CCS Overview

Rene Salmon

Center for

Computational Science

Introduction What is CCS?• June 2001• Establish new collaborations• Infrastructure to exchange ideas• Interdisciplinary research• Computational science research

High end workstations HPC Hardware and Software

Software Visualization• Techplot, AVS

Compilers• SGI, Absoft

Math Libraries• IMSL, BLAS

Finite Element Modeling• ABAQUS, PATRAN

Molecular Dynamics• NAMD, Gaussian, Amber, VMD

Matlab, Mathematica

High Performance Computing

Interconnect

Shared Memory Distributed Memory

SGI Linux Cluster

Shared Memory Distributed Memory

Multiprocessor Machines

Multiprocessor Machines

SGI 4 compute nodes 32 CPUs

• 700MHZ R16000 MIPS

8 GB RAM Memory bandwidth

• 3.2GB/sec peak

NUMAlink interconnect • 1.6GB/sec each direction

1 TB SGI storage array

Linux Cluster 34 nodes 68 CPUs

• 2.4 GHZ AMD Opteron 68 GB RAM Memory Bandwidth

• 12.8 GB/s Gigabit Ethernet

interconnect • 85MB/sec

1 TB storage array

Multiprocessor Machines• Single OS• Easier to program• OpenMP

• Inter-processcommunication

Multiple OS Harder to Program• MPI

Inter-processcommunication

Multiprocessor Machines High cost

• Complex Hardware• Support contract

Proprietary software • Irix• Compilers

Low cost• Commodity parts• Community driven support

Open source software• Linux• Compilers

Parallel Programming

OpenMP OpenMP(Open

specifications for Multiprocessing)• Library and compiler

directives Shared memory Process synchronization Thread based

MPI MPI(Message Passing

Interface)• Libraries

Distributed memory Process based• Process

synchronization• Master/slave mode

Process Threads Share a single

address space Access one another's

variables

Time & memory Interprocess

communication

OpenMP

program foobar

….

!$omp parallel do

do i=1, n

z(i)=a*x(i)+b

enddo

end program foobar

MPIprogram foobaruse mpi….call MPI_INIT(…)call MPI_COMM_RANK(..,myid,..)call MPI_COMM_SIZE(..,numprocs,..)data_chunk=SIZE_X/numprocsj=1+myid*data_chunkn=j+(data_chunk-1) x_local=x(j:n)do i=1, data_chunk

z_local(i)=a*x_local(i)+benddocall MPI_GATHER(z_local, …,z,…)call MPI_FINALIZE(… end program foobar

Queuing System PBSPro

Resource manager• Schedules/decides when job run• Allocates resources to jobs

Full featured • Supports preemption• Priorities• Supports parallel and single CPU jobs

CCS Queuing System Q1: Lowest priority• Access to all Tulane

community for research purposes only.

Q2: Provide intellectually to the leadership of CCS• Giving (or arrange)

seminars • Serving on CCS

committees

Q3Q3: Financially support : Financially support from individual grantsfrom individual grants• Personnel • Computer/Software

purchases • Computer/Software

maintenance Q4: Highest priority • Faculty and students

with CCS-funded projects

Grid Computing Login to Server Compile Move or prepare data Create and submit Job script to queue Monitor status Get results Move data Visualization

Grid Computing

Grids Nationally National Lambda Rail (NLR)

• Nationwide optical fiber infrastructure

Open Science Grid • DOE and NSF Roadmap • Join U.S. labs and

universities into a single, managed grid

• Goal: Build a national grid infrastructure for benefit of scientific applications

LONI: Louisiana Optical Network Initiative

March of 2004 secured NLR membership• Louisiana Board of Regents, Tulane, LSU • State allocated $40 million to create and

maintain LONI What is LONI?• Statewide optical network• Inter-connect universities and colleges

• Take advantage of NLR access

• 40 Gbps   • 1000 times faster

LONI: Louisiana Optical Network Initiative

LONI Members• Tulane University, Tulane HSC• LSU, LSU Medical Centers in Shreveport and

New Orleans• Louisiana Tech University• University of Louisiana at Lafayette• Southern University• University of New Orleans

LONI: Louisiana Optical Network Initiative

Provide NLR access• High-quality, high-definition videoconferencing• High-speed access to data• Remote visualization• Remote instrumentation• High Performance Computing

Collaborative research projects and grants Attract better research faculty Increased potential of receiving national

and international grant funding

LONI: Louisiana Optical Network Initiative

End of summer 2005 • $500,00.00 High Performance computer• All Connected via LONI

Tulane Pilot Grid• SURA test bed• Experience • Grid Research

Accessing Resources

Go to website: http://www.ccs.tulane.edu Resource request form Access local CCS and national Grid

resources