Heat-shock response of E. coli
The heat-shock response of E. coli (HSR) is a very stiff model of 28 species and 61 reaction channels which models the response of E. coli to heat stress. At elevated temperatures, proteins begin to denature; the response is the activation of several genes that produce chaperone enzymes, some of which help to refold denaturing proteins, whilst others help to degrade denatured proteins.
A generally stiff system, HSR gets progressively stiffer as the simulation progresses (with the initial conditions used and a long enough simulation time), with large changes in the propensities of some reactions. Systems such as this were one of the principal motivations for the Sorting Direct Method.
HSR is chosen principally because it is a real-world system whose characteristics have made it popular as a benchmark, and its inclusion here facilitates ready comparisons with other published execution times.
Speed Comparison
The table below shows single-core speed comparisons on IA-32 between CellMC-produced executable and results published in the literature, showing CellMC to be approximately 9 times faster on comparable hardware for ensembles of 500s HSR trajectories. Since CellMC achieves near-perfect linear speedup on multiprocessor shared-memory IA32 systems, its real-world performance is considerably better on modern dual- and quad-core machines.
| Description | Processor | GHz | Time (s) | Mrps |
|---|---|---|---|---|
| Cao et al. | Intel Pentium 4 | 1.4 | 76.5 | - |
| McCollum et al. | Intel Pentium 4 | 2.0 | 52.56 | 0.88 |
| Yoshimi et al. (using StochKit) | Intel Core 2 Quad | 2.4 | - | 1.61 |
| CellMC | AMD Athlon 64 | 2.0 | 7.63 | 8.09 |
| CellMC | Intel Core 2 | 1.86 | 6.11 | 10.38 |
| CellMC | Intel Core 2 Quad | 2.5 | 4.22 | 14.74 |
