Bio-IT for Core Facility Managers

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Bio-IT For Core Facility LeadersTips, Tricks & Trends

2012 NERLCSD Meeting - www.nerlscd.org

Wednesday, October 31, 12

http://www.nerlscd.org

http://www.nerlscd.org

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Meta-Issues (The Big Picture)

Infrastructure Tour

Compute & HPC

Storage

Intro

Cloud & Big Data

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6Wednesday, October 31, 12

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I’m Chris.

I’m an infrastructure geek.

I work for the BioTeam.

@chris_dagWednesday, October 31, 12

Who, what & whyBioTeam

‣ Independent consulting shop‣ Staffed by scientists forced to

learn IT, SW & HPC to get our own research done

‣ 12+ years bridging the “gap” between science, IT & high performance computing

‣ www.bioteam.net


http://www.bioteam.net

http://www.bioteam.net

Seriously.Listen to me at your own risk

‣ Clever people find multiple solutions to common issues

‣ I’m fairly blunt, burnt-out and cynical in my advanced age

‣ Significant portion of my work has been done in demanding production Biotech & Pharma environments

‣ Filter my words accordingly5


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Infrastructure Tour

Compute & HPC

Storage

Intro

Cloud & Big Data

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Meta-IssuesWhy you need to track this stuff ...


Why this stuff matters ...

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Big Picture

‣ HUGE revolution in the rate at which lab instruments are being redesigned, improved & refreshed

• Example: CCD sensor upgrade on that confocal microscopy rig just doubled your storage requirements

• Example: That 2D ultrasound imager is now a 3D imager

• Example: Illumina HiSeq upgrade just doubled the rate at which you can acquire genomes. Massive downstream increase in storage, compute & data movement needs


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The Central Problem Is ...

‣ Instrumentation & protocols are changing FAR FASTER than we can refresh our Research-IT & Scientific Computing infrastructure

• The science is changing month-to-month ...

• ... while our IT infrastructure only gets refreshed every 2-7 years

‣ We have to design systems TODAY that can support unknown research requirements & workflows over many years (gulp ...)


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The Central Problem Is ...

‣ The easy period is over‣ 5 years ago you could toss inexpensive storage and

servers at the problem; even in a nearby closet or under a lab bench if necessary

‣ That does not work any more; IT needs are too extreme‣ 1000 CPU Linux clusters and petascale storage is the

new normal; try fitting THAT in a closet!


What core facility leadership needs to understandThe Take Home Lesson

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‣ The incredible rate of cost decreases & capability gains seen in the lab instrumentation space is not mirrored everywhere

‣ As gear gets cheaper/faster, scientists will simply do more work and ask more questions. Nobody simply banks the financial savings when an instrument gets 50% cheaper -- they just buy two of them!

‣ IT technology is not improving at the same rate; we also can’t change our IT infrastructures all that rapidly


If you get it wrong ...

‣ Lost opportunity‣ Frustrated & very vocal researchers‣ Problems in recruiting ‣ Publication problems


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Infrastructure Tour

Compute & HPC

Storage

Intro

Cloud & Big Data

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Infrastructure TourWhat does this stuff look like?


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Self-contained single-instrument infrastructure


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Ilumina GA


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Instrument Control Workstation


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SOLiD Sequencer ...


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sits on top of a 24U server rack...


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Another lab-local HPC cluster + storage


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More lab-local servers & storage


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Small core w/ multiple instrument support


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Small cluster; large storage


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Mid-sized core facility


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Large Core Facility


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Large Core Facility


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Large Core Facility


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Colocation Cages


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Inside a colo cage


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Linux Cluster + In-row chillers (front)


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Linux Cluster + In-row chillers (rear)


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1U “Pizza Box” Style Server Chassis


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Pile of “pizza boxes”


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4U Rackmount Servers


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“Blade” Servers & Enclosure


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Hybrid Modular Server


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Integrated: Blades + Hypervisor + Storage


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Petabyte-scale StorageWednesday, October 31, 12

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Yep. This counts.

