Thomas Benchmarks

Here we present the results of our benchmarking of MMM Thomas. The benchmarks we are running are our HECBioSim benchmark suite here. Our benchmarks aren't too heavily tuned as these are designed to be used by our community to work out how much HPC time to ask for on this resource, so are set at a level that would be reasonable for any normal biomolecular MD simulation. More information on the benchmarks themselves can be found at the above link.

Thomas is the Tier2 HPC resource run by the Materials and Molecular Mobelling Hub. It is composed of Intel(R) Xeon(R) CPU E5-2650 v4 @ 2.20GHz with 24 cores per node and infiniband interconnect. This service is now deprecated and finishing service early 2021.

AMBER 16

	20K atoms	61K atoms	465K atoms	1400K atoms	3000K atoms
Cores	ns/day	ns/day	ns/day	ns/day	ns/day
24	34.7	11.1	1.4	0.5	0.2
48	55.8	18.4	2.4	0.8	0.4

Gromacs 2019.3

	20K atoms	61K atoms	465K atoms	1400K atoms	3000K atoms
Cores	ns/day	ns/day	ns/day	ns/day	ns/day
24	84.9	26.4	2.8	1.2	0.56
48	141.7	48.5	5.3	2.4	1.1

LAMMPS 7Aug19

	20K atoms	61K atoms	465K atoms	1400K atoms	3000K atoms
Cores	ns/day	ns/day	ns/day	ns/day	ns/day
24	10.1	3.3	0.42	0.14	failed
48	17.6	6	0.79	0.27	failed

NAMD 2.13

	20K atoms	61K atoms	465K atoms	1400K atoms	3000K atoms
Cores	ns/day	ns/day	ns/day	ns/day	ns/day
24	17.3	5.8	0.8	0.3	0.1
48	31.4	11.6	1.7	0.6	0.2

We had a very restricted account to benchmark Thomas meaning we could only go as far as two nodes.