File - GARUDA Access Portal
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1. be the protein database present in the current working directory and outputfilename can be of user s choice The input file the protein query sequence for blast program needs to be uploaded by Browse a Once the user clicks on Run button the client code will run on the SOA grid node where the service is hosted Client code will automatically invoke the Service and will pass the above values as input to the Service Once the outputs are generated user can download them from the following page AGSG User Manual Page 15 of 17 CDAC Servlet ServiceResult Mozilla Firefox File Edit wiew History Bookmarks Tools Help QB Cc x A EE http 192 168 60 40 8087 AG56Client ServiceResut Most Visited 4 Getting Started Latest Headlines ouie v dovoad Figure 4 User Interface to download output This is the download page From this page the user can select the output file to save the output of Service execution AGSG User Manual Page 16 of 17 CDAC 4 Contact Details Center for Development of Advanced Computing Address CDAC Knowledge Park No 1 Old Madras Road Opp HAL Aero engine Div Byappanahalli Bangalore 560038 URL www cdac in Email ssg cdac in Tel No 080 66116320 Fax No 080 25247724 AGSG User Manual Page 17 of 172. directory there is no need to give any Command Line arguments AGSG User Manual Page 12 of 17 CDAC 3 1 2 Advanced Service Creation When some application runs it requires a specific directory structure to be present at run time This specific directory structure can be given as explained below vi Project Directory Structure Optional If user wants the executable input files and any supported library files under one project directory the structure of project directory can be specified by him For example if a project directory structure contain a lib and input subdirectories then it can be specified as shown in figure below This will create the directories lt applicationname gt lib and lt applicationname gt input under the application directory lib input vii Output Directory structure Optional If user wants all the outputs to be placed in a particular directory then he can mention the output directory structure Ex Outputs All outputs will be sent to lt applicationname gt Outputs viii Supported Files Optional a Additional Files If the application needs any additional or supported files these can upload by browsing and uploading the files from the local machine b Library Files User can also upload any required library files These library files will be linked with LD_LIBRARY_PATH E enekivencki Pol Browse J Clickto ADD Library files User can upload multiple
3. libraries by clicking Click to add Library files And if any directory structure needs to be maintained for the library files the user can specify AGSG User Manual Page 13 of 17 CDAC the same in Relative Path in Application Directory Structure This is optional 3 2 Service Deployment After filling in the AGSG form User can click on Create Service for generation of service This process will generate a Grid ARchive GAR file The service that is generated is bundled into a GAR file This gar file needs to be deployed into globus container on the suitable SOA based grid nodes Since the GAR file needs to be deployed in the Globus container it can be done only by the Grid Administrator Hence user needs to send an e mail request to the GARUDA System Administrator s of the grid center where he desires to deploy the service The tool automatically generates a mail along with the gar file attachment Figure below shows the template for requesting deployment of service The User only needs to provide his her mail id in the From address field The gar file sent will be deployed by the System Administrator Once the service is deployed the System Administrator has to send a mail notification to the user providing the URI of the service Client can use this service URI later for future job submissions GG BLR Admin mohans cdacb ermet in Deploy GAR File Dear Sir Madam I have created a service called Ma
4. or any datatype supported by java language b Executable followed by multiple parameters Ex exec i inputfile1 p1 parami p2 param2 p3 param3 p4 param4 Input parameters having options as pvalue1 having option param1 c Executable followed by input and multiple parameters Ex exec inputfile1 p1 param p2 param2 p3 param3 d Executable with input as stdin Ex exec lt inputfile1 e Executable followed by parameter values AGSG User Manual Page 9 of 17 CDAC Ex exec param param2 param3 f Redirecting default output stdout to a file Ex exec gt outfile g Executable only Input file taken by default Input file should be available in current working directory Case a exec inputfile1 inputfile2 Where the inputfile1 and inputfile2 are parameters of the type file Suppose an executable accepts two matrices i e MatixA and MatrixB as input file for addition Note Input parameter name can be given according to user s choice Datatype File can only be given in case user uploads any file as input from client code If input file is already present in the current working directory when file is uploaded as supported file then the Datatype of input file should be String Case b exec i inputfile1 p1 param p2 param2 p3 param3 p4 param4 In case b the application executable needs multiple input parameters In such case user needs to give the types of each parameter value of ea
