CD-EXCALIBUR-FMS0023-M3.3.2_ReportDesignPatternsSpecificationsPrototypes
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   :description: technical note

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ExCALIBUR,Report,on,design,patterns,specifications,and,prototypes,M3.3.2,Abstract,The,report,describes,work,for,ExCALIBUR,project,NEPTUNE,at,Milestone,3.3.2.,Report,on,design,patterns,and,prototypes,specifications,for,tokamak,edge,simulation.,UKAEA,REFERENCE,AND,APPROVAL,SHEET,Client,Reference:,UKAEA,Reference:,CD/EXCALIBUR-FMS/0023,Issue:,Date:,1.00,12,August,2020,Project,Name:,ExCALIBUR,Fusion,Modelling,System,Prepared,By:,Name,and,Department,Wayne,Arter,Ed,Threlfall,Joseph,Parker,Stan,Pamela,Signature,N/A,N/A,N/A,N/A,Date,12,August,2020,12,August,2020,12,August,2020,12,August,2020,BD,Reviewed,By:,Rob,Akers,16,August,2020,Advanced,Dept.,Manager,Computing,2,1,Introduction,This,report,has,two,aims,as,prefigured,in,the,report,[1].,The,central,Section,2,mainly,focusses,on,design,patterns,to,be,used,in,NEPTUNE,,but,also,pursues,the,prototyping,process.,It,begins,in,Section,2.1,by,outlining,in,some,detail,the,design,patterns,that,historically,have,proven,useful,in,large,software,engineering,projects,,starting,with,general,software,design,before,specialising,in,Section,2.2,to,scientific,programming,and,multiscale,physics,simulation.,In,Section,2.3,,considera-,tion,is,given,to,the,past,and,current,contexts,of,software,development,processes:,it,is,worth,noting,that,,today,,the,HPC,landscape,is,in,something,of,a,state,of,flux,with,the,rise,of,heterogeneous,architectures,and,the,corresponding,coding,tools.,There,is,a,final,summary,Section,3.,The,original,design,pattern,concept,is,credited,by,Sommerville,([2],,p.209),to,architect,and,design,theorist,Christopher,Alexander,,who,in,his,1977,book,A,Pattern,Language:,Towns,,Buildings,,Construction,[3],presented,a,compendium,of,‘certain,common,patterns,of,building,design,that,are,inherently,pleasing,and,effective’.,His,text,outlines,some,253,such,patterns,,described,collectively,as,a,‘design,lexicon’,or,even,an,entirely,new,tongue:,to,quote,Alexander,himself,‘All,253,patterns,together,form,a,language.’.,A,similar,approach,was,applied,to,object-oriented,software,architecture,in,the,‘90s,,resulting,in,the,publication,of,Design,Patterns:,Elements,of,Reuseable,Object-Oriented,Software,[4],,the,au-,thors,of,which,have,become,known,as,the,Gang,of,Four,(Go4,,also,abbreviated,GoF).,This,book,proposed,23,design,patterns,that,are,classified,according,to,a,trinity,of,themes:,creational,pat-,terns,,concerning,object,generation;,structural,patterns,,to,do,with,classes,and,composition,,and,behavioural,patterns,,dealing,with,interactions,between,objects.,These,will,be,discussed,with,a,view,of,how,germane,each,is,to,project,NEPTUNE,(it,is,also,relevant,that,,during,the,time,since,the,publication,of,[4],,some,of,the,original,patterns,have,been,elevated,to,the,status,of,permanent,language,features,in,some,object-oriented,languages).,Note,that,there,is,now,a,fourth,class,of,design,patterns,(as,exhibited,in,the,Wikipedia,article,[5]),concerning,concurrency,patterns.,Aside,from,these,general,concerns,,there,also,exist,patterns,which,apply,specifically,to,scientific,software.,As,detailed,in,Section,2.2.1,,the,textbook,by,Rouson,,Xia,and,Xu,[6],develops,most,of,a,framework,explicitly,targeted,to,multiphysics,workflows,for,Exascale,HPC,,starting,from,a,founda-,tion,of,object-oriented,principles.,Their,text,presents,a,viewpoint,on,the,most,useful,Go4,design,patterns,in,the,context,of,scientific,programming,and,also,offers,some,novel,patterns,tailored,specifically,to,this,field.,Consideration,is,given,in,Section,2.2.2,to,the,ComPat,project,[7],,which,,being,a,framework,and,software,suite,to,study,multiscale,fusion,plasmas,on,HPC,systems,,constitutes,a,further,speciali-,sation,in,the,direction,of,project,NEPTUNE.,Design,patterns,here,are,used,to,provide,separation,of,concerns,,with,the,full,physics,being,represented,by,an,interchangeable,set,of,submodels,in,a,coupling,framework.,Attention,is,given,to,the,preservation,of,good,scaling,to,Exascale,HPC,in,such,a,framework.,Section,2.2.3,gives,more,details,of,the,Verified,Exascale,Computing,for,Mul-,tiscale,Applications,(VECMA),project,[8],which,essentially,represents,a,continuation,of,ComPat,,using,updated,versions,of,the,same,components,eg.,the,multiscale,coupling,framework,MUSCLE.,The,associated,VECMA,toolkit,[9],provides,a,platform,for,VVUQ.,Although,not,a,pattern,in,the,strict,sense,,this,suite,is,of,interest,as,it,employs,several,more,fundamental,patterns,(for,example,the,Go4,Adapter),in,a,framework,which,includes,the,management,of,a,set,of,interrelated,jobs,on,3,either,a,cluster,or,an,HPC,machine,,and,the,provision,of,graphical,and,Python,interfaces.,In,software,engineering,,prototyping,is,normally,described,as,a,quick,way,to,produce,something,that,potential,customers,can,explore,,primarily,with,a,view,to,improving,the,user-interface.,Only,Booch,[10,,§,8.1],admits,that,it,may,help,the,developer,understand,the,technical,aspects,of,the,problem,better,,and,this,work,predates,design,patterns.,As,indicated,in,the,previous,report,[11],,little,formal,description,has,been,found,of,the,role,of,prototyping,in,scientific,computing.,However,the,highlighted,‘idea’,paper,of,Dubey,and,McInnes,[12],does,include,both,these,applications,and,is,further,discussed,in,Section,2.3.1.,4,2,Task,Work,2.1,General,design,patterns,2.1.1,Gang,of,Four,The,design,patterns,introduced,by,the,Gang,of,Four,will,be,described,briefly,,bearing,in,mind,their,likely,relevance,to,project,NEPTUNE.,It,is,notable,that,,in,the,light,of,the,decades,of,software,engineering,practice,that,have,followed,the,publication,of,[4],,developments,in,object-oriented,languages,themselves,have,incorporated,some,of,the,patterns,directly.,Note,that,the,Wikipedia,articles,on,these,patterns,are,largely,of,good,quality,and,provide,also,UML,representations,and,(polyglot),code,examples.,Note,additionally,that,the,Wikipedia,article,on,Software,design,pattern,[5],contains,patterns,in,addition,to,those,in,the,Go4,text,,particularly,a,fourth,category,,concerning,concurrency,patterns,,which,would,seem,quintessential,to,our,case.,Creational,Design,Patterns,These,are,associated,with,object,creation.,Abstract,factory,-,this,provides,an,interface,for,creating,families,of,related,objects,without,specify-,ing,their,concrete,class.,Derived,factory,classes,create,,for,example,,documents,with,a,style,(fonts,etc.),common,to,the,concrete,factory,,the,documents,being,represented,by,derived,types,eg.,fan-,cyLetter,,businessLetter,,...,,,businessReport.,The,client,only,knows,about,the,abstract,document,types,(letter,,report,...),and,