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Job submission into the LHC Grid ( Job Management + JDL)

This tutorial introduces the job management and Job Description Language (JDL) aspects of the LHC Grid. Learn how to interact with the Grid via the Workload Management System (WMS) and submit and manage jobs efficiently.

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Job submission into the LHC Grid ( Job Management + JDL)

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  1. Job submission into the LHC Grid (Job Management + JDL) edited by Gabor Hermann MTA SZTAKI EGEE is funded by the European Union under contract IST-2003-508833 EGEE Summer School Grid Systems – 3-8 July 2006 - 1

  2. Acknowledgement • This tutorial is based on the work of many people: • Fabrizio Gagliardi, Flavia Donno and Peter Kunszt (CERN) • Simone Campana (INFN) • the EDG developer team • the EDG training team • the NeSC training team • the SZTAKI training team EGEE Summer School Budapest, 3-8 July 2006

  3. Job Management • The user interacts with Grid via a Workload Management System(WMS) • 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 on the “best resources” • The WMS tries to optimize the usage of resources • To get information about their status • To retrieve their output EGEE Summer School Budapest, 3-8 July 2006

  4. WMS Components • WMS is currently composed of the following parts: • Workload Manager, which is the core component of the system • Match-Maker(also called Resource Broker), whose duty is finding the best resource matching the requirements of a job (match-making process). • Job Adapter, which prepares the environment for the job and its final description, before passing it to the Job Control Service. • Job Control Service (JCS), which finally performs the actual job management operations (job submission, removal. . .) • Logging and Bookkeeping services (LB) : store Job Info available for users to query EGEE Summer School Budapest, 3-8 July 2006

  5. Job Preparation:Let’s think the way the Grid thinks! • Information to be specified • Job characteristics • Requirements and Preferences of the computing system • including software dependencies • Job Data requirements • Specified using a Job Description Language (JDL) EGEE Summer School Budapest, 3-8 July 2006

  6. RLS UI Network Server RB node Inform. Service Workload Manager Job Contr. - CondorG SE characts & status CE characts & status Computing Element Storage Element Job Submission EGEE Summer School Budapest, 3-8 July 2006

  7. RLS UI submitted Network Server RB node Inform. Service Workload Manager UI: allows users to access the functionalities of the WMS (via command line, GUI, C++ and Java APIs) Job Contr. - CondorG SE characts & status CE characts & status Computing Element Storage Element Job Submission Job Status EGEE Summer School Budapest, 3-8 July 2006

  8. RLS UI submitted Network Server RB node Inform. Service Workload Manager Job Description Language (JDL) to specify job characteristics and requirements edg-job-submit myjob.jdl(glite-job-submit) Myjob.jdl JobType = “Normal”; Executable = "$(CMS)/exe/sum.exe"; InputSandbox = {"/home/user/WP1testC","/home/file*”, "/home/user/DATA/*"}; OutputSandbox = {“sim.err”, “test.out”, “sim.log"}; Requirements = other. GlueHostOperatingSystemName == “linux" && other.GlueCEPolicyMaxWallClockTime > 10000; Rank = other.GlueCEStateFreeCPUs; Job Contr. - CondorG SE characts & status CE characts & status Computing Element Storage Element Job Submission Job Status EGEE Summer School Budapest, 3-8 July 2006

  9. NS: network daemon responsible for accepting incoming requests RLS UI Job submitted Network Server RB node Inform. Service waiting Workload Manager Input Sandbox files RB storage Job Contr. - CondorG SE characts & status CE characts & status Computing Element Storage Element Job Submission Job Status EGEE Summer School Budapest, 3-8 July 2006

  10. RLS UI submitted Network Server RB node Inform. Service waiting Workload Manager RB storage WM: responsible to take the appropriate actions to satisfy the request Job Contr. - CondorG SE characts & status CE characts & status Computing Element Storage Element Job Submission Job Status EGEE Summer School Budapest, 3-8 July 2006

  11. RLS UI Match- Maker/ Broker submitted Network Server RB node Inform. Service waiting Workload Manager Where must this job be executed ? RB storage Job Contr. - CondorG SE characts & status CE characts & status Computing Element Storage Element Job Submission Job Status EGEE Summer School Budapest, 3-8 July 2006