5. CDAC Automatic Grid Service Generator Version 1 0 USER MANUAL Wish CDAC Table of Contents 2 3 AGSG PRAUIIGS vciiucnsisvadsnsirnscourioneseusiedinoneceiniduncerciourdouvaduscedeneusieindsmeneniniusisisesensusnes 6 3 Generating Grid Service amp Corresponding Client csccsccccccccccesssssssssessesseeees 8 o A E EAE OTEO E AEE A TEA E AI EE AE EAE E 8 EE G 3s nC eee a eee ee reer e Te eee een emer ener eer cen er eee ern 15 a el xg 1S dl 110 gt ee eee ee eee EA a eer Eevee eee eee a eee ener er 16 Ue E ceded eaten nig eh ent gs edged a 18 AGSG User Manual Page 2 of 17 CDAC 1 Introduction The Automatic Grid Service Generator AGSG is a web tool to automatically generate Grid services It can convert an existing executable file as a grid service The AGSG tool can work on any Globus 4 x based grid This tool is useful for application developers or programmers who wish to build a Grid Service from his her application 1 1 Grid Services Overview Grid Services are like Web Services but with improved characteristics to address fundamental issues in distributed grid computing relating to how to name create discover monitor and manage the lifetime of stateful services Grid Services are Stateful and potentially transient services support Notifications PortType extension Lifecycle management etc A Grid Service adheres to the WSRF OGSI specification The layered diagram below shows the relat
6. ce the grid service is deployed a URI Uniform Resource Identifier is generated and multiple clients users can invoke the service using the URI The URI will be like this https lt IP_Address Port_Number gt wsrf services lt ApplicationPackageNa me gt lt ServiceName gt Service For Example If Math is service name and package of application is example core first then URI will be https 192 168 60 168 8443 wsrf services examples core first MathService AGSG User Manual Page 4 of 17 CDAC 2 AGSG Tool 2 1 Pre Requisites User should preferably use Browser IE Version 6 0 and above or Mozilla Firefox 3 0 7 and above 2 2 Accessing the AGSG Tool The tool can be accessed from any machine connected to the GARUDA grid through the Garuda Portal Note Garuda Portal URI is http 192 168 60 40 GridPortal1 3 on Garuda network or http 203 200 36 236 GridPortal1 3 via internet In order to access the AGSG tool click the Service Generator link in the Garuda Portal The Service Generator link has two sub links called Service Creator and Service Invoker e Click Service Creator link for creating a new Grid Service and e Click Service Invoker link for invoking a published service using its URI 2 3 AGSG Features The Automatic Grid Service Generator tool can generate Grid services from already existing executable files It frees the user from the complexity involved in maki
7. ch parameter and order if any to be maintained Then the parameters need to be specified in AGSG interface Suppose if parameter for the application is optional i e the client may may not use this parameter while invoking the service Such optional parameters of the service can be specified by ticking the optional check box Description for each parameter can be provided in Description field inputfile NOME d param BBENONE io Sara For example The Basic Local Alignment Search Tool BLAST is a bio informatics application which does sequence analysis on protein database to search for a sequence of Amino Acid AGSG User Manual Page 10 of 17 CDAC The command line execution for BLAST application is executable p lt program name gt i lt File Containing query string gt d lt Database file gt o lt Output file gt blastall p blastp i hahu aa d yeast aa o outfile p is for program name i input file name contains query sequence to search d Database file sequence database file containing multiple sequences o output file name So the inputs parameters required for this application is specified in the AGSG interface as shown below Se ate Serio FO reeset Case c exec inputfile1 p1 param1 p2 param2 p3 param3 In some cases the input parameter to executable have label As param1 param2 pram3 have labels p1 p2 and p3 respectively Inputfile1 does not have label Suppo
8. erested to use this service can understand what it does Ex MathMulFunction is used for matrix multiplication MathMulFunction can be used for matrix multiplication It requires 2 input square matrices with equal dimensions iii Select Cluster and Enter Home Directory In this field the user should select the cluster where the application is pre compiled and he wants to use this pre compiled executable of his application for creating a Grid Service User also needs to provide his home directory path in the selected cluster AGSG User Manual Page 8 of 17 CDAC GG CHE fhome mohans iv Upload Executable file User needs to upload the required executable file If user is using an interpreted language to develop his application then the corresponding interpreter must be specified in the provided field iv Relative Path in Application Directory Structure Optional Some applications require that the executable should reside in particular directory In such cases the path can be supplied with this field Relative Path in Application Directory Structure v Input Parameters The input parameters if any required by the application can be given in this field There may be some applications that do not require any input and some applications which require multiple inputs For Example a Executable name followed by either one input or multiple inputs Ex exec inputfile1 inputfile2 Input can be file
9. ionship between the Open Grid Services Architecture OGSA Web Services Resource Framework WSRF and Globus Toolkit 4 GT4 Standards in the works GGF VO management Security Grid applications are based Applications Resource management on the high level services Job Management defined by OGSA Data services i e not implemented from OGSA etc ankaa biel GT4 includes many of the services required by OGSA WSRF Standardized Oasis Web Services and implemented GT4 Standardized W3C and implemented e g Apache Axis Figure 1 Layered Relationship Diagram 1 2 Building a Grid Service Following are the basic steps to create a Grid Service in GT4 1 Define the service s interface Define the public interfaces for the service This is done with GWSDL 2 Implement the service Write the server amp client source files describing the implementtaion of the interface This is done with Java AGSG User Manual Page 3 of 17 CDAC 3 Define the deployment parameters Specify the container level service configuration information This is done with WSDD and JNDI 4 Compile everything and generate GAR file This is done with Ant Ant is an open source tool similar to make that helps to build large projects 5 Deploy service The service will execute in a hosting environment i e the service container of the Globus Toolkit 4 Hence the gar file has to be deployed inside the globus container On
