File - GARUDA Access Portal
Contents
1. scssessssessesseeeees 14 Appendix 3 Resource Specification Language e sseesssesssesssecssocssoossosossoossssesssoessoosso 15 Appendix 4 MyPrOXy wicscscisccsnsccosssciancdecscsssnacsconvcsssnsssesesiovebeaseoniescesens ensesoenssseressoncssen 16 Kepler Workflow User Guide June 2010 Version 1 0 Page i CDAC Chapter 1 Introduction 1 0 Kepler Kepler is free and open source scientific workflow designed to help scientists analysts and computer programmers create execute and share models and analyses across a broad range of scientific and engineering disciplines The Kepler software is developed and maintained by the cross project Kepler collaboration which is led by a team consisting of several key institutions that originated the project UC Davis UC Santa Barbara and UC San Diego Kepler is a java based application that is maintained for the Windows OSX and Linux operating systems The Kepler Project supports the official code base for Kepler development as well as provides user manuals mechanism to report bugs suggest enhancements discussion forum etc Kepler allows the user to create a workflow and execute the same from GUI Once created a workflow can also be run from command line as it allows saving a workflow in xml or kar format and executed via command line 1 1 Kepler Features Kepler provides a graphical user interface and a run time engine that can execute workflows either from within2. Usage garuda_job_ submit lt garuda_resv_id gt lt gridway job_template gt Example garuda_job_ submit 99 gg hyd cdac org in tmp test jt Modifying a grid compute reservation opt garudaresv bin garuda_compute_ reserve modify command can be used to modify an unexpired compute node reservation Usage garuda_compute_reserve modify lt garuda resv_id gt lt number_of_nodes gt Example garuda compute reserve modify 99 gg hyd cdac org in 1 Kepler Workflow User Guide June 2010 Version 1 0 Page 14 CDAC Appendix 3 Resource Specification Language RSL Common notation for exchange of information between components RSL provides e Resource requirements Machine type number of nodes memory etc e Job configuration executable path arguments environment etc Important RSL tags Argument count Directory environment Executable job jobType stdin stdout stderr queue Simple RSL example lt job gt lt executable gt bin echo lt executable gt lt argument gt Welcome to C DAC lt argument gt lt environment gt lt name gt LD LIBRARY PATH lt name gt lt value gt home soademo lib lt value gt lt environment gt lt queue gt batch lt queue gt lt job gt RSL MPI Job lt job gt lt executable gt tmp hello lt executable gt lt argument gt C DAC lt argument gt lt directory gt home soademo tools lt directory gt lt stdin gt dev null lt stdin gt lt stdout gt stdout GLOBUS USER N
3. 0 Page 9 CDAC Chapter 4 Frequently Asked Questions 1 How can I start kepler Login to gateway m c through ssh and to gridfs m s cd usr local EADS_AAOW kepler sh Before this pls check if the JAVA _ HOME is set to usr local jdk1 6 0_1 And ANT HOME is set to usr local EADS_AAOW ant apache ant 1 8 0 And path set as ANT_HOME bin 2 How can I invoke the grid actors Since the globus4 0 7 is not present in the kepler repository it has to be manually instantiated onto the workflow canvas To instantiate a component on the menu bar Tools gt Instantiate component gt Type in the correct class name of the component to be instantiated For instance some of the globus actors and their classnames Actor classname GlobusWSJob org kepler actor globus wsgram GlobusWSJob MyProxy org kepler actor MyProxy GridFtpCopy org kepler actor globus GridFtpCopy 3 How to connect the actors Once the actors have been instantiated on the workflow canvas each actor has to be connected which can be done by clicking on of the port and dragging it until the other actor s port 4 How can an actor be configured Each actor has to be configured which can be done either by double clicking the actor or by right click gt configure actor Enter the appropriate values and commit the entries 5 What is a director Kepler uses a director actor metaphor to visually represent the various components of a workflow A director controls