the,abstract,factory,,the,concrete,choice,of,which,determines,the,style,of,documents,received,by,the,client.,Builder,-,this,separates,the,construction,of,a,complex,object,from,the,representation,of,that,object.,Instead,of,having,classes,call,the,object’s,constructor,,they,call,a,separate,Builder,method,that,constructs,the,objects.,Altering,this,Builder,means,the,object,can,be,constructed,differently,without,having,to,change,the,object;,also,,selecting,a,different,Builder,means,that,the,type,of,object,created,can,be,changed.,Factory,method,-,this,decouples,the,construction,of,objects,from,the,objects,themselves,,allowing,the,creation,of,objects,whose,concrete,type,is,not,determined,at,compile,time.,Prototype,-,this,creates,objects,by,cloning,an,existing,object.,The,point,is,that,a,Clone(),method,may,be,called,on,an,object,of,unspecified,concrete,type,-,this,is,similar,to,the,aim,of,the,Factory,method,above.,Singleton,-,this,restricts,a,class,to,having,a,solitary,instance,(or,none,at,all).,Constructors,are,hidden,by,making,them,private,and,the,sole,instance,is,accessed,via,a,GetInstance(),method,,which,provides,global,access,and,can,be,used,to,provide,lazy,initialization,-,creating,the,singleton,only,when,it,is,required.,5,Figure,1:,Class,diagram,for,the,(object),Adapter,pattern,(there,is,also,a,very,similar,class,Adapter,version).,Figure,2:,Class,diagram,for,the,Composite,pattern.,Structural,Design,Patterns,These,are,to,do,with,composition,,inheritance,etc.;,some,of,them,seem,very,straightforward.,Oth-,ers,appear,directly,relevant,for,NEPTUNE,:,these,examples,are,presented,first,and,are,illustrated,with,the,appropriate,UML,diagram,(all,of,which,were,created,using,the,free,graphing,software,yEd,[13]).,Adapter,-,sometimes,known,as,a,wrapper,,an,Adapter,is,simply,an,object,that,translates,between,otherwise-incompatible,interfaces,,thus,allowing,objects,to,co-operate,without,changes,to,their,in-,terfaces.,Arguably,one,goal,of,good,interface,design,is,to,avoid,the,need,for,this,pattern;,however,,and,with,no,pejorative,intended,,since,pre-written,third-party,code,may,be,used,in,NEPTUNE,It,is,also,of,note,that,modern-day,unified,APIs,for,,,it,may,well,be,necessary,to,use,Adapters.,heterogeneous,computing,are,,fundamentally,,implementations,of,this,pattern,(eg.,a,SYCL,plug-in,acts,basically,as,an,Adapter,for,CUDA,in,order,to,harness,NVidia,GPUs).,Composite,-,this,means,the,provision,of,a,unified,interface,for,part,and,whole;,eg.,resizing,a,collection,of,shapes,is,simply,resizing,each,shape.,Branches,forward,request,to,leaves,(shapes,in,this,case);,another,example,is,printing,a,collection,of,graphics,objects,(which,boils,down,to,printing,each,object).,This,is,certainly,relevant,to,a,graph-based,approach,and,indeed,it,is,used,in,the,Arcos,framework.,6,Figure,3:,Class,diagram,for,the,Facade,pattern.,Figure,4:,Class,diagram,for,the,Proxy,pattern.,Facade,-,this,means,the,provision,of,a,simplified,API,that,delegates,to,interfaces,of,subsystems;,it,can,thus,be,used,to,provide,a,greater,or,lesser,degree,of,automation,and,it,also,means,that,all,controls,of,a,set,of,related,subsystems,are,located,conveniently,in,one,place,(perhaps,a,reason-,able,analogy,is,having,all,the,controls,needed,to,drive,a,car,in,front,of,the,driver).,This,paradigm,seems,central,to,making,software,easy,to,use,and,understand,and,thus,seems,to,be,of,great,import.,Proxy,-,this,means,a,class,functioning,as,a,stand-in,for,something,else,and,sharing,the,same,interface.,Clients,cannot,necessarily,distinguish,between,the,object,and,its,proxy,,but,the,latter,could,provide,,for,example,,additional,checking,for,reasonableness,of,inputs,,or,security,checking,,or,implement,load-on-demand,of,data.,The,idea,of,loading,large,data,objects,only,when,explicitly,required,is,of,great,utility,,particularly,in,a,parallel,computing,scenario.,The,remaining,structural,patterns,were,judged,to,be,of,lesser,interest,for,project,NEPTUNE,.,Bridge,-,this,decouples,abstraction,from,interface;,the,bridge,object,associates,an,abstraction,(=in-,terface),with,its,implementation,at,run-time.,This,seems,very,similar,to,virtual,functions,(run-time,polymorphism).,It,seems,that,the,goal,of,this,pattern,can,be,accomplished,with,virtual,methods.,7,Figure,5:,Class,diagram,for,the,Command,pattern.,Decorator,-,this,means,adding,functionality,to,a,particular,object,without,affecting,the,behaviour,of,other,objects,of,same,class.,The,Decorator,object,just,wraps,the,class,and,either,overrides,or,forwards,requests.,The,constructor,of,the,Decorator,has,a,reference,to,the,decorated,object,as,its,argument.,This,seems,a,rather,ad,hoc,way,to,add,functionality,ex,post,facto.,Flyweight,-,this,seems,to,mean,the,sharing,of,data,between,similar,objects,to,save,memory,,eg.,not,storing,all,the,letters,in,a,document,but,rather,storing,each,letter,once,(ie.,an,alphabet!),and,then,the,document,is,represented,by,a,collection,of,references,to,these.,It,is,clearly,useful,when,objects,occur,in,large,numbers,(again,,letters,in,a,document).,The,jargon,is,that,intrinsic,data,(eg.,the,glyph,for,each,letter),can,be,shared;,extrinsic,data,cannot.,Note,that,,perhaps,counter-,intuitively,,Flyweight,objects,are,generally,big,(‘bulky,data’);,they,are,addressed,by,references,that,store,only,the,extrinsic,data,(in,the,document,example,,this,would,be,the,positions,of,the,letters).,The,reasoning,behind,the,name,seems,to,be,that,the,amount,of,data,stored,would,be,much,larger,or,heavier,if,the,object,was,fully,described,at,each,occurrence.,Thus,in,the,example,of,letters,in,a,document,,if,each,were,stored,with,its,case,,font,type,and,size,,this,would,use,up,far,more,store,than,stating,the,font,at,the,beginning.,Behavioural,Design,Patterns,Three,of,these,patterns,were,judged,to,be,of,somewhat,greater,interest:,Command,-,this,means,having,an,encapsulated,Command,object,(constituted,by,all,the,informa-,tion,needed,to,perform,an,action).,This,can,be,used,in,scripting,,macro,recording,,multi-level,undo,,parallel,processing,,thread,pools,...,this,is,,potentially,,a,key,part,of,overall,program,coordination.,Observer,-,the,subject,(an,object),maintains,a,list,of,dependants,and,notifies,them,automatically,of,any,state,changes.,It,enables,commands,to,be,broadcast,to,all,relevant,parties,(one,might,draw,the,analogy,of,hormones,in,animal,bodies,,or,pheromones,in,eusocial,insect,colonies).,This,would,appear,to,be,a,powerful,tool,for,program,coordination.,Also,,it,is,very,useful,in,GUIs,for,making,sure,all,aspects,of,the,interface,are,updated,to,reflect,changes,in,user,inputs,or,data.,Strategy,-,also,known,as,Policy,,this,pattern,enables,the,selection,of,an,algorithm,at,run-time,,perhaps,through,the,use,of,a,run-time-assigned,function,pointer.,It,allows,the,algorithm,to,vary,independently,from,the,clients,that,use,it.,This,can,be,very,useful,for,the,dynamical,coupling,of,objects,of,arbitrary,type.,8,Figure,6:,Class,diagram,for,the,Observer,pattern.,Figure,7:,Class,diagram,for,the,Strategy,pattern.,In,the,interest,of,completeness,,the,remaining,behavioural,patterns,follow.,Chain,of,Responsibility,-,in,this,pattern,,a,command,object,emitted,by,a,source,is,passed,along,a,(possibly,branching),chain,of,potential,processing,objects,,representing,a,dynamical,‘if,...,else,if,...,else,if,...’;,it,seems,to,require,a,nerve-like,chain,to,conduct,the,command.,The,removal,of,close,coupling,appeals,,though,the,Observer,pattern,appears,more,flexible,as,it,removes,the,need,for,the,chain,/,tree,of,command.,Interpreter,-,this,means,basically,providing,a,domain-specific,language,with,its,own,grammar,,rather,than,hard-coding,each,individual,command.,Example:,instead,of,writing,DO,A,WITH,B(),the,grammar,is,Execute(DO,A,WITH,B).,This,is,useful,because,grammar,can,make,the,driver,syntax,much,cleaner.,Iterator,-,this,means,the,ability,to,access,elements,of,an,aggregate,object,without,exposing,the,underlying,representation.,Note,that,one,criticism,of,Go4,is,that,it,listed,features,that,ought,to,have,been,part,of,C++,and,now,it,seems,that,some,of,the,patterns,have,been,incorporated,in,the,language,-,I,believe,the,STL,Iterator,implements,this,pattern.,This,pattern,would,appear,to,be,already,present,in,C++,,in,a,sense;,otherwise,,it,seems,simply,to,mean,that,the,API,of,an,aggregate,object,should,hide,the,implementation,,which,is,something,of,a,given.,Mediator,-,this,is,intended,to,reduce,close,coupling,between,objects,,as,they,communicate,via,the,mediator,,rather,than,directly.,Again,it,is,nice,that,close,coupling,is,reduced,but,this,scheme,does,introduce,the,central,control,object,(mediator),,which,may,not,always,be,desirable.,A,single,mediator,object,may,have,unwanted,consequences,in,a,massively-parallel,environment,(though,9,one,can,imagine,hierarchies,of,mediators).,Memento,-,this,involves,the,provision,of,the,ability,to,restore,an,object,to,a,past,state,(eg.,for,rollback,undo).,It,seems,that,an,object,must,store,a,copy,of,its,past,self,and,some,additional,information,about,how,to,get,from,that,copy,to,the,present,version,(mathematically,,this,seems,like,the,Markov,property).,State,-,means,allowing,an,object,to,alter,its,behaviour,when,its,internal,state,changes.,One,defines,State,objects,(and,derives,special,cases,of,States),,then,classes,delegate,state-specific,behaviour,to,their,State,object.,The,advantages,of,this,pattern,are,presently,unclear;,it,seems,there,are,also,cases,when,one,wants,objects,not,to,have,internal,state,data,at,all,...,Template,method,-,here,,the,skeleton,of,a,method,is,located,in,a,superclass;,the,‘template’,that,is,never,overridden,,this,contains,invariant,parts,of,the,algorithm.,Its,components,are,overridden;,for,example,,one,might,have,a,computer,game,with,invariant,structure,Initialize(),,Startplay(),,Endplay(),,all,of,which,are,overrides.,This,might,be,quite,useful,for,different,physics,solvers;,it,is,obviously,logical,to,have,only,one,copy,of,common,code.,Visitor,-,this,means,adding,new,virtual,functions,to,a,family,of,classes,without,modifying,the,classes,or,defining,a,new,operation,for,a,class,without,changing,the,class:,one,calls,a,Visitor,method,on,an,object,and,the,Visitor,does,something,to,the,object.,It,is,useful,for,performing,an,It,is,operation,on,a,wide,variety,of,classes,without,having,to,put,a,new,method,in,each,class.,obviously,good,‘economics’,to,have,only,one,copy,of,common,code.,2.1.2,Post-Go4,Patterns,The,Wikipedia,page,on,software,design,pattern,[5],outlines,a,further,16,concurrency,patterns,,defining,them,as,‘those,types,of,design,patterns,that,deal,with,the,multi-threaded,programming,paradigm’.,Five,of,these,are,to,be,found,in,the,text,Pattern-Oriented,Software,Architecture,Vol.2:,Patterns,for,Concurrent,and,Networked,Objects,by,Schmidt,,Stal,,Rohnert,and,Buschmann,(an-,other,gang,of,four),[14].,Given,the,lie,of,the,current,high-performance,computing,landscape,,these,would,seem,of,particular,relevance,to,NEPTUNE,and,so,,a,brief,outline,of,each,is,given,here.,Active,object,-,method,execution,is,here,decoupled,from,method,invocation,in,order,to,avoid,race,conditions,on,an,object’s,data,(or,indeed,the,need,to,write,additional,code,to,synchronize,such,Instead,of,object,methods,acting,directly,on,the,object,,the,work,is,delegated,to,a,task,cases).,scheduler:,the,upshot,is,that,only,one,thread,may,ever,modify,the,internal,state,of,an,object.,The,pattern,uses,asynchronous,method,invocation,,itself,a,further,pattern.,Balking,-,this,means,that,an,action,is,performed,on,an,object,solely,if,that,object,is,in,a,particular,state.,There,is,some,debate,as,to,the,validity,of,this,as,a,pattern,and,one,might,argue,that,an,API,should,not,support,requests,that,are,‘invalid’,in,the,sense,of,being,inconsistent,with,the,internal,state,of,the,object.,Regardless,,the,pattern,can,be,used,to,ensure,that,a,worker,object,only,accepts,new,jobs,if,it,is,not,in,a,‘busy’,state,,for,example.,Binding,properties,-,though,the,Wikipedia,article,is,somewhat,unclear,,it,seems,that,this,means,having,multiple,observers,enforce,synchrony,(or,some,other,consistency),of,the,properties,of,some,other,object;,it,would,give,a,way,of,automatically,enforcing,mutual,consistency,of,properties,10,of,different,objects.,Compute,kernel,-,this,is,a,routine,compiled,for,execution,on,an,accelerator,,for,example,a,shader,routine,of,a,GPU,that,is,called,by,the,main,program.,The,kernel,corresponds,roughly,to,the,‘inner,loop’,ie.,the,actual,work.,SIMD,intrinsics,would,seem,an,example,of,this,paradigm,also.,More,succinctly:,the,same,computation,,many,times,in,parallel.,Double-checked,locking,-,this,seems,to,mean,doing,a,check,on,a,lock,using,a,criterion,(known,as,the,‘lock,hint’),before,explicitly,acquiring,the,lock.,Locking,only,proceeds,in,the,lock,hint,indicates,that,locking,is,required.,It,is,a,method,of,reducing,overhead,by,doing,a,quick,(and,possibly,dirty,-,the,Wikipedia,article,cautions,that,the,pattern,can,be,unsafe,on,certain,combinations,of,hardware,/,software,/,language),check,before,proceeding,with,an,operation.,Event-based,asynchronous,-,this,seems,intended,to,address,problems,with,the,asynchronous,method,invocation,(referred,to,above,,in,Active,object),,also,known,as,simply,the,asynchronous,pattern,,which,means,that,a,long-running,method,returns,immediately,a,‘working,...’,response,and,notifies,the,caller,on,later,completion,of,the,work.,One,says,the,caller,is,not,‘blocked’,(that,is,the,meaning,of,asynchronous;,the,Wikipedia,article,[5],does,not,detail,the,precise,meaning,of,event-based,asynchronous).,Guarded,suspension,-,seemingly,an,alternative,to,the,balking,pattern,,this,pattern,prevents,acqui-,sition,of,a,lock,until,a,precondition,is,satisfied,(it,is,a,way,of,making,a,program,wait,before,doing,something,,for,example,waiting,for,an,queue,to,contain,an,object,before,attempting,to,operate,on,an,object,in,the,queue).,Join,-,join-patterns,refer,to,the,high-level,(as,opposes,the,nitty-gritty,of,threads,and,locks),practice,of,making,programs,work,in,parallel,by,message,passing,,enabling,scalability.,The,article,linked,from,[5],contains,much,detail,on,join-calculus.,Lock,-,this,is,a,foundation,of,multi-threaded,programming:,one,thread,puts,a,‘lock’,on,a,resource,,preventing,other,threads,from,accessing,or,modifying,that,until,the,lock,is,released,by,the,subject,thread.,Messaging,design,pattern,(MDP),-,this,describes,how,a,communications,protocol,works,,for,ex-,ample,request-response,(like,HTTP),or,one-way,(like,UDP),,or,request,with,optional,response.,Monitor,object,-,this,seems,to,refer,to,using,mutexes,(which,can,be,implemented,simply,as,the,acquisition,of,a,lock),in,order,to,permit,access,to,the,methods,of,an,object,on,a,serial,basis,only.,Succinctly:,an,object,whose,methods,are,subject,to,mutual,exclusion.,Reactor,-,this,is,‘an,object,providing,an,asynchronous,interface,to,resources,that,must,be,han-,dled,synchronously’,(Wikipedia).,The,object,(or,service,handler),is,said,to,demultiplex,incoming,requests,and,pass,them,on,in,a,synchronous,manner.,Read-write,lock,-,this,means,the,provision,of,concurrent,read,but,serial,write,access.,Scheduler,-,this,means,the,means,by,which,work,is,doled,out,to,threads;,clearly,the,issue,of,load-,balancing,and,overall,rate-limiting,steps,raise,their,heads,here.,Aside,-,this,concept,also,allowed,multi-tasking,back,in,the,days,of,single-processor,architectures.,Thread,pool,-,this,refers,to,a,set,of,threads,that,are,available,to,be,assigned,work;,the,threads,may,be,organized,in,some,way,eg.,as,a,queue.,11,Thread-specific,storage,-,‘Static,or,‘global’,memory,local,to,a,thread.’,([5]).,12,2.2,Scientific,patterns,2.2.1,Rouson’s,patterns,The,book,by,Rouson,,Xia,and,Xu,[6],could,be,seen,as,template,for,designing,and,writing,the,software,to,be,written,for,NEPTUNE,,since,it,starts,with,an,introduction,to,object-oriented,pro-,gramming,and,finishes,with,a,description,of,the,Morfeus,multiphysics,framework,aimed,ultimately,at,Exascale,HPC.,Since,most,code,examples,are,presented,in,both,languages,,the,book,may,also,be,regarded,as,a,‘Rosetta,stone’,for,scientific,programming,in,C++,and,Fortran,2003,,see,Table,1,,and,including,a,chapter,(§,11),devoted,to,discussion,of,the,interoperability,of,the,two,languages.,Notably,too,,Rouson,et,al,[6,,§,4.2.3],describe,how,one,of,the,first,examples,of,object-oriented,scientific,programming,,described,in,the,book,by,by,Gardner,and,Manduchi,[15],,is,an,application,in,nuclear,fusion,,namely,a,data,acquisition,code,written,in,Java.,Table,1:,Rouson,,Xia,and,Xu,as,a,‘Rosetta,Stone’,–,Table,2.1,from,[6],on,Object-Oriented,Pro-,gramming,nomenclature.,Fortran,2003,Derived,type,Component,Class,select,type,Type-bound,procedure,Parent,type,Extended,type,Module,Generic,interface,Final,procedure,Defined,operator,Defined,assignment,Deferred,procedure,binding,Procedure,interface,Intrinsic,type/procedure,General,Abstract,data,type,(ADT),Attribute,C++,Class,Data,member,Dynamic,Polymorphism,(emulated,via,dynamic,cast),Virtual,Member,function,Base,class,Subclass,Namespace,Function,overloading,Destructor,Overloaded,operator,Overloaded,assignment,op-,erator,Pure,virtual,member,function,Abstract,method,Function,prototype,Primitive,type/procedure,Method,,operation,Parent,class,Child,class,Package,Static,polymorphism,Procedure,signature,Built-in,type/procedure,In,this,report,,the,focus,is,on,design,patterns,,to,which,concept,Rouson,et,al,[6],contribute,the,idea,of,“domain-specific,design,patterns”,,where,the,domain,is,the,scientific,one,encompassing,NEPTUNE.,Rouson,and,coworkers,also,describe,language-specific,design,patterns,,namely,Sur-,rogate,[6,,§,7],for,Fortran,2003,and,Compute,Globally,,Return,Locally,(CGRL),[16],for,Co-array,Fortran,(CAF).,These,are,necessary,because,of,deficiencies,in,the,programming,language(s),and,will,not,be,further,discussed.,In,Rouson,et,al,[6,,§,5],,the,concept,of,object,(which,they,pedantically,describe,as,a,language-,specific,pattern,because,it,is,not,fundamental,to,either,the,Fortran,2003,or,C++,languages),un-,derlies,their,discussion,of,design,patterns.,The,book,also,emphasises,the,importance,of,UML,in,describing,patterns,[6,,§,B].,Table,2,which,is,reproduced,from,[6],,summarises,the,generic,design,13,patterns,found,useful,for,scientific,work,in,the,book,,either,directly,or,because,they,inspired,related,scientific,design,patterns.,Table,2:,Useful,Go4,design,patterns,and,summary,descriptions,–,Table,4.1,from,[6],,augmented,with,pointers,to,sections,in,the,book,Allow,Varying,of,Subclass,of,instantiated,object,§,9,Location,or,method,of,accessing,an,object,Object,structure,and,composition,(§,9.2),Interface,to,a,subsystem,§,6,How,an,aggregate’s,elements,are,accessed,§,5.4,How,and,which,objects,interact,with,each,other,§,8,An,algorithm,§,7,Pattern,Factory,Method,Proxy,Composite,Facade,Iterator,Mediator,Strategy,Template,Method,Step(s),of,an,algorithm,§,9.4,Singleton,Abstract,Factory,Global,variable(s),§,9.3,Factory,method,§,9,The,Strategy,pattern,is,shown,to,be,directly,useful,in,scientific,programming,,with,the,example,of,enabling,an,easy,switch,between,different,methods,for,integrating,a,PDE,forward,in,time,,such,as,forward,Euler,or,2nd,order,Runge-Kutta.,The,next,novelty,arises,from,the,perceived,need,for,a,multiphysics,program,with,‘separation,of,concerns’,to,be,adaptable,at,the,level,of,mathemat-,ical,abstraction,of,the,vector,calculus,,or,more,precisely,the,tensor,calculus.,This,leads,to,the,introduction,in,ref,[6,,§,6],of,the,Abstract,Data,Type,or,ADT,calculus,for,PDEs,,referred,to,as,‘ab-,stract,calculus’,where,say,partial,derivative,with,respect,to,time,(∂/∂t),and,Laplacian,operator,∇2,have,special,representations,in,software,,cf.,overloading,operators.,Externally,,the,Abstract,Cal-,culus,pattern,exhibits,many,aspects,of,the,Facade,design,pattern,,whereas,internally,the,separate,operators,may,be,regarded,as,Template,Methods.,There,is,criticism,of,the,Mediator,pattern,see,Figure,8,,because,of,the,linear,growth,in,its,complex-,ity,with,the,number,of,objects,it,has,to,connect,,hence,the,introduction,of,the,Puppeteer,pattern,,see,Figure,9.,The,key,distinction,is,that,the,connected,objects,need,know,nothing,about,the,Puppeteer.,The,application,of,Abstract,Factory,pattern,to,Abstract,Calculus,is,to,define,discrete,properties,to,be,applied,to,a,field