AWS Compute Blog

Category: AWS Batch

Creating an AWS Batch environment for mixed CPU and GPU genomics workflows

This post is courtesy of Lee Pang – AWS Technical Business Development  I recently worked with a customer who needed to process a bunch of raw sequence files (FastQs) into Hi-C format (*.hic), which is used for the structural analysis of DNA/chromatin loops and sequence accessibility. The tooling they were interested in using was the Juicer […]

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GPU workloads on AWS Batch

Contributed by Manuel Manzano Hoss, Cloud Support Engineer I remember playing around with graphics processing units (GPUs) workload examples in 2017 when the Deep Learning on AWS Batch post was published by my colleague Kiuk Chung. He provided an example of how to train a convolutional neural network (CNN), the LeNet architecture, to recognize handwritten digits […]

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Building Simpler Genomics Workflows on AWS Step Functions

This post is courtesy of Ryan Ulaszek, AWS Genomics Partner Solutions Architect and Aaron Friedman, AWS Healthcare and Life Sciences Partner Solutions Architect In 2017, we published a four part blog series on how to build a genomics workflow on AWS. In part 1, we introduced a general architecture highlighting three common layers: job, batch and […]

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Building a tightly coupled molecular dynamics workflow with multi-node parallel jobs in AWS Batch

Contributed by Amr Ragab, HPC Application Consultant, AWS Professional Services and Aswin Damodar, Senior Software Development Engineer, AWS Batch At Supercomputing 2018 in Dallas, TX, AWS announced AWS Batch support for running tightly coupled workloads in a multi-node parallel jobs environment. This AWS Batch feature enables applications that require strong scaling for efficient computational workloads. Some of […]

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Using Cromwell with AWS Batch

Contributed by W. Lee Pang and Emil Lerch, WWPS Professional Services DNA is often referred to as the “source code of life.” All living cells contain long chains of deoxyribonucleic acid that encode instructions on how they are constructed and behave in their surroundings. Genomics is the study of the structure and function of DNA […]

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Deploy an 8K HEVC pipeline using Amazon EC2 P3 instances with AWS Batch

Contributed by Amr Ragab, HPC Application Consultant, AWS Professional Services AWS provides several managed services for file- and streaming-based media encoding options. Amazon Elastic Transcoder and AWS Elemental MediaConvert each provide several options for video/audio transcoding, optimized for various client devices. AWS Elemental Live provides online streaming-based encoding from edge camera devices. Through AWS Greengrass, edge […]

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Using AWS CloudFormation to Create and Manage AWS Batch Resources

This post courtesy of Arya Hezarkhani. AWS CloudFormation allows developers and systems administrators to easily create and manage a collection of related AWS resources (called a CloudFormation stack) by provisioning and updating them in an orderly and predictable way. CloudFormation users can now deploy and manage AWS Batch resources in exactly the same way that […]

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Building High-Throughput Genomics Batch Workflows on AWS: Workflow Layer (Part 4 of 4)

This post is courtesy of Aaron Friedman – Healthcare and Life Sciences Partner Solutions Architect at AWS and Angel Pizarro – Scientific Computing Technical Business Development Manager at AWS This post is the fourth in a series on how to build a genomics workflow on AWS. In Part 1, we introduced a general architecture, shown below, and […]

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Building High-Throughput Genomic Batch Workflows on AWS: Batch Layer (Part 3 of 4)

This post is courtesy of Aaron Friedman – Healthcare and Life Sciences Partner Solutions Architect at AWS and Angel Pizarro – Scientific Computing Technical Business Development Manager at AWS This post is the third in a series on how to build a genomics workflow on AWS. In Part 1, we introduced a general architecture, shown below, and […]

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Building High-Throughput Genomics Batch Workflows on AWS: Job Layer (Part 2 of 4)

This post is courtesy of Aaron Friedman – Healthcare and Life Sciences Partner Solutions Architect at AWS and Angel Pizarro – Scientific Computing Technical Business Development Manager at AWS This post is the second in a series on how to build a genomics workflow on AWS. In Part 1, we introduced a general architecture, shown below, and […]

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