ARCHER Benchmarks

archer machine photo Here we present the results of our benchmarking of ARCHER. 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.

ARCHER is hosted by the EPCC and is comprised of the CRAY XC30 architecture and is the current tier1 UK national machine. ARCHER is composed of 4,920 nodes with each compute node having two 2.7 GHz, 12-core E5-2697 v2 (Ivy Bridge) series processors bringing a total of 118,080 cores. The majority of these nodes 4544 (109,056 cores) having 64GB of RAM whilst 376 (9,024 cores) have high memory (128GB RAM). The compute nodes are connected via a high speed Aries interconnect for fast parallel computation and have access to high performance parallel filesystems. This service is now finished and the machine decommissioned as of February 2021.

AMBER 14

20k atoms			61k atoms			465k atoms			1.4M atoms			3M atoms
cores	ns/day	ns/kAU	cores	ns/day	ns/kAU	cores	ns/day	ns/kAU	cores	ns/day	ns/kAU	cores	ns/day	ns/kAU
24	29.13	3.372	24	9.99	1.156	24	1.17	0.135	24	0.36	0.042	24	0.17	0.019
48	53.36	3.088	48	17.87	1.034	48	2.07	0.120	48	0.67	0.039	48	0.30	0.017
96	86.58	2.505	96	29.67	0.859	96	3.46	0.100	96	1.09	0.032	96	0.54	0.016
192	88.60	1.282	192	42.06	0.609	192	5.35	0.077	192	1.69	0.024	192	0.85	0.012
384	81.83	0.592	384	44.68	0.323	384	6.63	0.048	384	2.29	0.017	384	1.18	0.009
768	59.89	0.217	768	38.04	0.138	768	6.63	0.024	768	2.61	0.009	768	1.47	0.005
1536	28.27	0.051	1536	27.32	0.049	1536	5.10	0.009	1536	2.37	0.004	1536	1.42	0.003
			3072	10.40	0.009	3072	4.05	0.004	3072	2.05	0.001	3072	0.97	0.0009

Gromacs 2020.2 Single Precision

20k atoms			61k atoms			465k atoms			1.4M atoms			3M atoms
cores	ns/day	ns/kAU	cores	ns/day	ns/kAU	cores	ns/day	ns/kAU	cores	ns/day	ns/kAU	cores	ns/day	ns/kAU
24	76.065	8.804	24	22.281	2.579	24	2.520	0.292	24	1.047	0.121	24	0.474	0.055
48	127.506	7.379	48	39.130	2.264	48	4.916	0.284	48	2.047	0.118	48	0.939	0.054
72	172.436	6.653	96	64.163	1.857	96	9.625	0.279	96	3.744	0.108	96	1.833	0.053
96	165.494	4.789	192	99.429	1.438	192	15.987	0.231	192	5.485	0.079	192	3.553	0.051
120	194.908	4.512	288	124.272	1.199	384	33.097	0.239	384	9.739	0.070	384	6.250	0.045
144	122.152	2.356	384	148.792	1.076	768	25.094	0.091	768	18.549	0.067	768	10.058	0.036
168	208.652	3.449	480	183.417	1.061	1536	30.450	0.055	1536	21.395	0.039	1536	14.689	0.027
192	214.384	3.102	576	89.313	0.431	1920	28.591	0.041	3072	21.990	0.020	3072	21.651	0.020
288	197.441	1.904	672	160.534	0.664	2304	32.456	0.039	4608	27.207	0.016	4608	18.163	0.011
384	129.391	0.936	768	163.934	0.593	2688	30.378	0.031	6144	26.536	0.012	6144	20.437	0.009
480	failed	-	864	98.624	0.317	3072	29.925	0.027	7680	26.168	0.009	7680	19.331	0.007
576	98.835	0.477	960	79.584	0.230	3840	29.637	0.021	9216	26.059	0.008	9216	23.931	0.006
			1056	83.766	0.220	4608	25.966	0.016	10752	25.547	0.007	10752	23.886	0.006
			1152	105.749	0.255	5376	31.041	0.016	12288	22.438	0.005	12288	24.767	0.005
						6144	26.812	0.012	13824	24.334	0.005	13824	27.101	0.005
						6912	27.070	0.011	15360	21.294	0.004	15360	27.784	0.005

