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Overview of Research Computing ITS Research Computing Mark Reed. Overview – Research Computing. Resources Services Projects. ReCo Resources. Computational Resources compute clusters: Killdevil , Kure Special purpose servers: galaxy, bioapps , sapientia , ICISS, eruditio Software

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Overview of Research Computing ITS Research Computing

Mark Reed

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Overview – Research Computing

  • Resources

  • Services

  • Projects

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ReCo Resources

  • Computational Resources

    • compute clusters: Killdevil, Kure

    • Special purpose servers:

      • galaxy, bioapps, sapientia, ICISS, eruditio

  • Software

    • licensed

    • open source

  • Data Storage

  • Virtual Computing Lab (VCL)

  • Access to National Resources

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ReCo Services

  • Technical Support

  • Training and Development

  • Engagement and Collaboration

  • Research Database Support

  • Secure Data Exchange

  • Data Grids – iRODS

  • Desktop Support - THL

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ReCo Projects

  • EFRC

  • HTS and Seqware

  • Digital Humanities

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Compute Cluster Advantages

  • fast interconnect, tightly coupled

  • aggregated resources

    • compute cores

    • memory

  • installed software base

  • high availability

  • large (scratch) file spaces

  • scheduling and job management

  • data backup

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Multi-Purpose Killdevil Cluster

  • High Performance Computing

    • Large parallel jobs, high speed interconnect

  • High Throughput Computing (HTC)

    • high volume serial jobs

  • Large memory jobs

    • special nodes for extreme memory

  • GPGPU computing

    • computing on Nvidia processors

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Killdevil Nodes

  • Three types of nodes:

    • compute nodes

    • large memory nodes

    • GPGPU nodes

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Killdevil Compute Cluster

Infiniband4x QDR Interconnect

priority usage for patrons

Buy in is cheap


large lustre scratch file system IB connected


  • Heterogeneous Research Cluster

  • Dell Blades

  • 700+ Compute Nodes mostly

    • Xeon 5670 2.93 GHz

    • 9600 cores

    • Nehalem Microarchitecture

    • Dual socket, hex core and octcore

    • 48 GB memory

    • some higher memory nodes

  • GPGPU Nodes

    • 64 Nvidia Tesla M2070

  • Extreme Memory Nodes

    • two 1 TB node, 32 cores

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  • A HPC/HTC research compute cluster in RC

  • Named after the beach in North Carolina

  • It’s pronounced like the Nobel prize winning physicist and chemist, Madame Curie

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Kure Compute Cluster

priority usage for patrons

Buy in is cheap


/netscr, /proj

  • Heterogeneous Research Cluster

  • Hewlett Packard Blades

  • 200+Compute Nodes, mostly

    • Xeon 5560 2.8 GHz

    • Nehalem Microarchitecture

    • Dual socket, quad core

    • 48 GB memory

    • over 1800 cores

    • some higher memory nodes

  • Infiniband4x QDR

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Getting an account:

For Kure, KillDevil and Mass Storage

  • http://onyen.unc.edu

  • Subscribe to Services

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Licensed Software

  • over 20 licensed software applications (some are site or volume licensed, others restricted)

    • SAS, Matlab, Maple, Mathematica, Gaussian, Accelrys Materials Studio and Discovery Studio modules, Sybyl, Schrodinger, Stata, ArcGIS, NAG, IMSL, Totalview, Envi/IDL, JMP, and JMP Genomics

  • compilers (licensed and otherwise)

    • intel, PGI, gnu, CUDA compiler

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Large Installed Software Base

  • Numerous other packages provided for research and technical computing

    • including BLAST, PyMol, SOAP, PLINK, NWChem, R, Cambridge Structural Database, Amber, Gromacs, Petsc, Scalapack, Netcdf, Babel, Qt, Ferret, Gnuplot, Grace, iRODS, XCrySDen, and many more.

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long term archival storage

easy to access and use

“limitless” capacity

2 TB free

looks like ordinary disk file system – data is actually stored on tape

data is backed up

Mass Storage

Recently Upgraded!

“To infinity … and beyond” - Buzz Lightyear

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Virtual Computing Lab (VCL)

  • Collaboration with NC State to establish VCL infrastructure for UNC.

  • VCL provides on-demand access to high-end computing resources, via highly customized, virtual Windows and Linux machines.

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Virtual Computing Lab (VCL)

  • Users can log on from anywhere at any time to make a reservation to use a machine

  • Lots of software available!

    • ArcGIS

    • SAS

    • MATLAB

    • Adobe

    • MS Office

    • LaTEX

    • SigmaPlot

    • MUCH MORE!

