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Performance Analysis of HPC Applications on Several Dell PowerEdge 12

Generation Servers

The PowerEdge M620 and PowerEdge M420 are blade based servers. The PowerEdge M620 is a half-

height blade; the PowerEdge M1000e chassis can house up to 16 such blades. The PowerEdge M420 is a

denser, quarter-height blade and the same PowerEdge M1000e chassis can house up to 32 such blades.

A full chassis of servers was used in each case to allow meaningful power measurements and to

properly amortize the shared infrastructure cost of power supplies, fans, and so on. The other

differences in the size of the clusters are due to resource limitations; however the results sections

compares performance based on the number of cores to eliminate total cluster size as a factor.

The PowerEdge M420 supports only SSD drives. The operating system for the server was installed on this

drive. None of the applications were configured to write local files on each compute node; therefore,

the choice of SSD versus SAS is not relevant to the results in this study.

The BIOS on all the servers are set to Dell HPC defaults, which include the Performance per Watt

Optimized DAPC System Profile, Node Interleaving disabled and Logical Processor disabled. This System

Profile balances power saving and performance options by enabling Turbo Boost, C states and C1-E. The

Power Profile is set to DAPC (Dell Advanced Power Controller) and the Memory Frequency is set to max

performance.

StackIQ Rocks+ 6.0.1 Dell edition [5] was used to deploy and manage the cluster.

Table 3 illustrates the applications that were studied, the benchmarks used, and their characteristics.

The applications chosen are a mix of open source and commercial applications.

Application and benchmark details Table 3.

Application

Domain

Version

Benchmark data set

High Performance

Linpack

Floating point CPU intensive

system benchmark

Intel MKL

v10.3.9.293

Problem size set to 90

percent of total memory.

Stream

Memory Bandwidth micro-

benchmark

v5.9

Array size 160000000

ANSYS Fluent

Computational Fluid Dynamics

application

v14.0.0

truck_poly_14m and

truck_111m

WRF

Weather modeling application

v3.1

Conus 12k

NAMD

Molecular Dynamics application

v2.9

STMV

MILC

Quantum Chromo-dynamics

application

v7.6.3

fnl-2009-intel.in

Based on Medium-NSFt3

Lower-upper decomposition,

physical systems

NPB v3.3.1

Class D

For HPL, the performance metric used for comparison is GFLOPS and for WRF, the performance metric

used is the average time step. For NAMD, the performance metric used is days per nanosecond. For all

other applications the metric used is rating. Rating is defined as the number of times an application

can be executed in a single day. In addition to quantifying the performance on the above mentioned

server platforms, the power consumed is also measured by using a rack power distribution unit (PDU).

Because an apples to apples comparison is not possible with the test bed configuration, a cluster level

comparison of power consumption is provided in Power Consumption and Energy Efficiency.

A previous study [1] characterized the performance and energy impact of different BIOS tuning options

on the PowerEdge M620 servers. The PowerEdge M620 cluster test bed and applications used in that

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