From the Benchtop to the Datacenter: HPC Requirements in Life Science Research

From the Benchtop to the DatacenterHPC Requirements in Life Science Research

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HPC User Forum 2015; Norfolk, VA.

Ari E. Berman, Ph.D.

Who am I?

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General Manager of Government Services at BioTeam

I’m a fallen scientist - Ph.D. Molecular Biology, Neuroscience, Bioinformatics

I’m an HPC/Infrastructure geek - 17 years

I help enable science!

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BioTeam

‣ Independent consulting shop

‣ Staffed by scientists forced to learn IT, SW & HPC to get our own research done

‣ Infrastructure, Informatics, Software Development, Cross-disciplinary Assessments

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

‣ Our wide-ranging work is what gets us invited to speak at events like this ...

What do we do?BioTeam

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Laboratory Knowledge


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Converged Solution


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Converged Solution

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OK, so why am I here talking to you?

We have a unique perspective across much of life sciences

We’ve noticed a few things

‣ Big Data has arrived in Life Sciences

‣ Data is being generated at unprecedented rates

‣ Research and Biomedical Orgs were caught off guard

‣ IT running to catch up, limited budgets

‣ Money is tight, Orgs reluctant to invest in Bio-IT

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25% of all Life Scientists will require HPC in 2015!

It’s being made harder by lack of support and infrastructure that works for them

Research is hard

‣ Scientists are getting frustrated

‣ Stubborn, fight for what they need

‣ They will build a cluster under their desk if it gets the job done

‣ In general they will win against IT, eventually

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It’s a risky time to be doing HPC for life science

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Big Picture / Meta Issue

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

‣ IT not a part of the conversation, running to catch up

Science progressing way faster than IT can refresh/change

The Central Problem Is ...

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

• Bench 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 new normal for informatics

If IT gets it wrong ...

‣ Lost opportunity

‣ Missing capability

‣ Frustrated & very vocal scientific staff

‣ Problems in recruiting, retention, publication & product development

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It’s a risky time to be doing Bio-IT

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What are the drivers in Bio-IT today?

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Genomics: Next Generation Sequencing (NGS)

It’s like the hard drive of life

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The big deal about DNA

‣ DNA is the template of life

‣ DNA is read --> RNA

‣ RNA is read --> Proteins

‣ Proteins are the functional machinery that make life possible

‣ Understanding the template = understanding basis for disease

Sequencing by SynthesisHow does NGS work?

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Reference assembly, variant callingHow does NGS work?

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Gateway to personalized medicineThe Human Genome

‣ 3.2 Gbp

‣ 23 chromosomes

‣ ~21,000 genes

‣ Over 55M known variations

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...and why NGS is the primary driver

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The Problem...

‣ Sequencers are now relatively cheap and fast

‣ Some can generate a human genome in 18 hours, for $2,000

‣ Everyone is doing it

‣ Can generate 3TB of data in that time

‣ First genome took 13 years and $2.7B to complete

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Other Methodologies Not Far Behind

High-throughput Imaging

‣ Robotics screening millions of compounds on live cells 24/7 • Not as much data as genomics in

volume, but just as complex • Data volumes in the 10’s TB/week

‣ Confocal Imaging • Scanning 100’s of tissue sections/

week, each with 10’s of scans, each with 20-40 layers and multiple florescent channels

• Data volumes in the 1’s - 10’s TB/week

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High-power, dense detector MRI scanners in use 24/7 at large research hospitals

High-res medical imaging

‣ Creating 3D models of brains, comparing large datasets

‣ Using those models to perform detailed neurosurgery with real-time analytic feedback from supercomputer in the OR (cool stuff)

‣ Also generates 10’s of TB/week

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This is a huge problem

‣ Causing a literal deluge of data, in the 10’s of Petabytes

‣ NIH generating 1.5PB of data/month

‣ First real case in life science where 100Gb networking might really be needed

‣ But, not enough storage or compute

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But wait! There’s more!

