October 2003

• 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

SGI Origin 2800
– 128 CPUs
– 64 GB Memory
– 1.6 Terabytes of Disk
SGI Origin 200
– 1 Processor
– 256 MB Memory
Current Systems
Cray C916
– 10 Processors
– 1 Gigaword Memory
– 512 megaword solid-state storage device (SSD)
– 460 Gigabytes of Disk
Space
SGI Onyx 10000
– 8 Processors
– Infinite Reality Graphics
October 2003
Linux Beowulf
– 219 Node Cluster of
Compaq, Dell, Gateway,
& CSI Intel Processors

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)
+ 2 nd 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

Applications
• Guassian 98
• GAMESS
• NWChem
• PETSc
Mimosa
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

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.

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.edu
Email assist@mcsr.olemiss.edu
Call (662) 915-7206; ask for a supercomputer consultant
Walk in to 1 st floor, Powers Hall
Schedule or attend Workshops/Seminars
Read MCSR News Flashes www.mcsr.olemiss.edu/newsflash
Emailed to research accounts (mcsr-users mailing list) news | pg
MCSR E-Newsletter
MCSR Account Manager (accounts, grants, email addresses)
October 2003

October 2003
Supported Research Funds
$40,000,000
$35,000,000
$30,000,000
$25,000,000
$20,000,000
$15,000,000
$10,000,000
$5,000,000
$0
FY
19
99
FY
20
00
FY
20
01
FY
20
02
FY
20
03
Supported
Research Funds
Reported research funds were $35,480,858 in FY2003, up 242% since FY1999

October 2003
Fiscal Year Budget
$2,500,000
$2,000,000
$1,500,000
$1,000,000
$500,000
$0
FY
19
99
FY
20
00
FY
20
01
FY
20
02
FY
20
03
Fiscal Year Budget
MCSR FY2003 budget: $1,213,234 in FY2003, down from $1,913,110 in FY1999

October 2003
Number of Research Accounts
800
700
600
500
400
300
200
100
0
FY1999 FY2000 FY2001 FY2002 FY2003
Number of Research
Accounts
MCSR supported a total of 722 research accounts across all systems in FY2003

October 2003
Central Processor Hours Generated, SGI Origin
600,000
500,000
400,000
300,000
200,000
100,000
0
FY
19
99
FY
20
00
FY
20
01
FY
20
02
FY
20
03
Central Processor Hours
Generated, SGI Origin
537,762 CPU hours were generated on the SGI Origin Supercomputer for MCSR researchers in FY2003

System Billings Units, Cray supercomputer
4,000,000
3,500,000
3,000,000
2,500,000
2,000,000
1,500,000
1,000,000
500,000
0
FY1999 FY2000 FY2001 FY2002 FY2003
October 2003
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)
$35.00
$30.00
$25.00
$20.00
$15.00
$10.00
$5.00
$0.00
FY1999 FY2000 FY2001 FY2002 FY2003
Return of Investment
($Research/$MCSR
Budget)
There were over $29 in active research grants for every $1 spent on MCSR in FY2003

Tonight’s Presentations:
Mr. David Roach
Director, Mississippi Center for Supercomputing Research
University, Mississippi
Mr. Eigoro Hashimoto
Senior Research Scientist
Naval Oceanographic Office (NAVOCEANO)/Lockheed Martin Space Operations
Major Shared Resource Center (MSRC)
October 2003
Stennis Space Center, MS

October 2003

• 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

SGI Origin 2800
– 128 CPUs
– 64 GB Memory
– 1.6 Terabytes of Disk
SGI Origin 200
– 1 Processor
– 256 MB Memory
Current Systems
Cray C916
– 10 Processors
– 1 Gigaword Memory
– 512 megaword solid-state storage device (SSD)
– 460 Gigabytes of Disk
Space
SGI Onyx 10000
– 8 Processors
– Infinite Reality Graphics
October 2003
Linux Beowulf
– 219 Node Cluster of
Compaq, Dell, Gateway,
& CSI Intel Processors

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)
+ 2 nd 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

Applications
• Guassian 98
• GAMESS
• NWChem
• PETSc
Mimosa
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

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.

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.edu
Email assist@mcsr.olemiss.edu
Call (662) 915-7206; ask for a supercomputer consultant
Walk in to 1 st floor, Powers Hall
Schedule or attend Workshops/Seminars
Read MCSR News Flashes www.mcsr.olemiss.edu/newsflash
Emailed to research accounts (mcsr-users mailing list) news | pg
MCSR E-Newsletter
MCSR Account Manager (accounts, grants, email addresses)
October 2003

October 2003
Supported Research Funds
$40,000,000
$35,000,000
$30,000,000
$25,000,000
$20,000,000
$15,000,000
$10,000,000
$5,000,000
$0
FY
19
99
FY
20
00
FY
20
01
FY
20
02
FY
20
03
Supported
Research Funds
Reported research funds were $35,480,858 in FY2003, up 242% since FY1999

October 2003
Fiscal Year Budget
$2,500,000
$2,000,000
$1,500,000
$1,000,000
$500,000
$0
FY
19
99
FY
20
00
FY
20
01
FY
20
02
FY
20
03
Fiscal Year Budget
MCSR FY2003 budget: $1,213,234 in FY2003, down from $1,913,110 in FY1999

October 2003
Number of Research Accounts
800
700
600
500
400
300
200
100
0
FY1999 FY2000 FY2001 FY2002 FY2003
Number of Research
Accounts
MCSR supported a total of 722 research accounts across all systems in FY2003

October 2003
Central Processor Hours Generated, SGI Origin
600,000
500,000
400,000
300,000
200,000
100,000
0
FY
19
99
FY
20
00
FY
20
01
FY
20
02
FY
20
03
Central Processor Hours
Generated, SGI Origin
537,762 CPU hours were generated on the SGI Origin Supercomputer for MCSR researchers in FY2003

System Billings Units, Cray supercomputer
4,000,000
3,500,000
3,000,000
2,500,000
2,000,000
1,500,000
1,000,000
500,000
0
FY1999 FY2000 FY2001 FY2002 FY2003
October 2003
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)
$35.00
$30.00
$25.00
$20.00
$15.00
$10.00
$5.00
$0.00
FY1999 FY2000 FY2001 FY2002 FY2003
Return of Investment
($Research/$MCSR
Budget)
There were over $29 in active research grants for every $1 spent on MCSR in FY2003

October 2003

The Hearin Center for Enterprise Science
Group Technology Problem
Travelling Salesman Problem
October 2003
Telecommunication Network Allocation

LIDAR Digital Terrain Model
LIDAR data point and CL profile LIDAR Terrain surface with CL profile
October 2003

Velocity Components for LSCC
October 2003

An example of coupling nesting procedure in Oceanographic Modeling
NCOM ¼ → NRLPOM 7km → NRLPOM 1.5km→ NRLPOM 0.5km
NOGAPS DAMPS_27 DAMPS_9 DAMPS_9 +tide
October 2003

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

JM

 j

V

 j
JM

,


2 J
1

1 



2 j
 
1
2


2 j
2 



1
1


2  
1



 1 / 2
 m n

 p
0 c n

2 n

1
1

/ 2 n 100 

0
K


 J

J
 jK 0 JK 
 j

K 0 JK n  0 K 

K
October 2003