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--- cluster:175 [2018/09/23 12:22]
hmeij07 [Gromacs]
+++ cluster:175 [2018/09/26 12:35]
hmeij07 [Lammps]
@@ Line 69: / Line 69: @@
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+==== 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 implying the cpu calculations are the bottleneck.
 ==== Gromacs ====
@@ Line 74: / Line 88: @@
 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).
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