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cluster:175 [2018/09/23 12:23]
hmeij07 [Gromacs] 		cluster:175 [2018/09/26 20:11]
hmeij07 [Gromacs 2018.3]
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 104: Line 118:
  
 </code> </code>
 +
 +==== Gromacs 2018.3 ====
 +
 +The multidir not running in Gromacs 2018 is a bug in the code clashing with the call MPI_Barrier (communication timing error).  It is fixed in Gromacs 2018.3 so we have some multidir results although gpu utilization has room for improvements (about 25% used, same as on GTX).
 +
 +<code>
 +
 +# multidir -gpu_id 0123 with four simultaneous gromacs processes
 +
 +-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 or about 146 ns/day/node (quad)
 +
 +-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 or about 100 ns/day/node (quad)
 +
 +multidir -gpu_id 00112233 with eight simultaneous gromacs processes
 +sharing the gpus, 2 processes per gpu
 +
 +-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>
 +
 +That last error when loading multiple processes per gpu is *not* according to their documentation. So the multidir performance is similar to previous single dir performance but still lags GTX performance by quite a bit. Albeit, there is room in utilization rate of the gpus.
 +
  
 ==== What to Buy ==== ==== What to Buy ====
cluster/175.txt ยท Last modified: 2018/11/29 18:00 by hmeij07

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