October 2003

MSRC High Performance Computing Outreach Program to Universities in Mississippi

Tonight’s Presentations:

Mr. David RoachDirector, Mississippi Center for Supercomputing Research

University, Mississippi

Mr. Eigoro HashimotoSenior Research Scientist

Naval Oceanographic Office (NAVOCEANO)/Lockheed Martin Space OperationsMajor Shared Resource Center (MSRC)

Stennis Space Center, MS

October 2003

The Mississippi Center for Supercomputing Research

October 2003

Background• History:

– 1987 Standard Oil Donates Cyber 205 Supercomputer to UM– 6 Supercomputers over the Past 14 Years– Separate from UM in budget of MS Legislature

• Mission: High Performance Computing Support– Provides Computing Cycles, Applications, and Support– Enhances Instructional and Research Climates– Serves all 8 Mississippi Public Universities– Helps Bring Research $$$ into Mississippi

October 2003

Why use MCSR?

• Reference us in proposals to secure grants for computationally intensive research.

• Leave the fast computing to us.

• Use our specialized math, science, and engineering packages in your instruction or research.

• Let your students learn on us.

• Tap into our experience in Unix, Linux, and Cluster Building.

October 2003

Current Systems SGI Origin 2800

– 128 CPUs

– 64 GB Memory

– 1.6 Terabytes of Disk

Cray C916– 10 Processors

– 1 Gigaword Memory

– 512 megaword solid-state storage device (SSD)

– 460 Gigabytes of Disk Space

Linux Beowulf– 219 Node Cluster of

Compaq, Dell, Gateway, & CSI Intel Processors

SGI Origin 200– 1 Processor

– 256 MB Memory

SGI Onyx 10000– 8 Processors

– Infinite Reality Graphics

October 2003

Magnolia • Cray C916/10-1024 running Unicos 10 (Unix)• Installed October, 1999• FORTRAN, C/C++ Compilers• Optimization via:

– Vectorization– Fortran autotasking– C Microtasking

October 2003

SGI Origin 2800 (Sweetgum) Hardware

– 128 CPUs • 64 R12000 300 MHz CPUs• 64 R10000 195 MHz CPUs

– 64 Gigabytes shared memory – 1.6 Terabyates of fiberchannel disk– Irix 6.5.17f (Unix)– Gigabit uplink to Internet2– Origin 2000 (1999) + 2nd Origin 2000 (2002) = Origin 2800

October 2003

SGI Origin 2800 (Sweetgum) Programming Environment• IRIX (Unix-based) OS (6.5.17f)• MIPSpro FORTRAN, C, C++ Compilers (7.3.1.3)• Math/Scientific Libraries - LAPACK, BLAS, ARPACK, LINPACK

• Optimization via Parallelization– Directives-based approach:

• Fortran, C, C++, HPF, OpenMP via compiler directives

• Automatically via Power Fortran Accelerator

– Message Passing Approach:• MPI (message library calls from Fortran/C/C++)

October 2003

SGI Origin 2800 (Sweetgum) Applications• GAMESS, Gaussian 94/98/03, UNICHEM

• IMSL

• MATLAB

• ABAQUS & PATRAN

• NCAR Graphics

• Xgnuplot

• PETSc

October 2003

Mimosa Hardware• 219 Intel single-processor nodes

– 1 Master + 212 Compute + 6 I/O = 219 nodes

– P4’s and P3’s with 500MB – 1GB memory each

– Dell, Compaq, Gateway, and CSI desktop systems

• 4 rows of cabinets

• Upgrading from 100Mbps to Gigabit Ethernet• http://www.mcsr.olemiss.edu/computing/diagrams/mimosa.htm

October 2003

Mimosa Programming Environment• RedHat Linux 8.0• PGI CDK w/Fortran, C/C++ compilers• PBS Pro• Optimization via Parallelization

– Fortran, C, C++ via compiler directives– Automatically via Power Fortran Accelerator– MPI - PGI MPI 4.1 and MPICH 1.2.4

• Math/Scientific Computing Libraries• LAPACK, BLAS, ARPACK

October 2003

Mimosa Applications• Guassian 98

• GAMESS

• NWChem

• PETSc

October 2003

Onyx Hardware• 8 R10000 195 MHz Processors• 2GB Memory• Infinite Reality Graphics Engine

supporting Sirius Video

Software

• Irix • MIPSPro Fortran, C/C++• OpenGL, GLUT

October 2003

MCSR Software/Applications

• Finite Element Analysis: Abaqus, Patran, Dyna-3D

• Chemistry: Gaussian, UniChem, NWChem

• Math: IMSL, Matlab

• Compilers: FORTRAN, C/C++, , HPF

• Parallel Programming: MPI (MPICH, LAM), Batch Jobs Systems: NQS, PBS

• Communications: Secure Shell, Xwin-32

October 2003

UM Research Server

• willow.olemiss.edu

• Sun 420R w/4 450 MHz CPU’s, 4096 MB, Solaris 7

• Generally, a UM resource (all students & faculty)– Exceptions granted to IHLs based on need and availability

• Computational Research, Instruction, Self-paced learning

• Math/Statistics: SAS, SPSS, Limdep, Lisrel, IMSL

• Programming: FORTRAN 77/90, C/C++ , Java, MySQL

• http://www.mcsr.olemiss.edu/computing/willow.html

October 2003

MCSR Services

• 3 Supercompting User Consultants; 1 Stats Consultant• Support: Email/Phone/Walk-in/On-site/Web (FAQs, Articles) • Unix/Linux Questions (Unix Help for Users)• Account and connectivity troubleshooting • Negotiating MCSR job queues; Optimization; Parallelization• Seminars/Tours (Unix/Linux, Parallel Programming, Clustering) • Linux clustering consulting• Mailing list management• Unix/Linux SysAdmin Troubleshooting

(Irix, Solaris)

October 2003

Who Uses MCSR Systems?

