A Distributed Problem Solving Environment (PSE) for Scientific Computing

Transcription

1 Presented at PSE Workshop held n 1st IEEE Internatonal Conference on e-scence and Grd Computng, Melbourne, Dec. 5, 005 A Dstrbuted Problem Solvng Envronment (PSE) for Scentfc Computng Shgeo Kawata 1), Hdeak Fuju 1), Hdeak Sugura 1), Yuch Satoh 1), Yoshkazu Hayase ), Takayuk Teramoto 3), Takash Kkuch 1), Htohde Usam 4), Hroyuk Kanazawa 5), Motohro Yamada 5), Yutaka Myahara 5), Masahde Fujsak 5) 1) Graduate School of Engneerng, Utsunomya Unversty 7-1- Yohtoh, Utsunomya , Japan,kwt@cc.utsunomya-u.ac.jp ) Department of Electronc Control Engneerng, Toyama Natonal College of Martme Technology, 1- Ebe Nerya, Shnmnato, Toyama, , Japan 3) Department of Electroncs and Computer Engneerng, Tsuyama Natonal College of Technology Numa 64-1, Tsuyama, , Japan 4) Natonal Insttute of Informatcs, Center for Grd Research and Development, Jnbocho Mtsubuldng 14F(NAREGI), 1-105, Kanda-Jnbocho, Chyoda-ku, Tokyo , Japan 5) Computatonal Scence and Engneerng Center, Fujtsu Lmted, Mhama-ku, Chba , Japan Abstract A dstrbuted Problem Solvng Envronment (PSE) s proposed to help users solve partal dfferental equaton (PDE) based problems n scentfc computng. The system nputs a problem descrpton and outputs a program flow, a C-language source code for the problem and also a document for the program. Each module s dstrbuted on dstrbuted computers. The PSE contans all the nformaton of the problem, PDEs, dscretzaton scheme, mesh nformaton, equaton manpulaton results, desgned program structure, varable and constant defntons and program tself. Therefore the documentaton support module generates a document for the generated program and the problem tself n the PSE. The module lason module generates an adapter module among the dstrbuted PSE modules. The job executon servce module deploys programs generated or prepared on dstrbuted computer resources and helps users run the programs on the dstrbuted computers. The concept of the dstrbuted PSE extends the potental of conventonal PSE systems. 1. Introducton Recently studes on Problem Solvng Envronment (PSE)[1-13] for partal dfferental equaton (PDE) based problems have been extensvely explored n order to support engneers, scentsts, students and so on to compute or smulate ther own problems on dstrbuted computers. Computer analyses and smulatons have been performed to desgn products, study scentfc ssues and more, and have been recognzed as the thrd method followng theoretcal and expermental methods. One of the major objectves n PSE researches s to help users compute or smulate ther problems wthout heavy tasks, for example, wthout complete knowledge[10, 11] for computatons or wthout a full programmng[1-1]. In ths sense the PSE provdes an nfrastructure for software for computatonal engneerng and scence. In PSE for PDEs, one of problems, whch should be solved, s to develop huge PSE systems, ncludng reusablty of legacy PSE softwares. In order to solve ths problem n PSE, a module-based PSE s proposed[14]; each PSE module solves a part of PSE tasks, for example, problem descrpton nterface, dscretzaton, scheme suggeston module, program flow desgner, program generator, data analyzer, vsualzer, and so on. If each module can be developed ndependently and works cooperatvely and smoothly to solve one PSE job, the heavy work of PSE development may be drastcally relaxed. On the other hand, n Hgh-Performance Computng (HPC) and smulatons n scence and technology, dstrbuted computer systems ncludng GRID systems [15, 16] are now popular and provde a flexble and costeffectve envronment. The dstrbuted computer system may be n a complex envronment of heterogeneous computer hardware and software. However, t s qute

