1. EGEE-II INFSO-RI-031688 Enabling Grids for E-sciencE www.eu-egee.org EGEE and gLite are registered trademarks Job Submission Fokke Dijkstra RuG/SARA Grid tutorial Utrecht September 2007

2. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Contents The LCG Workload Management System (WMS) in gLite Job Submission to EGEE –Job Preparation –A simple example & Job Lifecycle –Job Description Language (JDL) –Job Submission & Monitoring –Some more advanced topics

3. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 WMS ?

4. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 The LCG WMS The user submits jobs via the Workload Management System The Goal of WMS is the distributed scheduling and resource management in a Grid environment. What does it allow Grid users to do? To submit their jobs To execute them To get information about their status To retrieve their output The WMS tries to –Optimize the usage of resources –Execute user jobs as fast as possible

5. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Logging & Bookkeeping (LB) Resource Broker (RB) Job Submission Service (JSS) Storage Element (SE) Computing Element (CE) Information System (BDII) LCG File Catalog (LFC) JDL User Interface (UI) WMS components

6. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Job Preparation You need to provide –A complete (enough) job description  What program?  What data?  Any requirements on OS, installed software, ?? –Possibly a program  You’re submitting in unknown territory!  Program portably!  Don’t rely on hard-coded paths or special locations  The program you send may not even be in $HOME! –Perhaps some input data –Perhaps instructions on what to do with the output

7. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 How to Write a Job Description Here is a minimal job description (call it hello.jdl) We specified –The program to run and its arguments –Directed the standard error and output streams to files –Told it what to do with the output Executable = “/bin/echo”; Arguments = “Goedemiddag”; StdError = “stderr.log”; StdOutput = “stdout.log”; OutputSandbox = {“stderr.log”, “stdout.log”};

8. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Job Submission Example User issues a voms-proxy-init –enters his certificate’s password –Receives a valid Globus proxy User issues a: edg-job-submit mytest.jdl and gets back from the system a unique Job Identifier (JobId) User issues a: edg-job-status JobId to get logging information about the current status of his Job When the “OutputReady” status is reached, the user can issue a edg-job-get-output JobId and the system returns the name of the temporary directory where the job output can be found on the UI machine.

9. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Submitting it $ voms-proxy-init --voms tutor Your identity: /O=edgtutorial/O=users/O=rug/OU=rc/CN=Fokke Dijkstra Enter GRID pass phrase: Creating temporary proxy................................................................. Done Contacting mu4.matrix.sara.nl:30007 [/O=dutchgrid/O=hosts/OU=sara.nl/CN=mu4.matrix.sara.nl] "tutor" Done Creating proxy.............................................. Done Your proxy is valid until Mon Sep 11 23:22:12 2006 $ edg-job-submit hello.jdl Selected Virtual Organisation name (from UI conf file): tutor Connecting to host mu3.matrix.sara.nl, port 7772 Logging to host mu3.matrix.sara.nl, port 9002 ******************************************************************************* JOB SUBMIT OUTCOME The job has been successfully submitted to the Network Server. Use edg-job-status command to check job current status. Your job identifier (edg_jobId) is: - https://mu3.matrix.sara.nl:9000/Nz6PWWJCjtT7YY3PJWDu5Q ******************************************************************************* JobId

10. A Job Submission Example UI JDL Logging & Bookkeeping (LB) Resource Broker (RB) Job Submission Service (JSS) Storage Element (SE) Computing Element (CE) Information System (IS) Job Submit Event Input Sandbox Job Status submitted LCG File Catalog (LFC) User Interface (UI) Job Status waiting

11. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Checking the status $ edg-job-status https://mu3.matrix.sara.nl:9000/Nz6PWWJCjtT7YY3PJWDu5Q ************************************************************* BOOKKEEPING INFORMATION: Status info for the Job : https://mu3.matrix.sara.nl:9000/Nz6PWWJCjtT7YY3PJWDu5Q Current Status: Done (Success) Exit code: 0 Status Reason: Job terminated successfully Destination: mu6.matrix.sara.nl:2119/jobmanager-pbs-long reached on: Tue Jun 1 08:14:25 2004 *************************************************************