16 monster compute nodes + 22 GPU nodesCost? 30 bucks an hour via AWS Spot Market

Real world screenshot from earlier this month


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Physical data movement station


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Physical data movement station


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“Naked” Data Movement


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“Naked” Data Archive


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The cliche image


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Backblaze Pod: 100 terabytes for $12,000


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Infrastructure Tour

Compute & HPC

Storage

Intro

Cloud & Big Data

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ComputeActually the easy bit ...


Not a big deal in 2012 ...

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Compute Power

‣ Compute power is largely a solved problem‣ It’s just a commodity‣ Cheap, simple & very easy to acquire‣ Lets talk about what you need to know ...


Thinks you should be tracking ...Compute Trends

‣ Facility Issues‣ “Fat Nodes” replacing Linux Clusters‣ Increasing presence of serious “lab-local” IT


Facility Stuff

‣ Compute & storage requirements are getting larger and larger

‣ We are packing more “stuff” into smaller spaces

‣ This increases (radically) electrical and cooling requirements


Facility Stuff - Core issue

‣ Facility & power issues can take many months or years to address

‣ Sometimes it may be impossible to address (new building required ...)

‣ If research IT footprint is growing fast; you must be well versed in your facility planning/upgrade process


Facility Stuff - One more thing

‣ Sometimes central IT will begin facility upgrade efforts without consulting with research users

• This was the reason behind one of our more ‘interesting’ projects in 2012

‣ ... a client was weeks away from signing off on a $MM datacenter which would not have had enough electricity to support current research & faculty recruiting commitments


“Fat” Nodes Replacing Clusters


Fat Nodes - 1 box replacing a cluster

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‣ This server has 64 CPU Cores‣ .. and up to 1TB of RAM‣ Fantastic Genomics/Chemistry

system• A 256GB RAM version only

costs $13,000

‣ These single systems are replacing small clusters in some environments


Fat Nodes - Clever Scale-out Packaging

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‣ This 2U chassis contains 4 individual servers

‣ Systems like this get near “blade” density without the price premium seen with proprietary blade packaging

‣ These “shrink” clusters in a major way or replace small ones


The other trend ...


“Serious” IT now in your wet lab ...

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‣ Instruments used to ship with a Windows PC “instrument control workstation”

‣ As instruments get more powerful the “companion” hardware is starting to scale-up

‣ End result: very significant stuff that used to live in your datacenter is now being rolled into lab enviroments


“Serious” IT now in your wet lab ...

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‣ You may be surpised what you find in your labs in ’12

‣ ... can be problematic for a few reasons ...

1. IT support & backup2. Power & cooling3. Noise4. Security


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NetworkingAlso not particularly worrisome ...


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Networking

‣ Networking is also not super complicated‣ It’s also fairly cheap & commoditized in ’12‣ There are three core uses for networks:

1. Communication between servers & services

2. Message passing within a single application

3. Sharing files and data between many clients


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Networking 1 - Servers & Services

‣ Ethernet. Period. Enough said.‣ Your only decision is between 10-Gig and 1-Gig ethernet‣ 1-Gig Ethernet is pervasive and dirt cheap‣ 10-Gig Ethernet is getting cheaper and on it’s way to

becoming pervasive


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Networking 1 - Ethernet

‣ Everything speaks ethernet‣ 1-Gig is still the common interconnect for most things‣ 10-Gig is the standard now for the “core”‣ 10-Gig is the standard for top-of-rack and “aggregation”‣ 10-Gig connections to “special” servers is the norm


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Networking 2 - Message Passing

‣ Parallel applications can span many servers at once

‣ Communicate/coordinate via “message passing”

‣ Ethernet is fine for this but has a somewhat high latency between message packets

‣ Many apps can tolerate Ethernet-level latency; some applications clearly benefit from a message passing network with lower latency

‣ There used to be many competing alternatives

‣ Clear 2012 winner is “Infiniband”Wednesday, October 31, 12

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Networking 2 - Message Passing

‣ The only things you need to know ...‣ Infiniband is an expensive networking alternative that

offers much lower latency than Ethernet‣ You would only pay for and deploy an IB fabric if you had

an application or use case that requires it.‣ No big deal. It’s just “another” network.


