HPC/Benchmarks/Generation 1 vs 2

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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

Observations

  • 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).

Recommendations

For the given workload, the I recommend the following values for optimal performance with respect to the given objective.

Node type Objective
time → min charge → min time × charge → min
gen1 nodes=4:ppn=3 nodes=1:ppn=4 nodes=3:ppn=4
run=35
tmax=503.05
charge=4.47 		run=01
tmax=1138.83
charge=2.53 		run=33
tmax=544.74
charge=3.63
gen2 nodes=4:ppn=4 nodes=1:ppn=8 nodes=2:ppn=8
run=54
tmax=237.59
charge=2.11 		run=22
tmax=472.16
charge=1.05 		run=52
tmax=329.10
charge=1.46 








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