2. What is MCSR? Who is MCSR? What Does MCSR Do? Who Does MCSR Serve?
What Kinds of Accounts?
Why Does Mississippi Need Supercomputers?
What Kinds of Research?
What Kinds of Instruction?
What Kinds of Workshops?
How Much Does it Cost?
What Kinds of Software?
What Supercomputers and Clusters?

3. What is MCSR? Mississippi Center for Supercomputer Research
Established in 1987 by the Mississippi Legislature
Mission: Enhance Computational Research Climate at Mississippi’s 8 Public Universities
also: Support High Performance Computing (HPC) Education in Mississippi

4. What Does MCSR Do? We make Mississippi scientists:
- more competitive for federal grants
- more productive in research
We provide extraordinary learning opportunities for Mississippi college students
- instructional accounts
- computing workshops
- helpdesk support

5. Who Does MCSR Serve?
MCSR serves faculty, researchers, and students at all of Mississippi’s 8 public universities
Alcorn State University
Jackson State University
Mississippi Sate University
Mississippi Valley State University
The University of Southern Mississippi
Delta State University
The University of Mississippi
Mississippi University for Women

6. Who Uses More MCSR Computing Time?

7. What Types of Computing Access is Available?
Research Accounts
- provided for faculty and student “researchers”
- good for the duration of employment or enrollment
Instructional Accounts
- provided at an instructor’s request
- for all students enrolled in a semester course
- valid for the duration of the semester
- can be “converted” to research account

8. Research vs. Class Accounts?

9. Who Uses Research Accounts?

10. Who Uses Instructional Accounts?

11. What Types of Courses Use MCSR?
Over 82 University Courses Supported since 2000
C/C++, Fortran, MPI, OpenMP, MySQL, HTML, Javascript, Matlab, PHP, Perl, ….

12. Why Do Mississippi Researchers Need Supercomputers?
Economics: researchers in a poor state like Mississippi can still make a big splash.
Computational simulations are faster, cheaper, and safer than laboratory experiments alone.

13. What Kinds of Research @ MCSR?
90% of MCSR calculations are computational chemistry
Cleanup of high explosive materials.
Design of high energy density rocket fuels
The chemical underpinnings of high powered lasers
Mutation studies of enzyme activity
Designing weather-proofing coatings for machinery
Other Areas
Hurricane forecasting
Blast resistant Coatings
Better 3-D imaging for diagnosing brain tumors

14. What Types of Workshops by MCSR?
MCSR consultants taught over 140 free seminars in FY08.
Over 60 training topics available, and growing.
Fixed schedule or on-demand.
Unix/programming, Math Software, Stats Software, Computational Chemistry Software

16. Do Researchers and Students Pay to Use MCSR?
No. MCSR services are provided at no cost to the individual, department, or institution.
Funded researchers may ask for priority access.
Mississippi researchers may claim the value of MCSR computing services received as an in-kind contribution from their institution when seeking federal grants.

17. How Much Does MCSR Cost Mississippi?

18. What Is the Value of MCSR to Mississippi?
RETURN ON INVESTMENT =
GRANTS SUPPORTED / MCSR BUDGET
For FY 2008:
$32,832,097 / $845,535
= $38.30 per dollar spent

19. What Software Environments @ MCSR
Programming
C/C++, FORTRAN, Java, Perl, PHP, MPI…
Science/Engineering
PV-Wave, IMSL, GSL, Math Libraries, Abaqus
Math/Statistics
SAS, SPSS, Matlab, Mathematica
Chemistry
Gaussian, Amber, NWChem, GAMESS, CPMD, MPQC, MolPro, GROMACS

20. What Supercomputers @ MCSR?

21. Supercomputers at MCSR: sweetgum.
- SGI Origin CPU Supercomputer
- 64 GB of shared memory

22. Supercomputers at MCSR: redwood
NSF Expiration Sep 30, 2004; HPVCI Expiration Date Dec 31, 2002.
- 224 CPU SGI Altix 3700 Supercomputer GB of shared memory

23. Supercomputers at MCSR: mimosa
253 CPU Intel Linux Cluster – Pentium 4
Distributed memory – 500MB – 1GB per node
Gigabit Ethernet

24. Supercomputers at MCSR: mimosa

25. Supercomputers at MCSR: sequoia
22 nodes
176 cores
352 GB Memory
20 TB Storage
InfiniBand Interconnect

26. Supercomputers at MCSR: sequoia

27. Introduction to Parallel Programming at MCSR
Message Passing Computing
Processes communicate via calls to message passing library routines
Programmers “parallelize” algorithm and add message calls
At MCSR, this is via MPI programming with C or Fortran
Sweetgum – Origin 2800 Supercomputer (128 CPUs)
Mimosa – Beowulf Cluster with 253 Nodes
Redwood – Altix 3700 Supercomputer (224 CPUs)
Sequoia – Altix XE 310 InfiniBand Cluster (176 cores)
Shared Memory Computing
Threads coordinate/communicate results via shared memory variables
Care must be taken not to modify the wrong memory areas
At MCSR, this is via OpenMP programming with C or Fortran on sweetgum, redwood, or sequoia

28. Speed-Up

29. What MCSR Systems for USM Class Accounts
Sweetgum
MPI or OpenMP
1 to 16 CPUs
Up to 900mb per CPU
PBS scripts preferred
#PBS –l ncpus=4
Interactive computations will be killed after 30 minutes
Queues: SM-4P, SM-8P, MM-8P, MM-16P
Processors: Mix of 195 MHz and 300 MHz
O/S: Irix (like Unix)
Compilers: SGI’s Fortran, C/C++, GNU C/C++, w/ SGI MPT

32. What MCSR Systems for USM Class Accounts
Mimosa
MPI
1 to 18 nodes
400 GB Memory per node
PBS Scripts Only (no interactive jobs allowed)
#PBS –l nodes=4
Queues: MCSR-CA
Processors: single 1.4 GHz P4/node
O/S: SUSE Linux 10.3
Compilers: Portland Group (PGI) Fortran, C/C++ w/mpich
qstat –f (to find out what nodes your job is running on)

35. What MCSR Systems for USM Class Accounts
Sequoia
OpenMP (multiple processors on the same node)
MPI (multiple processors on the same or different nodes)
Hybrid (OpenMP within node, MPI across nodes)
1 to 4 nodes, 1 to 8 CPUs per node
PBS Queues: SM-4P (for up to 4 CPUs on 1 node)
MCSR-Test (up to 8 CPUs on each of 4 nodes)
PBS Scripts Only (no interactive jobs allowed)
#PBS –l nodes=4:ppn=8 (to run on all 8 CPUs of all 4 nodes)
#PBS –l ncpus=8:select=
16 GB Memory per node (2 GB per CPU)
qstat –f (to find out what nodes your job is running on)

38. Sequoia for USM Class Accounts
To run on 4 nodes, and 8 processors per node (32 processes)
#PBS –l nodes=4:ppn=8
To run on 2 nodes, and 4 processors per node (8 processes)
#PBS –l nodes=2:ppn=4
To run on 1 node, and up to 8 processors (OpenMP)
#PBS –l nodes=1:ppn=8
To run on 8 processors, regardless of number of nodes
#PBS –l ncpus=8
To run 8 processors, with preferences about node placement
#PBS –l place=scatter (distribute across as many nodes as can)
#PBS –l place=pack (pack processes onto as few nodes as can)
#PBS –l place=free (place processes on first available processors)

39. Parallel Efficiency
NSF Expiration Sep 30, 2004; HPVCI Expiration Date Dec 31, 2002.