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Networking 3 - File Sharing

‣ For ‘Omics this is the primary focus area‣ Overwhelming need for shared read/write access to files

and data between instruments, HPC environment and researcher desktops

‣ In HPC environments you will often have a separate network just for file sharing traffic


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Networking 3 - File Sharing

‣ Generic file sharing uses familiar NFS or Windows fileshare protocols. No big deal

‣ Always implemented over Ethernet although often a mixture of 10-Gig and 1-Gig connections

• 10-Gig connections to the file servers, storage and edge switches; 1-gig connections to cluster nodes and user desktops

‣ Infiniband also has a presence here• Many “parallel” or “cluster” filesystems may talk to the clients

via NFS-over-ethernet but internally the distributed components may use a private Infiband network for metadata and coordination.


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Storage.(the hard bit ...)


Setting the stage ...

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Storage

‣ Life science is generating torrents of data‣ Size and volume often dwarf all other research areas -

particularly with Bioinformatics & Genomics work‣ Big/Fast storage is not cheap and is not commodity‣ There are many vendors and many ways to spectacularly

waste tons of money‣ And we still have an overwhelming need for storage that

can be shared concurrently between many different users, systems and clients


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Life Science “Data Deluge”

‣ Scare stories and shocking graphs getting tiresome‣ We’ve been dealing with terabyte-scale lab instruments

& data movement issues since 2004• And somehow we’ve managed to survive ...

‣ Next few slides• Try to explain why storage does not stress me out all that

much in 2012 ...


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The sky is not falling.

‣ Overwhelming majority of us do not operate at Broad/Sanger levels

• These folks add 200+ TB a week in primary storage

‣ We still face challenges but the scale/scope is well within the bounds of what traditional IT technologies can handle

‣ We’ve been doing this for years• Many vendors, best practices, “war stories”, proven methods

and just plain “people to talk to…”

1. You are not the Broad Institute or Sanger Center


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‣ Yesteryear: Terascale .TIFF Tsunami‣ Yesterday: RTA, in-instrument data reduction‣ Today: Basecalls, BAMs & Outsourcing‣ Tomorrow: Write directly to the cloud

2. Instrument Sanity Beckons


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‣ Peta-scale storage has not been a risky exotic technology gamble for years now

• A few years ago you’d be betting your career

‣ Today it’s just an engineering & budget exercise• Multiple vendors don’t find petascale requirements particularly

troublesome and can deliver proven systems within weeks

• $1M (or less in ’12) will get you 1PB from several top vendors

‣ However, still HARD to do BIG, FAST & SAFE• Hard but solvable; many resources & solutions out there

3. Peta-scale storage is not really exotic or unusual any more.


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On the other hand ...


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OMG! The Sky Is Falling!Maybe a little panic is appropriate ...


The sky IS falling!

‣ As instrument output declines …

‣ Downstream storage consumption by end-user researchers is increasing rapidly

‣ Each new genome generates new data mashups, experiments, data interchange conversions, etc.

‣ MUCH harder to do capacity planning against human beings vs. instruments

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1. Those @!*#&^@ Scientists ...


The sky IS falling!

‣ Sequencing is already a commodity

‣ NOBODY simply banks the savings

‣ EVERYBODY buys or does more

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2. @!*#&^@ Scientific Leadership ...


The sky IS falling!

772007 2008 2009 2010 2011 2012

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BIG SCARY GRAPH

Gigabases vs. Moores LawOMG!!


The sky IS falling!

‣ Cost of acquiring data (genomes) falling faster than rate at which industry is increasing drive capacity

‣ Human researchers downstream of these datasets are also consuming more storage (and less predictably)

‣ High-scale labs must react or potentially have catastrophic issues in 2012-2013

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3. Uncomfortable truths


The sky IS falling!

‣ This is not sustainable• Downstream consumption

exceeding instrument data reduction

• Commoditization yielding more platforms

• Chemistry moving faster than IT infrastructure

• What the heck are we doing with all this sequence?

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5. Something will have to break ...


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CRAM it.


The sky IS falling!

