SBGrid in Your Lab
SBGrid in Your Lab
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. SBGrid members are roughly split between usage of Linux and Mac. Here are some things to consider:
SBGrid supports Linux and Mac operating systems:
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 two preconfigured systems: a standard 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 distributions will likely work (Ubuntu, Mint, SUSE), but might require additional fine-tuning. We currently support versions 7 and 8 of CentOS/RHEL/Scientific Linux and test all applications on these platforms, but recommend that users stick with CentOS 7, since CentOS8 will reach end-of-life at the end of 2021. 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.
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.
Site Installation
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 is 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 was historically installed in the /programs directory, but in early 2021 we will transition to using the installation path /opt/sbgrid. Your installation will run the most recent, stable 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.
Workstation Installation Manager
The Consortium also offers an installation manager that allows end users the flexibility to install the full collection or cherry-pick a subset of software titles, and to kick off updates when convenient. Users from member labs can submit a request for an SBGrid installation manager account here: www.sbgrid.org/registration/register/.
Support Wiki
Visit our Support Wiki at https://sbgrid.org/wiki/Home for more details on installing software, using the SBGrid Environment, GPU computing, running SBGrid on AWS, and support for site administrators.