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IBM Spectrum Scale Best Practices for Genomics Medicine Workloads

by Joanna Wong, Kevin Gildea, Kumaran Rajaram, Luis Bolinches, Monica Lemay, Piyush Chaudhary, Sandeep R. Patil, Ulf Troppens

April 2018

Intermediate to advanced

64 pages

2h 3m

English

IBM Redbooks

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April 2018, Second EditionDecember 2017, First Edition
1.1 Genomics medicine1.1.1 Genomics medicine overview1.1.2 Genomics workload1.2 Solution approach1.2.1 Composable infrastructure1.2.2 Composable building blocks1.2.3 Driven by design thinking1.2.4 Driven by agile development1.3 Blueprint capabilities1.3.1 Capabilities of the compute services1.3.2 Capabilities of the storage services1.3.3 Capabilities of the private network services1.4 Example environment1.4.1 Physical configuration1.4.2 Logical configuration
2.1 Overview2.1.1 Capabilities and solution elements2.1.2 Software levels2.2 Application layer2.2.1 The Broad Institute GATK2.3 Orchestration layer2.3.1 IBM Spectrum LSF2.4 Data layer2.5 General recommendations2.5.1 Designation of the compute nodes2.5.2 IBM Spectrum Scale node roles2.5.3 IBM Spectrum LSF host types2.5.4 IBM Spectrum LSF add-ons2.5.5 External dependencies2.5.6 Communication and security aspects2.6 Tuning2.6.1 Operating system2.6.2 Network2.6.3 IBM Spectrum Scale2.7 Monitoring
3.1 Overview3.1.1 Capabilities and solution elements3.1.2 Software levels3.2 File storage layer3.2.1 IBM Spectrum Scale file systems3.2.2 Recommendations for genomics medicine workloads3.2.3 IBM Spectrum Scale filesets3.3 Block storage layer3.3.1 IBM Elastic Storage Server3.4 File access layer3.4.1 NFS and SMB3.5 General recommendations3.5.1 Recommendations for IBM Spectrum Scale3.5.2 External dependencies3.5.3 Communication and security aspects3.6 Data management3.7 Tuning3.7.1 IBM Elastic Storage Server3.7.2 Protocol nodes3.8 Monitoring
4.1 Overview4.1.1 Capabilities and solution elements4.1.2 Shared network4.2 High-speed data network4.2.1 IBM Spectrum Scale network requirements4.2.2 Recommendations for genomics medicine workloads4.2.3 Miscellaneous comments4.3 Management networks4.3.1 Provisioning network4.3.2 Service network4.4 Network designs4.4.1 Network design for small configuration4.4.2 Network design for large configuration
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Content preview from IBM Spectrum Scale Best Practices for Genomics Medicine Workloads

Summary of changes

This section describes the technical changes that are made in this edition of the paper and in previous editions. This edition might also include minor corrections and editorial changes that are not identified.

Summary of Changesfor IBM Spectrum Scale Best Practices for Genomics Medicine Workloadsas created or updated on April 25, 2018.

April 2018, Second Edition

This revision reflects the addition, deletion, or modification of new and changed information, which is summarized here.

Changed Information

•Minor corrections and clarifications

December 2017, First Edition

New information

•GATK3 on Power8

•IBM Spectrum Scale Release 4.2.3.4

•IBM Elastic Storage Server 5.2

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Publisher Resources

ISBN: 9780738456751Other