AWS HPC Blog

Category: AWS Batch

BioContainers are now available in Amazon ECR Public Gallery

Today we are excited to announce that all 9000+ applications provided by the BioContainers community are available within ECR Public Gallery! You don’t need an AWS account to access these images, but having one allows many more pulls to the internet, and unmetered usage within AWS. If you perform any sort of bioinformatics analysis on AWS, you should check it out!

Rearchitecting AWS Batch managed services to leverage AWS Fargate

AWS service teams continuously improve the underlying infrastructure and operations of managed services, and AWS Batch is no exception. The AWS Batch team recently moved most of their job scheduler fleet to a serverless infrastructure model leveraging AWS Fargate. I had a chance to sit with Devendra Chavan, Senior Software Development Engineer on the AWS Batch team, to discuss the move to AWS Fargate and its impact on the Batch managed scheduler service component.

Analyzing Genomic Data using Amazon Genomics CLI and Amazon SageMaker

In this blog post, we demonstrate how to leverage the AWS Genomics Command line and Amazon SageMaker to analyze large-scale exome sequences and derive meaningful insights. We use the bioinformatics workflow manager Nextflow, it’s open source library of pipelines, NF-Core, and AWS Batch.

Blender on Batch

Efficient and cost-effective rendering pipelines with Blender and AWS Batch

This blog post explains how to run parallel rendering workloads and produce an animation in a cost and time effective way using AWS Batch and AWS Step Functions. AWS Batch manages the rendering jobs on Amazon Elastic Compute Cloud (Amazon EC2), and AWS Step Functions coordinates the dependencies across the individual steps of the rendering workflow. Additionally, Amazon EC2 Spot instances can be used to reduce compute costs by up to 90% compared to On-Demand prices.

Getting Started with NVIDIA Clara Parabricks on AWS Batch using AWS CloudFormation

In this blog post, we’ll show how you can run NVIDIA Parabricks on AWS Batch leveraging AWS CloudFormation templates. Parabricks is a GPU-accelerated tool for secondary genomic analysis. It reduces the runtime of variant calling on a 30x human genome from 30 hours to just 30 minutes, and leverages AWS Batch to provide an interface that scales compute jobs across multiple instances in the cloud.

Understanding the AWS Batch termination process

In this blog post, we help you understand the AWS Batch job termination process and how you may take actions to gracefully terminate a job by capturing SIGTERM signal inside the application. It provides you with an efficient way to exit your Batch jobs. You also get to know about how job timeouts occur, and how the retry operation works with both traditional AWS Batch jobs and array jobs.