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What is MCSR?

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?

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What is MCSR?

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  1. 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?

  2. 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

  3. 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

  4. 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

  5. Who Uses More MCSR Computing Time?

  6. 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

  7. Research vs. Class Accounts?

  8. Who Uses Research Accounts?

  9. Who Uses Instructional Accounts?

  10. What Types of Courses Use MCSR? Over 82 University Courses Supported since 2000 C/C++, Fortran, MPI, OpenMP, MySQL, HTML,Javascript, Matlab, PHP, Perl, …. http://www.mcsr.olemiss.edu/education.php

  11. 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.

  12. 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

  13. 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

  14. 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.

  15. How Much Does MCSR Cost Mississippi?

  16. 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

  17. 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

  18. What Supercomputers @ MCSR?

  19. Supercomputers at MCSR: sweetgum - SGI Origin 2800 128-CPU Supercomputer - 64 GB of shared memory

  20. Supercomputers at MCSR: redwood - 224 CPU SGI Altix 3700 Supercomputer- 224 GB of shared memory

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

  22. Supercomputers at MCSR: mimosa

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

  24. Supercomputers at MCSR: sequoia

  25. 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

  26. Speed-Up • http://www.mcsr.olemiss.edu/Engr692_TimingWorshkeet.xls

  27. 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

  28. 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)

  29. 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)

  30. 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 ncpus=8 #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)

  31. Parallel Efficiency

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