PowerEdge: NAMD Performance on R740 with Volta GPUs

There are several HPC applications  that can benefit from using NVIDIA GPUs and NAMD is one such application. Nanoscale Molecular Dynamics (NAMD) is open-source software for molecular dynamics simulation, using the CHARMM parallel programming model, designed for high-performance simulation of large biomolecular systems. 
To benefit from GPU acceleration, a CUDA build for NAMD is needed. Instructions to compile NAMD with CUDA support can be found here .

In this article, we are going to discuss the NAMD performance with NVIDIAs latest Volta GPU V100-32GB in a single Dell EMC PowerEdge R740 server.

The PowerEdge R740 is a 2U dual-socket server with Intel Skylake processors. It can be configured to support up to 3 double-wide GPUs and a high-speed networking adapter.

Table 1 shows information about the hardware configuration and application details used for the tests. A nightly build version of NAMD was compiled for this test dated 2018-08-17.

       

Table 1 Hardware and Software Configuration Details

Performance Results

NAMD was tested with three different datasets: ApoA1, F1ATPase, and STMV which consist of 92 K, 327 K, and 1066k atoms respectively. Apoa1 is a smaller dataset compared to F1ATPase and STMV. The performance metric here is "ns/days." The data shown in this section is based on the average of 10 tests.
Figure 1 shows the NAMD performance with CPU and multiple GPUs on three datasets. Instructions from Intel’s website were followed to compile NAMD for Intel Xeon processors. Performance improvement from CPU to GPUs is noted in the graph below.

 
                                                                         Figure 1 NAMD performance on CPU and GPUs

•     Performance is relative to the Dual-CPU results across the different datasets.
•     The GPU versions of NAMD provide up to 11.2x speed up compared to the CPU version for all three datasets.
•     An additional 23%-33% performance increase was measured when the second GPU card was added. A more modest 6-9% was observed from two GPUs to three GPU tests.
   

  NAMD was also tested with different numbers of CPU cores across 1, 2 & 3 GPUs to identify the minimum number of CPU cores needed for best performance.

   

                                                        Figure 2 STMV performance with different CPU core counts and GPUs

•     As seen in Figure 2 using too few CPU cores has a negative impact on performance and performance improves as we increase the number of cores
•     Testing one V100 with 20+ CPU cores achieved good performance. There is an additional 2-3% performance advantage when we use more than 20 cores.
•     This test was also performed on the other two datasets ApoA1 and F1ATPase. Similar performance behavior was observed with them.
   

  
   

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  Summary

  NAMD performance results on Dell EMC PowerEdge R740 server and NVIDIA Volta V100-32GB GPUs have been presented here. There is ~6.6x-11.2x speedup over CPU-only tests when using GPUs. A R740 server with 3 V100 cards provides the best performance while a R740 with 2 V100 cards is within 91% of the three GPU configuration. If there are budget limitations, one GPU per R740 would be a good choice as it gives up to 8x speed-up compared to CPU. Tests with varied CPU cores and GPUs were also conducted, and we noticed that using too few CPU cores (fewer than 20 cores in our tests) reduces NAMD performance on GPU tests.