Gromacs 2018.1 Single Precision

20k atoms			61k atoms			465k atoms			1.4M atoms			3M atoms
cores	ns/day	ns/kAU	cores	ns/day	ns/kAU	cores	ns/day	ns/kAU	cores	ns/day	ns/kAU	cores	ns/day	ns/kAU
24	76.065	8.804	24	22.281	2.579	24	2.520	0.292	24	1.047	0.121	24	0.474	0.055
48	127.506	7.379	48	39.130	2.264	48	4.916	0.284	48	2.047	0.118	48	0.939	0.054
72	172.436	6.653	96	64.163	1.857	96	9.625	0.279	96	3.744	0.108	96	1.833	0.053
96	165.494	4.789	192	99.429	1.438	192	15.987	0.231	192	5.485	0.079	192	3.553	0.051
120	194.908	4.512	288	124.272	1.199	384	33.097	0.239	384	9.739	0.070	384	6.250	0.045
144	122.152	2.356	384	148.792	1.076	768	25.094	0.091	768	18.549	0.067	768	10.058	0.036
168	208.652	3.449	480	183.417	1.061	1536	30.450	0.055	1536	21.395	0.039	1536	14.689	0.027
192	214.384	3.102	576	89.313	0.431	1920	28.591	0.041	3072	21.990	0.020	3072	21.651	0.020
288	197.441	1.904	672	160.534	0.664	2304	32.456	0.039	4608	27.207	0.016	4608	18.163	0.011
384	129.391	0.936	768	163.934	0.593	2688	30.378	0.031	6144	26.536	0.012	6144	20.437	0.009
480	failed	-	864	98.624	0.317	3072	29.925	0.027	7680	26.168	0.009	7680	19.331	0.007
576	98.835	0.477	960	79.584	0.230	3840	29.637	0.021	9216	26.059	0.008	9216	23.931	0.006
			1056	83.766	0.220	4608	25.966	0.016	10752	25.547	0.007	10752	23.886	0.006
			1152	105.749	0.255	5376	31.041	0.016	12288	22.438	0.005	12288	24.767	0.005
						6144	26.812	0.012	13824	24.334	0.005	13824	27.101	0.005
						6912	27.070	0.011	15360	21.294	0.004	15360	27.784	0.005

LAMMPS 11.5.2018

20k atoms			61k atoms			465k atoms			1.4M atoms			3M atoms
cores	ns/day	ns/kAU	cores	ns/day	ns/kAU	cores	ns/day	ns/kAU	cores	ns/day	ns/kAU	cores	ns/day	ns/kAU
24	13.318	1.541	24	4.279	0.495	24	0.529	0.061	24	0.178	0.020	24	0.088	0.010
48	20.089	1.163	48	7.951	0.460	48	1.015	0.059	48	0.346	0.020	48	0.173	0.010
72	24.146	0.932	72	11.213	0.432	96	1.962	0.057	96	0.651	0.019	96	0.338	0.010
96	37.732	1.092	96	14.283	0.413	192	3.664	0.053	192	1.233	0.018	192	0.614	0.009
120	41.903	0.970	192	21.927	0.317	384	6.721	0.049	384	2.487	0.018	384	1.197	0.009
144	49.646	0.958	288	27.683	0.267	768	10.344	0.037	768	4.027	0.016	768	2.264	0.009
168	49.840	0.824	384	34.909	0.253	1536	13.827	0.025	1536	6.232	0.011	1536	3.767	0.008
192	51.207	0.741	480	42.146	0.244	1920	13.878	0.020	3072	7.095	0.006	3072	5.586	0.007
288	42.271	0.408	576	42.613	0.206	2304	15.827	0.019	4608	7.753	0.005	4608	6.499	0.005
384	67.966	0.492	672	46.383	0.192	2688	12.095	0.012	6144	8.617	0.004	6144	7.431	0.004
480	38.593	0.223	768	55.877	0.202	3072	15.423	0.014	7680	7.889	0.003	7680	7.969	0.003
576	38.325	0.185	960	42.335	0.122	3840	15.795	0.011	9216	10.079	0.003	9216	8.324	0.003
672	44.097	0.182	1152	59.351	0.143	4608	17.432	0.011	10752	9.812	0.003	10752	7.992	0.002
768	44.255	0.160	1344	42.601	0.088	5376	17.932	0.009	12288	9.747	0.002	12288	7.796	0.002
864	38.616	0.124	1536	34.892	0.063	6144	14.753	0.007	13824	11.884	0.002	13824	7.867	0.002
960	38.641	0.111	1728	35.148	0.057	6912	15.053	0.006	15360	11.754	0.002	15360	7.969	0.001