‣ Minor improvements are useless; order-of-magnitude needed

‣ Some people are talking about radical new methods – compressing against reference sequences and only storing the diffs• With a variable compression “quality budget” to spend on

lossless techniques in the areas you care about

‣ http://biote.am/5v - Ewan Birney on “Compressing DNA”

‣ http://biote.am/5w - The actual CRAM paper

‣ If CRAM takes off, storage landscape will change81

CRAM it in 2012 ...


http://biote.am/5v

http://biote.am/5v

http://biote.am/5w

http://biote.am/5w

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What comes next?Next 18 months will be really fun...


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What comes next.

‣ Accept that science changes faster than IT infrastructure‣ Be glad you are not Broad/Sanger‣ Flexibility, scalability and agility become the key

requirements of research informatics platforms• Tiered storage is in your future ...

‣ Shared/concurrent access is still the overwhelming storage use case

• We’ll still continue to use clustered, parallel and scale-out NAS solutions

The same rules apply for 2012 and beyond ...


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What comes next.

‣ Many peta-scale capable systems deployed• Most will operate in the hundreds-of-TBs range

‣ Far more aggressive “data triage” • “.BAM only!”

‣ Genome compression via CRAM‣ Even more data will sit untouched & unloved‣ Growing need for tiers, HSM & even tape

In the following year ...


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What comes next.

‣ Broad, Sanger and others will pave the way with respect to metadata-aware & policy driven storage frameworks

• And we’ll shamelessly copy a year or two later

‣ I’m still on my cloud storage kick• Economics are inescapable; Will be built into storage

platforms, gateways & VMs

• Amazon S3 is only a HTTP RESTful call away

• Cloud will become “just another tier”

In the following year ...


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‣ What do DDN, Panasas, Isilon, BlueArc, etc. have in common?

• Under the hood they all run Unix or Unix-like OS’s on x86_64 architectures

‣ Some storage arrays can already run applications natively

• More will follow

• Likely a big trend for 2012

What comes next.Expect your storage to be smarter & more capable ...


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But what about today?


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Still trying to avoid this.(100TB scientific data, no RAID, unsecured on lab benchtops )


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Flops, Failures & FreakoutsCommon storage mistakes ...


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Flops, Failures & Freakouts

‣ Scientist: “My work is priceless, I must be able to access it at all times”

‣ Corporate/Enterprise Storage Guru: “Hmmm …you want high availability, huh?”

‣ System delivered:• 40TB Enterprise SAN

• Asynchronous replication to remote site

• Can’t scale, can’t do NFS easily

• ~$500K per year in operational & maintenance costs

#1 - Unchecked Enterprise Storage Architects


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‣ Scientist: “I do bioinformatics, I am rate limited by the speed of file IO operations. Faster disk means faster science. “

‣ System delivered:• Budget blown on top tier fastest-possible ‘Cadillac’ system

‣ Outcome:• System fills to capacity in 9 months; zero budget left.

#2 - Unchecked User Requirements


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‣ Common source of storage unhappiness

‣ Root cause:• Not enough pre-sales time spent on design and engineering

• Choosing Open Source over Common Sense

‣ System as built:• Not enough metadata controllers

• Issues with interconnect fabric

• Poor selection & configuration of key components

‣ End result:• Poor performance or availability

• High administrative/operational burden

#3 - D.I.Y Cluster & Parallel Filesystems


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Hard Lessons LearnedWhat these tales tell us ...


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‣ End-users are not precise with storage terms• “Extremely reliable” means no data loss;

Not millions spent on 99.99999% high availability

‣ When true costs are explained:• Many research users will trade a small amount of uptime or

availability for more capacity or capabilities

• … will also often trade some level of performance in exchange for a huge win in capacity or capability

Hard Lessons Learned


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‣ End-users demand the world but are willing to compromise

• Necessary for IT staff to really talk to them and understand work, needs and priorities

• Also essential to explain true costs involved

‣ People demanding the “fastest” storage often don’t have actual metrics to back their assertions



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‣ Software-based parallel or clustered file systems are non-trivial to correctly implement

• Essential to involve experts in the initial design phase

• Even if using ‘open source’ version …

‣ Commercial support is essential• And I say this as an open source zealot …



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The road aheadMy $.02 for 2012...


