HPC/Benchmarks/Generation 1 vs 2

Introduction

Earlier this year, we received 200 additional nodes with E5540 processors. The processors have 8 cores, and support Hyperthreading, a feature which allows 2 threads per core. This benchmark investigates the benefit of hyperthreading (HT), and suggests optimal values for the nodes and processors per node (ppn) parameters in PBS.

Data

• HPC/Generation-2 nodes/vasp/vasp.lst, grep-able
• File:Vasp.txt, tab-separated CSV
• File:Vasp.pdf, PDF

Observations and conclusions

• 4-core runs give a high numerical throughput in each node type (run=01 to 04)
• gen2 nodes are fine for VASP with nodes=1:ppn=8; gen1 nodes are not (run=22 vs. 21)
• Adding more nodes allows for the fastest run (run=54) or 40% slower and a better charge rate (run=52)
• Running two apps in a single job is mostly not worth the effort of managing them (run=04 vs. 22)
• HT allows for slightly better charge rates, but usually only with non-MPI jobs (or unsynced MPI jobs) (run=15, 25, 40, 55), and runtimes are nearly proportionately longer, making HT largely unattractive. This also holds for the only case tested for HT and napps=1 (run=50).