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MSRC High Performance Computing Outreach Program to Universities in Mississippi

MSRC High Performance Computing Outreach Program to Universities in Mississippi. Tonight’s Presentations: Mr. David Roach Director, Mississippi Center for Supercomputing Research University, Mississippi Mr. Eigoro Hashimoto Senior Research Scientist

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MSRC High Performance Computing Outreach Program to Universities in Mississippi

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  1. MSRC High Performance Computing Outreach Program to Universities in Mississippi 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) Stennis Space Center, MS

  2. The Mississippi Center for Supercomputing Research

  3. 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 Background

  4. 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.

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

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

  7. 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

  8. 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++)

  9. SGI Origin 2800 (Sweetgum) Applications • GAMESS, Gaussian 94/98/03, UNICHEM • IMSL • MATLAB • ABAQUS & PATRAN • NCAR Graphics • Xgnuplot • PETSc

  10. 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

  11. 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

  12. Mimosa Applications • Guassian 98 • GAMESS • NWChem • PETSc

  13. Onyx Hardware • 8 R10000 195 MHz Processors • 2GB Memory • Infinite Reality Graphics Engine supporting Sirius Video Software • Irix • MIPSPro Fortran, C/C++ • OpenGL, GLUT

  14. 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 MCSR Software/Applications

  15. 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 UM Research Server

  16. 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) MCSR Services

  17. Who Uses MCSR Systems? 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.

  18. 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….

  19. 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

  20. 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/

  21. 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 1st 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)

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

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

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

  25. 537,762 CPU hours were generated on the SGI Origin Supercomputer for MCSR researchers in FY2003

  26. 2,932,619 System Billing Unitswere generated for the Cray supercomputer in FY2003

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

  28. Examples of Research Projects at the Mississippi Center for Supercomputing Research

  29. The Hearin Center for Enterprise Science Group Technology Problem Travelling Salesman Problem Telecommunication Network Allocation

  30. LIDAR Digital Terrain Model LIDAR Terrain surface with CL profile LIDAR data point and CL profile

  31. Velocity Components for LSCC

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

  33. ARPACK Linear Algerbra Libraries • 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

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