,in,order,to,solve,a,PDE.,Rouson,et,al,give,the,example,of,the,flow,u(x,,t),as,a,solution,to,Burgers’,equation,,as,the,‘Field’,returned,by,reference,from,the,Factory,Method,create(),in,Figure,10,,where,the,Abstract,Factory,FieldFactory,uses,the,concrete,Periodic6thFactory,which,aggregates,(discrete),periodic,boundary,conditions,with,a,6th-order,Pad,´e,approximation.,The,point,is,that,other,boundary,conditions,and,approximations,may,be,easily,substituted,for,periodic,and,6th-order,Pad,´e,respectively,,but,the,create(),interface,remains,the,same.,Indeed,strictly,speaking,,these,other,substitutions,must,be,available,to,satisfy,the,definition,that,an,Abstract,Factory,is,capable,of,creating,a,family,of,related,objects.,Software,described,in,the,Rouson,et,al,book,apparently,culminates,with,the,Morfeus,framework,for,multiphysics.,The,reason,this,otherwise,seemingly,very,relevant,framework,is,not,described,in,the,report,[17],is,that,on,close,inspection,,what,ref,[6],contains,is,more,a,proposal,to,implement,the,design,patterns,in,the,book,than,a,finished,project.,The,only,related,public,repository,found,14,Figure,8:,UML,class,diagram,for,the,Mediator,pattern,showing,application,to,the,problem,of,ac-,cessing,an,atmospheric,state,defined,by,separate,data,describing,air,,cloud,and,ground,properties,–,After,Fig.,8.1,from,[6].,was,actually,set,up,very,recently,(2020),by,Rouson,,and,contains,Fortran,2003,code,only,[18].,15,(a),(b),Figure,9:,At,top,(a),,UML,class,diagram,for,the,Puppeteer,pattern,–,after,Fig.,8.2,from,[6].,Be-,low,(b),,UML,sequence,diagram,for,the,Puppeteer,pattern,–,Fig.,8.3,from,[6],,when,specifically,derivative,information,is,required,so,the,puppeteer,can,form,a,Jacobian,matrix.,16,Figure,10:,UML,class,diagram,for,the,Abstract,Factory,pattern,showing,application,to,solving,a,PDE,–,after,Fig.,9.1,from,[6].,17,2.2.2,ComPat,The,ComPat,project,[7,,19],is,an,extreme,scaling,design,pattern,targeting,the,multiscale,modelling,of,magnetic,confinement,fusion,(MCF),plasmas.,Models,of,MCF,plasmas,span,lengthscales,from,the,electron,gyroradius,∼,10−6,m,to,the,device,size,∼,10,m,,and,timescales,from,the,electron,gyro-,period,∼,10−10,s,to,the,confinement,time,∼,10,s.,Including,even,smaller,length-,and,timescales,from,atomic,and,sheath,physics,would,be,desirable.,The,different,physical,effects,within,an,MCF,plasma,are,also,characterized,by,models,of,different,dimensionality,,with,five-dimensional,gyro-,kinetic,turbulence,,two-,or,three-dimensional,edge,transport,,and,one-dimensional,core,transport,models.,The,ComPat,project,adopts,a,submodel,approach,to,modelling,MCF,plasmas,,using,single-scale,submodels,provided,by,different,codes,,and,coupling,these,together,by,passing,relevant,informa-,tion,in,an,agreed,format,through,middleware.,This,approach,has,a,number,of,benefits.,It,allows,the,separation,of,concerns:,using,existing,codes,as,submodels,means,that,the,components,are,developed,by,domain,specialists,,and,are,therefore,better,tested,and,validated.,Discrete,sub-,models,are,also,easier,to,maintain,and,optimize.,Further,,it,allows,users,to,change,which,code,is,used,for,each,submodel,,so,that,a,user,could,,for,example,,choose,between,continuum,and,particle-based,solvers,for,the,gyrokinetic,turbulence,,or,indeed,,between,gyrokinetic,and,gyrofluid,models.,The,drawback,of,separating,codes,in,this,manner,is,that,the,process,of,coupling,codes,introduces,complexity,and,runtime,overheads.,ComPat,is,a,framework,and,software,suite,designed,to,facilitate,studying,multiscale,fusion,plas-,mas,on,HPC,systems.,It,has,two,major,objectives,[20]:,(1),to,provide,a,collection,of,methods,and,software,to,aid,the,development,of,component-based,multiscale,simulations;,and,(2),to,create,generic,transformation,and,optimization,methods,to,ameliorate,coupling,overheads,and,improve,the,simulation’s,runtime,(and/or,other,performance,metric),on,a,targeted,set,of,execution,plat-,forms.,Different,workflow,configurations,may,be,used,depending,on,what,the,user,wishes,to,opti-,mize,,for,example,,minimizing,wall,clock,time,,minimizing,total,energy,consumption,,or,maximizing,scaling,efficiency.,Implementation,The,ComPat,software,stack,has,several,components.,Firstly,,it,uses,a,domain-,specific,language,,the,Multiscale,Modelling,Language,(MML),and,its,representation,in,XML,(xMML),to,allow,developers,to,give,a,high-level,description,of,submodels,and,their,interactions.,It,uses,the,tool,jMML,to,generate,a,topology,,task-graph,and,skeleton,configuration,file,for,the,coupling,frame-,work.,The,coupling,framework,used,is,MUSCLE2,(Multiscale,Coupling,Library,and,Environment).,This,itself,has,two,parts,,a,library,for,data,exchange,between,submodels,,and,a,runtime,envi-,ronment,to,manage,each,submodel’s,execution,on,(possibly),distributed,resources.,The,library,has,APIs,in,C,,C++,,Fortran,,Python,and,Java,,with,functions,allowing,users,to,query,parameters,,send,and,receive,data,,and,log,and,stage,files.,This,component-based,approach,means,that,the,framework,is,agnostic,towards,which,submodels,are,actually,used.,Submodels,(called,kernels,in,MUSCLE2,nomenclature),therefore,may,be,swapped,in,and,out,,and,different,multiscale,models,treated,within,the,same,framework.,ComPat,uses,QCG,middleware,[21],,as,a,resource,broker,to,set-up,and,execute,jobs.,The,QCG,client,provides,a,simple,interface,to,machines,through,batch,scripts,or,XML,files.,This,allows,cross-,18,cluster,jobs,to,be,configured,with,a,single,script,and,to,be,monitored,from,a,single,workstation.,Performance,Alowayyed,et,al.,[22],identify,three,Multiscale,Computing,Patterns,(MCPs):,Hetero-,geneous,Multiscale,Computing,(HMC),,Replica,Computing,(RC),And,Extreme,Scaling,(ES).,Com-,Pat,follows,the,Extreme,Scaling,Pattern,,as,the,computing,cost,of,one,submodel,(called,the,pri-,mary),dominates,that,of,all,other,submodels,(called,the,auxiliaries).,In,ComPat,,the,primary,is,the,model,for,microscale,turbulence.,Through,its,use,of,multiple,computing,resources,,the,extreme,pattern,introduces,an,extra,layer,of,parallelism,at,the,code,coupling,level,,meaning,that,coupling,overheads,may,be,hidden,,and,the,coupled,code,may,even,outperform,a,monolithic,implementa-,tion.,In,Luk,et,al.,[20],,a,further,optimization,is,found,by,solving,the,submodels,in,an,“asynchronous”,fashion.,A,simple,first,analysis,of,the,data,dependencies,in,ComPat,showed,that,the,different,mod-,els,needed,to,be,executed,sequentially,,and,that,consequently,the,primary,microturbulence,sub-,model,was,often,idle,,waiting,for,other,submodels,to,finish.,However,,by,considering,the,timescales,of,the,auxiliary,submodels,,Luk,et,al.,argue,that,the,longer-timescale,equilibrium,and,transport,solvers,do,not,change,their,input,to,the,turbulence,solver,significantly,from,one,time