2 dffcult for users to know the detal structure of the dstrbuted computer system they use. In a realstc and useful dstrbuted envronment users should be supported by assstant software [15], so that users can use the dstrbuted computer systems smoothly and effectvely wthout detal knowledge of the dstrbuted computer system tself. In ths paper a new dstrbuted PSE, called D-NCAS, s proposed n order to support users to generate a computer program and to work on dstrbuted computer systems. The PSE system nputs a problem nformaton ncludng dscretzaton and computaton schemes, and outputs a program flow, a C-language source code for the problem and also a document for the program and for the problem. On a host computer a user nputs hs/her problem, and the host navgates the user to solve the problem. The dstrbuted PSE for PDEs conssts of several modules: a problem descrpton module, a dscretzaton one, an equaton manpulaton one, a program desgn one, a program generaton one, documentaton support module, a module lason module and a job executon servce module. Each module s dstrbuted on dstrbuted computers, and all the nformaton s descrbed by the Extensble Markup Language (XML)[17] ncludng the Mathematcal Markup Language (MathML) [18]. Each dstrbuted module communcates wth the host module by usng XML documents, so that outputs from each module are vsualzed. Independent modules whch are developed by other engneers or users for one of the functons specfed above can be also used after adjustments to the dstrbuted PSE nterface, f necessary. Therefore the concept of the dstrbuted PSE extends the potental of conventonal PSE systems. The PSE contans all the nformaton of the problem tself, PDEs, dscretzaton scheme, mesh nformaton, equaton manpulaton results, desgned program structure, varable and constant defntons and program tself. Therefore the documentaton support module also generates a document for the generated program and the problem tself n the PSE. The module lason module generates an adapter module among the dstrbuted PSE modules. The adapter module generated by the module lason system nputs output data from precedng modules and/or external modules, and connects the data to the nput data for the next module. The job executon servce module deploys programs generated or prepared on dstrbuted computer resources and help users run the programs on the dstrbuted computers. The PSE tells users whch computers are avalable and approprate for ther specfc applcaton software by usng hardware and software nformaton specfed. Then the users deploy ther software on the dstrbuted computer systems. The PSE may open a new flexble hgh performance computng envronment.. Target Issues of PSE The present research target ssues of the PSE nclude the followngs: (1) Computer-asssted program generaton should be supported. () Smple and easy executon of users applcaton programs on dstrbuted computers. (3) Smple and easy deploy of users programs onto the dstrbuted computer envronment. Based on the PSE presented n ths paper, users may work smoothly on a dstrbuted computer system: users obtan smulaton programs generated by the PSE, also need not have precse nformaton about hardware locaton behnd the PSE, and execute ther software wthout dffcultes. The job executon servce module n the dstrbuted PSE holds all the nformaton about the dstrbuted computer system and manages all the nformaton relatng to hardware, software nstalled, job executon, network and the locaton of computaton results. 3. A Dstrbuted PSE In our dstrbuted PSE all the modules are dstrbuted on network-lnked computers. The nformaton for the dstrbuted modules and the computers are regstered n a host computer. Newly developed modules by some users or scentsts or so can be also regstered n the host PSE server. The dstrbuted PSE host server has the regstered nformaton for the modules orented to one specfc purpose, and users can obtan the nformaton for each module and can select one of the modules to perform one task n all the PSE process. The schematc dagram for the dstrbuted PSE s shown n Fg.1. At the begnnng of problem solvng process a user nputs hs/her problem nformaton and computaton scheme nformaton nto the host PSE server. All the nformaton s descrbed by XML, and s vsualzed to the user.

