minor formatting changes

- [Post-Installation Steps](#post-installation-steps)

- [SGI IRIX Software Branch](#sgi-irix-software-branch)

The SBGrid Software Suite can be installed on a single computer at your site and shared via a network filesystem (NFS) with the workstations or compute nodes on your network.

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


| Installation Requirements | |

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

| Branch | size |

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

| i386-mac | ~500 Gb |

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

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.

As state above, the `sbgrid-cli` utility should be used to install and manage an installation. This approach has a number of benefits over the script-based install. [See the sbgrid-cli recommened installation page for more information](sbgrid-cli-admin). A site installation can also be performed using the sbgrid-admin script : [sbgrid-admin](installation_admin) utility. This approach is currently supported but will be deprecated in the future.

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.

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.

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. If you would like access to SGI IRIX softare, please let us know at bugs@sbgrid.org. Also note that the IRIX branch is only compatible with _tcsh_; there is no sh-compatible configuration for this branch.

## General

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.

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.

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:

Other available versions: 4.4.3 4.2.6 4.6.0

Overrides use this shell variable: GNUPLOT_M

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.

Variable Setting Configuration

CCP4_M 6.3.0 personal

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

- There are significant benefits to installing software on a network filesystem, if available. NFS, SMB or AFP are all options for sharing a single software installation among multiple machines. Network installations have less administrative overhead, bandwidth and significant disk savings over a local installation.

- [Mac OS X](#mac-os-x)

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- libGLU is required for many structure visualization programs ( COOT, PyMOL, IMOD, Chimera, etc). This library is usually provided with the graphics card drivers, or in the

absence of that using the linux mesa package. For the standard CentOS repositories, running `yum install mesa-libGLU` (and potentially `yum install mesa-libGLU-devel`) as should provide non-hardware accelerated versions of these libraries.

- 64-bit machines need a number of 32-bit compatibility packages due to a number of legacy packages that are only available as 32-bit applications. Additional fonts for Tcl/Tk, Motif and Xview applications are also encouraged.

**32-bit compatibility libraries and fonts**

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

- XQuartz is required to provide X11 support on macOS. The latest Xquartz version can be downloaded from the MacOSForge site here: [https://www.xquartz.org ](https://www.xquartz.org/).