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Ready Solutions Engineering Test Results

Variant Calling (BWA-GATK) pipeline benchmark

with Dell EMC Ready Bundle for HPC Life Sciences

13G/14G server performance comparisons with Dell EMC Isilon and Lustre

Storage

Overview

Variant calling is a process by which we identify variants from sequence data. This process includes making a decision if there is single

nucleotide polymorphisms (SNPs)

, insertions and deletions (indels)

, and/or structural variants (SVs)

iii

at a given position in an

individual genome or transcriptome. The main goal of identifying genomic variations is linking to human diseases. Although not all

human diseases are associated with genetic variations, variant calling can provide a valuable guideline for geneticists working on a

particular disease caused by genetic variations. BWA-GATK is one of the Next Generation Sequencing (NGS) computational tools that

is designed to identify germline and somatic mutations from human NGS data. There are a handful of variant identification tools, and we

understand that there is not a single tool performs perfectly (Pabinger et al., 2014). However, we chose GATK which is one of most

popular tools as our benchmarking tool to demonstrate how well Dell EMC Ready Bundle for HPC Life Sciences can process complex

and massive NGS workloads.

The purpose of this blog is to provide valuable performance information on the Intel® Xeon

Gold 6148 processor and the previous

generation Xeon

E5-2697 v4 processor using a BWA-GATK pipeline benchmark on Dell EMC Isilon F800/H600 and Dell EMC Lustre

Storage. The Xeon

Gold 6148 CPU features 20 physical cores or 40 logical cores when utilizing hyper threading. This processor is

based on Intel’s new micro-architecture codenamed “Skylake”. Intel significantly increased the L2 cache per core from 256 KB on

Broadwell to 1 MB on Skylake. The 6148 also touts 27.5 MB of L3 cache and a six channel DDR4 memory interface. The test cluster

configurations are summarized in Table 1.

Table 1 Test Cluster Configurations

Dell EMC PowerEdge C6420 Dell EMC PowerEdge C6320

CPU

2x Xeon

Gold 6148 20c 2.4GHz (Skylake) 2x Xeon

E5-2697 v4 18c 2.3GHz (Broadwell)

RAM

12x 16GB @2666 MHz 8x 16GB @2400 MHz

RHEL 7.3

Interconnect

Intel

Omni-Path

BIOS System Profile

Performance Optimized

Logical Processo

Disabled

irtualization Technology

Disabled

0.7.15-r1140

Sambamba

0.6.5

Samtools

1.3.1

GATK

3.6

Summary of content (5 pages)

PAGE 1
Ready Solutions Engineering Test Results Variant Calling (BWA-GATK) pipeline benchmark with Dell EMC Ready Bundle for HPC Life Sciences 13G/14G server performance comparisons with Dell EMC Isilon and Lustre Storage Overview Variant calling is a process by which we identify variants from sequence data.
PAGE 2
Ready Solutions Engineering Test Results The test clusters and F800/H600 storage systems were connected via 4 x 100GbE links between two Dell Networking Z9100-ON switches. Each of the compute nodes was connected to the test cluster side Dell Networking Z9100-ON switch via single 10GbE. Four storage nodes in the Dell EMC Isilon F800/H600 were connected to the other switch via 8x 40GbE links. The configuration of the storage is listed in Table 2.
PAGE 3
Ready Specs Table 2 Storage Configurations Dell EMC Isilon F800 Dell EMC Isilon H600 Dell EMC Lustre Storage Number of nodes 4 4 2x Dell EMC PowerEdge R730iv as MDS 2x Dell EMC PowerEdge R730 as OSS CPU per node Intel® Xeon™ CPU E5-2697A v4 @2.60 GHz Intel® Xeon™ CPU E5-2680 v4 @2.40GHz 2 x Intel® Xeon™ E5-2630V4 @ 2.20GHz Memory per node Storage Capacity 256GB 256GB 256GB Total usable space: 166.8 TB, 41.7 TB per node Total usable space: 126.8 TB, 31.7 TB per node N/A 2.
PAGE 4
Ready Solutions Engineering Test Results 4 Performance Evaluation BWA-GATK Benchmark over Generations Dell EMC PowerEdge C6320s and C6420s were configured as listed in Table 1. The tests performed here are designed to demonstrate performance at the server level, not for comparisons on individual components. At the same time, the tests were also designed to estimate the sizing information of Dell EMC Isilon F800/H600 and Dell EMC Lustre Storage.
PAGE 5
Ready Specs The results with Dell EMC Isilon F800 that indicate C6320 with Broadwell/128GB RAM performs roughly 50 genomes per day less when 3 samples are processed per compute node and 30 genomes per day less when 2 samples are processed in each compute node compared to C6420. It is not clear if C6320’s performance will drop again when more samples are added to each compute node; however, it is obvious that C6420 does not show this behavior when the number of samples is increased on each compute node.