Need for Speed: Biotech Research Laboratories Speed Science with Wirespeed 10 Gig Ethernet Switching

IT Editorial

Thursday, 30 April 2009 15:34

Written by Joseph Ammirato

An emerging solution to both speed and budget, known as 10 Gigabit Ethernet (10G or 10GE) Switching fabrics, has been deployed in High Performance Computing clusters today.   An Ethernet Fabric is a purpose-built 10 Gigabit Ethernet switching solution for data center networks that enables a wire-speed, ultra-low latency, lossless, and scalable network infrastructure.  10G switching solutions speed exploding volumes of data traffic with efficiency and cost effectiveness previously unseen.   By leveraging standards-based Ethernet technology to improve productivity, researchers can now extend budgets and race live-saving science to market.

Win-win: Faster to market = More lives saved + More profit

Protein Dynamics

Biotech companies relentlessly sprint to bring new pharmaceuticals and drug therapies to market, not only for humane purposes, but also to optimize profits relative to their competitors.  Accelerating time to market, in many cases, hinges on increasing the number of analyses that can be performed; this includes mining ever-increasing sequencer data sets, amplifying molecular structure comparisons, expanding nucleotide correlations and screening additional cellular modeling results.  Many biotech companies are finding significant performance bottlenecks that choke off product development efficiencies.  All too often, researchers spend increasingly more budget on storage systems and have a continuing reliance on desktop tools.   Given the enormous volumes of data under analysis, under investment in the network interconnect between PCs, servers, and storage compromises biotech researchers’ ability to accelerate new products to market.

10 Gigabit Ethernet Switching & Biotech High Performance Computing

With 10 Gigabit Ethernet Switching, biotech research HPC clusters can now scale and perform at peak levels to deliver research results faster with lower cost.  One new networking vendor offers an exciting standards-based 10 Ethernet Switching solution that prevents network bottlenecks through an efficient 10G Switching biotech research cluster infrastructure that offers alternative paths (multipathing) for data to travel and, thereby, provides optional routes before primary routes become congested.

Purpose-built for scalable 10G switching architectures, fewer devices are required to achieve full wirespeed bandwidth, allowing researchers to speed up processing and establish a long-term biotech research IT investment for meeting critical research requirements.

10G Switching Enables Faster Access to Biotech Research Data

By increasing the volume of individual analysis, researchers achieve their biotech research goals more quickly:  Through faster harvesting of  data from numerous and larger sequencer data sets, increasing the number of molecular structure comparisons and nucleotide correlations, or screening more results from cellular modeling. 

 
Molecular model

Additional compute cores, storage nodes, and network connections -- in short, scale -- are required to manage this burgeoning data volume.  In addition to scale, different research teams depend on their biotech research HPC cluster to handle their individual research objectives.  For example, a research team may correlate nucleotides on a protein under study while another team improves their protein folding model.  If both teams work on the same protein using the same HPC cluster, the cluster -- and its network interconnect -- must accommodate different research parameters without custom tuning for each job run.

With 10G Ethernet Switching, biotech research HPC clusters can scale to thousands of compute and storage node connections – matching the scale requirements for computational analyses.   The new networking vendor noted above goes one step further through a standards-based innovation that eliminates network congestion by measuring, in real-time, all traffic flows’ latencies and reroutes traffic around any emerging bottlenecks in the biotech research HPC cluster. As a result, this 10GE switching solution delivers ultra-low latency and ultra-low jitter for any type of biotech research HPC traffic.  Moreover, independent of the type of research, this new 10 Gigabit Ethernet Switching solution dynamically balances traffic at wirespeed to provide the most efficient Ethernet network for analysis.

Pushing the Pedal to the Metal: Wirespeed 10GE Speeds Results

DNA sequencing

Speeding up the analytic process requires that compute nodes have faster processors and storage nodes have faster access times.  In addition, the network connections need to be larger and cannot be blocked.  When a cluster has more server connections feeding into less outgoing network connections, we have a condition called oversubscription.   This creates potential for blocked traffic when the total incoming server traffic bandwidth exceeds the total bandwidth of the outgoing network connections.   Any oversubscription of the network creates a bottleneck resulting in slower compute time for biotech research analysis.  Storage access is particularly impacted by oversubscription; packets drop, retransmits go out, transmit protocols throttle back – all causing the cluster to slow down.  Therefore, all network connections in the cluster need to be wirespeed in order deliver timely biotech research results.  All wirespeed 10 Gigabit Ethernet Switching networks prevent any throttling down to low efficiencies, and wirespeed maps directly to faster biotech research results.

However, not all 10GE switching solutions are equal; some are not capable of delivering a full end-to-end wirespeed networking solution for biotech research HPC clusters.  Researchers and their IT partners should carefully evaluate all vendors’ solutions as many will fall short of the high performance and budgetary needs for their biotech research.

Matching The Need for Speed with The Need for Budget

     
Molecular model

Economically, research teams should make sure that all biotech research HPC cluster costs are taken into account including hardware, operational expenses (power, cooling, footprint, etc.), training, and support for the HPC cluster.  In addition, when the cost of a cluster can be shared across multiple research, these teams can pool resources for an even faster, more efficient compute cluster.  The cost of 10G Ethernet Switching solutions is rapidly coming down to match price/performance gains from high performing servers and storage.  Researchers are encouraged to survey the entire networking vendor landscape as new innovations, especially from new more nimble entrants, makes the need for speed a need that can be fulfilled in the toughest of economic climates.

Biotech Research 10 Gigabit Ethernet Switching Checklist
Here’s a list of biotech HPC 10G networking requirements that biotech researchers can use to ensure their need for speed is met:

1. Does the 10GE Switching solution access results faster?
2. Exceed performance metrics for all user groups and all traffic   patterns?
3. Remove all storage bottlenecks and re-transmits?
4. Scale bandwidth to match cores and compute nodes?
5. Speed up processing with wirespeed 10G Switching?
6. Achieve unsurpassed 10G Switching connectivity?

7. Does the 10GE Switching solution Lower Biotech Operating Costs?
8. Lowest price per port?
9. Conserve compute and storage dollars?
10. Simplify operations?
11. Minimize power and reduce cooling?
12. Use familiar Ethernet to get up and running quickly?

About the Author: Joseph Ammirato is Vice-President of Marketing for Woven Systems (www.wovensystems.com).  Woven Systems is an innovative networking systems vendor that provides standards-based wirespeed 10 Gigabit Ethernet Switching solutions that fit today’s biotech IT budgets.  You can email Joseph at: jammirato@wovensystems.com.

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