  12. RLS UI Match- Maker/ Broker submitted Network Server RB node Inform. Service waiting Workload Manager Matchmaker: responsible to find the “best” CE where to submit a job RB storage Job Contr. - CondorG SE characts & status CE characts & status Computing Element Storage Element Job Submission Job Status EGEE Summer School Budapest, 3-8 July 2006

  13. Where are (which SEs) the needed data ? RLS UI Match- Maker/ Broker submitted Network Server RB node Inform. Service waiting Workload Manager What is the status of the Grid ? RB storage Job Contr. - CondorG SE characts & status CE characts & status Computing Element Storage Element Job Submission Job Status EGEE Summer School Budapest, 3-8 July 2006

  14. RLS UI Match- Maker/ Broker submitted Network Server RB node Inform. Service waiting Workload Manager CE choice RB storage Job Contr. - CondorG SE characts & status CE characts & status Computing Element Storage Element Job Submission Job Status EGEE Summer School Budapest, 3-8 July 2006

  15. RLS UI submitted Network Server RB node Inform. Service waiting Workload Manager Job Adapter RB storage Job Contr. - CondorG SE characts & status CE characts & status JA: responsible for the final “touches” to the job before performing submission (e.g. creation of wrapper script, etc.) Computing Element Storage Element Job Submission Job Status EGEE Summer School Budapest, 3-8 July 2006

  16. RLS UI submitted Network Server RB node Inform. Service waiting Workload Manager ready RB storage Job Contr. - CondorG SE characts & status JC: responsible for the actual job management operations (done via CondorG) CE characts & status Computing Element Storage Element Job Submission Job Status EGEE Summer School Budapest, 3-8 July 2006

  17. RLS UI submitted Network Server RB node Inform. Service waiting Workload Manager ready RB storage Job Contr. - CondorG scheduled SE characts & status CE characts & status Input Sandbox files Job Computing Element Storage Element Job Submission Job Status EGEE Summer School Budapest, 3-8 July 2006

  18. RLS UI submitted Network Server RB node Inform. Service waiting Workload Manager RB storage ready Job Contr. - CondorG scheduled running “Grid enabled” data transfers/ accesses Computing Element Storage Element Job Job Submission Job Status EGEE Summer School Budapest, 3-8 July 2006

  19. RLS UI submitted Network Server RB node Inform. Service waiting Workload Manager ready RB storage Job Contr. - CondorG scheduled Output Sandbox files running Computing Element done Storage Element Job Submission Job Status EGEE Summer School Budapest, 3-8 July 2006

  20. RLS UI submitted Network Server RB node Inform. Service waiting Workload Manager ready RB storage Job Contr. - CondorG edg-job-get-output <dg-job-id> glite-get-output scheduled running Computing Element done Storage Element Job Submission Job Status EGEE Summer School Budapest, 3-8 July 2006

  21. RLS UI submitted Network Server Output Sandbox files Inform. Service waiting Workload Manager ready RB storage RB node Job Contr. - CondorG scheduled running Computing Element done Storage Element cleared Job Submission Job Status EGEE Summer School Budapest, 3-8 July 2006

  22. RB node edg-job-status <dg-job-id> glite-job-status edg-job-get-logging-info <dg-job-id> glite-job-logging-info Network Server UI LB: receives and stores job events; processes corresponding job status. Checkpointing! Workload Manager Job status Job Contr. - CondorG Logging & Bookkeeping Log Monitor Log of job events Computing Element Job monitoring LM: parses CondorG log file (where CondorG logs info about jobs) and notifies LB EGEE Summer School Budapest, 3-8 July 2006

  23. Possible job states By system By User EGEE Summer School Budapest, 3-8 July 2006

  24. Job Submission syntax edg-job-submit (glite-job-submit)[–r <res_id>] [-c <config file>] [-vo <VO>] [-o <output file>]<job.jdl> -r the job is submitted directly to the computing element identified by <res_id> -c the configuration file <config file> is pointed by the UI instead of the standard configuration file -vo the Virtual Organisation (if user is not happy with the one specified in the UI configuration file) -o the generated edg_jobId is written in the <output file> Useful for other commands, e.g.: edg-job-status –i<input file> (or edg_jobId) -i the status information about edg_jobId contained in the <input file> are displayed EGEE Summer School Budapest, 3-8 July 2006