The Road Ahead

‣ Peta-capable platforms required

‣ Scale-out NAS still the best fit

‣ Customers will no longer build one big scale-out NAS tier

‣ My ‘hack’ of using nearline spec storage as primary science tier is probably obsolete in ’12

‣ Not everything is worth backing up

‣ Expect disruptive stuff98

Storage Trends & Tips for 2012


The Road Ahead

‣ Monolithic tiers no longer cut it

• Changing science & instrument output patterns are to blame

• We can’t get away with biasing towards capacity over performance any more

‣ pNFS should go mainstream in ’12

• { fantastic news }

‣ Tiered storage IS in your future

• Multiple vendors & types99

Trends & Tips for 2012


The Road Ahead

‣ Your storage will be able to run apps

• Dedupe, cloud gateways & replication

• ‘CRAM’ or similar compression

• Storage Resource Brokers (iRODS) & metadata servers

• HDFS/Hadoop hooks?

• Lab, Data management & LIMS applications

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Drobo Appliance running BioTeam MiniLIMS internally...


The Road Ahead

‣ Hadoop / MapReduce / BigData

• Just like GRID and CLOUD back in the day you’ll need a gas mask to survive the smog of hype and vendor press releases.

• You still need to think about it

• ... and have a roadmap for doing it

• Deep, deep ties to your storage

• Your users want/need it

• My $.02? Fantastic cloud use case101



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Disruptive Technology Example


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Backblaze Pod For Biotech


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Backblaze: 100Tb for $12,000


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Infrastructure Tour

Compute & HPC

Storage

Intro

Cloud & Big Data

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The ‘C’ wordDoes a Bio-IT talk exist if it does not mention “the cloud”?


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Defining the “C-word”

‣ Just like “Grid Computing” the “cloud” word has been diluted to almost uselessness thanks to hype, vendor FUD and lunatic marketing minions

‣ Helpful to define terms before talking seriously‣ There are three types of cloud‣ “IAAS”, “SAAS” & “PAAS”


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Cloud Stuff

‣ Before I get nasty ...‣ I am not an Amazon shill‣ I am a jaded, cynical, zero-loyalty consumer of IT

services and products that let me get #%$^ done‣ Because I only get paid when my #%$^ works, I am

picky about what tools I keep in my toolkit‣ Amazon AWS is an infinitely cool tool


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Cloud Stuff - SAAS

‣ SAAS = “Software as a Service”‣ Think:‣ gmail.com


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Cloud Stuff - SAAS

‣ PAAS = “Platform as a Service”‣ Think:‣ https://basespace.illumina.com/‣ salesforce.com‣ MS office365.com, Apple iCloud, etc.


https://basespace.illumina.com

https://basespace.illumina.com

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Cloud Stuff - IAAS

‣ IAAS = “Infrastructure as a Service”‣ Think:‣ Amazon Web Services‣ Microsoft Azure


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Cloud Stuff - IAAS

‣ When I talk “cloud” I mean IAAS‣ And right now in 2012 Amazon IS the IAAS cloud‣ ... everyone else is a pretender


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Cloud Stuff - Why IAAS

‣ IAAS clouds are the focal point for life science informatics

• Although some vendors are now offering PAAS and SAAS options ...

‣ The “infrastructure” clouds give us the “building blocks” we can assemble into useful stuff

‣ Right now Amazon has the best & most powerful collection of “building blocks”

‣ The competition is years behind ...Wednesday, October 31, 12

A message for thecloud pretenders…


No APIs?Not a cloud.


No self-service?Not a cloud.


Installing VMWare & excreting a press release?

Not a cloud.


I have to email a human?Not a cloud.


~50% failure rate when launching new servers?

Stupid cloud.


Block storage and virtual servers only?

(barely) a cloud;


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Private CloudsMy $.02 cents


Private Clouds in 2012:

‣ I’m no longer dismissing them as “utter crap”

‣ Usable & useful in certain situations

‣ Hype vs. Reality ratio still wacky

‣ Sensible only for certain shops• Have you seen what you have to do

to your networks & gear?