3 User Problem Descrpton XML Document Input Server A A1 A A3 : Server B B1 B B3 : Problem Descrpton & Computaton Scheme Informaton PSE Server Desgned Program Flow & C Program Server C C1 C C3 : Dtrbuted PSE Server Varable nformaton Dmenson n Space Varable nformaton Dscretzaton Scheme PDEs Varable Defnton Pont n Space & Tme Intal Condton Boundary Condton Dscretzaton Process Manpulate Process Basc Program Skeleton XML XML XML Vsualzed User Dscretzaton Manpulate Program Flow Fg. 1. Overvew of the dstrbuted PSE Problem Flow Descrpton XML Document XML Encodng User 1 Web Browser Java Applet WWW Server C-language Source Code for the Problem Output Servers User Web Browser Horb Fg. 3. Dstrbuted-PSE work flow Mod_Control1 Data_proxy Data_skeleton 1 Horb Server1 Mod_Control Data_proxy Data_skeleton Horb Server... Server_skeleton Dstrbuted PSE Server Data Base ServerObj3 ServerObj3 ServerObj3 Fg.. Structure of dstrbuted PSE Network The communcaton s accomplshed through an nterface usng WWW server and Applet. The PSE server sends an nformaton descrbed by XML to a module, and the module performs the task. The module sends the result based on the nput XML nformaton back to the PSE server. The result s vsualzed so that the user can check f the result s approprate. After successve processes, fnally the PSE generates a desgned program flow and then a C program. Fgure shows the network structure employed n the PSE. The program generaton PSE module provdes a workflow shown n Fg.3, and the user follows the workflow navgaton for a problem generaton. 4. Problem Solvng n Dstrbuted PSE 4.1 PSE modules for program generaton support In a problem descrpton XML document the followngs are specfed: dmenson n space, PDEs, constants, varables, varable defnton ponts n space and tme, ntal and boundary condtons, dscretzaton scheme, and space mesh defnton. Because all the nformaton s descrbed by XML, the nformaton s treated as tree-type nformaton. Fgure 4 shows a part of an example nput problem descrpton n XML, and the XML document s vsualzed to the user as shown n Fg.5. The PDEs and boundary condtons are also descrbed by the Math-ML (a subset of XML) as shown n Fg. 6. In the XML document for problem descrpton, a user nputs nformaton for dependent and ndependent varables, constant factors, n addton to the defnton n a space mesh and a tme mesh for varables. Based on the nformaton wth the mesh nformaton and the dscretzaton scheme nformaton, the PDEs are dscretzed and manpulated n order to obtan a matrx or a fnal form of each dscretzed PDEs. Frst we present example results of PDEs dscretzaton by fnte dfference method (FDM). The nput problem nformaton ncludes PDEs and a dscretzaton scheme specfed by a user. An FDM/FEM module transforms a PDEs XML document to another XML document for dscretzed PDEs, based on the nput nformaton. An Example dscretzaton s presented n the followngs: an example PDE for dffuson problem s Eq.1.

4 f T T + A + A = 0 (1) t x y When a user chooses the Euler explct scheme, the frst term s dscretzed as follows: <?xml verson="1.0" encodng="shift_jis"?> <?xml-stylesheet type="text/xsl" href="fdmxsl.xsl"?> <nformatonfdm> <header> <ttle>thermal Dffuson Problem</ttle> <dmenson></dmenson> </header> <mesh_condton> <tme> <factor>t</factor> <tme_type>unform</tme_type> <tmes sec="100"/> <tmestep sec="0.01"/> </tme> <space> <space_type>unform</space_type> <_coordnate mn="0" max="0" step="0.1"> x</_coordnate> <j_coordnate jmn="0" jmax="10" jstep="0.1"> Fg. 4. An example problem descrpton XML document f t = f n+1 f dt n where the superscrpt of 'n' s a tme ndex, the subscrpt of '' s space ndex and 'dt' shows the tme-step sze. The second and the thrd terms are dscretzed as shown n Eq. 3, dependng on the user s specfcaton. In ths case the central dfference scheme s employed. n n n T T + 1 T + T 1 = (3) x dx where 'dx' s the mesh sze. Fgure 6 shows a problem nformaton descrbed by an XML document for ths example. The followng example shows an advecton equaton, where the advecton term s dscretzed by the Upwnd dfference scheme. f f + u = 0 (4) t x where 'u' s a velocty of a convectve materal, for example, flud. In ths case the second term n Eq.4 may be transformed to Eq.5 f u u f f u u f f u n n n n + n n n n 1 = (5) x dx dx Fgure 7(a) shows the varable defnton ponts of 'f ' and 'T ' n Eq. 1 on a mesh. Fgure 7(b) shows an vsualzaton example for Eq.1 usng the XML document. The XML and Math-ML documents are vsualzed n a web browser by usng the software "techexplorer"[19]. The dscretzaton result s also shown n Fgure 7(c). () Fg. 5. Vsualzaton of an XML Problem Informaton usng an XSL Style Sheet <?xml verson="1.0"?> <reln dmenson=""> <eq/> <apply> <plus/> <apply solvatype="forwarddfference"> <plus/> <apply> <partaldff/> <bvar> <c attachment="n" defnetype="ndependence" relaton="tme" unform="true">t</c> </bvar> <fn> <c defnetype="dependence" defnton="0" relatve="0" jdefnton="0" jrelatve="0">f</c> </fn> </apply> </apply> <apply solvatype="centraldfference"> <plus/> <apply> <tmes/> Dscretzaton Scheme Varable Informaton Dscretzaton Scheme Fg. 6. A Problem Informaton for FDM n XML The PSE problem nput module sends an nput nformaton descrbed n XML to the FDM/FEM module, and the module performs the dscretzaton and equaton manpulaton tasks. Then the FDM/FEM module sends the result wrtten n the XML document back to the PSE host. The program-generaton PSE modules also help users generate MPI-based parallel smulaton programs based on partal-dfferental equatons (PDEs). The D-NCAS capablty explores possbltes to vsualze and steer the parallel program desgn process. At present D-NCAS supports a doman decomposton n a desgn of a parallel numercal smulaton program, and the doman decomposton s desgned or steered by users through a vsualzaton wndow. After desgnng the doman decomposton, the parallel program tself s also desgned

5 and generated n NCAS, and the desgned parallel program s vsualzed and steered by a PAD dagram. Man functon n a parallel program j y f T (a) x (b) Solver for Temperature Solver for Temperature (c) Fg. 7. a) Varable defnton postons n one mesh, b) a vsualzed example basc equaton and c) a dscretzaton result. Fg. 8. Example vsualzaton of a man part of a desgned parallel program by usng a PAD dagram n the parallel program generaton component n the PSE toolkt. In D-NCAS, MPI functons are employed for message passng, and a SPMD (sngle program multple data) model s supported. The vsualzaton and steerng capabltes provde users a flexble desgn possblty of parallel programmng The parallel program generaton module of D-NCAS nputs PDEs, boundary and ntal condtons, parallel program nformaton for a doman decomposton, CPU number employed, and mesh nformaton. All the processes are vsualzed and steered n order to meet the user s requrement. Fgure 8 shows an example of the vsualzaton for a generated program by a PAD dagram. Dscretzaton Scheme Term Frst term of LHS Second term of LHS Thrd term of LHS Frst term of RHS Second term of RHS Scheme Fg. 9. Example of a document generated by the parallel program generaton component n the PSE server. Ths module contans the nput nformaton of abstract problem nput nformaton, for example, PDEs, problem area, varables, etc. Therefore the document s also generated wth the MPI-based parallel program from the hgher level nformaton. At the same tme the program generaton module also generates a document for the generated program as shown n Fg. 9, because the D-NCAS component keeps all the the nformaton from the abstract problem descrpton, equatons and so on as descrbed above. 4. Lason for a dstrbuted PSE In our dstrbuted PSE (D-NCAS) all functons from an nput problem descrpton to a C program generaton and a document generaton are dvded nto separate functons. They are assgned to specfc modules dstrbuted on network-lnked computers. The

6 nformaton for the dstrbuted modules and the computers s regstered n a host computer, that s, a module regster PSE server. New modules developed by users can also be regstered n the host module regster PSE server. Users nput ther problem nformaton nto the PSE server through the PSE WEB server. The PSE server sends the nformaton descrbed n XML to the next module, and the module performs the task. The module sends the result based on the nput XML nformaton back to the PSE server. After successve processes, fnally the PSE server gets a desgned program flow and then a C program. Fgure 10 shows the structure of the module lason module. Each module of the dstrbuted module-based PSE may be developed by dfferent users. Although ths feature makes the PSE flexble and expandable as dscussed n Introducton, the nput/output data type and order may be dfferent from those of other modules. If they do not ft to those for other modules, the problem solvng process can not be accomplshed. Our module lason system provdes the data adapter to convert the nput/output data to the data ftted to those for the next module. As long as the nput/output data are descrbed by XML and ther nformaton ncludng the data type and the data order are known, the module lason system produces a data adapter to connect the modules n the dstrbuted PSE. In order to know the nput/output data nformaton, n ths paper we assume that each module has an example set of the nput/output data nformaton descrbed by XML, besdes a complete document for the data nput/output. Wthout the full nformaton of the nput/output data one can not use the module n a problem solvng process. Therefore ths assumpton s reasonable. Fgure 11 shows the nterface of the module regster PSE server. The module regster PSE server contans the module nformaton, ncludng the nput/output data nformaton, the locaton of the document and the module locaton URL (Unform Resource Locator), and t also has the nformaton of user-desgned workflows to solve a problem. Through the WEB page shown n Fg.11 users fnd the avalable module lst. The users connect the selected modules, and desgn the workflow for ther problem solvng tasks. At the module regstraton phase, the module nformaton of the module class name, ts method name and arguments are regstered together wth the data nput/output nformaton, the module locaton, etc. The module nformaton s descrbed by WSDL (web servce descrpton language). When the module s regstered to the module regster PSE server and s deployed on dstrbuted computers, the WSDD (web servce deployment descrptor) fle s also used as a usual web servce. Data Input module SOAP ADAPTER HTTP SOAP Regster PSE Server Dscretzaton Generaton HTTP SOAP Equaton Manpulaton SOAP Lason System WEB Browser C-Program Desgn & Generaton User Fg. 10. A module lason system Fg. 11. Interface of the module regster PSE server In a dstrbuted PSE a new module may be added or a legacy module may be updated by ndvdual users/developers. If the module lason system helps users connect the modules and provdes adaptors among the modules based on the nput/output data nformaton of the modules, the module lason system elevates the module-based dstrbuted PSE capablty further. Fgure 1 shows a concept of the data adapter module, generated by the module lason system. The precedng modules output data and the next module may nput the data together wth an external data n general. Each module has the nput/output data nformaton ncludng example nput/output data XML fles and a document for the data.