  25. Other (most relevant) UI commands • edg-job-list-match(glite-job-list-match) • Lists resources matching a job description • The - - rank option prints the ranking of each resource • Performs the matchmaking without submitting the job • See matchmaking section later • edg-job-cancel(glite-job-cancel) • Cancels a given job • edg-job-status(glite-job-status) • Displays the status of the job • edg-job-get-output(glite-get-output) • Returns the job-output (the OutputSandbox files) to the user EGEE Summer School Budapest, 3-8 July 2006

  26. Other (most relevant) UI commands • edg-job-get-logging-info (glite-job-logging-info) • Displays logging information about submitted jobs (all the events “pushed” by the various components of the WMS) • Different levels of verbosity (-v option) : • Verbosity 1 is the most suitable for debugging • Verbosity 2 is just too much info • About debugging a failed job • Understanding a job failure is not an easy task • Output of edg-job-get-logging-info not always straightforward to interpret • Short failure description • Difficult to distinguish a “grid” failure from a “user job” problem • Same error could be due to different causes (“in-famous” globus 155 …) • More useful info can be found in the logs of the RB • Not easily accessible by the end user • In principle can fetch them using gridftp but … come on … • User should try to log as much info as possible in the standard error file. • User should try to monitor the job/application • RGMA,GridIce for jobs status • RGMA for applications EGEE Summer School Budapest, 3-8 July 2006

  27. Job Flow Status and Errors • Status queries from the UI machine (static or dynamic): • job status queries are addressed to the LB database. • Resourcestatus queries are addressed to the BDII • If the site where the job is being run falls down, the job will be automatically resent to anotherCE that is analogue to the previous one, w.r.t. requirements the user asked for. • In the case that this new submission is disabled, the job will be marked as aborted. • Users can getinformation about what happened by simply questioning the LB service. EGEE Summer School Budapest, 3-8 July 2006

  28. Job Description Language EGEE Summer School Budapest, 3-8 July 2006

  29. Job Description Language • The supported attributes are grouped in two categories: • Job Attributes • Define the job itself • Resource expression attributes • Taken into account by the RB for carrying out the matchmaking algorithm (to choose the “best” resource where to submit the job) • Computing Resource • Used to build expressions of Requirements and/or Rank attributes by the user • Have to be prefixed with “other.” (external) or “self.” (internal) • Data and Storage resources • Input data to process, • SE where to store output data, • protocols spoken by application when accessing SEs EGEE Summer School Budapest, 3-8 July 2006

  30. JDL: some relevant attributes • JobType • Normal (simple, sequential job), Interactive, MPICH, Checkpointable • Or combination of them • Executable (mandatory) • The command name • Arguments (optional) • Job command line arguments • StdInput, StdOutput, StdError (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 will automatically staged to the remote resource • OutputSandbox (optional) • List of files, generated by the job, which have to be retrieved • VirtualOrganisation (optional) • A different way to specify the VO of the user EGEE Summer School Budapest, 3-8 July 2006

  31. JDL: some relevant attributes II • Input Data (Just a suggestion!) • DataAccessProtocol file|gridftp|rfio(Together with InputData) • Output Data {OutputFile= [CE path] [ StorageElement= SE ][ LogicalFileName = lfn:fileName ] }(Real Data movement) • OutputSE • rank • requirements • MyProxyServer • RetryCount • NodeNumber • JobSteps EGEE Summer School Budapest, 3-8 July 2006

  32. Example of JDL file [ JobType = “Normal”; Executable = "$(CMS)/exe/sum.exe"; InputSandbox = {"/home/user/WP1testC","/home/file*”, "/home/user/DATA/*"}; OutputSandbox = {“sim.err”, “test.out”, “sim.log"}; Requirements = (other. GlueHostOperatingSystemName == “linux") && (other.GlueCEPolicyMaxWallClockTime > 10000); Rank = other.GlueCEStateFreeCPUs; ] EGEE Summer School Budapest, 3-8 July 2006

