Research ComputingUniversity Of South Florida

Providing Advanced Computing Resources for Research

and Instructionthrough

Collaboration

Mission

• Provide advanced computing resources required by a major research universityo Softwareo Hardwareo Trainingo Support

User Base

• 40 Research groups• 6 Colleges• 100 faculty• 300 students

Hardware

• System was build on the condominium model and consists of 300 Nodes 2400 Processorso University provides infrastructure and some

computational resourceso Faculty funding provides bulk of computational

resources

Software

• Over 50 scientific codes o Installationo Integrationo Upgradeso Licensing

Support Personnel

• Provide all systems administration• Software support• One-on-one consulting• System efficiency improvements• Users are no longer just the traditional “number crunchers

Current Projects

• Consolidating the last standalone cluster (of appreciable size)

• Advanced Visualization Centero Group of 19 Faculty applied for fundingo Personnelo Trainingo Large Resolution 3D display

Current Projects

• New computational resourceso Approximately 100 nodeso GPU resourceso Upgrade parallel file system

• Virtual Clusterso HPC for the other 90 %

• FACC

Florida State University's Shared HPC

Building and Maintaining Sustainable Research

Computing at FSU

Shared-FSU HPC Mission

• Support multidisciplinary research• Provide a general access computing

platform• Encourage cost sharing by departments

with dedicated computing needs• Provide a broad base of support and

training opportunities

Turn-key Research SolutionParticipation is Voluntary

• University provides staffing• University provides general infrastructure

o Network fabricso Rackso Power/Cooling

• Additional buy-in incentiveso Leverage better pricing as a group o Matching funds

• Offer highly flexible buy-in optionso Hardware purchase onlyo Short-term Service Level Agreementso Long-term Service Level Agreements

• Shoot for 50% of hardware costs covered by Buy-in

Research Support @ FSU

• 500 plus users • 33 Academic Units• 5 Colleges

HPC Owner Groups• 2007

o Department of Scientific Computingo Center for Ocean-Atmosphere Prediction Studieso Department of Meteorology

• 2008 o Gunzburger Group (Applied Mathematics)o Taylor Group (Structural Biology)o Department of Scientific Computingo Kostov Group (Chemical & Biomedical Engineering)

• 2009 o Department of Physics (HEP, Nuclear, etc.)o Institute of Molecular Biophysicso Bruschweiler Group (National High Magnetic Field Laboratory)o Center for Ocean-Atmosphere Prediction Studies (with the Department of Oceanography)o Torrey Pines Institute of Molecular Studies

• 2010o Chella Group (Chemical Engineering)o Torrey Pines Institute of Molecular Studieso Yang Group (Institute of Molecular Biophysics)o Meteorology Departmento Bruschweiler Groupo Fajer Group (Institute of Molecular Biophysics)o Bass Group (Biology)

Research Support @ FSU

• Publicationso Macromoleculeso Bioinformaticso Systematic Biologyo Journal of Biogeographyo Journal of Applied Remote Sensingo Journal of Chemical Theory and Computationo Physical Review Letterso Journal of Physical Chemistryo Proceeding of the National Academy of Scienceo Biophysical Journalo Journal Chemical Theory Computationo Journal: J. Phys. Chem.o PLoS Pathogenso Journal of Virologyo Journal of the American Chemical Societyo The Journal of Chemical Physicso PLoS Biologyo Ocean Modelingo Journal of Computer-Aided Molecular Design

Sliger Data Center

Shared-HPC pfs

FSU’s Shared-HPCStage 1: Infiniband Connected Cluster

Single and Multiprocessor UsageYear 1

DSL BuildingSliger Data Center

Shared-HPC pfs

Condor

FSU’s Shared-HPCStage 2: Alternative Backfilling

Backfilling Single Proc Jobs on Non-HPC Resources Using Condor

Condor Usage

• ~1000 processor cores available for single processor computations

• 2,573,490 processor hours used since Condor was made available to all HPC users in September

• Seven users have been using Condor from HPC

• Dominate users are Evolutionary Biology, Molecular Dynamics, and Statistics (same users that were submitting numerous single proc. jobs)

• Two workshop introducing it to HPC users

Single vs. Multi-processor JobsYear 2

Single vs. Multi-processor JobsYear 3

DSL BuildingSliger Data Center

Shared-HPC pfs

Condor

SMP

FSU’s Shared-HPCStage 3: Scalable SMP

FSU’s Shared-HPCStage 3: Scalable SMP

• One MOAB Queue for SMP or very large memory jobs

• Three “nodes”o M905 blade with 16 cores and 64GB memo M905 blade with 24 cores and 64GB memo 3Leaf system with up to 132 cores and 528 GB

mem

DSL Building

DSL Data Center

Sliger Data Center

Shared-HPC pfs

Condor

SMP

2°fs

Vis

Interactive ClusterFunctions

• Facilitates data exploration• Provides venue for software not well suited for

a batch scheduled environmento (e.g., some MatLab, VMD, R, Python, etc.)