Faculty Research Accounts

UM

JSU

MSU

USM

DSU

We currently support over 722 research accounts on all MCSR systems and over 750 individual and class accounts. During our history, we have supported over 500 research projects.

October 2003

What kinds of research?FY 2003 saw over $35 million in active grants for MCSR researchers, covering research projects including:

• Assembling novel materials from molecular clusters• Silicon Stabilization of Alpha/beta silanes. • Automobile Crash Test Modeling• Seismic Vulnerability Modeling• Antennae Design• Routing/Scheduling Optimization• many others….

October 2003

MCSR Accounts

• MCSR accounts for students/faculty of 8 MS public Universities• UM Research Server accounts for UM students/faculty only• Non-Research Account Categories

• General/Instructional (open-ended for learning use)• Class (sets of class accounts for one semester only)

• Applying for an Individual Account• Individual Computer Account Request Form • IT Helpdesk (117 Powers Hall)• Copy of University ID• Signed Copy of UM Appropriate Use Policy

October 2003

MCSR Accounts (cont.)

• Research Accounts for MCSR servers only• Research Accounts have more privileged system use

• /ptmp directories• increased job priorities

• Research Categories• Thesis/Dissertation• Research (Open-ended Research without Funding)• Pending Funded Research (research w/pending grants)• Funded Research (one or more current grants)

• Apply for Research Accounts using Online Acct. Manager• https://secure.olemiss.edu/resdb/

October 2003

Communicating with MCSR

Browse www.mcsr.olemiss.eduEmail assist@mcsr.olemiss.eduCall (662) 915-7206; ask for a supercomputer consultantWalk in to 1st floor, Powers HallSchedule or attend Workshops/SeminarsRead MCSR News Flashes

www.mcsr.olemiss.edu/newsflashEmailed to research accounts (mcsr-users mailing list)news | pg

MCSR E-NewsletterMCSR Account Manager (accounts, grants, email addresses)

October 2003

Supported Research Funds

$0

$5,000,000

$10,000,000

$15,000,000

$20,000,000

$25,000,000

$30,000,000

$35,000,000

$40,000,000

FY1999

FY2000

FY2001

FY2002

FY2003

SupportedResearch Funds

Reported research funds were $35,480,858 in FY2003, up 242% since FY1999

October 2003

Fiscal Year Budget

$0

$500,000

$1,000,000

$1,500,000

$2,000,000

$2,500,000

FY1999

FY2000

FY2001

FY2002

FY2003

Fiscal Year Budget

MCSR FY2003 budget: $1,213,234 in FY2003, down from $1,913,110 in FY1999

October 2003

Number of Research Accounts

0

100

200

300

400

500

600

700

800

FY1999 FY2000 FY2001 FY2002 FY2003

Number of ResearchAccounts

MCSR supported a total of 722 research accounts across all systems in FY2003

October 2003

Central Processor Hours Generated, SGI Origin

0

100,000

200,000

300,000

400,000

500,000

600,000

FY1999

FY2000

FY2001

FY2002

FY2003

Central Processor HoursGenerated, SGI Origin

537,762 CPU hours were generated on the SGI Origin Supercomputer for MCSR researchers in FY2003

October 2003

System Billings Units, Cray supercomputer

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

3,000,000

3,500,000

4,000,000

FY1999 FY2000 FY2001 FY2002 FY2003

System Billings Units,Cray supercomputer

2,932,619 System Billing Units

were generated for the Cray

supercomputer in FY2003

October 2003

Return of Investment ($Research/$MCSR Budget)

$0.00

$5.00

$10.00

$15.00

$20.00

$25.00

$30.00

$35.00

FY1999 FY2000 FY2001 FY2002 FY2003

Return of Investment($Research/$MCSRBudget)

There were over $29 in active research grants for every $1 spent on MCSR in FY2003

October 2003

Examples of Research Projects at the Mississippi Center for Supercomputing Research

October 2003

The Hearin Center for Enterprise Science

Travelling Salesman Problem

Group Technology Problem

Telecommunication Network Allocation

October 2003

LIDAR Digital Terrain ModelLIDAR Digital Terrain Model

LIDAR Terrain surface with CL profile LIDAR data point and CL profile

October 2003

Velocity Components for LSCC

October 2003

NCOM ¼ → NRLPOM 7km → NRLPOM 1.5km→ NRLPOM 0.5kmNOGAPS DAMPS_27 DAMPS_9 DAMPS_9 +tide

An example of coupling nesting procedure in Oceanographic Modeling

October 2003

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Important features of ARPACK with respect to this QM calculation include: •Ability to return a select number of eigenvalues (k) where k is much, much smaller than the order of the matrix, n.•Small, fixed storage requirement.•Only the action of the matrix on a vector is needed

ARPACK Linear Algerbra Libraries