‣ There are easier ways


‣ Remain cynical (test vendor claims)‣ Due Diligence still essential‣ I personally would not deploy/buy anything that does not

explicitly provide Amazon API compatibility

Private Clouds: My Advice for ‘12


Most people are better off:1. Adding VM platforms to existing HPC clusters &

environments

2. Extending enterprise VM platforms to allow user self-service & server catalogs

Private Clouds: My Advice for ‘12


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Cloud AdviceMy $.02 cents


Don’t get left behind

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Cloud Advice

‣ Research IT Organizations need a cloud strategy today‣ Those that don’t will be bypassed by frustrated users‣ IaaS cloud services are only a departmental credit card

away ... and some senior scientists are too big to be fired for violating IT policy :)


Design Patterns

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Cloud Advice

‣ You actually need three tested cloud design patterns:

‣ (1) To handle ‘legacy’ scientific apps & workflows‣ (2) The special stuff that is worth re-architecting ‣ (3) Hadoop & big data analytics


Legacy HPC on the Cloud

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Cloud Advice

‣ MIT StarCluster• http://web.mit.edu/star/cluster/

‣ This is your baseline‣ Extend as needed


http://web.mit.edu/star/cluster/

http://web.mit.edu/star/cluster/

“Cloudy” HPC

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Cloud Advice

‣ Some of our research workflows are important enough to be rewritten for “the cloud” and the advantages that a truly elastic & API-driven infrastructure can deliver

‣ This is where you have the most freedom‣ Many published best practices you can borrow‣ Amazon Simple Workflow Service (SWS) look sweet‣ Good commercial options: Cycle Computing, etc.


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Hadoop & “Big Data”

‣ Hadoop and “big data” need to be on your radar‣ Be careful though, you’ll need a gas mask to avoid the

smog of marketing and vapid hype‣ The utility is real and this does represent the “future

path” for analysis of large data sets


Big Data HPC

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Cloud Advice - Hadoop & Big Data

‣ It’s gonna be a MapReduce world, get used to it‣ Little need to roll your own Hadoop in 2012‣ ISV & commercial ecosystem already healthy‣ Multiple providers today; both onsite & cloud-based‣ Often a slam-dunk cloud use case


What you need to know

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‣ “Hadoop” and “Big Data” are now general terms‣ You need to drill down to find out what people actually

mean‣ We are still in the period where senior mgmt. may

demand “hadoop” or “big data” capability without any actual business or scientific need



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‣ In broad terms you can break “Big Data” down into two very basic use cases:

1. Compute: Hadoop can be used as a very powerful platform for the analysis of very large data sets. The google search term here is “map reduce”

2. Data Stores: Hadoop is driving the development of very sophisticated “no-SQL” “non-Relational” databases and data query engines. The google search terms include “nosql”, “couchdb”, “hive”, “pig” & “mongodb”, etc.

‣ Your job is to figure out which type applies for the groups requesting “hadoop” or “big data” capability


Hadoop vs traditional Linux Clusters

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High Throughput Science

‣ Hadoop is a very complex beast‣ It’s also the way of the future so you can’t ignore it‣ Very tight dependency on moving the ‘compute’ as close

as possible to the ‘data’‣ Hadoop clusters are just different enough that they do

not integrate cleanly with traditional Linux HPC system‣ Often treated as separate silo or punted to the cloud



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‣ Hadoop is being driven by a small group of academics writing and releasing open source life science hadoop applications;

‣ Your people will want to run these codes‣ In some academic environments you may find people

wanting to develop on this platform


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Cloud Data MovementMy $.02 cents


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Cloud Data Movement

‣ We’ve slung a ton of data in and out of the cloud‣ We used to be big fans of physical media movement‣ Remember these pictures?‣ ...


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Physical data movement station 1


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Physical data movement station 2


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“Naked” Data Movement


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“Naked” Data Archive


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Cloud Data Movement

‣ We’ve got a new story for 2012‣ And the next image shows why ...