• Provides access to hardware not typically found on standard desktops/laptops/mobile devises (e.g. lots of memory, high-end GPUs)

• Provides licensing and configuration support for software applications and libraries

Interactive ClusterHardware Layout

• 8 high-end CPU based host nodeso Multi-core Intel or AMD processorso 4 to 8 GB of memory per coreo 16X PCIe connectivityo QDR IB connectivity to Luster storageo IP (read-only) connectivity to Panasaso 10 Gbps connectivity to campus network backbone

• One C410x external PCI chassiso Compacto IPMI managemento Supports up to 16 NVIDIA Tesla M2050

Up to 16.48 teraflops

DSL Building

DSL Data Center

Sliger Data Center

Shared-HPC pfs

Condor

SMP

2°fs

Vis

Db.Web

Web/Database HardwareFunction

• Facilitates creation of Data analysis Pipelines/Workflows

• Favored by external funding agencieso Demonstrated cohesive Cyberinfrastructure o Fits well into required Data Management Plans

(NSF) • Intended to facilitate access to data on

Secondary storage or cycles on owner share of HPC

• Basic Software Install, no development support

• Bare Metal or VM

Web/Database HardwareExamples

Web/Database HardwareExamples

FSU Research CI

HPC

HTC

SMP

1° storage

2°Storage

Vis and interactive

DB and Web

Florida State University's Shared HPC

• Universities are by design multifaceted and lack a singular focus of support

• Local HPC resources should also be multifaceted and have a broad basis of support

HPC Summit

University of Florida

HPC Center

HPC Summit

Short history

• Started in 2003• 2004 Phase I:

CLAS – Avery – OIT• 2005 Phase IIb:

o COE – 9 investors• 2007 Phase IIb:

o COE – 3 investors• 2009 Phase III:

o DSR – 17 investors - ICBR - IFAS • 2011 Phase IV:

o 22 investors

HPC Summit

Budget

• Total budgeto 2003-3004 $0.7 Mo 2004-2005 $1.8 Mo 2005-2006 $0.3 Mo 2006-2007 $1.2 Mo 2007-2008 $1.6 Mo 2008-2009 $0.4 Mo 2009-2010 $0.9 M

HPC Summit

Hardware

• 4,500 cores• 500 TB storage• InfiniBand connected• In three machine rooms

o Connected by 20 Gbit/sec Campus Research Network

HPC Summit

System software

• RedHat Enterprise Linux o through free CentOS distributiono upgrade once per year

• Lustre file systemo mounted on all nodeso Scratch onlyo Provide backup through CNS service

Requires separate agreement between researcher and CNS

HPC Summit

Other software

• Moab scheduler (commercial license)• Intel compilers (commercial license)• Numerous applications

o Open and commercial

HPC Summit

Operation

• Shared cluster• some hosted systems• 300 users• 90% - 95% utilization

HPC Summit

Investor Model

• Normalized Computing Unito $400 per NCUo Is one coreo In fully functional system (RAM, disk, shared

file system)o For 5 years

HPC Summit

Investor Model

• Optional Storage Unito $140 per OSUo 1 TB of file storage (RAID) on one of a few

global parallel file systems (Lustre)o For 1 year

HPC Summit

Other options

• Hosted systemo Buy all hardware, we operateo No sharing

• Pay as you goo Agree to pay monthly billo Equivalent (almost) to $400 NCU prorated on a

monthly basis• Or rates are 0.009 cents per hour

o Cheaper than Amazon Elastic Cloud

www.ccs.miami.edu

Mission Statement

• UM CCS is establishing nationally and internationally recognized research programs, focusing on those of an interdisciplinary nature, and actively engaging in computational research to solve the complex technological problems of modern society. We provide a framework for promoting collaborative and multidisciplinary activities across the University and beyond

CCS overview

• Started in June 2007• Faculty Senate approval in 2008• Four Founding Schools: A&S, CoE,

RSMAS, Medical• Offices in all Campus• ~30 FTEs• Data Center at the NAP of Americas

UM CCS Research Programs and Cores

Physical Science&

Engineering

Computational Biology&

Bioinformatics

Data Mining

Visualization

ComputationalChemistry

SoftwareEngineering

High PerformanceComputing

Social Systems Informatics

Quick Facts• Over 1,000 UM users• 5,200 cores of Linux Based Cluster• 1,500 cores of Power-based Cluster• ~2.0 PT of Storage• 4.0 PT of Back-up • More at:

o http://www.youtube.com/watch?v=JgUNBRJHrC4

o www.ccs.miami.edu

High Performance Computing

• UM Wide Resource Provides Academic Community & Research Partners with Comprehensive HPC Resources:o Hardware & Scientific Software Infrastructureo Expertise in Designing & Implementing HPC Solutionso Designing & Porting Algorithms & Programs to Parallel

Computing Models• Open Access of compute processing (first come

serve)o Peer Review for large projects – Allocation Committeeo Cost Center for priority access

• HPC serviceso Storage Cloudo Visualization and Data Analysis Cloud o Processing Cloud