White Papers

Figure 2: NAMD performance and acceleration on the five C4130 configurations.
Figure 2 shows the performance of NAMD on the PowerEdge C4130. Configurations “A”, “B” and “C” are four
GPU configurations. However the acceleration on NAMD also seems to be sensitive to number of CPUs, e.g., there
is a significant difference in the acceleration between “A” and “B”. “B” has an additional CPU compared to “A”.
Among the three quad GPU configurations the current version of NAMD performs best on configuration “C”. The
difference in two highest performing configurations “C” and “B” is the manner in which GPUs are attached to the
CPU. The balanced configuration “C” has 2 GPUs attached to 2 CPUs resulting in 7.8X acceleration over the CPU-
only case. The same four GPUs attached via a Switch module to a single CPU results in about 7.7X acceleration.
On the dual GPU configurations, “D” performs better with 5.9X acceleration compared to 4.4X in configuration “E”.
The fact that “D” does better is in line with the assumption that a 2
nd
CPU is helpful for NAMD, as we saw “B & C”
(the dual CPU quad GPU configurations) performing best.