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March 2012Wednesday, October 31, 12

Wow!Cloud Data Movement

‣ With a 1GbE internet connection ...‣ and using Aspera software ....‣ We sustained 700 MB/sec for more than 7 hours

freighting genomes into Amazon Web Services‣ This is fast enough for many use cases, including

genome sequencing core facilities*‣ Chris Dwan’s webinar on this topic:

http://biote.am/7e


http://biote.am/7e

http://biote.am/7e

Wow!Cloud Data Movement

‣ Results like this mean we now favor network-based data movement over physical media movement

‣ Large-scale physical data movement carries a high operational burden and consumes non-trivial staff time & resources


There are three ways to do network data movement ...Cloud Data Movement

‣ Buy software from Aspera and be done with it‣ Attend the annual SuperComputing conference & see

which student group wins the bandwidth challenge contest; use their code

‣ Get GridFTP from the Globus folks• Trend: At every single “data movement” talk I’ve been to in

2011 it seemed that any speaker who was NOT using Aspera was a very happy user of GridFTP. #notCoincidence


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Putting it all together


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Wrapping up

IT may just be a means to an end but you need to get your head wrapped around it

‣ (1) So you use/buy/request the correct ‘stuff’‣ (2) So you don’t get cheated by a vendor‣ (3) Because you need to understand your tools‣ (4) Because trends in automation and orchestration

are blurring the line between scientist & sysadmin


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Wrapping up - Compute & Servers

‣ Servers and compute power are pretty straightforward‣ You just need to know roughly what your preferred

compute building blocks look like‣ ... and what special purpose resources you require (GPUs,

Large Memory, High Core Count, etc.)‣ Some of you may also have to deal with sizing, cost and

facility (power, cooling, space) issues as well


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Wrapping up - Networking

‣ Networking is also not hugely painful thing‣ Ethernet rules the land; you might have to pick and choose

between 1-Gig and 10-Gig Ethernet

‣ Understand that special networking technologies like Infiniband offer advantages but they are expensive and need to be applied carefully (if at all)

‣ Knowing if your MPI apps are latency sensitive will help

‣ And remember that networking is used for multiple things (server communication, application message passing & file and data sharing)


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Wrapping up - Storage

‣ If you are going to focus on one IT area, this is it

‣ It’s incredibly important for genomics and also incredibly complicated. Many ways to waste money or buy the ‘wrong’ stuff

‣ You may only have one chance to get it correct and may have to live with your decision for years

‣ Budget is finite. You have to balance “speed” vs “size” vs “expansion capacity” vs “high availibility” and more ...

‣ “Petabyte-capable Scale-out NAS” is usually the best starting point. You deviate away from NAS when scientific or technical requirements demand “something else”.


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Wrapping up - Hadoop / Big Data

‣ Probably the way of the future for big-data analytics. It’s worth spending time to study; especially if you intend to develop software in the future

‣ Popular target for current and emerging high-scale genomics tools. If you want to use those tools you need to deploy Hadoop

‣ It’s complicated and still changing rapidly. It can be difficult to integrate into existing setups

‣ Be cynical about hype & test vendor claims


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Wrapping up - Cloud

‣ Cloud is the future. The economics are inescapable and the advantages are compelling.

‣ The main obstacle holding back genomics is terabyte scale data movement. The cloud is horrible if you have to move 2TB of data before you can run 2Hrs of compute!

‣ Your future core facility may involve a comp bio lab without a datacenter at all. Some organizations are already 100% virtual and 100% cloud-based


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The NGS cloud clincher.

700 mb/sec sustained for ~7 hoursWest Coast to East Coast USA


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Wrapping up - Cloud, continued

‣ Understand that for the foreseeable future there are THREE distinct cloud architectures and design patterns.

‣ Vendors who push “100% hadoop” or “legacy free” solutions are idiots and should be shoved out the door. We will be running legacy codes and workflows for many years to come

‣ Your three design patterns on the cloud:• Legacy HPC systems

(replicate traditional clusters in the cloud)

• Hadoop

• Cloudy (when you rewrite something to fully leverage cloud capability)


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Thanks! Slides online at: http://slideshare.net/chrisdag/


http://slideshare.net/chrisdag/

http://slideshare.net/chrisdag/

Date post:	12-May-2015
Category:	Technology
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