Tune OpenMP Performance on a Memory-Bound Genomics Pipeline
Overview
What this challenge is about.
Profile a genomics pipeline across 1–64 threads, fix NUMA and false sharing bottlenecks, and deliver a scaling study for a verifiable certificate.
The scenario
The lab (publicly funded, processing roughly 4,000 patient samples/month for partners) has a 48-hour per-sample turnaround when it should be 18 — the bottleneck is on this single node.
The Brief
What you'll do, and what you'll demonstrate.
Tune an OpenMP variant-calling pipeline from poor 16-thread scaling to at least 48-thread useful scaling on a dual-socket NUMA node.
Earning criteria — what you'll demonstrate
- Profile OpenMP code with Intel VTune to identify memory bottlenecks
- Apply NUMA-aware allocation on a multi-socket node
- Identify and eliminate false sharing through padding + restructuring
- Validate optimizations with before/after measurement, not intuition
Program Fit
Where this fits in your program.
Sharpens the same skills your degree expects you to demonstrate.
High-Performance and Scientific Computing
Master · Systems
Strong alignment
This challenge maps to High-Performance and Scientific Computing at the Master level. It sharpens the same practical skills your coursework expects — but in a real industry context with actual constraints and deliverables.
Skills
Skills you'll demonstrate.
Each one shows up on your verified credential.
- Openmp
Apply openmp to solve real industry problems and demonstrate production-level capability.
- Numa Awareness
Apply numa awareness to solve real industry problems and demonstrate production-level capability.
- False Sharing
Apply false sharing to solve real industry problems and demonstrate production-level capability.
- Cache Optimization
Apply cache optimization to solve real industry problems and demonstrate production-level capability.
- Intel Vtune
Apply intel vtune to solve real industry problems and demonstrate production-level capability.
- Performance Analysis
Apply performance analysis to solve real industry problems and demonstrate production-level capability.
Careers
Career paths this challenge builds toward
Completing this challenge demonstrates skills that transfer directly to these roles: