TN-14-1_ExcaliburNeptuneDslCodeDesignPatternNeptune
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   :description: technical note

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Excalibur-Neptune,report,2047356-TN-14-01,Task,4.3,DSL,and,code,design,pattern,for,NEPTUNE,Ben,Dudson,,Peter,Hill,,Edward,Higgins,,David,Dickinson,,and,Steven,Wright,University,of,York,David,Moxey,University,of,Exeter,March,31,,2022,Contents,1,Executive,summary,2,Approaches,to,Multi-Species,Simulations,3,DSL,Adoption,4,Conclusions,5,References,2,2,5,7,8,1,1,Executive,summary,In,this,report,we,discuss,approaches,to,code,design,and,the,adoption,of,domain,specific,languages,(DSLs),for,multi-species,simulations,in,the,BOUT++,[1],and,Nektar++,[2],solvers.,Specifically,this,report,covers:,1.,Approaches,to,code,design,in,Bout++,that,allow,for,single-species,plasma,simulations,to,be,extended,to,multiple,species.,2.,How,these,multi-species,models,are,expressed,in,a,high-level,DSL.,3.,An,overview,of,the,DSLs,that,exist,already,in,the,Bout++,and,Nektar++,frameworks,and,how,a,common,UFL-like,DSL,might,drive,both,Bout++,and,Nektar++,solvers.,2,Approaches,to,Multi-Species,Simulations,Our,previous,report,(2047356-TN-05),focuses,on,the,implementation,of,two,multi-fluid,simulations,within,the,BOUT++,framework.,When,developing,such,a,simulation,,if,only,a,small,number,of,species,are,re-,quired,,such,as,in,Hermes-2,[3],and,STORM,[4],,then,code,can,be,copied,and,modified,for,each,individual,species,relatively,easily.,However,,as,the,number,of,species,grows,,so,too,does,the,length,and,complexity,of,the,code.,This,makes,the,code,increasingly,error,prone,,difficult,to,test,and,difficult,to,maintain.,Instead,,our,previous,report,outlines,two,approaches,to,extending,from,single,species,simulations,to,multi,species,simulations.,Those,two,approaches,demonstrated,in,Bout++,are:,•,Subclassing,,where,the,class,hierarchy,is,used,as,a,base,from,which,to,adapt,and,specialise,the,behaviour,of,each,species.,•,State-Command,Pattern,,where,the,states,of,multiple,species,are,stored,in,a,dictionary,structure,,and,the,evolution,of,those,species,is,defined,by,a,collection,of,model,components.,2,These,two,approaches,are,implemented,in,the,BOUT++,framework,in,SD1D,[5],and,Hermes-3,[6],,respectively.,In,SD1D,,the,model,is,constructed,from,numerous,Species,classes,,which,repre-,sent,particular,atomic,or,ion,species,,and,Reaction,classes,which,represent,the,interactions,between,different,species.,These,interactions,are,orchestrated,by,a,central,object,representing,the,whole,system,,containing,a,list,of,participating,species,and,reaction,objects.,Figure,1,shows,this,simplistic,design.,Figure,1:,Subclassing,architecture,,in,which,Species,objects,describe,plasma,species,,and,Reactions,represent,interactions,between,them.,All,interactions,are,carried,out,through,exchange,of,sources.,The,main,time,look,for,SD1D,is,them,implemented,as,follows:,3,SpeciesReactiongetDensity()getTemperature()getVelocity()addParticleSource()addMomentumSource()addEnergySource()updateSpecies(species[])getParticleSources()getMomentumSources()getEnergySources()nTvstate,1,for,species,in,species_list,:,2,species,.,evolve,(),3,4,for,reaction,in,reaction_list,:,5,#,Calculate,reaction,rates,using,all,species,reaction,.,updateSpecies,(,species_list,),6,7,8,9,10,11,12,13,14,15,16,for,species_name,,,source,in,reaction,.,densityS,ources,(),:,#,Check,that,the,species,is,in,species_list,species_list,[,species_name,].,addDensity,(,source,),for,species_name,,,source,in,reaction,.,m,om,entum,So,urces,(),:,species_list,[,