10. ng a grid service steps discussed in Section 1 2 The AGSG tool internally creates files such as GWSDL WSDD JNDI and Service Implementation which are required while generating a grid service The features of AGSG are e Web Based tool e User Friendly GUI e Frees user from the complexity involved in making a grid service e Converts an executable file as a grid service e Support executables of different languages C C Fortran 77 amp 90 e Supports both compiled and interpreted language applications e Globus 4 x based grid AGSG User Manual Page 5 of 17 CDAC e Client stub generation e Client code generation Required for invoking a service e Generic Interface tested with different types of applications having different types and number of I O parameters e Enables Service generation and deployment on heterogeneous resources of GARUDA AGSG User Manual Page 6 of 17 3 Generati CDAC ng Grid Service amp Corresponding Client 3 1 Service Creator The Service Creator helps to automatically build a Grid Service from an executable file The GUI for Service Creator is shown below GG BLR 7 MathhdulFuctian MathMulFunction can be used for matrix multiplication It requires 42 input square matrices with egual dimentions fmatrixA matrix B Outputs O OO fhomesmohans C Documents and Setting OWS Matrix n put Matrix A S SE Matrix input Matrix B E T None Output ile rec
11. se an executable accepts two matrices i e MatixA and MatrixB as input file for addition And result will be produce in output file which have label o i e exec MatrixA MatrixB o Outputfile Then input parameters required for this application is specified in the AGSG interface as shown below Matrixa First Input matrix Second Input matri utputtile Output File Case d exec lt inputfile1 AGSG User Manual Page 11 of 17 CDAC Executable with input as stdin Suppose an executable accepts a matrix i e MatixA as input file from stdin to calculate Transpose of the matrix Le exec lt MatrixA Then inputs parameters required for this executable specified in the AGSG interface as shown below Delete Row Case e exec parami param2 param3 Executable followed by parameter values Suppose an executable calculate age of the user by accepting date of birth as input le exec Day Month Year Then inputs parameters required for this executable specified in the AGSG interface as shown below In this example there are no labels given to any of the parameters only the Description and Datatype of each parameter is specified Case f In case the output from the default output stdout needs to be redirected to a particular output file NONE i S Case g In case no parameter is required for the executable to run and by default if it picks the required input file from current
12. th Hence I need to deploy the GAR file in the globus container at GG BLAR I am sending GAR file as attachment Please Deploy the GAR File Thanks fhome agsg Math senice_ Figure 3 Request for deployment of GAR AGSG User Manual Page 14 of 17 CDAC 3 3 Service Invoker This is the client code to invoke the service generated this tool provides a GUI for invoking the service The client can be accessed from any machine connected to the GARUDA grid through the Garuda Portal using the links Service Generator gt Service Invoker The Service Invoker has a simple interface which accepts the URI of the published service and the corresponding parameters It invokes the service User should supply the URI in the Enter Service URI Once the URI is entered and submitted an interface will pop up showing the details of the required input parameters The service will run on target machine and output the results In the following example user at the time of service creation has given four input parameters as follows a programname of String Datatype with Label as p b inputfile of File Datatype with Label as i c databasename of String Datatype with Label as d d outputfilename of String Datatype with Label as o Now the user client needs to provide the value for programname inputfile databasename and outputfilename Ex For BLAST application programname will be blastp or blastn databasename will
13. ut ENE O fe z i i Cr armany Arr nents Ti B Figure 2 User Interface e In order to create a service the user needs to provide the following information Service Name Service Description Select cluster and Enter home directory on selected cluster Upload Executable file Specify Interpreter Input Parameters Project Directory Structure optional Output Directory structure optional Supported Files Optional AGSG User Manual Page 7 of 17 CDAC e Mandatory fields are marked with e Online help can be obtained for each feature by clinking the Each of these fields are illustrated with an example in this document 3 1 1 Basic Service Creation i Service name The user should give a name for the service to be generated It should be unique The service generated will be identified with this name For Example if service name is given as MathMulFunction MathhulFunction The URI Uniform Resource Identifier generated for the service will be like this https lt IP_Address Port_Number gt wsrf services lt ApplicationPackageName gt lt ServiceName gt Service For Example If MathMulFunction is service name and package of application is example core first then URI will be https 192 168 60 168 8443 wsrf services examples core first MathMulFu nctionService ii Service Description In this field the user should give a brief description of what the service offers so that people int
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