  33. A “real world” JDL file job attributes part [ JobType = "normal"; Executable = "lexor_wrap.sh"; StdOutput = "dc2.003020.digit.A8_QCD._01730.job.log.3"; StdError = {"dc2.003020.digit.A8_QCD._01730.job.log.3";} OutputSandbox {"metadata.xml", "lexor_wrap.log","dq_337704_stagein.log","dq_337704_stageout.log",\ "dc2.003020.digit.A8_QCD._01730.job.log.3" }; RetryCount = 0; Arguments = "dc2.003020.simul.A8_QCD._01730.pool.root,\ dc2.003020.digit.A8_QCD._01730.pool.root.3 100 0"; Environment = { "LEXOR_WRAPPER_LOG=lexor_wrap.log","LEXOR_STAGEOUT_MAXATTEMPT=5","LEXOR_STAGEOUT_INTERVAL=60","LEXOR_LCG_GFAL_INFOSYS=atlas-bdii.cern.ch:2170","LEXOR_T_RELEASE=8.0.7","LEXOR_T_PACKAGE=8.0.7.5/JobTransforms","LEXOR_T_BASEDIR=JobTransforms-08-00-07-05","LEXOR_TRANSFORMATION=share/dc2.g4digit.trf","LEXOR_STAGEIN_LOG=dq_337704_stagein.log","LEXOR_STAGEIN_SCRIPT=dq_337704_stagein.sh","LEXOR_STAGEOUT_LOG=dq_337704_stageout.log","LEXOR_STAGEOUT_SCRIPT=dq_337704_stageout.sh" }; MyProxyServer = "lxb0727.cern.ch"; VirtualOrganisation = "atlas"; rank = -other.GlueCEStateEstimatedResponseTime EGEE Summer School Budapest, 3-8 July 2006

  34. A “real world” JDL file (cont.) resource attributes part requirements = ( Member("VO-atlas-lcg-release-0.0.2", other.GlueHostApplicationSoftwareRunTimeEnvironment) && (other.GlueCEStateStatus == "Production“) && !Member("VO-atlas-has-m1", other.GlueHostApplicationSoftwareRunTimeEnvironment)) && (other.GlueCEInfoHostName != "lcgce02.gridpp.rl.ac.uk" ) && (other.GlueCEInfoHostName != "lcg-ce.lps.umontreal.ca" ) && (other.GlueCEInfoHostName != "lcgce02.triumf.ca" ) && (other.GlueCEInfoHostName != "ce-a.ccc.ucl.ac.uk" ) && Member("VO-atlas-release-8.0.7", other.GlueHostApplicationSoftwareRunTimeEnvironment)) && ( other.GlueCEPolicyMaxCPUTime >= (Member("LCG-2_1_0",other.GlueHostApplicationSoftwareRunTimeEnvironment) ? ( 36000000 / 60 ) : 36000000 ) / other.GlueHostBenchmarkSI00 ) ) && ( other.GlueHostNetworkAdapterOutboundIP == true ) && (other.GlueHostMainMemoryRAMSize >= 512 ) ); ] EGEE Summer School Budapest, 3-8 July 2006

  35. Requirements • Job requirements on the resources • Specified using GLUE attributes of resources published in the Information Service • Its value is a boolean expression • Only one requirements can be specified ( one C-like logic expression ) • if there are more than one, only the last one is taken into account • If not specified, default value defined in UI configuration file is considered • Default: other.GlueCEStateStatus == "Production" (the resource has to be able to accept jobs and dispatch them on WNs) EGEE Summer School Budapest, 3-8 July 2006

  36. Relevant Glue Attributes 1 (State) • State (objectclass GlueCEState) • GlueCEStateRunningJobs: • number of running jobs • GlueCEStateWaitingJobs: • number of jobs not running • GlueCEStateTotalJobs: • total number of jobs (running + waiting) • GlueCEStateStatus: • queue status: queueing (jobs are accepted but not run), production (jobs are accepted and run), closed (jobs are neither accepted nor run), draining (jobs are not accepted but those in the queue are run) • GlueCEStateWorstResponseTime: • worst possible time between the submission of a job and the start of its execution • GlueCEStateEstimatedResponseTime: • estimated time between the submission of a job and the start of its execution • GlueCEStateFreeCPUs: • number of CPUs available to the scheduler EGEE Summer School Budapest, 3-8 July 2006

