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Understanding the Role of Dell EMC Isilon SmartConnect in Genomics

Workloads

Kihoon Yoon. Dell EMC HPC Innovation Lab. November 2016

Coming together with EMC has opened many new opportunities for the Dell EMC HPC Team to develop

high-performance computing and storage solutions for the Life Sciences. Our lab recently stood up a

‘starter' 3 node Dell EMC Isilon X410 cluster. As a loyal user of the Isilon X210 in a previous role, I

couldn’t wait to start profiling genomics applications using the X410 with Dell EMC HPC System for Life

Sciences.

Because our current Isilon X410 storage cluster is currently fixed at the 3 node minimum, we aren’t set

up yet to evaluate the scalability of the X410 with genomics workflows. We will tackle this work once

our lab receives additional X nodes and the new the Isilon All-Flash node (formerly project Nitro).

In the meantime, I wanted to understand how the Isilon storage behaves relative to other storage

solutions and decided to focus on the role of Isilon SmartConnect.

Through a single host name, SmartConnect enables client connection load balancing and dynamic

network file system (NFS) failover and failback of client connections across storage nodes to provide

optimal utilization of the Isilon cluster resources.

Without the need to install client-side drivers, administrators can easily manage a large and growing

number of clients and ensure in the event of a system failure, in-flight reads and writes will successfully

finish without failing.

Traditional storage systems with two-way failover typically sustain a minimum 50 percent degradation in

performance when a storage head fails, as all clients must fail over to the remaining head. With Isilon

SmartConnect, clients are evenly distributed across all remaining nodes in the cluster during failover,

helping to ensure minimal performance impact.

To test this concept, I ran the GATK pipeline varying the number of samples and compute nodes without

and with SmartConnect enabled on the Isilon storage cluster.

The configuration of our current lab environment and whole human genome sequencing data used for

this evaluation are listed below.

Table 1 System configuration, software, and data

Dell EMC HPC System for Life Sciences

Server

40 x PowerEdge C6320

Processor

2 x Intel Xeon E5-2697 v4. 18 cores per socket, 2.3 GHz

Memory

128 GB at 2400 MT/s

Interconnect

10GbE NIC and switch for accessing Isilon &

Intel Omni-Path fabric

Software

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Understanding the Role of Dell EMC Isilon SmartConnect in Genomics Workloads Kihoon Yoon. Dell EMC HPC Innovation Lab. November 2016 Coming together with EMC has opened many new opportunities for the Dell EMC HPC Team to develop high-performance computing and storage solutions for the Life Sciences. Our lab recently stood up a ‘starter' 3 node Dell EMC Isilon X410 cluster.
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Operating System Red Hat Enterprise Linux 7.2 BWA 0.7.2-r1039 Samtools 1.2.1 Sambamba 0.6.0 GATK 3.5 Benchmark Data ERR091571 10x Whole human genome sequencing data from Illumina HiSeq 2000, Total number of reads = 211,437,919 As noted earlier, the Isilon in our environment is currently set up in a minimum 3 node configuration. The current generation of Isilon is scalable up to 144 nodes. As you add additional Isilon nodes, the aggregate memory, throughput, and IOPS scale linearly.
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Aligning & Sorting step is more sensitive to the number of samples. In this benchmark, GenotypeGVCFs is not a bottleneck since we used an identical sequence data for all the concurrent pipelines. In real data analysis, a large number of different samples are used, and GenotypeGVCFs becomes the major bottleneck. Table 3 Test results for BWA-GATK pipeline without and with Isilon SmartConnect enabled.
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If you are using Bright Cluster Manger and need some tips to set it up with Isilon SmartConnect, read this post.