TheThe MU3CMU3C ComputerComputer ClusterCluster ArchitectureArchitecture
MikeMike PoublonPoublon HopeHope CollegeCollege WhatWhat isis aa ComputerComputer Cluster?Cluster?
AA computercomputer clustercluster isis aa groupgroup ofof networkednetworked computerscomputers thatthat workwork togethertogether asas aa singlesingle highhigh performanceperformance computercomputer AA computercomputer clustercluster cancan speedspeed upup computecompute timestimes throughthrough parallelparallel executionexecution ComputerComputer clustersclusters provideprovide aa highhigh levellevel ofof performanceperformance atat aa lowlow costcost whenwhen comparedcompared toto traditionaltraditional supercomputerssupercomputers TheThe MU3CMU3C ComputerComputer ClusterCluster
KVM KVM switches switches
network compute switches nodes (rear)
compute nodes raid arrays keyboard & display head nodes compute nodes UPS (bottom) ComputerComputer ClusterCluster UsesUses
ClustersClusters cancan bebe usedused onon anyany computationalcomputational task,task, butbut performperform theirtheir bestbest whenwhen workingworking onon aa tasktask thatthat cancan bebe brokenbroken downdown intointo smaller,smaller, parallelparallel subtaskssubtasks Examples:Examples: – Molecular Modeling – Weather Prediction – Genetics Research – Physics Simulations – 3D Scene Rendering (Movies like Shrek, Bug’s Life, etc) WhyWhy UseUse aa ComputerComputer Cluster?Cluster?
ComputationsComputations cancan taketake largelarge amountsamounts ofof timetime onon aa singlesingle computercomputer duedue to:to: – High accuracy modeling – Highly dimensional calculations Examples:Examples: – 4 atom high accuracy PES takes 1 month compute time; 5 atoms takes 1 year – 1 nanosecond simulation of QM molecular dynamics takes 10 years ComputerComputer ClusterCluster AdvantagesAdvantages
ClusterCluster computers:computers: –– areare affordableaffordable whenwhen comparedcompared toto theirtheir supercomputersupercomputer cousinscousins –– runrun standardstandard softwaresoftware (Linux)(Linux) –– cancan bebe expandedexpanded overover timetime –– areare faultfault toleranttolerant inin manymany casescases MU3CMU3C ComputerComputer ClusterCluster LayoutLayout
Local Network or Internet Head Node Hope College Command Data Network Storage Node Network
Carleton Compute Node Gustavus- Macalester Adolphus
Jobs issued by the Parallel Node File sharing traffic head node (PBS) Communication (MPI) (NFS) MU3CMU3C HardwareHardware
HeadHead NodeNode StorageStorage NodeNode ComputeCompute NodeNode 22 xx 2.62.6 GHzGHz 22 xx 2.62.6 GHzGHz 22 xx 2.62.6 GHzGHz OpteronOpteron OpteronOpteron OpteronOpteron processorsprocessors processorsprocessors processorsprocessors 88 GBGB ramram 88 GBGB ramram 88 GBGB ramram 22 xx 250GB250GB 22 xx 250GB250GB 250GB250GB hardhard hardhard drivedrive hardhard drivedrive drivedrive (raid(raid 1)1) (raid(raid 1)1) 22 xx 55 TBTB raidraid arrayarray MU3CMU3C HardwareHardware TotalsTotals
112112 2.62.6 GHzGHz ProcessorsProcessors 448448 GBGB ramram 1414 TBTB ofof distributeddistributed (on(on node)node) storagestorage 1010 TBTB ofof centralcentral filefile storagestorage (on(on storagestorage node)node) ServicesServices ProvidedProvided
NTP: (Network Time Protocol) Synchronizes time inside the cluster Samba: Allows Mac and Windows computers to access files across the network WWW: Standard web server gives users easy access to documentation SSH/SCP: Users can log in to the cluster from their desktop computers to submit jobs PBS: Manages job schedules to efficiently use cluster resources MPI: Allows nodes to communicate in a parallel fashion ChemistryChemistry ProgramsPrograms
Aces2Aces2 AmberAmber 88 Gaussian03Gaussian03 GamessGamess (parallel)(parallel) MolproMolpro 20022002 (parallel)(parallel) MopacMopac NWChemNWChem QchemQchem TinkerTinker WhatWhat CanCan TheThe ClusterCluster DoDo ForFor Me?Me?
InitialInitial resultsresults showshow thatthat computationscomputations benefitbenefit greatlygreatly fromfrom parallelismparallelism
Molpro 2002 CCSD(T) Energy Calculation of HFCO (in sec.)
Processors 6-31g cc-pvtz aug-cc-pvtz cc-pvqz aug-cc-pvqz
1 3 250 1637 3590 21017
2 6 138 868 1871 10826
3 8 106 561 1249 7289 4 9 98 462 1003 5318 AggregateAggregate PerformancePerformance
PerformancePerformance measuredmeasured usingusing thethe HighHigh PerformancePerformance LinpackLinpack BenchmarkBenchmark www.Top500.orgwww.Top500.org –– 11st PlacePlace –– 280600280600 GflopsGflops (131072(131072 Processors)Processors) –– 100100th PlacePlace –– 39803980 GflopsGflops (2560(2560 Processors)Processors) –– 500500th PlacePlace -- 1645.71645.7 GflopsGflops (460(460 Processors)Processors) –– MU3CMU3C –– 343.5343.5 GflopsGflops (106(106 Processors)Processors) TopTop 100100 OverOver TheThe YearsYears
DateDate andand MaxMax SuperSuper ComputerComputer GflopsGflops ComputerComputer ClusterCluster 1010 yearsyears agoago 8585 1515 (170.4(170.4 GflopsGflops)) 55 yearsyears agoago 6363 3737 (4938(4938 GflopsGflops)) CurrentCurrent 2828 7272 (280600(280600 GflopsGflops)) SummarySummary
ComputerComputer clustersclusters allowallow computationcomputation ofof moremore complexcomplex problemsproblems ComputerComputer clustersclusters enableenable researchersresearchers toto achieveachieve resultsresults inin muchmuch lessless timetime ComputerComputer clustersclusters allowallow sharingsharing ofof expensiveexpensive resourcesresources amongamong multiplemultiple researchersresearchers AcknowledgmentsAcknowledgments
Dr.Dr. PolikPolik –– ResearchResearch MentorMentor DepartmentDepartment ofof Chemistry,Chemistry, HopeHope CollegeCollege ResearchResearch CorporationCorporation andand HowardHoward HughesHughes MedicalMedical InstituteInstitute NSFNSF