AWS HPC Blog

Benchmarking NVIDIA Clara Parabricks Somatic Variant Calling Pipeline on AWS

Somatic variants are genetic alterations which are not inherited but acquired during one’s lifespan, for example those that are present in cancer tumors. In this post, we will demonstrate how to perform somatic variant calling from matched tumor and normal genome sequence data, as well as tumor-only whole genome and whole exome datasets using an NVIDIA GPU-accelerated Parabricks pipeline, and compare the results with baseline CPU-based workflows.

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AI-based drug discovery with Atomwise and WEKA Data Platform

Drug discovery is an expensive proposition, with a $2.6 billion cost over 10 years and just a 12% success rate. AI promises to significantly improve the success rate by finding small molecule hits for undruggable targets. On the forefront of using AI in drug discovery is Atomwise, with its AtomNet® platform. In this blog, we will lay out the challenges of the drug discovery process, and show how AI/ML startups are solving these challenges using solutions from Atomwise, AWS, and WEKA.

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Figure 1: Comparison of simulation performance for the Le Mans test case run with Open MPI and Intel MPI. Intel MPI offers better performance compared to Open MPI.

Simcenter STAR-CCM+ price-performance on AWS

Organizations such as Amazon Prime Air and Joby Aviation use Simcenter STAR-CCM+ for running CFD simulations on AWS so they can reduce product manufacturing cycles and achieve faster times to market. In this post today, we describe the performance and price analysis of running Computational Fluid Dynamics (CFD) simulations using Siemens SimcenterTM STAR-CCM+TM software on AWS HPC clusters.

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Figure 2: Identification of redun jobs and grouping them into Array Jobs to run on AWS Batch. (Top) redun represents the workflow as an Expression Graph (top-left), and identifies reductions (red boxes) that are ready to be executed. The redun Scheduler creates a redun Job (J1, J2, J3) for each reduction and dispatches those jobs to Executors based on the task-specific configuration. The Batch Executor allows jobs to accumulate for up to three seconds (default) in order to identify compatible jobs for grouping into an Array Job, which are then submitted to AWS Batch (top-right). (Bottom) As jobs complete in AWS Batch, the success (green) and failure (red) is propagated back to Executors, the Scheduler, and eventually substituted back into the Expression Graph (bottom-left).

Data Science workflows at insitro: how redun uses the advanced service features from AWS Batch and AWS Glue

Matt Rasmussen, VP of Software Engineering at insitro, expands on his first post on redun, insitro’s data science tool for bioinformatics, to describe how redun makes use of advanced AWS features. Specifically, Matt describes how AWS Batch’s Array Jobs is used to support workflows with large fan-out, and how AWS Glue’s DynamicFrame is used to run computationally heterogenous workflows with different back-end needs such as Spark, all in the same workflow definition.

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Figure 1: Evaluating a sequence alignment workflow using graph reduction.** In redun, workflows are represented as an Expression Graph (left) which contain concrete value nodes (grey) and Expression nodes (blue). The redun scheduler identifies tasks that are ready to execute by finding subtrees that can be reduced (red boxes), substituting task results back into the Expression Graph (red arrows). The scheduler continues to find reductions until the Expression Graph reduces to a single concrete value (grey box, far right). If any reduction has been done before (determine by comparing an Expression's hash), the redun scheduler can replay the reduction from a central cache and skip task re-execution.

Data Science workflows at insitro: using redun on AWS Batch

Matt Rasmussen, VP of Software Engineering at insitro describes their recently released, open-source data science framework, redun, which allows data scientists to define complex scientific workflows that scale from their laptop to large-scale distributed runs on serverless platforms like AWS Batch and AWS Glue. I this post, Matt shows how redun lends itself to Bioinformatics workflows which typically involve wrapping Unix-based programs that require file staging to and from object storage. In the next blog post, Matt describes how redun scales to large and heterogenous workflows by leveraging AWS Batch features such as Array Jobs and AWS Glue features such as Glue DynamicFrame.

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Migrating to AWS ParallelCluster v3 – Updated CLI interactions

The AWS ParallelCluster version 3 CLI differs significantly from ParallelCluster version 2. This post provides some guidance on mapping between versions to help you with migrating to ParallelCluster 3. We also summarize new CLI features in ParallelCluster 3 to expose the things you just couldn’t do previously.

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Choosing between AWS Batch or AWS ParallelCluster for your HPC Workloads

It’s an understatement that AWS has a lot of services (more than 200 at the time of this post!). We’re usually the first to point out that there’s more than one way to solve a problem. HPC is no different in this regard, because we offer a choice: customers can run their HPC workloads using AWS […]

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