Go to http://vcl.unc.edu to sign on

For help, see “Getting Started on VCL” webpage http://help.unc.edu/CCM3_007680

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Access to National Resources

  • XSEDE – NSF funded leadership class infrastructure at 11 partner sites.

  • Open Science Grid – national shared computing and storage resources in a common grid infrastructure

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Services: Training

  • Courses are offered in the following areas:

    • Introductions to HPC resources

    • Research Applications

    • Linux

    • General Computing

    • Parallel Programming

  • Courses are taught throughout year by Research Computing, for listings and details, go to:

    • http://learnit.unc.edu/workshops

    • http://help.unc.edu/CCM3_008194

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Services: Technical Support

  • Technical support in using RC resources is available

    • Support in compiling, porting, using tools, submitting jobs, using software packages, storage and data management, …

  • online web forms

  • email research@unc.edu

  • 962-HELP (962-4357)

  • personal consultation

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Engagement, Support and Collaboration

  • Research scientists with experience in computational chemistry, physics, grid computing, environmental modeling, mathematics, parallel computing and the life sciences are available for consultation and collaboration.

  • Digital Humanities Specialist

  • Extensive technical support for utilizing research computing resources.

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Services: Secure Data Exchange

  • Capability to share secure and sensitive data using a secure “drop box” mechanism for anonymous or non-Onyen users or full FTP access for trusted Onyen accounts

  • Computing - challenges of flexibility needed for research and realities of cyber attacks

  • Networking – maximizing bandwidth for research endeavors vs. IPS/IDS inspection

  • Data – compliance requirements, data sharing, privacy, etc.

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Services: Data Grids –iRODS

  • Distributed data storage using the integrated Rule oriented Data System (iRodS). iRODS provides scientists with a secure, scalable system that can support many aspects of research data management

  • Enables data grids/repositories whose policies are implemented and enforced through rules

Research Computing is experimenting with hosting iRODS collections as a service.

Collaborating with UNC Libraries, Institute for the Environment, and RENCI.


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Desktop Computing –TarHeel Linux

Linux Image Pull

  • Desktop/Laptop Campus Machines

  • Build desktop machines tailored for the RC environment with additional customization by user.

  • Based on CentOS

  • Security Approved Build

    • nightly updates

  • Onyen

  • OpenAFS

  • Customized Applications

  • Firewall

  • http://tarheellinux.unc.edu

KickstartServer for Linux Distribution in ITS Manning Machine Room

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Services: Research Database Support

  • Full time DB admin to support UNC research databases

  • over 20 UNC Research Databases for research production, training and development

    • clients include School of Pharmacy, Lineberger Comprehensive Cancer Center (LCCC), Computer Science, SILS, Renci, Bioinformatics, Institute for the Environment, …

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Energy Frontier Research Centers


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Chemical Approaches to Artificial Photosynthesis. Modular Approach

Light absorption, sensitization

Electron transfer quenching

Vectorial electron/proton transfer, redox splitting

Catalysis of water oxidation and reduction

Photosystem II

Meyer, Accounts of Chemical Research1989, 22, 163.

Meyer, et. al. Inorg. Chem.2005, 6802; Acc. Chem Res 1989, 163.

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High Throughput Sequencing Approach

  • The High Throughput Sequencing Facility (HTSF) provides core services primarily for

  • Lineberger Comprehensive Cancer Center (LCCC) and the TCGA (The Cancer Genome Atlas) project

  • Renci – NIDA project (National Inst. Drug Abuse)

  • UNC life sciences

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High Throughput Deep Sequencing Infrastructure Approach

  • ~20 NextGen sequences

    • IlluminaHiSeq, Ion Torrent, …

  • RNAseqpipeline

  • DNAseqpipeline

  • Whole Genome pipeline

  • ChIP/FAIREseq pipeline

  • De novo assembly

  • Specialized Workflow Engine, Condor, LSF scheduling

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High Throughput Deep Sequencing Infrastructure Approach

Data Collection Infrastructure


1.7 PB

Aggregation Server

Compute Nodes

MaPSeq meta scheduler running multiple pipelines



Processing Pipeline

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Lumbee Approach Familial Political Factions

Malinda Maynor Lowery, History

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Brooklyn Renaissance Social Graph Approach

Melissa Bullard, History

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Questions and Comments? Approach

  • For assistance with any of our services, please contact Research Computing

    • Email: research@unc.edu

    • Phone: 919-962-HELP

    • Submit help ticket at http://help.unc.edu