archer machine photoHere 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