4. or directs the execution of a workflow just as a film director oversees a cast and crew The actors take their execution instructions from the Kepler Workflow User Guide June 2010 Version 1 0 Page 10 CDAC director In other words actors specify what processing occurs while the director specifies when it occurs Each workflow must have a director that controls the execution of the workflow using a particular model of computation For example workflow execution can be synchronous with processing occurring one component at a time in a pre calculated sequence SDF Director Alternatively workflow components can execute in parallel with one or more components running simultaneously which might be the case with a PN Director For more details refer Kepler User Manual Appendix 1 6 How to run a workflow To run the workflow click on the play gt button from the toolbar Otherwise the workflow can be run through the command line also with the following command ant run workflow no gui Dworkflow Sample xml 7 Can I run the workflow from command line With the following comman gui will not be invoked and you can run workflow ant run workflow no gui Dworkflow Sample xml 8 How to make an RSL file A sample rsl file is listed lt job gt lt executable gt testgg lt executable gt lt environment gt lt name gt GARUDA_RESV_ID lt name gt lt value gt R714 gg blr tfg lt value lt en
5. AME lt stdout gt lt stderr gt stderr execution lt stderr gt lt count gt 2 lt count gt lt jobType gt mpi lt jobType gt lt job gt For complete syntax of the Resource Specification Language RSL refer http www globus org toolkit docs 4 0 execution wsgram schemas gram_job_descript ion html Kepler Workflow User Guide June 2010 Version 1 0 Page 15 CDAC Appendix 4 MyProxy MyProxy Usage Instructions MyProxy is a open source software for managing X 509 Public Key Infrastructure PKI security credentials certificates and private keys It combines an online credential repository with an online certificate authority It allows users to securely obtain credentials when and where needed The advantage of using MyProxy is that the user need not keep their Certificates on Grid instead they can upload and get certificate from the secured Myproxy Server whenever required Storing a credential in the MyProxy repository Rather than storing your X 509 credentials certificate and private key on each machine you use you can store them in a MyProxy repository and retrieve a proxy credential from the MyProxy repository when needed To store a credential in the MyProxy repository run the myproxy init command on a computer where your Grid credentials are located For example myproxy info username gridmon owner DC IN DC GARUDAINDIA O C DAC OU CTSF CN Karuna karunap cdacb ernet in timele
6. For Kepler to be visible from remote machine a visual sharing tool like XManager needs to be used The X11 on gridfs machine has been enabled for desktop sharing 1 4 Pre requisite software e JAVA ver 1 6 e ANT ver 1 8 e Xmanager 2 0 or greater on client machine Kepler Workflow User Guide June 2010 Version 1 0 Page 2 CDAC Chapter 2 Usage Instructions 2 0 Procedure for Access to Kepler on GARUDA 1 Kepler is installed at grid headnode gridfs 203 200 36 236 at usr local EADS_AAOW ssh 203 200 36 236 1 username 2 For remotely accessing the Kepler GUI following are the steps a Invoke the Xmanager client on local desktop Xstart b In the Xstart dialog box the Execution Command field is used to specify whether to open complete remote desktop or only the remote terminal Hence Execution Command can have Execution Command usr bin gnome session display SDISPLAY Execution Command xterm c Fill out the Xstart dialog box and Run Xstart Session S gridfs z Save Host 203 200 36 236 7 SaveAs _ Protocol SSH 7 Setup Delete User Name Jaridmon Shortcut Password Execution Command ust bin gnome session display DISPLAY gt Options ji V Show status dialog box ii Show reply messages lose To configure advanced options click the Advanced button Advanced Help Figure 1 A sample Xstart Dialog Box Kepler Workflow
7. User Guide June 2010 Version 1 0 Page 3 CDAC 2 1 d Set the Environment variable and Path as below export JAVA_HOME usr local jdk1 6 0 10 export ANT _HOME usr local EADS AAOW ant apache ant 1 8 0 export PATH PATH SANT _HOME bin e Invoke Kepler through kepler sh Procedure for Job Submission on GARUDA Step 1 Reserving the resources When a person needs to submit a job to GARUDA he should first identify the resource RESERVATION of the GARUDA resources needs to be performed The Reservation ID obtained should be saved to be mentioned in the RSL file or Job script content Reservation command garuda_compute_reserve gg blr tfg 2010 04 20T11 30 00 2010 04 21T18 58 28 2 Output of Reservation Command R714 gg blr tfg Step 2 Check the credentials Submitting a job requires a valid proxy which is nothing but a short lived credential The user s credentials should be alive otherwise it needs to be invoked Proxy information can be obtained with the help of grid proxy info command grid proxy info subject DC IN DC GARUDAINDIA O C DAC OU CTSF CN Karuna karunap cdacb ernet in CN 237891045 CN 2012224773 CN 744875709 issuer DC IN DC GARUDAINDIA O C DAC OU CTSF CN Karuna karunap cdacb ernet in CN 237891045 CN 2012224773 identity DC IN DC GARUDAINDIA O C DAC OU CTSF CN Karuna karunap cdacb ernet in type Proxy draft pre RFC compliant impersonation proxy streng