  37. Relevant Glue Attributes 2 (Hardware) • Architecture (objectclass GlueHostArchitecture) • GlueHostArchitecturePlatformType: • platform description • GlueHostArchitectureSMPSize: • number of CPUs • Processor (objectclass GlueHostProcessor) • GlueHostProcessorVendor: • name of the CPU vendor • GlueHostProcessorModel: • name of the CPU model • GlueHostProcessorVersion: • version of the CPU • GlueHostProcessorOtherProcessorDescription: • other description for the CPU • […] EGEE Summer School Budapest, 3-8 July 2006

  38. Relevant Glue Attributes 3 (HW & Software) • Application software (objectclass GlueHostApplicationSoftware) • GlueHostApplicationSoftwareRunTimeEnvironment: • list of software installed on this host • Main memory (objectclass GlueHostMainMemory) • GlueHostMainMemoryRAMSize: • physical RAM • GlueHostMainMemoryVirtualSize: • size of the configured virtual memory • Benchmark (objectclass GlueHostBenchmark) • GlueHostBenchmarkSI00: • SpecInt2000 benchmark • GlueHostBenchmarkSF00: • SpecFloat2000 benchmark • Network adapter (objectclass GlueHostNetworkAdapter) • […] • GlueHostNetworkAdapterOutboundIP: • permission for outbound connectivity • GlueHostNetworkAdapterInboundIP: • permission for inbound connectivity EGEE Summer School Budapest, 3-8 July 2006

  39. Exercise: JDL Requirements • other.GlueCEInfoLRMSType == “PBS” && other.GlueCEInfoTotalCPUs > 1 (the resource has to use PBS as the LRMS and whose WNs have at least two CPUs) • Member(“CMSIM-133”, other.GlueHostApplicationSoftwareRunTimeEnvironment) (a particular experiment software has to run on the resource and this information is published on the resource environment) • TheMember operator tests if its first argument is a member of its second argument. Used in case of multi attribute. • RegExp(“cern.ch”, other.GlueCEUniqueId) (the job has to run on the CEs in the domain cern.ch) • Matches the regular expression • (other.GlueHostNetworkAdapterOutboundIP == true) && Member(“VO-alice-Alien”, other.GlueHostApplicationSoftwareRunTimeEnvironment) && Member(“VO-alice-Alien-v4-01-Rev-01”, other.GlueHostApplicationSoftwareRunTimeEnvironment) && (other.GlueCEPolicyMaxWallClockTime > 86000) (the resource must have some packages installed VO-alice-Alien and VO-alice-Alien-v4-01-Rev-01 and the job has to run for more than 86000 WallClock time units) EGEE Summer School Budapest, 3-8 July 2006

  40. Rank • Expresses preference (how to rank resources that have already met the Requirements expression) • It is expressed as a floating-point number • The CE with the highest rank is the one selected (see Matchmaking later on) • If not specified, default value defined in the UI configuration file is considered • Examples: • -other.GlueCEStateEstimatedResponseTime (the lowest estimated traversal time) • Usually the default • other.GlueCEStateFreeCPUs (the highest number of free CPUs) • Bad idea: number of free CPU published per QUEUE, not per VO • (other.GlueCEStateWaitingJobs == 0 ? other.GlueCEStateFreeCPUs : -other.GlueCEStateWaitingJobs) (the number of waiting jobs is used if this number is not null and the rank decreases as the number of waiting jobs gets higher; if there are not waiting jobs, the number of free CPUs is used) EGEE Summer School Budapest, 3-8 July 2006

  41. Relevant Glue Attributes about policy of LRMS • GlueCEPolicyMaxWallClockTime: • maximum wall clock time available to jobs submitted to the CE, in seconds (previously it was in minutes) • GlueCEPolicyMaxCPUTime: • maximum CPU time available to jobs submitted to the CE, in seconds (previously it was in minutes) • GlueCEPolicyMaxTotalJobs: • maximum allowed total number of jobs in the queue • GlueCEPolicyMaxRunningJobs: • maximum allowed number of running jobs in the queue • GlueCEPolicyPriority: • information about the service priority EGEE Summer School Budapest, 3-8 July 2006

