2.6

- Overrides use this shell variable: GNUPLOT_L

-

- Version information for: /programs/i386-mac/gnuplot

-

- Default version: 4.6.4

- Other available versions: 4.4.3 4.2.6 4.6.0

- Overrides use this shell variable: GNUPLOT_M

-

-

-## Overriding Default Versions

-

-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.

-

-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:

-

-`APPLICATION_X=1.2`

-

-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:

-

-| Software Directory | Shorthand Initial |

-| ------------------ | ----------------- |

-| i386-linux | _L |

-| x86_64-linux | _X |

-| i386-mac | _M |

-

-To quickly open the overrides file in your default $EDITOR, you can run *sbgrid-overrides -e*.

-

-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.

-

-The example output below shows CCP4 on linux being changed from the default version:

-

- Configuration options in effect for this shell:

- Variable Setting Configuration

- CCP4_M 6.3.0 personal

-

-

-## Disabling a Software Package

-To disable a specific software package, set its version to "disable" in your ~/.sbgrid.conf file.

-## General

-

-* 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.

-

-## Linux

-Information on configuring 3D stereo can be found [here](stereo)

-

-* 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:

-

- /programs/i386-linux/system/RPMs

- /programs/x86_64-linux/system/RPMs

-

-* SELinux must be disabled.

-

-* 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.

-

-Packages for RHEL 6, and 7 and compatible machines:

-

- yum install glibc.i686 libgcc.i686 libX11.i686 libXaw.i686 libXext.i686 ncurses.i686 \

- redhat-lsb.i686 xorg-x11-fonts-75dpi xorg-x11-fonts-100dpi xorg-x11-fonts-ISO8859-1-75dpi \

- xorg-x11-fonts-ISO8859-1-100dpi xorg-x11-fonts-misc libXScrnSaver

-

-

-* 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.

-`apt-get install libc6-i386 lsb tcsh gawk libjpeg62 curl libx11-6:i386 libxext6:i386`

-

-## Mac OS X

-Information on configuring 3D stereo can be found [here](stereo)