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Special Jobs

Special Jobs. Claudio Cherubino INFN Catania Fourth EELA Tutorial for Managers and Users Mexico City, 28 August-1 September 2006. Outline. MPI jobs on gLite DAG Job Collection Parametric jobs. MPI Overview.

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Special Jobs

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  1. Special Jobs Claudio Cherubino INFN Catania Fourth EELA Tutorial for Managers and Users Mexico City, 28 August-1 September 2006

  2. Outline • MPI jobs on gLite • DAG • Job Collection • Parametric jobs Fourth EELA Tutorial, Mexico City, 28 August-1 September 2006

  3. MPI Overview • Execution of parallel jobs is an essential issue for modern informatics and applications. • Most used library for parallel jobs support is MPI (Message Passing Interface) • At the state of the art, parallel jobs can run inside single Computing Elements (CE) only; • several projects are involved into studies concerning the possibility of executing parallel jobs on Worker Nodes (WNs) belonging to different CEs. Fourth EELA Tutorial, Mexico City, 28 August-1 September 2006

  4. Requirements & settings • In order to guarantee that MPI job can run, the following requirements MUST BE satisfied: • the MPICHsoftware must be installed and placed in the PATH environment variable on each WNs of the CE. • Some MPI’s applications require a shared filesystem among the WNs to run. • The variable VO_<name_of_VO>_SW_DIR will contain the name of a directory in case of SHARED filesystem. • The variable VO_<name_of_VO>_SW_DIR will contain “.” if there is NO SHARED filesystem. Fourth EELA Tutorial, Mexico City, 28 August-1 September 2006

  5. This attribute defines the required number of CPUs needed for the application • From the user’s point of view, jobs to be run as MPI are specified setting the JDL JobType attribute to MPICH and specifying the NodeNumber attribute as well. • E.g.: … • JobType = “MPICH”; NodeNumber = 4; … Fourth EELA Tutorial, Mexico City, 28 August-1 September 2006

  6. (other.GlueCEInfoTotalCPUs >= NodeNumber) && Member (“MPICH”,other.GlueHostApplicationSoftwareRunTimeEnvironment) • When the previous two attributes are included in a JDL, the User Interface (UI) automatically adds the following expression: to the JDL Requirements expression in order to find out the best resource where the job can be executed. Fourth EELA Tutorial, Mexico City, 28 August-1 September 2006

  7. MPI exercise Create the file “mpi-test.jdl” inside $HOME/gLite/Other and put this contents inside the file: [ Type = "Job"; JobType = "MPICH"; Executable = “cpi"; NodeNumber = 2; StdOutput = “cpi.out"; StdError = “cpi.err"; InputSandbox = {"cpi"}; OutputSandbox = {“cpi.err",“cpi.out"}; RetryCount = 0; ] Fourth EELA Tutorial, Mexico City, 28 August-1 September 2006

  8. MPI submission [glite-tutor] /home/claudio > glite-job-submit -o id mpi-test.jdl Selected Virtual Organisation name (from proxy certificate extension): gilda Connecting to host glite-rb.ct.infn.it, port 7772 Logging to host glite-rb.ct.infn.it, port 9002 ========== glite-job-submit Success ====================== The job has been successfully submitted to the Network Server. Use glite-job-status command to check job current status. Your job identifier is: - https://glite-rb.ct.infn.it:9000/bsrbbzbcXZWSzU3iUYlm6g The job identifier has been saved in the following file: /home/claudio/id ========================================================== Fourth EELA Tutorial, Mexico City, 28 August-1 September 2006

  9. MPI status and output Query the status of the job using the following command: [glite-tutor] /home/claudio > glite-job-status -i id ……………………………………………. When the status of the job is “DONE”, you can retrieve output with the following command: [glite-tutor] /home/claudio > glite-job-output -i id …………………………………………… Fourth EELA Tutorial, Mexico City, 28 August-1 September 2006

