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cluster:175 [2018/09/23 12:07]
hmeij07 [P100 vs GTX & K20] 		cluster:175 [2018/09/25 12:39]
hmeij07 [Lammps]
Line 69: Line 69:
  
 </code> </code>
 +
 +== Lammps (PMMA) ==
 +
 +Material called PMMA (https://en.wikipedia.org/wiki/Poly(methyl_methacrylate). 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.
 +
 +a) 1GPU with X CPUs
 + 
 +#cpus   ns/day
 +4           89.6
 +2           61.6
 +1           34.3
 +
 +b) 4 GPUs with 4 CPUs
 +92 ns/day
 +
 +----------
 +compare these results to 
 +
 +1 K20 GPU + 4 CPUs  37 ns/day
 +1 K20 GPU + 6 CPUs  47 ns/day
 +1 GTX GPU + 4 CPUs  73 ns/day
 +1 GTX GPU + 6 CPUs  90 ns/day
 +
 +
 +
 +
  
 ==== Gromacs ==== ==== Gromacs ====
Line 74: Line 100:
 Gromacs has shown vastly improved performance between versions. v5 delivered about 20 ns/day per K20 server and 350 ns/day on GTX server. v2018 delivered 75 ns/day per K20 server and 900 ns/day on GTX server. A roughly 3x improvement. Gromacs has shown vastly improved performance between versions. v5 delivered about 20 ns/day per K20 server and 350 ns/day on GTX server. v2018 delivered 75 ns/day per K20 server and 900 ns/day on GTX server. A roughly 3x improvement.
  
-On the P100 test node, I could not invoke the multidir option of gromacs (have run it on GTX, weird). The utilization of the gpu drops as more and more gpus are deployed.  The optimum performance was with dual gpus achieving 36 ns/day. Four one gpu jobs would deliver 136 ns/day/server, far short of the 900 ns/day for our GTX server. (We only have dual P100 nodes quoted).+On the P100 test node, I could not invoke the multidir option of gromacs (have run it on GTX, weird). The utilization of the gpu drops as more and more gpus are deployed.  The optimum performance was with dual gpus achieving 36 ns/day. Four one gpu jobs would deliver 120 ns/day/server, far short of the 900 ns/day for our GTX server. (We only have dual P100 nodes quoted).
  
 <code> <code>
Line 83: Line 109:
 localhost,localhost,localhost,localhost,localhost,localhost,\ localhost,localhost,localhost,localhost,localhost,localhost,\
 localhost,localhost,localhost,localhost,localhost,localhost,localhost \ localhost,localhost,localhost,localhost,localhost,localhost,localhost \
-gmx_mpi mdrun -gpu_id 0123 -ntmpi 0 \+gmx_mpi mdrun -gpu_id 0123 -ntmpi 0 -nt 0 \
  -s topol.tpr -ntomp 4 -npme 1 -nsteps 20000 -pin on -nb gpu  -s topol.tpr -ntomp 4 -npme 1 -nsteps 20000 -pin on -nb gpu
  
cluster/175.txt ยท Last modified: 2018/11/29 18:00 by hmeij07

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