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Molecular Dynamics Benchmarking with

Intel Xeon Phi 7120P Coprocessors

Authors: Saeed Iqbal and Deepthi Cherlopalle

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular

systems. NAMD can benefit greatly from the Intel Xeon Phi family of coprocessors. Intel’s MIC is based on the x86-

technology and it run on Linux OS. Among the several coprocessors in this family, the 7120P with 61 cores has one

of the highest performance ratings of 1.22 TFLOPS. The 7120P also has the highest memory per card of 16 GB and

maximum memory bandwidth of 352 GB/s.

In this blog we evaluate NAMD performance with 7120P coprocessors on PowerEdge C4130 Server. Three proteins

ApoA1, F1ATPase and STMV are used in our study due to their relatively large problem size. ApoA1 is high density

lipoprotein found in plasma, which helps extraction of cholesterol from tissues to liver. F1ATPase is one of the most

abundant, responsible for the synthesizing of the molecule adenosine tri-phosphate. STMV stands for satellite

tobacco mosaic which worsens the symptoms of infections by tobacco mosaic virus. The performance measure is

“days/ns”, that shows the number of days required to simulate 1 nanosecond of real-time. Table 1 shows the

problem size for different systems.

Table 1: Problem Size of Proteins

Proteins

Number of Atoms

ApoA1

92,224

F1ATPase

327,506

STMV

1,066,628

NAMD tests are performed on Dell PowerEdge C4130 which can accommodate up to four 7120P Phis in a 1U form

factor. The PowerEdge C4130 also offers a configurable system design (“A” through “E”), potentially making it a

better fit, for MD codes in general. The three configurations “C” (a four Phi configuration), “D” (a two Phi

configuration) and “E” (a two Phi configuration) are compared. Part of the goal is to see performance variations

with different configurations for NAMD. Table 2 gives more information about the hardware configuration and

application details used for the tests.

Summary of content (4 pages)

PAGE 1
Molecular Dynamics Benchmarking with Intel Xeon Phi 7120P Coprocessors Authors: Saeed Iqbal and Deepthi Cherlopalle NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD can benefit greatly from the Intel Xeon Phi family of coprocessors. Intel’s MIC is based on the x86technology and it run on Linux OS. Among the several coprocessors in this family, the 7120P with 61 cores has one of the highest performance ratings of 1.22 TFLOPS.
PAGE 2
Table 2: Hardware Configuration and Application Details Server Processor GPU C4130 Prototype System 2 * Intel Xeon CPU E5-2690 v3 @ 2.6 GHz (12 core) 2 or 4 * Intel Xeon Phi Coprocessor 7120P Memory -16GB # of cores - 61 Processor Base Frequency- 1.238 GHz Max Turbo Frequency - 1.33GHz Power supply 2 x 1600W Operating RHEL 6.5 – kernel 2.6.32-431.el6.
PAGE 3
Figure 1: NAMD performance and acceleration on C4130 configurations C and D. Figure 1 illustrates the performance of NAMD on the PowerEdge C4130 Server. NAMD can benefit performance boost by adding coprocessors to the server. Configuration C has 2 CPU’s with 4 coprocessors, 2 coprocessors are connected to each CPU. Configuration D has 2 CPU’s with 2 coprocessors; each coprocessor is connected to a single CPU whereas Configuration E has 2 coprocessors connected to 1 CPU.
PAGE 4
Figure 2: NAMD Power Consumption results on CPU-only, C, D and E Configurations. As shown in Figure 2, the power consumption for C configuration is about 2.4X whereas for Configuration D it is 1.7X. Power consumption is higher in configuration C when compared to Configuration D because of two additional coprocessors in the server. Power consumption for Configuration E is 1.4X which is low when compared to Configuration D this is because “E” does not have an additional CPU.