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Hardware options

www.knome.com/knoSYS © 2014 Knome, Inc. All rights reserved.200 5th Avenue, Waltham, MA 02451 617-715-1000

The k100 model The k100 is a self-contained, high-performance processing center with compute, storage, network, and power management components.

ComputeThe k100 features four compute nodes each with two 8-core Intel E5-2600 series processors for a total of 128 virtual core “threads” of computer power. Using the lvy Bridge chips from Intel, the k100 compute nodes can handle processing hundreds of whole genomes with ease.

Each node contains 128 gigabytes of RAM for a total of 512 gigabytes in the 4-node system.

Additionally, all of the k100 CPU’s have an on-board Advanced Vector Extensions (AVX) instruction set for accelerating floating point operations. This instruction set has been used by the Broad Institute to accelerate the main routines of GATK variant calling substantially.

A fifth server acts as a database server with two 8-core E5-2600 Ivy Bridge processors and 128 gigabytes of memory.

The compute servers have an “open” architecture meaning that multiple align and call modules can be installed and performance compared for optimal results.

StorageIn addition to the compute servers, the k100 comes with a ClusterStor Lustre Storage Appliance with 60 terabytes of usable storage.

The knoSYS® system provides labs with a scalable, production-grade informatics system for the analysis, annotation, and interpretation of human next-gen sequence data. The platform includes both user-friendly software and powerful hardware.

While many organizations rely on the cloud to store their data, hospitals with a clinical focus are sensitive to security, versioning, and upload/download speeds. Having a locally-installed turnkey solution provides peace of mind and control over your data from end-to-end.

Performance studies with the system have shown sustained I/O rates of 1 gigabyte per second, meaning less time waiting and more time analyzing.

A RAID 6 configuration is used for failure tolerant storage so that in the instance of a drive failure (or even

if two drives fail), no data is lost and work can continue while the disk is replaced.

The k100 rack has space for two optional Lustre units to expand to 180 usable terabytes of storage. In addition to gaining storage space, the storage network is designed to increase in the available I/O bandwidth as drives are added, up to 7 gigabytes per second.

NetworkAs all eight servers need to “talk” to each other, the k100 has two networks: one for communication traffic and one for storage traffic. In addition, a 10 gigabit Ethernet card is provided for uploading and downloading files to and from the system.

These networks make interactions between the different components of the k100 seamless.

Power managementIncluded with the k100 is an uninterruptable power supply (UPS) and two power distribution units (PDU’s). These allow for sufficient back-up power for five minutes of operation, thereby enabling controlled shutdown of the system. All servers include a redundant, failover power supply. If a customer has their own racks, UPS, and PDU’s, these components aren’t necessary.

Massimo Delledonne of the University of Verona stands next to his k100.

www.knome.com/knoSYS © 2014 Knome, Inc. All rights reserved.200 5th Avenue, Waltham, MA 02451 617-715-1000

Load files into memory quickly A Mellanox Infiniband Switch manages traffic to the storage units and can also connect to external storage units with speeds of up to 40 gigabits per second, expandable to 56 gigabits per second.

Easily transfer data to (or off) the k100 Getting large data on and off any system is always a challenge and usually takes a long time. Two choices are provided: Infiniband or 10 gigabit Ethernet. Users can attach their Infiniband-equipped storage solution to the on-board Infiniband switch or can run a cable from their 10GbE switch to the 10GbE card on the k100. These enable 40 Gb/second or 10 Gb/second transfer speeds thus facilitating communication with an institution’s network.

Storage traffic network

Communication traffic network

Four high performance computing servers

Database server

Storage management unit

Storage unit

Expandable storage unit (optional)

Expandable storage unit (optional)

Power supply

It just worksTo enable all of the servers inside of the k100 to communicate with each other, an HP ProCurve 1 gigabit switch is included.

Spend less time waiting and more time analyzingMore data often means slower performance as all that data takes time to crunch. With the k100 high-performance computing servers and database server, waiting is never an issue. The HPC nodes and database nodes are Ivy Bridge Intel chips with 128 gigabytes of RAM. On-board AVX instruction sets accelerate processes, such as GATK calling, even further.

No worries about storageAs everyone in genetics knows, human genome data can get really big. Enter the ClusterStor Management Unit with Lustre Storage Units. Each storage unit comes with 60 terabytes of usable storage up to 180 terabytes with additional units. A RAID 6 configuration means that your data is well protected in case of hard drive failure.Peace of mind when the power goes out

Back-up power is included with the k100 for five minutes of operation so that you can shut down the system if there is a power outage. (Optional, depending on whether the k100 is in a pre-existing server room.)

