White Papers

22 Dell HPC Omni-Path Fabric: Supported Architecture and Application Study June 2016
5.4 NAMD
NAMD [9] is a parallel molecular dynamics code designed for high-performance simulation of large bio-
molecular systems. Three proteins ApoA1 (92,224 atoms), F1ATpase (327,506 atoms) and STMV (1,066,628)
are used in our study due to their relatively large problem size.
Figure 13 illustrates the performance of NAMD for three different datasets apoa1, f1atpase and stmv. All
the datasets show results for node counts from 1 to 32. All the data points in the graph are relative to one
node and a higher value represents better performance. Most of the MPI time is spent on broadcasting for
these datasets and the performance scales linearly at higher node counts.
Figure 13 NAMD performance graph
5.5 ANSYS
®
Fluent
®
At the time of publication of this whitepaper, Intel Omni-Path was not officially supported by ANSYS
®
Fluent
®
. In order to obtain preliminary performance data for this application, the MPI software was modified
to use the appropriate Intel Omni-Path library.
Multiple cases from Fluent benchmark suites v15 and v16 were tested on the lab test system. The relative
performance of twelve benchmark cases are presented in this section.
The graphs in Figure 14 and Figure 15 show the relative performance of the benchmarks on 1 to 32 nodes
using 28 to 896 cores. Each data point on the graphs represents the relative performance of the specific
benchmark data set using the number of cores marked on the x-axis in a parallel simulation. The results are
presented as performance relative to the performance of a single node or 28 cores. A higher value
represents better performance. The results are divided into two charts for easy readability. Figure 14
presents’ benchmarks that scale relatively well up to 32 nodes and Figure 15 presents benchmarks that do
not scale as well, due to smaller model sizes.
1
2
4
7.9
13.2
39.7
1
2
3.8
7.5
14.9
29.8
1
2
3.8
7.7
15.2
29.3
0
5
10
15
20
25
30
35
40
45
1 2 4 8 16 32
Relative to one node
No. of Nodes
NAMD
apoa1 f1atpase stmv