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ISAMBARD Benchmarks

isambard server photoHere we present the results of our benchmarking of ISAMBARD. 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.

ISAMBARD is a UK tier2 service and is a Cray XC50 system which comprises 20,992 cores, and is one of the worlds first production Arm-based supercomputers. While ISAMBARD is not based on the more common x86 processors from Intel and AMD, most software compiles and runs on ISAMBARD with no or minimal changes.

Each of the 329 compute nodes contain two 32-core Marvell ThunderX2 processors running at 2.5 GHz. 160 nodes have 256 GB and 169 have 512 GB of memory, both at DDR4-2666MHz. The nodes are connected via Cray Aries interconnect in a Dragonfly topology. A Cray Sonexion 3000 storage cabinet provides 900 terabytes of Lustre storage.

 

Gromacs 2020.2

20k atoms 61k atoms 465k atoms 1400k atoms 3000k atoms
cores ns/day cores ns/day cores ns/day cores ns/day cores ns/day
64 72.56 64 26.16 64 2.8 64 1.23 64 0.58
128 144.62 128 45.29 128 5.64 128 2.44 128 1.15
192 200.14 192 failed 256 10.94 256 4.8 256 2.28
256 236.62 256 83.79 384 17.23 384 7.05 384 3.29
320 244.48 320 99.88 512 21.15 512 9.58 512 4.24
384 255.67 384 112.95 640 26.29 640 11.18 640 5.23
448 278.86 448 128.23 768 31.92 768 13.15 768 6.1
512 168.37 512 124.38 960 failed 960 16.1 960 7.43
576 failed 576 134.67 1280 failed 1280 20.08 1280 9.68
640 failed 640 157.75 1600 53.82 1600 24.52 1600 11.6
    704 163.07 1920 57.68 1920 27.43 1920 13.82
    768 171.93 2240 57.87 2240 30.79 2240 15.64
    832 177.81 2880 66.55 2880 31.52 2880 19.01
    896 failed 3840 74.82 3840 38.12 3840 20.38
    960 failed            

 

LAMMPS 7/08/2019

20k atoms 61k atoms 465k atoms 1400k atoms 3000k atoms
cores ns/day cores ns/day cores ns/day cores ns/day cores ns/day
64 19.39 64 6.3 64 0.81 64 0.27 64 0.13
128 31.42 128 11.04 128 1.54 128 0.52 128 0.26
192 37.25 192 15.17 256 2.89 256 1.02 256 0.49
256 39.22 256 17.91 384 3.95 384 1.44 384 0.71
320 37.44 320 18.55 512 4.98 512 1.83 512 0.93
384 34.93 384 19.05 640 6.08 640 2.23 640 1.16
448 37.12 448 18.65 768 6.93 768 2.63 768 1.35
512 43.34 512 21.32 960 7.68 960 3.14 960 1.61
576 43.06 576 24.39 1280 9.28 1280 3.82 1280 1.91
640 47.1 640 25.81 1600 10.7 1600 4.43 1600 2.3
704 45.99 704 26.34 1920 11.1 1920 5.1 1920 2.75
768 51.94 768 28.17 2240 11.84 2240 5.69 2240 3.18
832 53.06 832 28.23 2880 12.78 2880 6.66 2880 3.69
896 43.7 896 27.29 3840 13.18 3840 7.57 3840 4.21
960 45.46 960 28.49            

 

NAMD 2.13

20k atoms 61k atoms 465k atoms 1400k atoms 3000k atoms
cores ns/day cores ns/day cores ns/day cores ns/day cores ns/day
64 24.06 64 9.03 64 1.27 64 0.44 64 0.17
128 37.82 128 16.08 128 2.31 128 0.79 128 0.36
192 53.52 192 18.34 256 3.07 256 1.3 256 0.71
256 68.54 256 15.5 384 5.17 384 1.66 384 0.99
320 77.13 320 17.72 512 6.44 512 2.54 512 1.22
384 88.3 384 26.18 640 7.63 640 2.88 640 1.33
448 76.16 448 29.15 768 10.07 768 3.54 768 2.09
512 80.67 512 28.31 960 12.33 960 4.19 960 2.48
576 76.81 576 30.01 1280 13.23 1280 5.47 1280 3.13
640 77.37 640 28.09 1600 13.84 1600 6.73 1600 3.54
704 73.82 704 35.62 1920 13.4 1920 7.58 1920 3.76
768 76.01 768 33.87 2240 10.65 2240 9.13 2240 4.52
832 61.07 832 31.11 2880 19.84 2880 10.98 2880 5.51
896 59.48 896 40.4 3840 20.55 3840 12.54 3840 6.95
960 66.65 960 30.3