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Figure 2: NAMD Performance within 1 P100-PCIe node
Figure 3: NAMD Performance across Nodes
GROMACS
GROMACS (for GROningen MAchine for Chemical Simulations) primarily does simulations for biochemical
molecules (bonded interactions). But because of its efficiency in calculating non-bonded interactions
(atoms not linked by covalent bonds), the user base is expanding to non-biological systems. Figure 4 shows
the performance of GROMACS on CPU, K80 GPUs and P100-PCIe GPUs. Since one K80 has two internal
GPUs, from now on when we mention one K80 it always refers to two internal GPUs instead of one of the
two internal GPUs. When testing with K80 GPUs, the same P100-PCIe GPUs based servers were used.
Therefore, the CPUs and memory were kept the same and the only difference is that P100-PCIe GPUs
were replaced to K80 GPUs. In all tests, there were four GPUs per server and all GPUs were utilized. For
2.41
2.84
2.77
2.20
2.30
2.40
2.50
2.60
2.70
2.80
2.90
1 P100 2 P100 4 P100
ns/day (higher the better)
NAMD Performance with STMV Dataset within 1 node
0.30
2.84
4.20
4.92
5.08
2.77
3.78
4.36
4.98
0.00
1.00
2.00
3.00
4.00
5.00
6.00
1 2 3 4
ns/day (higher the better)
Number of nodes
NAMD Performance with STMV Dataset
2 x 2690 v4 CPU P100 2/node P100 4/node