8. ft 0 00 00 S myproxy init Your identity DC IN DC GARUDAINDIA 0O C DAC OU CTSF CN Karuna karunap cdacb ernet in E Enter GRID pass phrase for this identity Creating PrOXY sie hall tii ere We Se ae a ee E Done Proxy Verify OK Your proxy is valid until Mon Jun 14 14 40 18 2010 Enter MyProxy pass phrase Verifying Enter MyProxy pass phrase A proxy valid for 168 hours 7 0 days for user gridmon now exists on hyd0l The myproxy init command prompts first for the pass phrase of your private key similar to grid proxy init and then prompts twice for a new pass phrase to use to secure the credentials on the MyProxy server By default the credential is stored under your Unix username for 7 days and can be used to retrieve credentials with 12 hour lifetimes Kepler Workflow User Guide June 2010 Version 1 0 Page 16 CDAC Retrieving a credential from the MyProxy repository Once you ve stored a credential in the MyProxy repository you can retrieve a proxy credential whenever you need one with the myproxy logon command For example myproxy logon s hyd0l Enter MyProxy pass phrase A credential has been received for user gridmon in tmp x509up u502 The myproxy logon command prompts for the pass phrase you set previously with myproxy init retrieves a proxy credential for you and stores it in the correct default location for use with other Globu
9. h fusr local GARUDA GLOBUS 4 0 7 AXIS ClientConfigFile Path Jusr local GARUDA GLOBUS 4 0 7 client config wsdd Add Remove Restore Defaults Preferences Help Cancel 1 Job Script Content This parameter gives the details of the job to be executed by the particular actor The complete RSL file can be copy paste into this field Please ensure that no extra white spaces are included inadvertently 2 Globus Host This parameter indicates which machine cluster in which the job should execute As it is desired to run on the GG BLR cluster of Garuda grid please mention gg blr tfg in this field 3 Batch Mode The default is taken as batch job 4 Job Scheduler Type Job scheduling on the GG BLR cluster is accomplished by the Portable Batch System PBS The appropriate job scheduler should be given in this parameter 5 GLOBUS_LOCATION Path The absolute path on the cluster GG BLR in this case where Globus is installed 6 AXISClientConfigFilePath The absolute path of the client config wsdd in the GLOBUS_LOCATION Step 6 Executing the Workflow Once the workflow is created it can be run from the GUI click on the play gt button from the toolbar Also the workflow can be run through the command line also with the following command ant run workflow no gui Dworkflow lt saved workflow name gt E g ant run workflow no gui Dworkflow lt sample xml gt ant run workflow no gui Dworkflow lt my
10. he commands related to grid compute node reservation are located at opt garudaresv bin directory of gridfs ctsf cdac org in machine Command for getting the free resources in a particular time slot opt garudaresv bin garuda_freeresources can be used to find the free compute nodes available in a particular time slot This command will return the cluster FQDN with number of free cpus Usage garuda_freeresources lt start_time gt lt end_time gt Example garuda_freeresources 2008 08 05T 14 38 28 2008 08 05T 14 58 28 The date and time that appears as single digit must be made to double digit by prepending 0 For example August 5 2008 must be specified as 2008 08 05 and not 2008 8 5 Same is applicable to time also Making a compute reservation The command opt garudaresv bin garuda_ compute reserve can be used to create a compute reservation This command will return the grid reservation id for the corresponding reservation slot Usage garuda compute reserve lt Cluster FQDN gt lt start_time gt lt end_time gt lt number_of CPU gt Example garuda_compute_reserve gg hyd cdac org in 2008 08 05T 14 38 28 2008 08 05T 14 58 28 1 Job submission with reservation id The command opt garudaresv bin garuda_job_ submit can be used to submit jobs in a cluster corresponding to a compute node reservation The command must be used to submit job only when the corresponding reservation slot is running or active