We have them allFile & Data Types

‣ Massive text files

‣ Massive binary files

‣ Flatfile ‘databases’

‣ Spreadsheets everywhere

‣ Directories w/ 6 million files

‣ Large files: 600GB+

‣ Small files: 30kb or smaller25

Application characteristics

‣ Mostly SMP/threaded apps performance bound by IO and/or RAM

‣ Hundreds of apps, codes & toolkits

‣ 1TB - 2TB RAM “High Memory” applications (large graphs, genomic assembly)

‣ Lots of Perl/Python/R

‣ MPI is rare • Well written MPI is even rarer

‣ Few MPI apps actually benefit from expensive low-latency interconnects* • *Chemistry, modeling and structure work is

the exception

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Up to a two line subtitle, generally used to describe the takeaway for the slide

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HPC in Life Sciences

Don’t just build for performanceBuild for the Use Case!

‣ Building for performance is short-sighted

‣ System needs to solve problems, not create more for scientists

‣ Fun to engineer for speed, but not terribly useful in LifeSci

‣ That means: take the time to understand the use cases, and design to that. Way more fun in the long-term

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If you have it, they will break itLife Scientists: Thugs of HPC

‣ Every kind of file you can imagine

‣ Every kind of algorithm (good, bad, ugly)

‣ Want it all, right now

‣ They keep everything

‣ Don’t want to pay for it

‣ Your health might depend on it (seriously!)

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Compute related design patterns largely static

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Core Compute

‣ Linux compute clusters are the baseline compute platform

‣ Mostly commodity server based - not a ton of capability SC in this space

‣ Need for capability SC is growing though - life sciences catching up

‣ Even our lab instruments know how to submit jobs to common HPC cluster schedulers

Power is the new commodityCore Compute

‣ Power efficiency is becoming a requirement as 0.5 - 1PF+ becomes commonplace (30,000+ cores)

‣ High core density in multi-server racks is key

‣ Better distribution of power

‣ Custom chassis with extreme densities are the best at power efficiency

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New and refreshed HPC systems running many node types

Compute: Diversity in node types

‣ HPC compute resources no longer homogenous; many types and flavors now deployed in single HPC stacks

‣ Newer clusters mix-and-match to match the known use cases: • ‘Fat’ nodes with many CPU cores • ‘Thin’ nodes with super-fast CPUs • Large memory nodes (1TB - 3TB) • GPU nodes for compute and visualization • Co-processor nodes (Xeon Phi, FPGA) • Analytic nodes with SSD, FusionIO, flash

or large local disk for ‘big data’ tasks

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Storage & Data Management

‣ Storage and network are the biggest headaches in life sciences

‣ Require connectivity to HPC, labs, and externally for data sharing

‣ Needs to be scalable: Life Sciences now well into petascale

‣ Starting to need performance, especially with medium - large HPC

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Storage & Data Management‣ LifeSci code very I/O-bound

• Huge number of r/w calls per second • CPU utilization may be low - most of

the operations are data wrangling from disk

• Load average will be through the roof • More than a few of these will bring your

storage to its knees

‣ IOPS are critical in 2015

‣ Throughput per core: 100MB/s, ideally (1 TB/s for 10k cores!) • Not at all realistic! Lucky to get 10MB/s

on sizable systems34

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Storage & Data Management‣ NAS = “easiest” option

• Scale Out NAS products are the mainstream standard

• Don’t deliver performance to cores

‣ Parallel & Distributed storage becoming more standard in LifeSci • GPFS: major proportion in market • Lustre: gaining ground, but worse than

GPFS with small files • Global buffers: reordering random IO • IOP Tiers: Millions of IOPS as scratch • Object stores! • Local SSDs for scratch

1Gb and 10Gb are not going to cut it with these requirements

Cluster Networking

‣ Building for IO requires very high-performance network

‣ Infiniband FDR/EDR

‣ Eliminating traditional ethernet: many benefits • High-speed network, much lower

cost (56Gb+) • IP can work with ipoverib (lose some

performance, but with LifeSci, that’s OK)

