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GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules

GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules (→ see this article for more information). It is a molecular dynamics calculations toolbox providing a rich set of calculation types, preparation and analysis tools. It runs well on almost all of the recent and past hardware platforms because of well implemented parallel algorithms and modern programming software design.

 

NCSA role in DEEP-EST project

 

NCSA responsibilities in the project encompass installation and performance optimizations of the MD simulator and the other tools for running on the Extreme Scale Booster, Data Analytics Module and Cluster Module, respectively.

 

Depending on the problem size of the simulation run GROMACS runs on different parts of the DEEP-EST system: 

 

Workflow Tk 1.3

Small runs will run on the CM and medium size simulation will run on the ESB/DAM. When running on the ESB/DAM all computationally intensive parts will be executed on the GPUs while CPUs will manage data transactions and CUDA kernel execution.

 

For larger simulations one needs the GPUs from the ESB but also stronger CPUs like on the CM. So large simulation run in an offload version on CM+ESB:

WP1 Workflow

Being able to use the advantages of two different modules improves the performance of large GROMACS runs on the DEEP-EST system:

 

Here a use case with 80 million atoms is used to scale on the DEEP-EST ESB. Each ESB node here as a partner CM node for the PME calclations.