  10. MPI on the web… • LCG-2 User Guide Manuals Series • https://edms.cern.ch/file/454439/LCG-2-UserGuide.pdf • http://oscinfo.osc.edu/training/ • http://www.netlib.org/mpi/index.html • http://www-unix.mcs.anl.gov/mpi/learning.html • http://www.ncsa.uiuc.edu/ Fourth EELA Tutorial, Mexico City, 28 August-1 September 2006

  11. Workload Manager Proxy Fourth EELA Tutorial, Mexico City, 28 August-1 September 2006

  12. WMProxy overview • WMProxy (Workload Manager Proxy) • is a new service providing access to the gLite Workload Management System (WMS) functionality through a simple Web Services based interface. • has been designed to efficiently handle a large number of requests for job submission and control to the WMS • the service interface addresses the Web Services and SOA architecture standards, in particular adhering to WS-I • developed in C++ using gsoap 2.7.6b as soap stubs generator Fourth EELA Tutorial, Mexico City, 28 August-1 September 2006

  13. New request types • Support for new types strongly relies on newly developed JDL converters and on the DAG submission support • all JDL conversions are performed on the server • a single submission for several jobs • All new request types can be monitored and controlled through a single handle (the request id) • each sub-jobs can be however followed-up and controlled independently through its own id • “Smarter” WMS client commands/API • allow submission of DAGs, collections and parametric jobs exploiting the concept of “shared sandbox” • allow automatic generation and submission of collections and DAGs from sets of JDL files located in user specified directories on the UI Fourth EELA Tutorial, Mexico City, 28 August-1 September 2006

  14. WMProxy : submission & monitoring • In order to submit jobs with WMProxy, it’s mandatory to delegate credentials: • The submission/monitoring commands are slightly different, but most of the “old” options are supported glite-wms-job-delegate-proxy -d del_ID glite-wms-job-submit -d del_ID collection.jdl glite-wms-job-status jobID glite-wms-job-output \ https://glite-rb.ct.infn.it:9000/LHIIGaCVdl7Olm sz0jpI_g Fourth EELA Tutorial, Mexico City, 28 August-1 September 2006

  15. DAG job nodeA nodeB nodeC NodeF nodeD • A DAG job is a set of jobs where input, output, or execution of one or more jobs can depend on other jobs • Dependencies are represented through Directed Acyclic Graphs, where the nodes are jobs, and the edges identify the dependencies Fourth EELA Tutorial, Mexico City, 28 August-1 September 2006

  16. JDL structure Fourth EELA Tutorial, Mexico City, 28 August-1 September 2006

  17. Attribute: Nodes Fourth EELA Tutorial, Mexico City, 28 August-1 September 2006

  18. Attribute: Dependencies Fourth EELA Tutorial, Mexico City, 28 August-1 September 2006

  19. DAG jdl [ type = "dag"; max_nodes_running = 4; nodes = [ nodeA = [ file ="nodes/nodeA.jdl" ; ]; nodeB = [ file ="nodes/nodeB.jdl" ; ]; nodeC = [ file ="nodes/nodeC.jdl" ; ]; nodeD = [ file ="nodes/nodeD.jdl"; ]; dependencies = { {nodeA, nodeB}, {nodeA, nodeC}, { {nodeB,nodeC}, nodeD } } ]; ] Node description could also be done here, instead of using separate files Fourth EELA Tutorial, Mexico City, 28 August-1 September 2006

  20. Job Collection • A job collection is a set of independent jobs that user wants to submit and monitor via a single request • Jobs of a collection are submitted as DAG nodes without dependencies • JDL is a list of classad, which describes the subjobs [ Type = "collection"; VirtualOrganisation = “gilda"; nodes = { [ <job descr 1 >], [ <job descr 2 >], … }; ] Fourth EELA Tutorial, Mexico City, 28 August-1 September 2006

