Dell NAMD Benchmarking Guide on a 4-Node Cluster with Intel Xeon Phi 7120P Coprocessors
Summary
Explore advanced computational capabilities for molecular dynamics research with this detailed analysis of NAMD benchmarks. The guide evaluates the performance scaling and power efficiency of massive biological simulations using Intel Xeon Phi co-processors across a four-node High Performance Computing (HPC) cluster. Ideal for computational scientists, bioinformaticians, and researchers requiring high-throughput, energy-efficient simulation platforms for large biomolecular systems. Discover significant performance gains up to 8.5 times through optimized hardware integration.
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NAMD benchmarking on 4 nodes cluster with Intel Xeon Phi 7120P Coprocessors
by Ashish Kumar Singh
This blog explores the application performance analysis of NAMD (NAnoscale Molecular Dynamics) for large data
sets on cluster of Power Edge R730 servers with Intel Xeon Phi 7120Ps. All the runs were carried out with Hyper
Threading (logical processors) disabled. IB verbs version of NAMD was used for all the runs.
Test Cluster Configuration:
The test cluster consisted of four Power Edge R730 servers with two Intel Xeon Phi 7120P co-processors each. Each
Power Edge R730 had two Intel Xeon E5-2695v3 @ 2.3GHz CPU and eight 16GB DIMMS of 2133MHz making it a
total of 128GB of memory per server. Each Power Edge R730 consisted of one Mellanox FDR Infiniband HCA card in
the low-profile x8 PCIe Gen3 slot (Linked with CPU2).
Compute node configuration
Page Summary Contents For Dell NAMD Benchmarking Guide on a 4-Node Cluster with Intel Xeon Phi 7120P Coprocessors
Manual Details
| Brand | Intel |
|---|---|
| Pages | 4 |
| File Size | 211.76 KB |
| Published | May 29, 2026 |
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Frequently Asked Questions
What function does NAMD perform in this system?
NAMD is a parallel, object-oriented simulation package designed for high performance of large bimolecular systems.
Should Hyper Threading be enabled for these runs?
No, all the performance analysis and benchmark tests were performed with Hyper Threading disabled.
How did using two Intel Xeon Phi 7120P impact power efficiency?
When compared to CPU-only configurations, power efficiency increased by 2.4 times in the STMV benchmark.
What is the total memory capacity of a single PowerEdge R730 server unit?
Each PowerEdge R730 server has eight 16GB DIMMs installed, giving it 128GB of memory.