12. A Job Submission Example UI JDL Logging & Bookkeeping (LB) Resource Broker (RB) Job Submission Service (JSS) Storage Element (SE) Computing Element (CE) Information System (IS) LCG File Catalog (LFC) Job Status submitted waiting User Interface (UI) Job Status ready BrokerInfo scheduled Job Status running Input Sandbox Output Sandbox doneoutputready

13. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Getting the Output $ edg-job-get-output https://mu3.matrix.sara.nl:9000/Nz6PWWJCjtT7YY3PJWDu5Q Retrieving files from host: mu3.matrix.sara.nl ( for https://mu3.matrix.sara.nl:9000/Nz6PWWJCjtT7YY3PJWDu5Q ) ******************************************************************************* JOB GET OUTPUT OUTCOME Output sandbox files for the job: - https://mu3.matrix.sara.nl:9000/Nz6PWWJCjtT7YY3PJWDu5Q have been successfully retrieved and stored in the directory: /tmp/jobOutput/fokke_Nz6PWWJCjtT7YY3PJWDu5Q ******************************************************************************* $ cat /tmp/jobOutput/fokke_Nz6PWWJCjtT7YY3PJWDu5Q/std.out Goedemiddag

14. A Job Submission Example UI JDL Logging & Bookkeeping (LB) Resource Broker (RB) Job Submission Service (JSS) Storage Element (SE) Computing Element (CE) Information System (IS) LCG File Catalog (LFC) Output Sandbox cleared submitted waiting ready scheduled running done Job Status outputready Job Status

15. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Job Description Language (JDL) Based upon Condor’s CLASSified ADvertisement language (ClassAd) ClassAd is an extensible language Sequence of attributes (key,value pairs) separated by semi-colons. Executable = “/bin/echo”; Arguments = “Goedemiddag”; StdError = “stderr.log”; StdOutput = “stdout.log”; OutputSandbox = {“stderr.log”, “stdout.log”};

16. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Types of Attributes The supported attributes are grouped in two categories: –Job Define the job itself –Resources  Taken into account by the RB for carrying out the matchmaking algorithm  Computing Resource (Attributes) Used to build expressions of Requirements and/or Rank attributes by the user Have to be prefixed with “other.”  Data and Storage resources (Attributes) Input data to process, SE where to store output data, protocols spoken by application when accessing SEs

17. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Job Definition Attributes Executable (mandatory) –The command name Arguments (optional) –Job command line arguments StdInput, StdOutput, StdErr (optional) –Standard input/output/error of the job Environment (optional) –List of environment settings InputSandbox (optional) –List of files on the UI local disk needed by the job for running –The listed files are staged from the UI to the remote CE OutputSandbox (optional) –List of files, generated by the job, which have to be retrieved

18. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Resource Attributes Requirements –Job requirements on computing resources –Specified using attributes of resources published in the Information System –If not specified, default value defined in UI configuration file is considered  Default: other.GlueCEStateStatus == "Production" (the resource has to be in the Production grid) Rank –Expresses preference (how to rank resources that have already met the Requirements expression) –Specified using attributes of resources published in the Information Service –If not specified, default value defined in the UI configuration file is considered  Default: - other.GlueCEStateFreeCPUs (the highest number of free CPUs)

19. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 “Data” Attributes InputData (optional) –Refers to data used as input by the job: these data are published in the Replica Catalog and stored in the SEs) –PFNs and/or LFNs DataAccessProtocol (mandatory if InputData specified) –The protocol or the list of protocols which the application is able to speak with for accessing InputData on a given SE OutputSE (optional) –The hostname of the output SE –RB uses it to choose a CE that is compatible with the job and is close to SE OutputData (optional) –Output Data that will be registered at the end of the job

20. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Example JDL File Executable = “gridTest”; StdError = “stderr.log”; StdOutput = “stdout.log”; InputSandbox = {“/home/joda/test/gridTest”}; OutputSandbox = {“stderr.log”, “stdout.log”}; InputData = “lfn:/grid/tutor/testbed0-00019”; DataAccessProtocol = “gridftp”; Requirements = other.Architecture==“INTEL” && \ other.OpSys==“CentOS” && other.FreeCpus >=4; Rank = “other.GlueHostBenchmarkSF00”;

21. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Job Submission edg-job-submit [–r ] [–n ] [-c ] [-o ] -r the job is submitted by the RB directly to the computing element identified by -c the configuration file is used by the UI instead of the standard configuration file -o the generated edg_jobId is written in the Useful for other commands, e.g.: edg-job-status –i (or edg_jobId) -i the status information about edg_jobId contained in the are displayed --vo the VO under which the job will be run

22. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Other WMS UI Commands edg-job-list-match Lists resources matching a job description Performs the matchmaking without submitting the job edg-job-cancel Cancels a given job edg-job-status Displays the status of the job edg-job-get-output Returns the job-output (the OutputSandbox files) to the user edg-job-get-logging-info Displays logging information about submitted jobs (all the events “pushed” by the various components of the WMS) Very useful for debug purposes

23. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 WMS Match Making The RB is the core component of WMS. It has to find the best suitable computing resource (CE) where the job will be executed It interacts with Data Management service and Information System They supply RB with all the information required for the resolution of the matches The CE chosen by RB has to match the job requirements (e.g. runtime environment, data access requirements, and so on) If 2 or more CEs satisfy all the requirements, the one with the best Rank is chosen

24. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Direct Job submission The RB has to deal with three possible scenarios. Scenario 1: Direct Job Submission  Job is scheduled on a given CE (specified in the edg-job- submit command via –r option)  RB doesn’t perform any matchmaking algorithm  Take care if InputData is specified!

25. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Brokered Job Submission, No InputData Scenario 2: Job Submission without data-access Requirements  Neither CE nor input data are specified.  RB starts the matchmaking algorithm, which consists of two phases: Requirements check (RB contacts the IS to check which CEs satisfy all the requirements) If more than one CE satisfies the job requirements, the CE with the best rank is chosen by the RB

26. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Brokered Job Submission, Grid Data Scenario 3: CE is not specified in the JDL  RB contacts Data Management service to find out which SE’s have copies of the requested input data sets  RB makes best effort match between Computing resources for which user is authorized SE’s “nearby” which can provide the requested data sets via the requested transfer protocol Any optional output SE specified in the job description  RB strategy consists of submitting jobs close to data!  The main two phases of the match making algorithm remain unchanged: Requirements check Rank computation  The matchmaking is only performed for CEs satisfying the data-access requirements (i.e. which are close to data)

27. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Proxy Renewal Why? –To avoid job failure because it outlived the validity of the initial proxy WMS support automatic proxy renewal mechanism as long as the user credentials are handled by a proxy server. 1.Create a proxy using voms-proxy-init 2.Register this proxy with the MyProxy server using myproxy-init –s [-t -c ] –d -n server is the server address (e.g. px.matrix.sara.nl) cred is the number of hours the proxy should be valid on the server proxy is the number of hours renewed proxies should be valid 3.Short term proxies can then be used to start jobs using grid-proxy-init –hours command 4.The Proxy is automatic renewed by WMS without user intervention for all the job life

28. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 MPI jobs MPI –Message passing –Link with parallel library –Run on multiple processors gLite –Limited support –Some sites can run MPI jobs JobType –JobType=”MPICH”; –NodeNumber = 8; –Adds MPICH support as requirement –Executable run in paralllel on 8 CPU’s

29. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Other JobTypes Interactive –StdOutput, StdInput and StdError forwarded to user –default X window –Other tools Checkpointable –Job must save checkpoints –Checkpoints can be retrieved –Not fully supported yet

30. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Further Information The gLite User Guide! http://glite.web.cern.ch/glite/documentation/default.asp ClassAd https://www.cs.wisc.edu/condor/classad/ https://www.cs.wisc.edu/condor/classad/ Sara Grid pages http://www.sara.nl/userinfo/grid/ http://www.sara.nl/userinfo/grid/