• Whole cluster can work for all job types, good IPC for simulations, etc

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Fat tree: Scalable TopologyCluster Networking

‣ Can be built with expansion in mind: no recabling

‣ Possible to have non-blocking network; cost savings at 2:1 blocking

‣ Can build in gateways that talk IP outside the network; Mellanox VPI makes this easier

‣ Can hang data transfer nodes (DTN) off of them, use as fast data transfer point

‣ Storage at the root37

Why go to all this trouble? 10Gb is fine!Cluster Networking

‣ This is true, for now, especially in Life Sciences

‣ Faster than 10Gb doesn’t really help most bad bioinformatics code units own; but at scale, things get messy

‣ Landscape is changing: code is being optimized, datasets are still increasing in size exponentially, lab tech developing at a rate that is off the scale

‣ Have to build for the unpredictable! (Scary)38

DRMs, OS’s, and Protocols, Oh My!Software stack

‣ Distributed Resource Managers: • Still see a ton of SGE/OGS out

there • Giving away to Univa pretty

quickly: very rich feature set • slurm has a growing following,

especially with SchedMD • Torque/maui & Moab • Even still see some PBS Pro and

LSF - but rare

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‣ Key Features in 2015 ‣ Resource mapping (cgroups);

map GPU to CPU ‣ Core-based scheduling ‣ Rich resource management:

threads, memory, accelerators, mixed environments

‣ Metascheduling (hybrid environments)

‣ Application aware scheduling40


‣ Big Data analytic frameworks ‣ Hadoop - slow to adopt, lots of

talk, very little walk: not dedicated instances - tends to live on core storage (schedulable)

‣ Database stacks: MySQL still most popular, Oracle still lives

‣ mongoDB is gaining popularity in code, but more for the savvy

‣ Heard some talk of Neo4j, but haven’t seen it in the wild

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Networking to/from Cluster

‣ May surpass storage as our #1 infrastructure headache

‣ Why? • Petascale storage meaningless if

you can’t access/move it • Enterprise network security

usually inhibits research data flow • 10-Gig, 40-Gig and 100-Gig

networking will force significant changes elsewhere in the ‘bio-IT’ infrastructure

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Network: ‘ScienceDMZ’

‣ Very fast “low-friction” network links and paths with security policy and enforcement specific to scientific workflows

‣ “ScienceDMZ” concept is real and necessary

‣ BioTeam will be building them in 2014 and beyond

‣ Central premise: • Legacy firewall, network and security methods architected

for “many small data flows” use cases • Not built to handle smaller #s of massive data flows

• Also very hard to deploy ‘traditional’ security gear on 10Gigabit and faster networks

‣ More details, background & documents at http://fasterdata.es.net/science-dmz/

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Background traffic or

competing bursts

DTN traffic with wire-speed

bursts

10GE

10GE

10GE

http://fasterdata.es.net/science-dmz/

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Simple Science DMZ:

Image source: “The Science DMZ: Introduction & Architecture” -- esnet

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What’s the future look like?

Also known as hybrid cloudsHybrid HPC‣ Relatively new idea

• small local footprint • large, dynamic, scalable, orchestrated

public cloud component

‣ DevOps is key to making this work

‣ High-speed network to public cloud required

‣ Software interface layer acting as the mediator between local and public resources

‣ Good for tight budgets, has to be done right to work

‣ Not many working examples yet46

Converged Infrastructure

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The meta issue

‣ Individual technologies and their general successful use are fine

‣ Unless they all work together as a unified solution, it all means nothing

‣ Creating an end-to-end solution based on the use case (science!): converged infrastructure

Necessary for ScienceConvergence

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Converged Solution


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Converged Solution

People matter tooConvergence

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Converged Solution

Not so distant future!Fully converged laboratories

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Converged Solution


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Converged Solution

New Bottleneck!


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Laboratory


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Laboratory

Knowledge

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end; Thanks!

Date post:	15-Jul-2015
Category:	Technology
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From the Benchtop to the Datacenter: HPC Requirements in Life Science Research

Technology