CCS Overview
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Transcript of CCS Overview
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CCS Overview
Rene Salmon
Center for
Computational Science
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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
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Software Visualization• Techplot, AVS
Compilers• SGI, Absoft
Math Libraries• IMSL, BLAS
Finite Element Modeling• ABAQUS, PATRAN
Molecular Dynamics• NAMD, Gaussian, Amber, VMD
Matlab, Mathematica
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High Performance Computing
Interconnect
Shared Memory Distributed Memory
SGI Linux Cluster
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Shared Memory Distributed Memory
Multiprocessor Machines
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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
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Multiprocessor Machines• Single OS• Easier to program• OpenMP
• Inter-processcommunication
Multiple OS Harder to Program• MPI
Inter-processcommunication
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Multiprocessor Machines High cost
• Complex Hardware• Support contract
Proprietary software • Irix• Compilers
Low cost• Commodity parts• Community driven support
Open source software• Linux• Compilers
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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
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Process Threads Share a single
address space Access one another's
variables
Time & memory Interprocess
communication
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OpenMP
program foobar
….
!$omp parallel do
do i=1, n
z(i)=a*x(i)+b
enddo
end program foobar
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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
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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
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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
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Grid Computing Login to Server Compile Move or prepare data Create and submit Job script to queue Monitor status Get results Move data Visualization
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Grid Computing
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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
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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
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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
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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
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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
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Accessing Resources
Go to website: http://www.ccs.tulane.edu Resource request form Access local CCS and national Grid
resources
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