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HPC Benchmarks and Applications Performance

Study on Broadwell-EP 4S Processor

Author: Neha Kashyap, August 2016 (HPC Innovation Lab)

The intent of this blog is to illustrate and analyze the performance obtained on Intel Broadwell-EP 4S processor with the focus on

HPC applications, two synthetic benchmarks along with four applications namely, High Performance Linpack (HPL), STREAM,

Weather Research and Forecasting (WRF), NAnoscale Molecular Dynamics (NAMD) and Fluent. These runs have been performed

on a standalone single server PowerEdge R830. Combinations of System BIOS profiles and Memory Snoop modes are compared

for better analysis.

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

Server

Dell PowerEdge R830

Processor

4 x E5-4669 v4 @2.2GHz, 22 core, 135W, 55M L3 Cache

AVX Base Frequency @1.7GHz

Memory

32 x 16GB DDR4 @ 2400MHz (Total=512GB)

Power Supply

2 x 1600W

Operating System

Red Hat Enterprise Linux 7.2 (3.10.0-327.el7.x86_64)

BIOS options

System profile – Performance and Performance Per Watt

(DAPC)

Snoop modes – Cluster on Die (COD) and Home Snoop (HS)

Logical Processor and Node Interleaving – Disabled

I/O Non-Posted Prefetch – Disabled

BIOS Firmware

1.0.2

iDRAC Firmware

2.35.35.35

STREAM

v5.10

HPL

From Intel MKL (Problem size is 253440)

Intel Compiler

From Intel Parallel studio 2016 update3

Intel MKL

11.3

MPI

Intel MPI – 5.1.3

NetCDF

4.4.0

NetCDF-Fortran

4.4.2

FFTW

2.1.5

WRF

3.8

Summary of content (7 pages)

PAGE 1
HPC Benchmarks and Applications Performance Study on Broadwell-EP 4S Processor Author: Neha Kashyap, August 2016 (HPC Innovation Lab) The intent of this blog is to illustrate and analyze the performance obtained on Intel Broadwell-EP 4S processor with the focus on HPC applications, two synthetic benchmarks along with four applications namely, High Performance Linpack (HPL), STREAM, Weather Research and Forecasting (WRF), NAnoscale Molecular Dynamics (NAMD) and Fluent.
PAGE 2
NAMD Ansys Fluent 2.11 v16.0 The server used for obtaining results is Dell’s PowerEdge 13th generation server. It is a high-performance four-socket, 2U rack server. It supports massive memory density (up to 3TB). The Intel® Xeon® Processor E5-4669 v4 (Product Family E5-4600 v4) is a 14nm die supporting two snoop modes in 4 socket systems - Home Snoop and Cluster on Die (COD). It is based on the microarchitecture code named Broadwell-EX. Default snoop mode being Home Snoop mode.
PAGE 3
Figure 2: STREAM Memory Bandwidth on DAPC.COD Here, figure 2 shows the performance obtained with STREAM Triad memory bandwidth in DAPC.COD configuration taking into account local, local NUMA and remote bandwidth. The full system memory bandwidth is ~ 226 GB/s. To obtain the local memory bandwidth, the processes are bind to a socket and only the memory local to that socket is accessed (same NUMA node with NUMA enabled).
PAGE 4
Figure 3: HPL Performance and Efficiency Figure 3 illustrates HPL performance benchmark. From this graph, it is clear that DAPC and Performance profiles are giving almost similar results whereas there is difference when comparing HS with COD. With DAPC, COD is 6.2% higher than HS whereas with Performance profile, COD yields 6.6% higher performance than HS. The HPL performance is analyzed in “GFLOP/second”. The Efficiency is more than 100% because of the AVX base frequency.
PAGE 5
E54669v4 Total no. of cores 88 CONUS12km MPI Processes 44 OMP Processes 2 CONUS2.5km TILES 44 Figure 4: Performance with WRF, CONUS12km MPI Processes 44 OMP Processes 2 TILES 56 Figure 5: Performance with WRF, CONUS2.5km Figure 4 illustrates CONUS 12km. With COD there is 4.5% improvement in the average time step when compared with HS. While for CONUS2.5km, DAPC and Performance profiles are showing a variance from 0.4% to 1.6% for HS and COD respectively. COD performs ~2.1% - 3.2% better than HS.
PAGE 6
Figure 6: Performance of NAMD on BIOS Profiles (The Lower the Better) The performance obtained on ApoA1 across BIOS profiles is same while for ATPase it is almost similar. The difference is visible in case of STMV (larger dataset) over other two datasets since the number of atoms increases which in turn helps in proper utilization of processors. In case of STMV, DAPC and Performance profiles vary from 0.7% to 1.3% for HS and COD respectively. Also the COD snoop mode performs ~6.1% - 6.7% better than HS.
PAGE 7
To conclude, the R830 platform is performing upto the mark with all expected output. It is a good pick for HPC workloads giving best results with DAPC.COD system BIOS profile. It is a great choice in terms of overall system architecture improvements and supporting latest processor.