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 [email protected] (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
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