,step,to,the,next.,Therefore,,they,introduce,an,”asynchronous”,mode,,where,the,microturbulence,model,takes,equilibrium,and,transport,data,from,the,previous,timestep.,This,removes,the,data,dependency,,and,allows,the,submodels,to,run,in,parallel.,This,asynchronous,workflow,decreases,the,total,wall,clock,time,by,around,6%,without,appreciably,changing,the,simulation,results.,Despite,this,improvement,,the,runtime,is,still,limited,by,the,scaling,performance,of,microturbulence,submodel,,which,only,scales,well,to,16,cores,per,flux,tube.,This,emphasises,that,in,the,Extreme,Scaling,Pattern,it,is,necessary,to,optimize,both,the,workflow,and,the,raw,scaling,performance,of,the,submodels,(that,are,on,the,critical,path),in,order,to,obtain,good,scaling,performance,at,Exascale.,19,Figure,11:,Usage,of,VECMAtk,,taken,from,the,website,[9].,2.2.3,VECMA,toolkit,The,Verified,Exascale,Computing,for,Multiscale,Applications,(VECMA),project,[8],in,many,impor-,tant,respects,follows-on,from,the,Computing,Patterns,for,High,Performance,Multiscale,Comput-,ing,(ComPat),project,[7].,Thus,the,ComPat,website,[19],lists,the,following,software,•,FabSim,•,QCG,–,Quality,in,Cloud,and,Grid,•,MUSCLE,2,–,The,Multiscale,Coupling,Library,and,Environment,whereas,the,VECMA,toolkit,(VECMAtk),website,[9],lists,(and,provides,links,to):,•,FabSim3,•,QCG,Pilot,Job,(QCGPJ),,QCG-Now,,QCG-Broker,and,QCG-Client,•,MUSCLE,3,•,EasyVVUQ,–,Facilitate,verification,,validation,and,uncertainty,quantification,(VVUQ),•,EasyVVUQ-QCGPJ,where,the,EasyVVUQ,software,represents,the,VVUQ,capability,developed,by,the,VECMA,project.,20,The,roles,played,by,FabSim,,QCG,and,MUSCLE,2,appear,to,have,been,taken,over,by,FabSim3,,QCGPJ,and,MUSCLE,3,respectively,in,the,more,recent,project,,and,as,they,are,described,in,Section,2.2.2,will,not,be,described,further.,MUSCLE,3,,updating,MUSCLE,2,,is,effectively,a,separate,development,from,VECMAtk,,that,pro-,vides,a,coupling,capability,between,different,codes.,It,is,of,additional,interest,because,it,has,the,capability,not,only,to,implement,but,also,to,create,couplings,using,the,Multiscale,Modeling,and,Simulation,Language,(MMSL),which,was,developed,in,tandem,with,the,original,MUSCLE.,Un-,fortunately,,as,of,mid-2020,,there,is,no,further,funding,for,developing,or,supporting,MUSCLE,3,,but,it,will,continue,to,be,supported,by,Lourens,Veen,at,the,Netherlands,eScience,center,in,his,“spare,time”.,Figure,11,indicates,how,the,components,of,VECMAtk,,apart,from,MUSCLE,3,(which,would,be,confined,to,the,HPC,Resource),,interact.,VECMA,toolkit,is,not,a,software,pattern,in,the,strict,sense,in,that,it,typically,spans,a,network.,The,QCG,software,devloped,in,Poland,at,the,Poznan,Supercomputing,and,Networking,Center,(PSNC),provides,the,user,with,a,system-independent,approach,to,the,problem,of,executing,a,set,of,interrelated,jobs,on,a,cluster,of,machines,or,as,indicated,in,the,figure,,a,HPC,machine,in,the,background.,QCG-Now,is,a,desktop,GUI,interface,to,the,other,components,of,the,QCG-Client,,of,which,the,most,important,for,VECMAtk,is,QCGPJ.,EasyVVUQ,[23],is,a,Python,library,to,help,produce,computational,“campaigns”,to,enable,UQ,of,simulations,on,HPC,machines,in,combination,with,QCGPJ,,with,which,it,is,specially,packaged,as,EasyVVUQ-QCGPJ.,The,intent,appears,to,be,that,EasyVVUQ-QCGPJ,will,replace,FabSim3,which,provides,similar,functionality,also,using,Python.,The,basic,pattern,in,EasyVVUQ-QCGPJ,is,in,fact,the,straightforward,[24],1.,Produce,ensemble,of,calculations,(“campaign”),,2.,Execute,unmodified,simulation,code,for,each,set,of,parameters,3.,Correlate,results,of,ensemble,so,that,EasyVVUQ-QCGPJ,is,non-intrusive,in,the,sense,that,like,most,UQ,packages,it,simply,wrappers,existing,code.,Indeed,it,exploits,Feinberg’s,chaospy,library,[25],to,help,generate,the,ensembles,via,sampling,from,distributions,provided,by,the,library,[26].,21,2.3,Prototype,Specification,2.3.1,Dubey’s,patterns,There,are,many,well-documented,software,development,processes,,such,as,waterfall,,spiral,,rapid,application,development,(RAD),and,agile.,The,purpose,of,these,processes,is,to,decompose,software,development,into,its,constituent,components,,so,that,developers,can,focus,on,the,quality,of,each,component,separately,,raising,the,quality,of,the,software,overall.,Dubey,and,McInnes,[12],discuss,software,lifecycle,processes,in,the,context,of,scientific,software,development.,They,note,that,,in,contrast,to,most,non-scientific,software,development,where,the,goal,is,software,creation,,in,scientific,software,development,,software,is,the,means,of,conducting,research,,not,the,product,of,it.,Therefore,they,argue,that,conventional,processes,of,software,development,are,not,well-suited,to,scientific,software,development.,In,[12],,Dubey,and,McInnes,describe,a,scientific,software,lifecycle,,formalizing,the,approaches,already,used,in,various,projects,,such,as,SAMRAI,[27],,FLASH,[28],,Enzo,[29],and,Amanzi,[30].,The,key,point,is,that,scientific,software,can,be,thought,of,as,consisting,of,two,components:,the,infrastructure,code,and,the,scientific,capability,code.,The,infrastructure,code,handles,tasks,like,discretizations,and,I/O.,It,is,relatively,stable,,and,it,may,be,developed,using,any,standard,soft-,ware,lifecycle,pattern.,The,scientific,capability,code,describes,the,scientific,model,itself.,Its,re-,quirements,are,research-driven,,and,the,code,itself,is,constantly,evolving.,Dubey,and,McInnes,introduce,a,software,development,lifecycle,for,the,scientific,capability,code,,and,describe,how,this,should,interface,with,the,development,process,of,the,infrastructure,code.,Isolating,the,scientific,code,from,the,infrastructure,code,and,limiting,the,points,of,contact,between,them,allows,rapid,prototyping,and,development,of,scientific,code,,without,undermining,the,stability,or,functionality,of,infrastructure,code.,Scientific,capability,development,process,The,development,lifecycle,proposed,by,Dubey,and,McInnes,is,shown,schematically,in,Figure,12(a).,The,essential,components,are,connected,by,solid,lines.,The,process,is,this:,first,,requirements,for,the,software,are,gathered,,and,the,target,phenomena,are,described,using,a,mathematical,model.,Next,,approximations,are,introduced,as,necessary,to,simplify,the,model,or,make,it,tractable.,Then,the,equations,are,discretized,,and,appropriate,numerical,algorithms,implemented,to,solve,the,model.,The,resulting,software,is,then,tested,for,correctness,–,i.e.,that,is,solves,the,correct,equations,–,and,its,stability,and,convergence,properties,are,studied.,This,produces,software,of,the,required,standard,,but,it,does,not,ensure,that,the,underlying,mathematical,model,adequately,describes,the,target,phenomena.,The,code,is,therefore,then,validated,against,calibrated,observations,,with,the,mathematical,model,feeding