  42. WMS Matchmaking EGEE Summer School Budapest, 3-8 July 2006

  43. The Matchmaking algorithm • The matchmaker has the goal to find the best suitable CE where to execute the job • To accomplish this task, the WMS interacts with the other EGEE/LCG components (File Catalog, and Information Service) • There are three different scenarios to be dealt with separately: • Direct job submission • Job submission without data-access requirements • Job submission with data-access requirements EGEE Summer School Budapest, 3-8 July 2006

  44. The Matchmaking algorithm: direct job submission CE defined in the JDL • The WMS does not perform any matchmaking algorithm at all • The job is simply submitted to the specified CE CE defined during the edg-job-submit (glue-job-submit) command: • If the CEId is specified then the WMS • Does NOT check whether the user is authorised to access the CE • Does NOT interacts with the File Catalog for the resolution of files requirements • Only checks the JDL syntax, while converting the JDL into a ClassAd • Syntax:edg-job-submit --resource <ce_id> <nome.jdl> command ce_id = hostaname:port/jobmanager-lsf-grid01 EGEE Summer School Budapest, 3-8 July 2006

  45. The Matchmaking algorithm: job submission without data access requirements (I) • The user JDL contains some requirements • Once the JDL has been received by the WMS and converted in ClassAd, the WMS invokes the matchmaker • The matchmaker has to find if the characteristics and status of Grid resources match the job requirements EGEE Summer School Budapest, 3-8 July 2006

  46. The Matchmaking algorithm: job submission without data access requirements (II) • There are two phases of evaluation: • Requirements check: • The Matchmaker contacts the BDII in order to create a set of suitable CEs compliant with user requirements and where the user is authorized to submit jobs • The Matchmaker creates the set of suitable CEs • Ranking phase: • The Matchmaker contacts the BDII again to obtain the values of those attributes that are in the rank expression (used to contact GRISes) • The CE with maximum rank value is selected • If 2 or more CE have same rank, Matchmakes selects random one • Can adopt a stochastic selection (enabling fuzzyness) • The user has to set the JDL FuzzyRank attribute to true • The rank value = probability to select the CE • The higher the rank value is, the higher the probability is. EGEE Summer School Budapest, 3-8 July 2006

  47. FC Match- Maker/ Broker IS The Matchmaking algorithm: job submission with data access requirements (I) • The user can specify in the JDL the following attributes • InputData represents the input files • InputData = {“lfn:my-file-001"} • lfn=logical file name, see Data Management • OutputSE represents the SE where the output file should be staged • OutputSE = "gilda-se-01.pd.infn.it"; • OutputData represents the output files • OutputFile = "dummy.dat"; • StorageElement = "gilda-se-01.pd.infn.it"; • LogicalFileName = "lfn:iome_outputData"; • DataAccessProtocol represents the protocol spoken by the application to access the file • DataAccessProtocol = "gsiftp"; EGEE Summer School Budapest, 3-8 July 2006

  48. The Matchmaking algorithm: job submission with data access requirements (II) • The Matchmaker finds the most suitable CEs taking into account • the SEs where input data are physically stored • the SE where output data should be staged • Previous to requirements and ranking checks, the broker • Performs a pre-match processing • interacts with File Catalog • Filters CEs satisfying both data access and user authorization requirements EGEE Summer School Budapest, 3-8 July 2006

  49. The Matchmaking algorithm: job submission with data access requirements(III) Summaray • The Matchmaker interacts with a File Catalogue and the Information Service • The FC is used to resolve the location of data (see Data Management talk for more details ) • The Matchmaker finds most sutable CEs considering • SEs where both input data are physically stored • SEs where output data should be staged • Previous to requirements and ranking checks, the broker • Performs a pre-match processing (access the FC) • Filters CEs satisfying both data access and user authorization requirements EGEE Summer School Budapest, 3-8 July 2006

  50. Job types in LCG-2 EGEE Summer School Budapest, 3-8 July 2006

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