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SBGridTV

SBGrid in Your Lab

Choices, choices! Before you set up SBGrid in your lab you will need to make a few decisions and find someone with a bit of technical/IT expertise. About half of our members choose Linux, the other half Mac. Here are some things to consider:

SBGrid applications are supported under Linux and OS X operating systems:

Linux Tux

Linux?

Many of our Linux users choose Nvidia graphics cards, which provide accelerated graphics with selected cards offering 3D support. Although any PC workstation can, in principle, be configured with a Linux operating system, we recommend purchasing from an established Linux integrator. Our local vendor, Thinkmate, offers three preconfigured systems: a 2D workstation, a 3D workstation, and a GPU-enabled workstation for EM computing. These configurations are updated regularly and can be further fine-tuned to your specific needs. You can order directly from Thinkmate or send the configuration details to your local or institution-approved vendor. We always suggest that you consult your institutional IT department before making any computer purchases, since there may be limitations on the hardware they can support.

The SBGrid software collection is fully compatible with three different distributions of Linux - Red Hat Enterprise, CentOS, and Scientific Linux and is usually compatible with Fedora linux. CentOS and Scientific Linux are very similar and are the preferred distribution for SBGrid. Other Linux distibutions will likely work (Ubuntu, Mint, SUSE), but might require additional fine-tuning. We currently support versions 6.x and 7.x of CentOS/RHEL/Scientific Linux and test all applications on these platforms. Very recent versions of Fedora may not be 100% compatible out of the box, but we will work to correct any reported issues.

Linux systems can be readily configured in a networked, multi-user environment with NFS and NIS/LDAP protocols for file sharing and authentication support. In an ideal setup, a Linux workstation would mount storage from an enterprise level institutional provider. Relying on your institutional infrastructure might eliminate the need for an interdependent backup solution. Most members coordinate with their local research computing groups to design a sustainable and robust solution.

Thinkmate

Mac OS X

Mac?

iMacs, Mac Minis, and MacBook Pros can support most standard structural biology computations. These Macs are usually configured for a single-user environment and do not offer 3D functionality. Software directories can be shared between workstations or duplicated on individual computers. The standard Mac SBGrid software installation is usually deployed to a single file server at your institution. We then provide you with scripts to further synchronize applications to individual workstations.

SBGrid recently released a new installation script that allows users to install software directly from our servers at Harvard University to their computers. The process is often slower than when installing software from your institutional server, but it allows you to customize the list of installed applications and will work from any location that has internet connectivity.

Software Environment

Once your hardware is in place setting up the SBGrid software environment is relatively straightforward. The SBGrid suite is designed for installation on a central server at member sites. This single installation can then be shared via NFS to all local workstations. Users will then simply source a single SBGrid startup configuration file that will detect your operating system and configure all applications. SBGrid software is always installed in the /programs directory. Your installation will run the most recent version of a given application by default, but you can use your own .sbgrid configuration file to easily switch to older versions. For NFS-mounted systems, all software updates are transparent and require no user intervention. For detached computers, the user must initiate software updates. More detailed instructions on installing and using the SBGrid suite are provided in the SBGrid Forum.

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