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cluster:175 [2018/09/23 12:23]
hmeij07 [Gromacs] 		cluster:175 [2018/09/26 20:01]
hmeij07 [Gromacs]
Line 69: Line 69:
  
 </code> </code>
 +
 +==== Lammps (PMMA) ====
 +
 +Using a material called PMMA (https://en.wikipedia.org/wiki/Poly(methyl_methacrylate) aka acrylic glass or plexiglas ("safety glass"). The PMMA simulations require the calculation of molecular bonds, which is not implemented in GPU hence more CPU cores are required than the Coillod example. The optimal ratio cpu:gpu appears to be 4-6:1.
 + 
 +^  gpu  ^  cpus  ^  ns/day  ^  quad  ^  ns/day/node  ^
 +|  1 P100  |  4  |  89  |  x4  |  356  |
 +|  1 GTX  |  6  |  90  |  x4  |  360  |
 +|  1 K20  |  6  |  47  |  x4  |  188  |
 +
 +That means the P100 works as well as the GTX. The K20 works at 50% the performance level of the others which is impressive for this old gpu.
 +
 +
 +
  
 ==== Gromacs ==== ==== Gromacs ====
Line 103: Line 117:
 0, Tesla P100-PCIE-16GB, 36, 7048 MiB, 9232 MiB, 97 %, 4 % 0, Tesla P100-PCIE-16GB, 36, 7048 MiB, 9232 MiB, 97 %, 4 %
  
 +</code>
 +
 +==== Gromacs 2018.3 ====
 +
 +<code>
 +multidir -gpu_id 0123
 +-np  8 -ntomp  4 -npme 1 -maxh 0.1 -pin on -nb gpu
 +01/md.log:Performance:       36.692        0.654
 +02/md.log:Performance:       36.650        0.655
 +03/md.log:Performance:       36.623        0.655
 +04/md.log:Performance:       36.663        0.655
 +-np 16 -ntomp  8 -npme 1 -maxh 0.1 -pin on -nb gpu
 +01/md.log:Performance:       25.151        0.954
 +02/md.log:Performance:       25.257        0.950
 +03/md.log:Performance:       25.247        0.951
 +04/md.log:Performance:       25.345        0.947
 +
 +multidir -gpu_id 00112233
 +-np  8 -ntomp  4 -npme 1 -maxh 0.1 -pin on -nb gpu
 +Error in user input:
 +The string of available GPU device IDs '00112233' may not contain duplicate
 +device IDs
 </code> </code>
  
cluster/175.txt ยท Last modified: 2018/11/29 18:00 by hmeij07

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