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Measuring Performance of Intel

Broadwell-EP Processors with

WRF and NAMD Applications

Authors: Ashish K Singh, Mayura Deshmukh, Neha Kashyap

This blog describes the performance of Intel Broadwell processors with HPC applications, Weather Research and

Forecasting (WRF) and NAnoscale Molecular Dynamics (NAMD). This is the second blog in the series of four blogs on

“Performance study of Intel Broadwell”. The first blog characterizes the Broadwell-EP processors with HPC

benchmarks like HPL and STREAM. This study compares five different Broadwell processors E5-2699 v4 @2.2GHz

(22 cores), E5-2698 v4 @2.2GHz (20 cores), E5-2697A v4 @2.6GHz (16 cores), E5-2690 v4 @2.6GHz (14 cores),

and E5-2650 v4 @2.2GHz (12 cores) in PowerEdge 13

generation servers. It characterizes the performance of the

system for WRF and NAMD by comparing five Broadwell processors models with previous generations of Intel

processors. For the generation over generation comparison, previous results from Intel Xeon X5600 series Westmere

(WSM), Intel Xeon E5-2600 series Sandy-Bridge (SB), Intel Xeon E5-2600 v2 series Ivy-Bridge (IVY), Intel Xeon E5-

2600 v3 series Haswell (HSW) and Intel Xeon E5-2600 v4 series Broadwell (BDW) processors were used. This blog

also describes the impact of BIOS tuning options on WRF and NAMD performance with Broadwell. Table 1 below lists

the server configuration and the application details for the Broadwell processor based tests. The software versions

were different for the older generation processors and results are compared against what was best configuration at that

time. Due to big architectural changes in servers and processors generation over generation, the changes in software

versions is not a significant factor.

Table 1: Details of Server and HPC Applications used with Intel Broadwell processors

Serve

Dell PowerEd

e R730

Processors E5-2699 v4 @2.2GHz, 22 cores, 145W

E5-2698 v4 @2.2GHz, 20 cores, 135W

E5-2697A v4 @2.6GHz, 16 cores, 145W

E5-2690 v4 @2.6GHz, 14 cores, 135W

E5-2650 v4

2.2GHz, 12 cores, 105W

Memor

16 x 16GB DDR4

2400MHz (Total=256GB)

Summary of content (11 pages)

PAGE 1
Measuring Performance of Intel Broadwell-EP Processors with WRF and NAMD Applications Authors: Ashish K Singh, Mayura Deshmukh, Neha Kashyap This blog describes the performance of Intel Broadwell processors with HPC applications, Weather Research and Forecasting (WRF) and NAnoscale Molecular Dynamics (NAMD). This is the second blog in the series of four blogs on “Performance study of Intel Broadwell”. The first blog characterizes the Broadwell-EP processors with HPC benchmarks like HPL and STREAM.
PAGE 2
Power Supply Operating System BIOS options 2 x 1100W Red Hat Enterprise Linux 7.2 (3.10.0-327.el7.x86_64) System profile – Performance and Performance Per Watt (DAPC) Logical Processor – Disabled Power Supply Redundant Policy – Not Redundant Power Supply Hot Spare Policy – Disabled I/O Non-Posted Prefetch - Disabled Snoop modes – COD, ES, HS and OSB BIOS Firmware iDRAC Firmware Intel Compiler MPI WRF NetCDF NetCDF-Fortran NAMD FFTW Node Interleaving - Disabled 2.0.0 2.30.30.
PAGE 3
WRF decomposes the domain into tasks or patches. Each patch can be further decomposed into tiles that are processed separately, but by default there is only one tile for every run. If the single tile is too large to fit into the cache of the CPU and/or core, it slows down computation due to WRF’s memory bandwidth sensitivity. In order to reduce the size of the tile, it is possible to increase the number of tiles by defining “numtile = x” in input file or defining environment variable “WRF_NUM_TILES = x”.
PAGE 4
Figure 1: Performance for Intel Broadwell processors with WRF Figure 1 compares performance among five Broadwell processors by using small and large size of WRF benchmarks. WRF was compiled with the “sm + dm” mode. The combinations of MPI and OpenMP processes that were used are mentioned in Table2. The “X” value in the graph on top of each bar show the performance relative to the 12 core Broadwell processor (which is set as baseline, 1.0).
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Figure 2: Performance of Intel Broadwell processors with NAMD Figure 2 plots the simulation speed of NAMD benchmarks with Broadwell processors. The “X” value in the graph on top of each bar show the performance relative to the 12 core Broadwell processor (which is set as baseline, 1.0). As seen from the graph, the relative performance of the different processors models is nearly same irrespective of the NAMD benchmark dataset (small, medium or large).
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Figure 4: BIOS profile comparison with ApoA1 (92,224 Atoms) Figure 5: BIOS profile comparison with ATPase (327,506 Atoms)
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Figure 6: BIOS profile comparison with STMV (1,066,628 Atoms) Figure 4, 5 and 6 show the performance characteristics of snoop modes available for Broadwell processors with three (small, medium and large) NAMD benchmarks. The left graphs compare snoop modes with the default BIOS Profile (OSB snoop mode with DAPC system profile, which is shown as the red line set at 1). The performance of all NAMD benchmarks across all snoop modes are almost the same for all the datasets.
PAGE 8
dots show the performance relative to WSM processor. It can be easily seen from the graph, the performance of the 14 core Broadwell processor is 20% better than the 14 core HSW processor. The performance of all the Broadwell processors is better than the Haswell E5-2697 v3. The performance improves up to 33% for top bin processor relative to Haswell E5-2697 v3. The performance for the 20 and 22 core Broadwell processors is the same and that is likely because of the lower memory bandwidth per core.
PAGE 9
Figure 9: Performance comparison of multiple generations of Intel processors with ApoA1 benchmark Figure 9 shows the comparison of multiple generations of Intel processors IVB, HSW and BDW with small sized (92,224 Atoms) NAMD benchmark named ApoA1. The bars show the NAMD performance of the processors in “days/ns”. As seen from the graph, HSW performs 40% better than IVB. While, BDW’s performance improvement varies from 23 to 52% except for the 12 core BDW.
PAGE 10
Figure10: Performance comparison of multiple generations of Intel processor with F1ATPase benchmark Figure 10 compares performance of multiple generations of Intel processors with the medium sized (327,506 Atoms) NAMD benchmark, named F1ATPase. It can be seen from the graph that HSW performance improvement is 33% better than IVB and BDW performance is up to 62% better than HSW.
PAGE 11
Figure 11: Performance comparison of multiple generations of Intel processors with STMV benchmark Figure 11 plots the performance comparison graph among multiple generations of Intel processors for the large size (1,066,628 Atoms) NAMD benchmark. As per this graph, the BDW processors are performing up to 63% better than HSW processor.