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Improvements in DNA sequencing technology have lead to a 10,000 fold increase in our data output over the past 5 years. I will describe the lessons we learned whilst scaling our IT infrastructure and ...

Improvements in DNA sequencing technology have lead to a 10,000 fold increase in our data output over the past 5 years. I will describe the lessons we learned whilst scaling our IT infrastructure and tools to cope with the vast amount of data.

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Guy Coates Guy Coates Presentation Transcript

  • Big Data:Sanger Experiences Guy Coates Wellcome Trust Sanger Institute gmpc@sanger.ac.uk
  • The Sanger InstituteFunded by Wellcome Trust.• 2nd largest research charity in the world.• ~700 employees.• Based in Hinxton Genome Campus, Cambridge, UK.Large scale genomic research.• Sequenced 1/3 of the human genome. (largest single contributor).• Large scale sequencing with an impact on human and animal health.Data is freely available.• Websites, ftp, direct database access, programmatic APIs. • Some restrictions for potentially identifiable data.My team:• Scientific computing systems architects.
  • DNA Sequencing TCTTTATTTTAGCTGGACCAGACCAATTTTGAGGAAAGGATACAGACAGCGCCTG AAGGTATGTTCATGTACATTGTTTAGTTGAAGAGAGAAATTCATATTATTAATTA TGGTGGCTAATGCCTGTAATCCCAACTATTTGGGAGGCCAAGATGAGAGGATTGC ATAAAAAAGTTAGCTGGGAATGGTAGTGCATGCTTGTATTCCCAGCTACTCAGGAGGCTG TGCACTCCAGCTTGGGTGACACAG CAACCCTCTCTCTCTAAAAAAAAAAAAAAAAAGG AAATAATCAGTTTCCTAAGATTTTTTTCCTGAAAAATACACATTTGGTTTCA ATGAAGTAAATCG ATTTGCTTTCAAAACCTTTATATTTGAATACAAATGTACTCC 250 Million * 75-108 Base fragments ~1 TByte / day / machineHuman Genome (3GBases)
  • Economic Trends:Cost of sequencing halves every 12months.The Human genome project:• 13 years.• 23 labs.• $500 Million.A Human genome today:• 3 days.• 1 machine.• $8,000.Trend will continue:• $1000 genome is probable within 2 years.
  • The scary graphPeak Yearly capillary Current weekly sequencing:sequencing: 30 Gbase 7-10 Tbases
  • Gen III Sequencers this year?
  • What are we doing with all these genomes?UK10K• Find and understand impact of rare genetic variants on disease.Ensembl• Genome annotation.• Data resources and analysis pipelines.Cancer Genome Project• Catalogue causal mutations in cancer.• Genomics of tumor drug sensitivity.Pathogen Genomics• Bacterial / viral genomics• Malaria Genetics• Parasite genetic / tropical diseases.All these programmes exist inframeworks of external collaboration.• Sharing data and resources is crucial.
  • IT RequirementsNeeds to match growth insequencing technology. Disk StorageGrowth of compute & storage 12000• Storage /compute doubles every 12 10000 months. • 2012 ~17 PB Usable 8000 TerabytesEverything changes, all the time. 6000• Science is very fluid. 4000• Speed to deployment is critical. 2000Moores law will not save us. 0 1995 1997 1999 2001 2003 2005 2007 2009 1994 1996 1998 2000 2002 2004 2006 2008 2010$1000 genome* Year• *Informatics not included
  • Sequencing data flow. Processing/ ComparativeSequencer Archive Internet QC analysis Unstructured data Structured data (Flat files) (databases) Raw data Sequence Alignments Variation data Feature (10 TB) (500GB) (200GB) (1GB) (3MB)
  • Agile SystemsModular design.• Blocks of network, compute and storage.• Assume from day 1 we will be adding more.• Expand simply by adding more blocks.• Lots of automation. Disk Disk Disk DiskMake storage visible fromeverywhere.• Key enabler; lots of 10Gig. Network Compute Compute Compute Compute
  • Compute ModulesCommodity Servers• Blade form-factor.• Automated Management.Generic intel/AMD CPUs• Single threaded / embarrasingly parallel workload.• No FPGAs or GPUs.2000-10,000 core per cluster• 3 Gbyte/s memory per core.• A few bigger memory machines (0.5TB).
  • Storage ModulesTwo flavours:Scale up (Fast)• DDN storage arrays.• Lustre. 250-500TB per filesystem.• High performance. Expensive.Scale out (Slow)• Linux NFS servers.• Nexsan Storage arrays.• 50-100TB per filesystem.• Cheap and cheerful.How large?• More modules = more management overhead.• Fewer modules = large unit of failure.• 100-500 TB
  • Actual ArchitectureCompute Silos• Beware of over- Fast consolidation. disk Fast• Some workflows interact Slow disk disk badly with one another.• Separate out some work onto different clusters. Fast diskLogically rather thanphysically separated.• LSF to manage workflow. Network• Simple software re-config to move capacity between silos. Farm 1 LSF Farm2 LSF Farm3
  • Some things we learnedKISS! Keep It Simple, Stupid.• Simple solution may look less reliable on paper than the fully redundant failover option.• Operational reality: • Simple solutions are much quicker to fix when they break.• Not always possible (eg lustre use).Good communication between science and IT teams.• Expose the IT costs to researchers.Build systems Iteratively.• Constantly evolving systems.• Groups start out with everything on fast storage, but realise they can get away with slower stuff.• More cost effective to do 3x1 yearly purchase rather than 1x 3 yearly?Data Triage• What do we really want to keep?