NAMD 2.12

20k atoms			61k atoms			465k atoms			1.4M atoms			3M atoms
cores	ns/day	ns/kAU	cores	ns/day	ns/kAU	cores	ns/day	ns/kAU	cores	ns/day	ns/kAU	cores	ns/day	ns/kAU
24	19.944	2.308	24	6.154	0.712	24	0.823	0.095	24	0.271	0.031	24	0.097	0.011
48	35.222	2.038	48	12.070	0.698	48	1.617	0.094	48	0.549	0.031	48	0.194	0.011
72	51.172	1.974	72	16.983	0.655	96	3.147	0.091	96	1.092	0.031	96	0.376	0.011
96	62.371	1.805	96	22.024	0.637	192	6.153	0.089	192	2.135	0.031	192	1.003	0.015
120	74.911	1.734	192	40.420	0.585	384	11.831	0.086	384	4.166	0.030	384	1.968	0.014
144	79.063	1.525	288	55.425	0.535	768	21.709	0.079	768	7.903	0.029	768	3.698	0.013
168	83.865	1.387	384	59.313	0.430	1536	33.060	0.060	1536	14.495	0.026	1536	6.871	0.012
192	76.058	1.100	480	67.728	0.392	1920	37.310	0.054	3072	24.345	0.022	3072	11.472	0.010
288	85.402	0.823	576	70.612	0.341	2304	failed	-	4608	31.638	0.019	4608	14.064	0.008
384	76.658	0.555	672	74.877	0.310	2688	45.724	0.047	6144	34.694	0.016	6144	17.024	0.008
480	81.278	0.470	768	45.454	0.164	3072	47.895	0.043	7680	36.188	0.013	7680	20.078	0.007
576	88.658	0.428	960	48.711	0.141	3840	52.451	0.038	9216	32.218	0.010	9216	21.718	0.007
672	93.670	0.387	1152	59.706	0.144	4608	60.150	0.036	10752	37.310	0.010	10752	22.740	0.006
768	56.985	0.206	1344	53.204	0.110	5376	37.465	0.019	12288	36.272	0.008	12288	22.519	0.005
864	63.266	0.203	1536	63.429	0.114	6144	50.640	0.022	13824	46.617	0.009	13824	24.488	0.005
960	65.893	0.191	1728	74.995	0.121	6912	51.201	0.021	15360	47.127	0.009	15360	26.508	0.005
			1920	74.934	0.108	7680	52.455	0.019
			2112	77.720	0.102	8448	43.258	0.014
			2304	65.241	0.079	9216	44.116	0.013
			2496	86.505	0.096	9984	45.773	0.013
			2688	64.530	0.067
			2880	66.546	0.064
			3072	63.840	0.058
			3264	47.565	0.040