,into,the,calibration,by,defining,regimes,in,which,the,model,is,valid.,The,validation,phase,then,feeds,back,into,the,approximation,,algorithm,and,(occasionally),the,discretization,phases,,if,it,is,necessary,to,make,changes,to,ensure,that,the,model,describes,the,target,phenomena.,This,feedback,from,simulations,into,planning,is,an,integral,part,of,the,evolution,of,scientific,code,requirements,capture.,The,wide-dashed,arrows,from,mathematical,models,and,numerical,algorithms,indicate,phases,that,may,be,skipped,in,certain,cases.,For,example,,calibration,may,not,be,needed,in,simple,cases,where,a,mathematical,model,is,universally,applicable.,Similarly,,some,correctness,,stability,and,22,(a),(b),Figure,12:,Lifecycle,patterns,proposed,by,Dubey,and,McInnes,[12]:,(a),the,scientific,software,lifecycle,pattern;,and,(b),the,interaction,of,the,infrastructure,and,scientific,capability,patterns.,These,graphics,are,respectively,Figures,3,and,4,of,ref,[12],,the,latter,also,corresponds,to,Figure,1,of,ref,[1].,23,convergence,checks,may,not,be,required,if,the,software,uses,third-party,libraries,or,externally-,verified,software,suites.,Finally,,the,narrow-dashed,lines,indicate,how,the,software,development,cycle,interfaces,with,other,concerns,like,simulation,planning,and,scientific,developments,in,the,field.,Planning,,such,as,de-,termining,available,compute,resources,can,necessitate,changes,to,the,numerical,implementation,to,make,a,set,of,simulations,feasible.,Analysis,of,simulation,results,can,lead,to,an,improved,un-,derstanding,of,the,target,phenomena,,which,can,result,in,modifications,to,the,mathematical,model,and,approximations,used.,The,above,description,treats,a,single,mathematical,model.,In,more,complex,multiscale,or,multi-,physics,systems,,there,will,be,multiple,mathematical,models,,but,the,same,software,lifecycle,may,be,used,for,each,model,independently.,Interfacing,development,processes,Now,we,must,consider,how,to,connect,the,development,process,for,scientific,capability,code,described,above,with,a,standard,development,process,used,Ideally,,there,will,be,few,points,of,contact,between,the,two,processes,,for,infrastructure,code.,as,this,will,allow,separation,of,concerns,,and,for,the,two,software,lifecycles,to,proceed,at,their,differing,rates,largely,independent,of,one,another.,Dubey,and,McInnes,[12],propose,the,approach,shown,in,Figure,12(b),,where,high-level,descriptions,of,the,infrastructure,and,scientific,capability,codes,are,given,in,the,left-,and,right-hand,columns,respectively.,There,are,only,three,coupling,points,between,the,two,lifecycles.,The,primary,coupling,point,is,through,the,design,of,the,API.,A,well-designed,module,structure,will,ensure,that,discrete,modules,communicate,their,data,through,a,fairly,stable,API.,However,,improvements,in,scientific,understanding,might,reveal,necessary,changes,in,the,data,dependencies,between,modules,,that,would,be,reflected,in,changes,to,the,API.,The,other,coupling,points,are,where,the,scientific,capability,code,interfaces,with,the,infras-,tructure’s,testing,framework,,and,where,improving,the,scientific,capability,of,the,code,(by,perhaps,adding,a,feature),means,that,the,functionality,of,infrastructure,code,must,also,be,extended.,These,coupling,points,are,however,very,limited,,and,therefore,the,infrastructure,and,scientific,capability,code,can,be,developed,with,largely,independent,lifecycles.,24,3,Summary,The,role,of,software,design,patterns,is,probably,best,summed,up,by,Barr,[31,,§,7],,who,argues,that,even,the,simplest,ones,such,as,Singleton,are,a,useful,start,to,creating,a,common,language,for,documenting,and,communicating,code,details.,The,Go4/GoF,Strategy,pattern,is,singled,out,as,making,it,much,easier,to,extend,software,capabilities.,The,same,pattern,is,also,mentioned,by,Hewitt,[32,,§,7],as,a,way,of,producing,more,flexible,and,reusable,software,,and,Rouson,et,al,[6],show,a,scientific,application,to,the,choice,of,discrete,time,integration,scheme.,Hewitt,[32,,§,8],also,describes,use,of,the,Proxy,(particularly),and,the,Facade,patterns,as,a,very,useful,way,of,saving,time,when,developing,software,,for,much,the,same,reasons,given,in,Section,2.1.1,,and,uses,Builder,to,help,describe,another,(specification),concept.,When,it,comes,to,scientific,application,however,,Rouson,et,al,take,most,Go4,design,patterns,only,as,an,inspiration,for,developing,their,own,Abstract,Calculus,and,Puppeteer,patterns.,It,becomes,clearer,how,design,patterns,fit,into,the,landscape,of,software,reuse,[2,,§,15],,although,it,is,perhaps,more,appropriate,to,think,of,a,hierarchy,rather,than,a,landscape.,At,the,top,level,of,a,given,piece,of,software,,there,might,be,a,framework,which,calls,other,code,that,in,turns,uses,lower-level,libraries,which,may,be,written,specially,for,the,project,,from,open-source,repositories,or,provided,by,the,machine,vendor.,The,middle-level,code,is,where,design,patterns,come,into,play,,and,perhaps,more,as,abstractions,,ie.,‘concept,reuse’,[2,,7.3.1].,This,would,seem,to,sum,up,best,the,use,of,the,design,pattern,concept,by,Rouson,et,al,[6].,In,the,context,of,reuse,,Sommerville,also,mention,components,and,component,frameworks,,ie.,‘collections,of,objects,and,object,classes,that,operate,together,to,provide,related,functions,and,services’,,but,these,do,not,seem,to,have,found,much,application,in,scientific,programming,[6,,§,1.4].,(‘Component’,is,also,used,to,mean,a,stand-alone,piece,of,software,such,as,might,form,an,element,of,a,workflow,,as,in,VECMAtk,,and,further,as,an,addition,to,the,C++,Standard,Template,Library.),It,would,of,course,be,helpful,to,be,able,to,reuse,the,work,of,the,ComPat,and,VECMAtk,projects,,but,the,results,obtained,so,far,in,application,to,fusion,(Section,2.2.2,andSection,2.2.3),have,been,disappointing,because,of,load-balancing,issues,,and,it,is,not,immediately,evident,how,to,remedy,this,situation,within,their,general,framework.,The,preferred,way,to,proceed,is,perhaps,to,examine,more,problem-specific,formulations,using,the,NEPTUNE,proxyapps.,Given,the,lack,of,design,patterns,for,scientific,work,,arguably,the,most,important,practical,aspect,of,patterns,as,far,as,NEPTUNE,is,concerned,,is,the,concept,reuse,aspect,when,it,extends,to,concepts,like,Resource,acquisition,is,initialization,(RAII).,Such,concepts,are,invoked,as,a,means,to,avoid,deficiencies,in,C++,,which,in,the,case,of,RAII,,is,a,lack,of,ability,to,monitor,memory,leakage.,Thread-safety,is,another,issue,,and,as,prefigured,in,Section,1,associated,patterns,have,become,part,of,languages,like,Rust,[33],,but,which,are,sadly,not,in,common,use,on,HPC.,However,these,‘safety-first’,concepts,need,to,feed,into,instructions,as,to,how,the,main,NEPTUNE,software,is,coded,,particularly,when,C++,is,used.,Regarding,prototyping,,as,might,be,expected