  21. ‘Scattered’ Input Sandboxes • Input Sandbox can contain • file paths on the UI machine (i.e. the usual way) • URI pointing to files on a remote gridFTP/HTTPS server InputSandbox = { "gsiftp://neo.datamat.it:2811/var/prg/sim.exe", "https://ghemon.cnaf.infn.it:8443/data/idat_1", "file:///home/pacio/myconf“ }; • A base URI to be applied to all sandbox files can also be specified InputSandboxBaseURI = "gsiftp://matrix.datamat.it:2811/var"; • Only local files (file://) are uploaded to the WMS node • File pointed by URIs are directly downloaded on the WN by the JobWrapper just before the job is started Fourth EELA Tutorial, Mexico City, 28 August-1 September 2006

  22. ‘Scattered’ Output Sandboxes • JDL has been enriched with new attributes for specifying the destinations for the files listed in the OutputSandbox attribute list OutputSandbox = { "jobOutput", "run1/event1", "jobError" }; OutputSandboxDestURI = { "gsiftp://matrix.datamat.it/var/jobOutput", "https://grid003.ct.infn.it:8443/home/cms/event1", "gsiftp://matrix.datamat.it/var/jobError" }; • A base URI to be applied to all sandbox files can also be specified OutputSandboxBaseDestURI = "gsiftp://neo.datamat.it/home/run1/"; • Files are copied when the job has completed execution by the JobWrapper to the specified destination without transiting on the WMS node Fourth EELA Tutorial, Mexico City, 28 August-1 September 2006

  23. Job collection example [ type = "collection"; InputSandbox = {"date.sh"}; RetryCount = 0; nodes = { [ file ="jobs/job1.jdl" ; ], [ [ Executable = "/bin/sh"; Arguments = "date.sh"; Stdoutput = "date.out"; StdError = "date.err"; OutputSandbox ={"date.out", "date.err"}; ] ], [ file ="jobs/job3.jdl" ; ] }; ] All nodes will share this Input Sandbox Fourth EELA Tutorial, Mexico City, 28 August-1 September 2006

  24. Parametric Job • A parametric job is a job where one or more of its attributes are parameterized • Values of attributes vary according to a parameter • Job monitoring / managing is always done through an unique jobID, as if the job was single (see submission of collection [ JobType = "Parametric"; Executable = "/bin/sh"; Arguments = "md5.sh input_PARAM_.txt"; InputSandbox = {"md5.sh", "input_PARAM_.txt"}; StdOutput = "out_PARAM_.txt"; StdError = "err_PARAM_.txt"; Parameters = 4; ParameterStart = 1; ParameterStep = 1; OutputSandbox = {"out_PARAM_.txt", "err_PARAM_.txt"}; ] Fourth EELA Tutorial, Mexico City, 28 August-1 September 2006

  25. Parametric job / 2 • Parameter can be also a list of string • InputSandbox (if present) has to be coherent with parameters [ui-test] /home/giorgio/param>cat param2.jdl [ JobType = "Parametric"; Executable = “/bin/cat"; Arguments = “input_PARAM_.txt”; InputSandbox = "input_PARAM_.txt"; StdOutput = "myoutput_PARAM_.txt"; StdError = "myerror_PARAM_.txt"; Parameters = {earth,moon,mars}; OutputSandbox = {“myoutput_PARAM_.txt”}; ] [ui-test] /home/giorgio/param > ls inputEARTH.txt inputMARS.txt inputMOON.txt param2.jdl Fourth EELA Tutorial, Mexico City, 28 August-1 September 2006

  26. References • JDL attributes specification for WM proxy • https://edms.cern.ch/document/590869/1 • WMProxy quickstart • http://egee-jra1-wm.mi.infn.it/egee-jra1-wm/wmproxy_client_quickstart.shtml • WMS user guides • https://edms.cern.ch/document/572489/1 Fourth EELA Tutorial, Mexico City, 28 August-1 September 2006

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