Optimizing GPU Heterogeneous Parallel Performance (GROMACS) with E-HPC CloudMetrics

What Is GROMACS?

Molecular Dynamics (MD) simulation is a computer simulation method for studying and analyzing the structure and properties of molecules and molecular systems using classical Newton mechanics. It is the key that can open up the world of microscopic motion. As one of the important areas of research in the HPC field, MD simulation is widely used in the development of new materials, chemical industry simulations, bio-medicine, and other fields.

GPU Performance Monitoring Function of CloudMetrics

Using CloudMetrics to Provide Guidance for GROMACS Performance Optimization

In the following example, the GPU version of GROMACS runs on an ecs.gn5 instance (8 cores, 16 vCPUs, 120 GB of memory, and 2 P100s), and the system resource usage information monitored by CloudMetrics is used for optimization.

  1. The CPU usage is constantly above 85%.
  2. The GPU usage ranges from 45% to 70% and fluctuates significantly.
  3. The video RAM usage of the GPU is about 25%.
  4. The PCI-E transmission bandwidth of the GPU generally does not exceed 2 Gbit/s.
  1. The CPU usage drops between 30% and 35%.
  2. The GPU usage is generally above 70%, with small fluctuations.
  3. The video RAM usage of the GPU increases by more than 50%.
  4. The PCI-E transmission bandwidth of the GPU is above 3 Gbit/s.
  5. While the load remains the same, the execution time is reduced by 50% after optimization.

Conclusion

CloudMetrics can monitor the usage of cluster resources, such as computing, memory, network, disk, and accelerator card resources, and present the results to users in a systematic manner. Users can conveniently compare and analyze the performance data provided by CloudMetrics to quickly locate the performance bottlenecks and optimize their applications accordingly.

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