,on,the,basis,of,previous,comments,,little,use,has,been,made,of,design,patterns,in,scientific,applications,and,more,generally,,little,further,literature,was,found,on,how,best,to,deal,with,the,specific,needs,of,prototyping,scientific,software,beyond,the,work,of,Dubey,and,McInnes,[12].,It,is,worth,remarking,that,as,Dubey,and,McInnes,themselves,explain,,their,document,[12],is,not,meant,to,be,definitive,for,scientific,prototyping,work,,instead,25,more,as,an,approach,to,be,tested,for,its,suitability,by,different,groups,for,different,projects.,In,the,context,of,the,NEPTUNE,project,,their,approach,could,be,used,separately,to,develop,each,of,the,proxyapps.,There,is,a,higher,level,to,NEPTUNE,,however,,whereby,the,experience,gained,by,producing,each,proxyapp,feeds,into,the,design,and,development,of,subsequent,ones.,Thus,there,might,be,added,a,second,loop,on,the,right,of,Figure,12(b),indicating,changes,to,the,way,the,software,is,designed,,developed,,validated,and,integrated,in,the,light,of,experience,,and,feeding,into,aspects,of,the,model,definition.,Acknowledgement,The,support,of,the,UK,Meteorological,Office,and,Strategic,Priorities,Fund,is,acknowledged.,References,[1],L.,Anton,,W.,Arter,,and,D.,Samaddar.,NEPTUNE:,Report,on,system,requirements.,Technical,Report,CD/EXCALIBUR-FMS/0014-1.00-M3.1.1,,UKAEA,,2020.,[2],I.,Sommerville.,Software,Engineering.,5th,Edition,(10th,Edition,,2017).,Addison-Wesley,,1997.,[3],C.,Alexander,,S.,Ishikawa,,M.,Silverstein,,M.,Jacobson,,I.,Fiksdahl-King,,and,S.,Angel.,A,Pattern,Language:,Towns,,Buildings,,Construction.,Oxford,University,Press,,1977.,[4],E.,Gamma,,R.,Helm,,R.,Johnson,,and,J.,Vlissides.,Design,Patterns:,Elements,of,Reusable,Object-Oriented,Software.,Addison-Wesley,,1995.,[5],Software,Design,Pattern,wiki.,https://en.wikipedia.org/wiki/Software_design_,pattern,,2020.,Accessed:,July,2020.,[6],D.,Rouson,,J.,Xia,,and,X.,Xu.,Scientific,software,design:,the,object-oriented,way.,Cambridge,University,Press,,2011.,[7],ComPat,Project.,Computing,Patterns,for,High,Performance,Multiscale,Computing,ComPat,website.,https://www.compatproject.eu/,,2020.,Accessed:,July,2020.,[8],VECMA,Project.,Verified,Exascale,Computing,for,Multiscale,Applications,VECMA,website.,http://www.vecma.eu,,2020.,Accessed:,July,2020.,[9],VECMA,Project.,VECMA,VVUQ,Toolkit,VECMAtk,website.,http://www.vecma-toolkit.eu,,2020.,Accessed:,July,2020.,[10],G.,Booch.,Object,Oriented,Design,with,applications.,Benjamin/Cummings,,Redwood,,1991.,[11],L.,Anton,,W.,Arter,,and,D.,Samaddar.,NEPTUNE:,Background,information,and,user,re-,quirements,for,design,patterns.,Technical,Report,CD/EXCALIBUR-FMS/0015-1.00-M3.3.1,,UKAEA,,2020.,26,[12],A.,Dubey,and,L.C.,McInnes.,Idea,paper:,The,lifecycle,of,software,for,scientific,simulations.,Technical,report,,Argonne,National,Lab.(ANL),,Argonne,,IL,(United,States),,2016.,[13],yEd,Graph,Editor.,https://www.yworks.com/products/yed,,2020.,Accessed:,July,2020.,[14],D.C.,Schmidt,,M.,Stal,,H.,Rohnert,,and,F.,Buschmann.,Pattern-Oriented,Software,Architec-,ture,Volume,2:,Patterns,for,Concurrent,and,Networked,Objects.,Wiley,,2000.,[15],H.,Gardner,and,G.,Manduchi.,Design,Patterns,for,e-Science.,Springer,,2007.,[16],M.,Haveraaen,,K.,Morris,,D.,Rouson,,H.,Radhakrishnan,,and,C.,Carson.,High-performance,design,patterns,for,modern,Fortran.,Scientific,Programming,,Article,ID,942059,,14,pages,,2015.,[17],W.,Arter,,E.,Threlfall,,J.,Parker,,and,S.,Pamela.,Report,on,user,frameworks,for,tokamak,multiphysics.,Technical,Report,CD/EXCALIBUR-FMS/0022-M3.1.2,,UKAEA,,2020.,[18],Morfeus,-,Multi-physics,Object-oriented,Reconfigurable,Fluid,Environment,for,Unified,Simu-,lations.,https://github.com/sourceryinstitute/MORFEUS-Source,,2020.,Accessed:,Au-,gust,2020.,[19],ComPat,Project.,Software,resources,for,ComPat,website.,https://www.compatproject.eu/,software-resources/,,2020.,Accessed:,July,2020.,[20],O.O.,Luk,,O.,Hoenen,,A.,Bottino,,B.D.,Scott,,and,D.P.,Coster.,Compat,framework,for,multi-,scale,simulations,applied,to,fusion,plasmas.,Computer,Physics,Communications,,239:126–,133,,2019.,[21],Poznan,Supercomputing,and,Networking,Center.,QCG,website.,http://www.qoscosgrid.,org/trac/qcg,,2020.,Accessed:,June,2020.,[22],S.,Alowayyed,,D.,Groen,,P.V.,Coveney,,and,A.G.,Hoekstra.,Multiscale,computing,in,the,exas-,cale,era.,Journal,of,Computational,Science,,22:15,–,25,,2017.,[23],R.A.,Richardson,,D.W.,Wright,,W.,Edeling,,V.,Jancauskas,,J.,Lakhlili,,and,P.V.,Coveney.,Easyvvuq:,A,library,for,verification,,validation,and,uncertainty,quantification,in,high,perfor-,mance,computing.,Journal,of,Open,Research,Software,,8(1),,2020.,[24],D.W.,Wright,,R.A.,Richardson,,W.,Edeling,,J.,Lakhlili,,R.C.,Sinclair,,V.,Jancauskas,,D.,Suleimenova,,B.,Bosak,,M.,Kulczewski,,T.,Piontek,,P.,Kopta,,I.,Chirca,,H.,Arabnejad,,O.O.,Luk,,O.,Hoenen,,J.,Weglarz,,D.,Crommelin,,D.,Groen,,and,P.V.,Coveney.,Building,confidence,in,simulation:,Applications,of,EasyVVUQ.,Advanced,Theory,and,Simulations,,page,1900246,,2020.,[25],J.,Feinberg,and,H.P.,Langtangen.,Chaospy:,An,open,source,tool,for,designing,methods,of,uncertainty,quantification.,Journal,of,Computational,Science,,11:46–57,,2015.,[26],Jonathan,Feinberg.,ChaosPy,–,Uncertainty,Quantification,Library.,readthedocs.io/en/master/index.html,,2020.,Accessed:,July,2020.,https://chaospy.,27,[27],Lawrence,Livermore,National,Laboratory,Center,for,Applied,Scientific,Computing.,SAMRAI,Structured,Adaptive,Mesh,Refinement,Application,Infrastructure.,https://computation.,llnl.gov/casc/SAMRAI/.,August,2020.,[28],A.,Dubey,,K.,Antypas,,M.K.,Ganapathy,,L.B.,Reid,,K.,Riley,,D.,Sheeler,,A.,Siegel,,and,K.,Weide.,Extensible,component-based,architecture,for,FLASH,,a,massively,parallel,,multi-,physics,simulation,code.,Parallel,Computing,,35(10-11):512–522,,2009.,[29],G.L.,Bryan,,M.L.,Norman,,B.O’Shea,,T.,Abel,,J.H.,Wise,,M.J.,Turk,,D.R.,Reynolds,,D.C.,Collins,,P.,Wang,,S.W.,Skillman,,B.,Smith,,R.P.,Harkness,,J.,Bordner,,J.-h.,Kim,,M.,Kuhlen,,H.,Xu,,N.J.,Goldbaum,,C.B.,Hummels,,A.G.,Kritsuk,,E.J.,Tasker,,S.,Skory,,C.M.,Simpson,,O.,Hahn,,J.S.,Oishi,,G.,So,,F.,Zhao,,R.,Cen,and,Y.,Li.,ENZO:,an,adaptive,mesh,refinement,code,for,astrophysics.,Astrophysical,Journal,Supplement,Series,,211(2):19,,2014.,[30],J.D.,Moulton,,S.,Molins,,J.N.,Johnson,,E.,Coon,,K.,Lipnikov,,M.,Day,,and,E.,Barker.,Amanzi:,An,open-source,multi-process,simulator,for,environmental,applications.,In,AGU,Fall,Meeting,Abstracts,,2014.,[31],A.,Barr.,The,problem,with,software:,Why,smart,engineers,write,bad,code.,MIT,Press,,2018.,[32],E.,Hewitt.,Semantic,Software,Design:,A,New,Theory,and,Practical,Guide,for,Modern,Archi-,tects.,O’Reilly,Media,,2019.,[33],Rust,programming,language.,https://www.rust-lang.org/,,2020.,Accessed:,August,2020.,28

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