Molecular dynamic (MD) simulations can be used to analyze the physical movements in atoms or molecules and perform nucleotide and genomic sequencing. These calculations and simulations are computationally intensive and can take several months using a cluster of traditional on-premises high-performance computers.
Research organizations require scalable, robust infrastructure. But it’s hard for researchers to justify buying an on-premises cluster with the speed required when the cluster can sit idle throughout the year. Researchers from around the world are working with Oracle for Research and using Oracle Cloud to accelerate discoveries. For example, researchers in the Clancy and Vorobyov laboratories at the University of California, Davis (UC Davis) developed advanced molecular dynamics (MD) simulations on Oracle Cloud to better understand and predict the likelihood of pharmaceutical compounds to cause drug-induced cardiotoxicity.
Why run molecular dynamic simulations in the cloud?
Oracle Cloud Infrastructure (OCI) provides access to the latest, cutting-edge hardware on-demand and offers enterprise-scale computing with a wide variety of options from bare metal to virtual machine (VM) GPU shapes. By using NVIDIA GPU Cloud (NGC) with OCI in combination with a GPU-enabled software tool like NVIDIA Clara Parabricks Pipelines, GROMACS, or NAMD, researchers can accelerate the analysis of whole genomes from days to under an hour.
Oracle recently conducted a benchmark study that demonstrates the performance gains and cost savings associated with running simulations in a faster, more efficient manner. The test compared the NVIDIA V100 Tensor Core GPU-enabled VM.GPU3.1, VM.GPU3.2, VMGPU3.4, and the BM.GPU3.8 instances with the new BM.GPU4.8 instance powered by the NVIDIA A100 Tensor Core GPU. On average, the BM.GPU4.8 had 32% greater overall performance increase compared to the BM.GPU3.8.
Reference architecture
The Oracle Architecture Center allows you to automate the entire process of deploying and provisioning the infrastructure for running NVIDIA Clara Parabricks Pipelines, GROMACS, or NAMD applications on OCI. Each reference architecture provides the Terraform code, available on GitHub. You can pull the code into Resource Manager with a single click, create the stack, and deploy it. Alternatively, you can download the code from GitHub to your computer, customize the code, and deploy the architecture by using the Terraform CLI. Each reference architecture introduces a platform topology, using architectural diagrams, a component overview, and recommendations for best practices, including availability, performance, security, and costs.
Deploy NVIDIA Clara Parabricks Pipelines
NVIDIA Clara Parabricks Pipelines is an accelerated computational framework supporting genomics applications by providing quick and accurate genome analysis tools, supporting germline, somatic, and RNA workflows. The NVIDIA GPU-based solution speeds up analysis of whole genomes from days to under an hour. Clara Parabricks Pipelines can meet the demands of any project and scale to thousands of genomes.
Figure 1: Deploy genomics applications framework and NVIDIA Clara Parabricks
Deploy GROMACS
GROMACS is a molecular dynamics package primarily designed to simulate complicated bonded interactions of biochemical molecules such as proteins, lipids, and nucleic acids. Because of its ability to quickly calculate non-bonded interactions, many groups also use GROMACS for research on non-biological systems. GROMACS is free, open source software that is user-friendly and includes a fully automated topology builder. It also comes with a large selection of flexible tools for trajectory analysis.
Figure 2: Deploy molecular dynamics and GROMACS applications
Deploy nanoscale molecular dynamics (NAMD)
Nanoscale molecular dynamics (NAMD) is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD uses the popular molecular graphics program visual molecular dynamics (VMD) for simulation setup and trajectory analysis. NAMD is free, open source software that offers source code and precompiled binaries.
Figure 3: Deploy molecular dynamics and NAMD applications
Unlock discoveries with Oracle Cloud
We recognized that configuring cloud infrastructure can be complex, but we’re here to help enable your success. These references architectures automate the entire process of deploying and provisioning infrastructure as code. Regardless of the GPU-enabled software that you run, you can provision and destroy compute resources for a simulation on demand to meet your scale requirements. In addition, our pay-for-use capacity keeps costs low.
Every use case is different. The only way to know if Oracle Cloud Infrastructure is right for you is to try it. You can select either the Oracle Cloud Free Tier or 30-day free trial, which includes US$300 in credit to get you started with a range of services, including compute, storage, and networking.