species_name,].,addMomentum,(,source,),for,species_name,,,source,in,reaction,.,energySources,(),:,species_list,[,species_name,].,addEnergy,(,source,),Figure,2:,Psuedo-code,for,the,main,time,loop,in,SD1D,,showing,how,polymor-,phism,is,used,to,evolve,multiple,species.,4,In,Hermes-3,,a,state-command,pattern,is,used,,where,instead,each,individ-,ual,species,is,specified,in,a,nested,dictionary-like,structure,,based,on,a,simple,schema,,e.g.,,state["species"]["h+"]["density"],for,the,number,density,of,hydrogen,ions.,A,collection,of,composable,model,components,are,then,defined,that,evolve,the,simulation,state,,performing,calculations,on,single,species,or,multiple,species,at,once,(e.g.,collisions,,etc).,Figure,3,shows,this,design,pat-,tern.,Figure,3:,State-Command,pattern:,The,State,of,the,simulation,system,is,In,the,first,pass,passed,through,a,sequence,of,Components,in,two,passes.,(transform(),calls),,components,can,modify,the,state;,in,the,second,pass,(finally(),calls),the,state,cannot,be,modified,,but,is,used,to,update,com-,ponent,internal,states.,Alternative,approaches,are,also,outlined,in,our,previous,report,including,the,use,of,an,Entity-Component,System,(ECS),and,a,task,graph,approach.,The,ECS,approach,is,not,dissimilar,to,our,state-command,approach,detailed,above,,while,a,task,graph,approach,can,be,taken,together,with,either,of,our,stated,approaches.,Task,graphs,are,particularly,of,interest,since,they,can,be,mapped,directly,to,the,SYCL/DPC++,programming,model,[7].,3,DSL,Adoption,While,our,previous,report,covered,the,code,structures,that,might,be,required,to,process,multi-fluid,simulations,in,Bout++,,it,did,not,elaborate,how,this,might,be,exposed,to,a,developer,through,a,domain,specific,language,(DSL).,In,the,T/NA086/20,[DSL,and,code,generation],work,package,,a,number,of,DSLs,are,outlined,that,exist,at,different,levels,of,abstraction.,Report,2057699-TN-02,details,some,of,these,DSLs,and,embedded,DSLs,(eDSLs),that,are,relevant,to,Project,NEPTUNE.,5,ComponentComponentComponenttransform()transform()transform()finally()finally()finally()DoneState,At,the,lowest,level,are,DSLs,like,RAJA,,Kokkos,and,SYCL,that,provide,mech-,anisms,to,specify,regions,of,code,for,parallel,execution.,At,a,higher,level,,there,are,DSLs,such,as,OP2,and,OPS,,where,a,developer,are,exposed,to,particular,structures,such,as,meshes,,and,they,can,write,kernels,that,execute,over,elements,of,these,structures,(e.g.,iterate,over,edges,,nodes,,etc.).,At,the,highest,level,are,DSLs,such,as,UFL,(used,by,Firedrake,and,FEniCS),and,Bout++,,where,PDEs,can,be,represented,directly,in,code.,It,is,possible,(and,perhaps,desirable),that,multiple,levels,of,DSL,are,used,within,a,single,application.,This,approach,is,already,taken,by,Bout++.,At,its,core,,Bout++,is,implemented,in,C++,with,MPI;,there,are,ongoing,efforts,to,merge,the,low-level,RAJA,DSL,with,some,of,the,core,code,,in,order,to,provide,het-,erogeneous,loop-level,parallelism.,Bout++,then,exposes,a,high-level,eDSL,to,developers,,allowing,PDEs,to,be,expressed,relatively,naturally,in,code.,This,approach,is,very,similar,to,UFL.,The,C++,core,is,heavily,templated,,allowing,the,eDSL,code,to,be,translated,at,compile,time,to,efficient,code,for,execution.,The,psuedo-code,in,Figure,2,provides,an,example,of,how,to,use,Bout++’s,primary,DSL,to,create,the,SD1D,code,(the,implementation,can,be,seen,in,sd1d.cxx).,Bout++,also,contains,a,secondary,DSL,(at,a,higher-level,still),in,its,input,files.,This,is,used,in,the,Hermes-3,simulation,detailed,above.,Within,the,input,DSL,,we,can,specify,multiple,species,and,define,their,parameters,and,reactions.,Figure,4,demonstrates,this,DSL.,Version,5.0,of,the,Nektar++,framework,introduces,a,python,interface,for,users,that,are,less,familiar,with,spectral,elements,and,the,Nektar++,framework,it-,self,[8].,This,interface,exists,at,a,similar,level,to,that,of,the,UFL,and,primary,Bout++,DSL.,Given,the,broad,similarity,in,the,three,DSLs,exposed,by,FEniCS,,Bout++,and,Nektar++,,it,is,possible,that,common,features,could,be,extracted,from,the,languages,to,form,a,common,DSL,that,can,drive,both,Bout++,and,Nektar++,frameworks.,However,,defining,a,common,DSL,and,building,solvers,that,im-,plement,such,a,DSL,will,be,a,significant,undertaking.,Extending,this,DSL,to,multi-fluid,reactions,will,also,require,that,additional,functionality,is,added,to,the,Nektar++,framework.,6,1,[hermes],2,components,=,d+,,d,,t+,,t,,e,,collisions,,sheath_boundary,,recycling,,reactions,3,4,#,properties,of,each,component,5,[d+],6,type,=,evolve_density,,evolve_momentum,,evolve_pressure,,anomalous_diffusion,7,AA,=,2,8,charge,=,1,#,Atomic,mass,9,10,[t],11,...,12,13,[reactions],14,type,=,(,15,16,17,),d,+,e,->,d+,+,2e,,t,+,e,->,t+,+,2e,,#,Deuterium,ionisation,#,Tritium,ionisation,Figure,4:,An,example,of,the,Bout++,Ini,input,file,describing,a,simple,simulation,with,deuterium,and,tritium,ions,and,atoms.,The,reactions,are,described,in,the,input,file.,4,Conclusions,In,this,report,,we,have,outlined,how,Bout++,has,been,extended,to,support,multi-fluid,simulations.,As,part,of,this,,the,Bout++,DSLs,have,required,exten-,sion,to,allow,us,to,represent,the,complex,reactions,present,in,a,multi-species,simulation.,In,order,to,extend,Bout++,to,multi-fluid,simulations,,the,embed-,ded,input,DSL,has,also,required,extension,,allowing,run-time,specification,of,component,reactions.,While,there,are,significant,similarities,in,the,interfaces,exposed,by,Bout++,and,Nektar++,(and,indeed,to,UFL),,there,are,areas,of,significant,divergence,in,approach,,meaning,that,it,is,likely,to,be,challenging,to,drive,both,frameworks,from,a,common,DSL.,7,5,References,[1],BOUT++,contributors.,BOUT++,manual.,https://bout-dev.,readthedocs.io/.,[2],C.D.,Cantwell,,D.,Moxey,,A.,Comerford,,A.,Bolis,,G.,Rocco,,G.,Mengaldo,,D.,De,Grazia,,S.,Yakovlev,,J.-E.,Lombard,,D.,Ekelschot,,B.,Jordi,,H.,Xu,,Y.,Mohamied,,C.,Eskilsson,,B.,Nelson,,P.,Vos,,C.,Biotto,,R.M.,Kirby,,and,S.J.,Sherwin.,Nektar++:,An,open-source,spectral/hp,element,framework.,Computer,Physics,Communications,,192:205–219,,2015.,[3],Ben,Dudson,,Jarrod,Leddy,,Hasan,Muhammed.,Hermes-2,hot,ion,drift-,reduced,model.,https://github.com/bendudson/hermes-2.,[4],L.,Easy,,F.,Militello,,T.,Nicholas,,J.,Omotani,,F.,Riva,,N.,Walkden,,UKAEA.,Hermes-2,hot,ion,drift-reduced,model.,https://github.com/,boutproject/STORM.,[5],Ben,Dudson,et,al.,SD1D,SOL,and,Divertor,model,in,1D.,https://github.,com/boutproject/SD1D.,[6],Ben,Dudson.,Hermes-3.,https://github.com/bendudson/hermes-3.,[7],Cheng-Hsiang,Chiu,,Dian-Lun,Lin,,and,Tsung-Wei,Huang.,An,experimental,study,of,sycl,task,graph,parallelism,for,large-scale,machine,learning,work-,loads.,Technical,report,,2021.,[8],David,Moxey,,Chris,D.,Cantwell,,Yan,Bao,,Andrea,Cassinelli,,Giacomo,Castiglioni,,Sehun,Chun,,Emilia,Juda,,Ehsan,Kazemi,,Kilian,Lackhove,,Ju-,lian,Marcon,,Gianmarco,Mengaldo,,Douglas,Serson,,Michael,Turner,,Hui,Xu,,Joaquim,Peir´o,,Robert,M.,Kirby,,and,Spencer,J.,Sherwin.,Nektar++:,Enhancing,the,capability,and,application,of,high-fidelity,spectral/hp,el-,ement,methods.,Computer,Physics,Communications,,249:107110,,2020,,doi:https://doi.org/10.1016/j.cpc.2019.107110.,8

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