11. on Language RSL script to describe the executable input output and other parameters of the job An Example RSL file is shown below lt executable gt bin echo lt executable gt lt argument gt Welcome to C DAC lt argument gt lt environment gt lt name gt LD LIBRARY PATH lt name gt lt value gt home soademo lib lt value gt lt environment gt lt queue gt batch lt queue gt lt job gt For complete syntax of the Resource Specification Language RSL Script file to be used on Globus based GARUDA grid please refer Appendix 3 For each job submission actor in the workflow the corresponding job description file can be obtained by tweaking the sample RSL above The RSL has to be given as input in the Job Script Content of the Kepler GlobusWSJob actor Step 5 Create the workflow using Kepler actors Kepler uses the GlobusWSJob actor for submitting jobs to Globus Globus WSJob actor parameters are as shown in figure 1 Job Script Content 2 Globus Host 3 Batch Mode 4 Job Scheduler Type 5 GLOBUS_LOCATION Path 6 AXISClientConfigFilePath Kepler Workflow User Guide June 2010 Version 1 0 Page 6 Oma parameters for GlobusWSJob a Job Script Content r gt lt count gt 8 lt count gt lt jobType gt mpi lt jobType gt lt queue gt default lt queue gt lt job gt Globus Host gg blr tfg Batch Mode v Job Scheduler Type PBS GLOBUS_LOCATION Pat
12. s Toolkit programs The detailed list of MyProxy Command reference can be found at http www globus org toolkit docs 4 0 security myproxy Cred_Mgmt MyProxy Inter face _Commandline Frag html or MyProxy Information Kepler Workflow User Guide June 2010 Version 1 0 Page 17
13. th 1024 bits path tmp x509up u502 timeleft 0 00 00 Kepler Workflow User Guide June 2010 Version 1 0 Page 4 Proxy can be created by the grid proxy init command grid proxy init Your identity DC IN DC GARUDAINDIA O C DAC OU CTSF CN Karuna karunap cdacb ernet in Enter GRID pass phrase for this identity Creating proxy Done Your proxy is valid until Tue Jun 8 02 38 47 2010 The job will get a limited proxy Step 3 Upload credentials to MyProxy Now user has valid credentials to submit a job in GARUDA grid Certificates should be available in My proxy server myproxy init Your identity DC IN DC GARUDAINDIA O C DAC OU CTSF CN Karuna karunap cdacb ernet in Enter GRID pass phrase for this identity Creating proxy Done Proxy Verify OK Your proxy is valid until Mon Jun 14 14 40 18 2010 Enter MyProxy pass phrase Verifying Enter MyProxy pass phrase A proxy valid for 168 hours 7 0 days for user gridmon now exists on hyd0l For retrieving the certificates myproxy logon s hyd01 Enter MyProxy pass phrase A credential has been received for user gridmon in tmp x509up _u502 For complete usage instructions of MyProxy please refer Appendix 4 Kepler Workflow User Guide June 2010 Version 1 0 Page 5 CDAC Step 4 Create Job Description The job description file has to be input into the Globus job submission actor Globus uses a Resource Specificati
14. the graphical interface or from a command line Kepler uses a director actor metaphor to visually represent the various components of a workflow A director controls or directs the execution of a workflow The actors take their execution instructions from the director In other words actors specify what processing occurs while the director specifies when it occurs Actors are ready to use processing components that can be easily customized connected and then run to perform complex applications efficiently Kepler has a searchable library containing nearly 350 actors Kepler workflows can be nested allowing complex tasks to be composed from simpler components Kepler workflows can leverage the computational power of grid technologies e g Globus SRB etc It supports job submission actor for Globus MyProxy actor for authentication and GridFTP actor for file transfer Kepler workflows and customized components can be saved reused and shared with colleagues using the Kepler ARchive format KAR 1 2 GARUDA Grid GARUDA is a nation wide grid spread across 17 cities of the country comprising of collaboration of science researchers computational nodes mass storage and scientific instruments with an aim to provide the technological advances required to enable data and compute intensive science for the 21st century GARUDA is based on the Globus Toolkit 4 0 7 The Globus Alliance has adopted the Open Grid Standards Infras
15. tructure OGSI standards based on convergence of Web Kepler Workflow User Guide June 2010 Version 1 0 Page 1 CDAC Services and Grid Computing technology The various technology components of GARUDA include a Portal for access and job submission program development tools scheduler reservation manger and storage resource manager and tools for monitoring and management of the system Access to GARUDA is through certificates obtained from the Indian Grid Certification Authority IGCA The GARUDA grid has a grid head node to which various compute resources are connected The cluster under consideration for this project is composed of Xeon Quad Core Dual CPU Processor X5460 nodes having 16GB RAM connected by Infiniband with RHEL 5 1 on Rocks v5 0 The GARUDA grid can be accessed from Internet through the gateway machine 1 3 Kepler on GARUDA Grid Kepler development version 2 0 has been identified based on discussion with the Kepler Forum as it provides Job Submission Actors for Globus The Kepler source code was compiled on the grid head node referred to as Gridfs IP as 203 200 36 236 The Kepler actor packages are deployed on Gridfs at usr local EADS_AAOW The job submission actor requires inputs Job script content which is an RSL script Cluster name Globus path and Scheduler type The executable name needs to be mentioned in the rsl script tag as lt executable gt executablename lt executable gt
