Senior High-Performance Compute (HPC) Engineer

Key Skills

AWS, Bash scripting, Data pipelines, Database, DevOps, Google Analytics, Google Cloud Platform (GCP), Java Programming, Planning and organization, PostgreSQL, Python Programming, Site Reliability Engineering (SRE), Typing skills, User support and Troubleshooting

Job Description

Invitae is dedicated to bringing comprehensive genetic information into mainstream medicine to improve healthcare for billions of people. Our team is driven to make a difference for the patients we serve. We are leading the transformation of the genetics industry, by making genetic testing affordable and accessible for everyone to guide health decisions across all stages of life.

We are looking for an expert Systems Engineer to help support our terrestrial data center High-Performance Computing (HPC) environment and cloud-based systems. Our Systems Engineers work closely with DevOps and Site Reliability Engineers (SRE) as well as a large Software Engineering organization. Our Systems Engineers work closely with production and development teams. They will assist with development work, operational support for new and existing services, and supply to the constant improvement of production systems. Candidates should be able to perform functions required to configure, support and tackle issues with large scale computing environments hosted in a co-lo facility and in Amazon Web Services (AWS).

What you’ll do :

• Work with our AWS Operations and EKS teams to stage and test running our PIPE Platform services and bioinformatics workloads in AWS.
• Coordinate with our Networking team for operational support and incident management
• Help configure and maintain our cluster workload manager (Univa/Altair Grid Engine) and cluster nodes to help ensure optimal resource allocation based on organizational needs.
• Support cluster users with troubleshooting and execution of their Nextflow bioinformatics workflows
• Support PIPE Platform colleagues in managing production and development operational services
• Support cluster users with troubleshooting and performance profiling of HPC jobs using systems monitoring and our PostgreSQL HPC job database
• Participate in on-call responses to incidents including crafting fixes or workarounds and improving systems
• Help maintain our petabytes of on prem state-of-the-art all-flash storage.

What you bring :

• 12 years of technical experience supporting scientific and/or high-performance computing on prem or in the cloud. 
• Hands-on experience with managing computational and large-scale storage resources in a multi-user environment 
• Scripting or programming skills in Bash, Go, Python, or Java in a Linux environment
• Strong Linux troubleshooting skills, curiosity, and interest in Linux OS configuration and system internals.
• Experience supporting containerized workflows (Singularity/Apptainer, Docker, or Podman ) in production and development environments
• Strong desire to identify and mitigate performance bottlenecks
• Experience with using Salt or willingness to learn
• Preferred: Experience deploying AWS environments via TerraForm or Cloudformation.

At Invitae, you’ll work alongside some of the world’s specialists in genetics and healthcare at the forefront of genetic medicine. Our teams thrive in our dynamic organization which has been crafted to empower them to make the biggest impact they can for our patients. We give our employees the ability to explore interests and capabilities broadly within the organization. We prize freedom with accountability and offer significant flexibility. We also provide excellent benefits and competitive compensation in a fast-growing organization.

At Invitae, we’re changing healthcare to change lives. Join us!