7 Legacy Legacy modules or New External Data Output Data Adaptor Data Converson Input Data 4.3 Job executon servce module PSE Next or New Fg. 1. Adapter generated by the module lason system. The adapter converts the output data from precedng modules and may combne the external data to produce the nput data to the next module. The scentfc computng tends to requre hgh performance computers, whch may be dstrbuted locally or globally. At present network lnked dstrbuted computer systems ncludng Grd systems are wdely avalable for researchers and engneers. However, t s dffcult for researchers to obtan detal nformaton on dstrbuted hardware and software resources, whch may be a large system, conssted of many computers. When the users work on the dstrbuted resources, the users need to fnd computng resources, data analyss servers and data storage servers. The job executon management ncludng these functons s essentally mportant for scentfc computng on the dstrbuted resources. The job executon servce module does not need any specal Grd mddleware to construct t, and the clent can use ths system by accessng the Web page for the job executon servce system. The job executon servce module conssts of dynamc system management servers, executon servers and data servers. The dynamc system management server s duplcated n order to keep the system robust, and has an assstant management server. The dynamc system management server has a functon of the job executon system management, ncludng software deployment, program complaton, job executon, job status retreval and computng data retreval. Ths system does not requre specal mddleware such as Globus or UNICORE or GLte or etc. Users access the web page on the dynamc system management server, and the clents submt jobs. After the submtted job fnshes, the dynamc system management server collects the nformaton from other dstrbuted computers. The dynamc management server and ts assstant server move dynamcally to new servers, f the present servers become busy. The dynamc system management server also demands the executon server to transfer the result data to the optmal data server. The dynamc system management server copes the computng data and sends the compressed computng data to another optmal data server n order for a robust data storage system. The clents can deploy ther programs, execute jobs and retreve the result data by accessng only the web page n the dynamc system management server. Ths job executon management server also has a functon of automatc system constructon, so that the users can manage the setup of the job executon management system easly on ther closed dstrbuted computers. Dynamc assstant server Dynamc system management server Web browser Clent 5. Conclusons In ths paper we presented the dstrbuted PSE of D- NCAS to help users work on dstrbuted computers. The role and vablty of the PSE n the dstrbuted computer system are demonstrated. The PSE server provdes a smooth and flexble envronment n the HPC on the dstrbuted computers. The dstrbuted PSE supports generaton of smulaton program and ts documentaton for PDEs-based problems, and also supports the job executon task on a dstrbuted computer envronment. The job executon servce module n the dstrbuted PSE encapsulates the complex nformaton of dstrbuted system so that on the PSE users can perform HPC as f dstrbuted computers are under users hand. The dstrbuted PSE may open a new envronment for HPC world. Acknowledgements Ths work was partly supported by the NAREGI (Natonal Research Grd ntatve) project n Japan. The authors would lke to express ther apprecatons to Prof. K. Mura ( the leader of the NAREGI project ), Dr. Motohro Yamada, Dr. Yutaka Myahara, Prof. yosho Tago, Prof. Yuko Umetan and Dr. Hroyuk Kanazawa for ther frutful dscussons on ths subject. References Synchronzaton SSL MPI executon server Job executon and data servers Job executon servce system Job submsson, Acquston of result data etc. Fg. 13. Structure of the job executon servce system

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