How can I run GOLD in parallel?
For very large virtual-screening tasks, we provide the GOLD Cluster tool. For smaller-scale parallelization, e.g. on a computational chemist's workstation or a local compute server, we do not have a specific product, but options are available.
This tool runs GOLD, inside a Singularity container, on an HPC compute cluster managed by Slurm. The GOLD Cluster tool and its User Guide are available to customers via our Downloads site under 'CSD-Discovery > GOLD'.
GOLD Cluster can be run on a Slurm cluster running in a Linux VM. Thus, in principle, this tool could be used to parallelize GOLD docking on a workstation. However, the setup involved isn't trivial and might not be straightforward on all platforms. A simpler solution for this use-case is thus required and a script is available which illustrates the use the CSD Docking API and the Python standard-library multiprocessing module to parallelize GOLD docking. This approach should be suitable for docking some hundreds or perhaps thousands of ligands, depending on the compute resource available and the docking protocol chosen. For further information, please contact firstname.lastname@example.org.
CSD Python API scripts repository (the script mentioned above is in
Platforms no longer supported
We no longer support the GOLD Cloud tool (which ran GOLD inside a Docker container on a Kubernetes cluster) or the use of GOLD with Parallel Virtual Machine (PVM). We also do not currently provide tooling or support for running GOLD on Grid Engines, although there is nothing in principle that should prevent this being done.