Installing SBGrid Software
Using the SBGrid Environment
Support for Site Administrators
Hardware Support Notes
Getting Help
Support for Developers
The majority of structural biology computing happens on linux; there are several vendors providing linux workstation or server configurations we've had good experience with: ThinkMate, Exxact, Microway. Please feel free to contact us at help@sbgrid.org regarding upcoming hardware, or if you have another hardware vendor to mention.
System configurations can be targeted to particular compute-intenstive workflows (for example, Cryo-EM or small molecule docking). We're in the process of assembling benchmark workflows, datasets and results to help guide hardware decisions.
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 arrangement with their Apple representative. SBGrid has several labs that run exclusively on Macs and OS X, though these are not advised for CryoEM data processing.
| System | Runtime (s) | Notes |
|---|---|---|
| Workstation 1 | 712 | |
| Workstation 2 | 398 | 2x GPU |
| GPU Node 1 | 281 | 4x GPU |
Core counts determined via "nproc" output, and include hyperthreading where enabled.
Plasmodium ribosome data set from Wong et al, 2014 ( EMD 2660 , EMPIAR-10028 ); courtesy of the Relion Wiki.
To allow for shorter runtimes during 2D classification benchmarks, input STAR files were truncated by removal of partical entries.