16. ver 1 0 June 2010 Submitted to Zeus Numerix Pvt Ltd amp EADS Bangalore India CDAC CENTRE FOR DEVELOPMENT OF ADVANCED COMPUTING C DAC Knowledge Park No 1 Old Madras Road Byappanahalli Bangalore 560 038 Tel 91 80 2534 1909 Fax 91 80 2524 7724 www cdacb in CDAC Table of Contents Chapter 1 Introducti n issssssssisssssssossossssssesosssoesossossoosso ssoossssssecosssoossss svevo osssooossss soss 1 1 0 DEB og ase E E E E E E de te deter enmensetaieece 1 1 1 Kepler Feature Sns eers eanne eera eaeau E EEE A ET ORERE EEES T ERT Ti 1 1 2 GARUDA Grider Cseesedigassisines boep aas ar aaun EN Aa EIAS Eaa DEE aE O Ea 1 1 3 Kepl r on GARUDA Gils psucsipatccaibnacanisaasistacntiananieaaaieainaaiiancsteaeene 2 1 4 Pre requisite software spine caidcaccansabeatsecnsdaer aurenuirrnnere etn nennees 2 Chapter 2 Usage Instructions us cidconcdcmiuciconniminiunimandinaumanimanna 3 2 0 PROCEDURE FOR ACCESS TO GARUDA s ssssesssesssersseessresreeesseetsseesstersteereressreessees 3 2 1 Procedure for Job Submission on GARUDA sssssssssssessseesssssssseessessrssressesse 4 Chapter 3 Testing ienniaseaaicnun cieaniansnioanienuanniind aban mancueaiaen 8 Chapter 4 Frequently Asked Questions sccccssccssssecssscccsssscsscsssscssssssesssscssesees 10 Appendix 1 Detailed Kepler User Manual sccscssccssssccscsccsscssescsssssscssssceeeene 13 Appendix 2 GARUDA Compute Reservation Commands
17. vironment gt lt stdout gt home tools gridmon kepler stdout testgg23 out wrapper lt stdout gt lt stderr gt home tools gridmon kepler stdout testgg23 err wrapper lt stderr gt lt count gt 8 lt count gt lt jobType gt mpi lt jobType gt lt queue gt default lt queue gt lt job gt 9 What is the command to obtain the reservation ID garuda_compute_ reserve gg blr tfg 2010 04 20T 11 30 00 2010 04 21T18 58 28 2 Refer Appendix 2 10 What are the parameters of the GlobusWSjob actor GlobusWSJob actor parameters are 1 Job Script Content Kepler Workflow User Guide June 2010 Version 1 0 Page 11 CDAC 2 Globus Host 3 Batch Mode 4 Job Scheduler Type 5 GLOBUS_LOCATION Path 6 AXISClientConfigFilePath usr local GARUDA GLOBUS 4 0 7 client config wsdd 11 Can workflows be saved and run at later point of time It can be saved and run as ant run workflow no gui Dworkflow Test xml Kepler Workflow User Guide June 2010 Version 1 0 Page 12 CDAC Appendix 1 Detailed Kepler User Manual The project website http www kepler project org contains the complete source code and documentation for Kepler Workflow software The Kepler User manual is available at https kepler project org users documentation Kepler Workflow User Guide June 2010 Version 1 0 Page 13 CDAC Appendix 2 GARUDA Compute Reservation Commands GARUDA grid compute reservations commands T
18. workflow kar gt Note A workflow can be saved from the File gt Save menu in xml or kar Kepler Workflow User Guide June 2010 Version 1 0 Page 7 CDAC Chapter 3 Testing Exhaustive testing has been done with the Kepler deployed on GARUDA Workflows containing combination of both serial and parallel MPT jobs were tried out Also Kepler was tested for access and job submission from different user logins Testing of the Kepler tool has been carried out with respect to the following Job submission Actor of Kepler for both sequential and parallel job submission MPI and Pthread jobs RSL with Reservation ID GARUDA certificates MyProxy Small workflow submission Both GUI and command line Kepler toolbars through remote visualization Access via Internet Ds get Bee UYN a j v D u a bsi aF ag h a a OL e EAE ATRAE tow Paine i q wee dearth I umpunenis IE cour m D encase Bi wan M E Ery Figure 1 A sample workflow using SDF director using Gloubs WSJob and GridFtpCopy actor SDF Synchronous Dataflow Refer Chapter 4 FAQ 5 Kepler Workflow User Guide June 2010 Version 1 0 Page 8 CDAC t d Dirinte ula urA dig w A heme A FPF te AEA Enga He i n A A athlewenas Figure 3 Submitting of jobs using PN director PN Process Network Refer Chapter 4 FAQ 5 Kepler Workflow User Guide June 2010 Version 1
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