Conceptual architecture and key components of PlayMolecule Sample Clauses

Conceptual architecture and key components of PlayMolecule. All PlayMolecule applications are containerized with Singularity to ensure easy deployment and reproducibility. For visualisation of the user interfaces and the results, PlayMolecule offers a web server which integrates a state-of-the-art 3D molecular viewer. HPC resources can be leveraged by PlayMolecule both to serve a larger number of users as well as to provide faster computation. Applications such as AdaptiveSampling depend on multiple GPUs being available so that multiple simulations can be run in a high-throughput parallel manner to explore faster protein conformational space, or protein-ligand interactions and thus can fully leverage large computing clusters. PlayMolecule applications mostly run in an embarrassingly parallel manner and thus scale linearly to the number of resources which are available and jobs which are run. Network usage is limited to the transfer of input and output files for jobs which execute on cluster nodes. The data transfer is done from the applications to the PlayMolecule backend which in turn stores the files in the XxxXX server. Output files are typically in the order of a few megabytes, however applications such as SimpleRun and AdaptiveSampling generate molecular dynamics trajectories of multiple gigabytes and thus can increase network traffic. Computation time varies between applications ranging from a few seconds in ProteinPrepare to multiple weeks in AdaptiveSampling. Ongoing work in PlayMolecule is focused on reducing data duplication between cluster nodes, the XxxXX server and the web server to also reduce network load as well as storage requirements. All PlayMolecule singularity applications are built using internal Python libraries which we regularly evaluate for performance and algorithms.
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