  • Sequencing data flow. General Farm (6K core) IRODs Sequencing Processing/ ComparativeSequencer (1K cores) Archive Internet QC UK10K Farm analysis (1.5K core) CGP Farm (2K cores) Structured data Unstructured data (Flat files) (databases) Slow Fast Fast Slow Fast Slow Slow Slow
  • That was easy!
  • Sequencing data flow. Processing/ ComparativeSequencer datastore Internet QC analysis Unstructured data Structured data (Flat files) (databases) Pbytes! Raw data Sequence Alignments Variation data Feature (10 TB) (500GB) (200GB) (1GB) (3MB)
  • People = Unmanaged DataInvestigators take data and “do stuff” with it.Data is left in the wrong place.• Typically left where it was created. • Moving data is hard and slow.• Important data left in scratch areas, or high IO analysis being run against slow storage.Duplication.• Everyone take a copy of the data, “just to be sure.”Capacity planning becomes impossible.• Who is using our disk space? • “du” on 4PB is not going to work...
  • Not Just an IT Problem#df -hFilesystem Size Used Avail Use% Mounted onlus02-mds1:/lus02 108T 107T 1T 99% /lustre/scratch102#df -iFilesystem Inodes IUsed IFree IUse% Mounted onlus02-mds1:/lus02 300296107 136508072 163788035 45%/lustre/scratch102 100TB filesystem, 136M files. • “Where is the stuff we can delete so we can continue production...?”
  • Lost productivityData management impacts on research productivity.• Groups spend large amounts of time and effort just keeping track of data.• Groups who control their data get much more done. • But they spend time writing data tracking applications.Money talks:• “Group A only need ½ the storage budget of group B to do the same analysis.” • Powerful message.Need a common site-wide data management infrastructure.• We need something simple so people will want to use it.
  • Data managementiRODS: Integrated Rule-Oriented Data System.• Produced by DICE Group (Data Intensive Cyber Environments) at U. North Carolina, Chapel Hill.Successor to SRB.• SRB used by the High-Energy-Physics (HEP) community. •20PB/year LHC data.• HEP community has lots of “lessons learned” that we can benefit from.
  • iRODS User interface Web, command line, fuse, API Irods Server Data in S3 Irods Server ICAT Rule Engine Data in databaseCatalogue Implements policiesdatabase Irods Server Data on disk
  • iRODSQueryable metadata• SQL like language.Scalable• Copes with PB of data and 100,000M+ files.• Data replication engine.• Fast parallel data transfers across local and wide area network links.Customisable Rules• Trigger actions on data according to policy. • Eg generate thumbnail for every image uploaded.Federated• iRODS installs can be federated across institutions.• Sharing data is easy.Open Source• BSD licensed.
  • Sequencing ArchiveFinal resting place for all oursequencing data.• Researchers pull data from irods for further analysis.2x 800TB space.• First deployment; KISS!Simple ruleset.• Replicate & checksum data.• External scripts periodically scrub data.Positively received.• Researchers are pushing us for new instances to store their data.Next Iterations:• Experiments with WAN, external federations, complex rules.
  • Architecture ICAT Oracle 10g RAC Irods Server Replica 1 Replica 2 (red datacentre) (green datacentre)275TB 120TB (Nexan) 275TB 120TB (Nexan)(Nexsan) 480TB (Nexsan) 480TB (DDN) (DDN)
  • Some thoughts on CloudsLargest drag on response is dealing with real hardware.• Delivery lead times, racking, cabling etc.To the cloud!Nothing about our IT approach precludes/mandates cloud.• Use it where it makes sense.Public clouds for big-data.• Uploading data to the cloud takes along time.• Data Security. • Need to do your due-diligence • (just like you should be doing in-house!) • Cloud may be more appropriate than in house.Currently cheaper for us to do production in-house.• But: Purely an economic decision.
  • Cloud ArchivesDark Archives• You can get data, but cannot compute across it.• Nobody is going to download 400TB of sequence data.Cloud Archives• Cloud models allow compute to be uploaded to the data and run “in- place.”• Private clouds may simplify data governance.• Can you do it more cheaply than public providers?
  • SummaryModular Infrastructure.Manage Data.Data Triage.Strong Collaboration / Dialogue with Researchers.
  • AcknowledgementsSanger Systems Team• Phil Butcher (Director of IT)• Informatics Systems Group.• Networking, DBA, Infrastructure & helpdesk teams.• Cancer, human-genetics, uk10k informatics teams.Resources:• http://www.sanger.ac.uk/research• http://www.uk10k.org• http://www.sanger.ac.uk/genetics/cgp/cosmic• http://www.ensembl.org• http://www.irods.org• http://www.nanoporetech.com