Inside a k100The k100 is the ultimate optimization of price and performance when it comes to hardware for genomic interpretation. Flexibility (parts can be upgraded and expanded) and robustness were paramount as the system was designed. The k100 ships in a standalone server rack or the components can be integrated into existing server facilities. The dense configuration of the system means less rack space is required for local installations. Hosted options are also available.

www.knome.com/knoSYS © 2014 Knome, Inc. All rights reserved.200 5th Avenue, Waltham, MA 02451 617-715-1000

Connections and communications � Intel Dual-Port I350 1GbE Ethernet Controller and Intel

10GbE 1-port Controller

Compute and storage � Two 8-core/16 thread, 2.0GHz, E5-2640v2 processors

with 20MB cache � 256GB of DDR3-1600 ECC memory � Storage includes 4 x 4TB 6Gb/sec SAS drives � LSI 9271-8i 6Gb/sec RAID controller � Storage in RAID6 configuration, 24TB usable � 1 x 300GB Intel DC S3500 Series MLC (6Gb/s) 2.5”

SATA SSD � Optical Drive: Low-Profile DVD+/-RW Drive � Power Supply: Redundant 740W with PMBus 80 PLUS

Platinum Certified

Size & weight Height 3.5 in (89 mm) Width 17.2 in (437 mm) Depth 25.5 in (648 mm) Weight 85 lbs (38.6 kg)

Electrical and operating requirements � Line voltage: 100V to 240V AC � Plug/Receptacle: NEMA L5-30 or L6-30 or IEC 60309

332P6/R6 � Frequency: 50Hz to 60Hz � Current: 30A, RoSH compliant � Power: ~594 VA

Connections and communications � Two networks: 40Gb/sec Infiniband QDR via a Mellanox

Switch for storage traffic and a HP ProCurve 1Gb/sec switch for network traffic.

� Also includes a 10GbE Ethernet card for uploading and downloading files.

High-performance computing cluster � Four nodes, each node with two 8-core/16 thread,

2.6GHz, E5-2650v2 processors with 20MB cache, 128GB of DDR3-1600 ECC memory

� Storage includes 2 x 2TB 7,200RPM, 6Gb/sec SATA drives

� Power Supply: Shared, Redundant 1620W Power Supply with PMBus - 80 PLUS Platinum Certified

Database server � 1 node with two 8-core/16 thread, 2.0GHz, E5-2640v2

processors with 20MB cache, 128GB of DDR3 ECC 1600 memory

� Storage includes 2 x 2TB 7,200RPM, 6Gb/sec SATA drives

� Power Supply: Redundant 750W with PMBus & 12C 80 PLUS Gold Certified

ClusterStor Management Unit � A 6-core/12 thread 2.4 GHz, E5-2609 processor with

32GB RAM � 16 x 10K RPM 2.5” 450GB SAS Compass HDDs � Power Supply: Redundant 764W Power Supply with

PMBus - 80 PLUS Platinum Certified

Scalable Lustre Storage Unit, 60TB usable (expandable to 180 TB)

� A 6-core/12 thread 2.4 GHz, E5-2609 processor with 16GB RAM

� 20 x 4TB 7,200 RPM 3.5” SAS HDDs plus 1 x 4TB 3.5” SAS drive as a global hot spare

� 2 x 15K RPM 300GB Yellow Jacket HDDs � Power Supply: Four (4) 580W Power Supplies - 80

PLUS Platinum Certified

Electrical and operating requirements � Line voltage: 200V to 240V AC � Plug/Receptacle: NEMA L6-30 or IEC 60309 332P6/R6 � Frequency: 50Hz to 60Hz � Current: 30A, RoSH compliant � Power: ~3,845 VA � Operating temperature: 50° to 95° F � UPS included 208V, 30A � Maximum operating altitude: 10,000 feet � Power consumption: 4,000 VA (peak) � Requires two (2) 30A L6-30 sockets

Size & weight In rack In shipping crate Height 47.17 in (1,198 mm) 53.15 in (1,350 mm) Width 23.62 in (600 mm) 35.39 in (899 mm) Depth 42.13 in (1,070 mm) 47.99 in (1,219 mm) Weight 699 lbs (317 kg) 949 lbs (423.9 kg)

Enclosure � The k100 ships fully integrated inside of a 24U

NetShelter SX server room rack.

The k25 modelFor organizations focusing on gene panels and smaller numbers of exome and whole genomes, the k25 is the perfect-sized option. Laboratories that are just getting started with next-generation sequencing may also find the k25 suits their needs. The k25 was released in 2014 in response to requests by labs that don’t currently have the high-volume NGS processing demands the k100 was designed to handle.

Components are similar to those of the k100; however, there are fewer of them. One dual CPU node (Intel Ivy Bridge model) contains 32 virtual core “threads” of compute power and 256 gigabytes of RAM. These CPU’s also come standard with an on-board Advanced Vector Extensions (AVX) instruction set which can be used to speed up floating point operations, such as GATK variant calling.

The storage server offers 24 terabytes of usable storage and still boasts a RAID 6 array for failure tolerance. Similar to the k100, the k25 provides reassurance

in knowing that data will not be lost if a drive fails or becomes corrupted.

The k25 is equipped with both 1 gigabit and 10 gigabit Ethernet cards to facilitate communication and uploading and downloading files to the k25.

The k25 is installed in an existing server rack and relies on existing infrastructure for power. If back-up power is not available, the k25 can be plugged into a UPS directly in case of power outage.

Hosted hardwareBoth the k100 and k25 models are traditionally installed in an organization’s existing server facilities, either in a bundled server rack or as individual components.

The option to purchase either model and have it hosted at Knome’s secure facility is also available; users log in remotely to the system.

k25 specificationsk100 specifications

Knome does not provide medical advice, diagnosis of a disease or other conditions or in the cure, mitigation, treatment, or prevention of a disease or to affect the structure or function of the body. Analyses and reports provided by Knome are for informational purposes only and are subject to change. Knome’s products and services are not for use in diagnostic procedures.