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WMS tricks & tips – further scripting

WMS tricks & tips – further scripting. Giuseppe La Rocca INFN – Catania giuseppe.larocca@ct.infn.it Training the Trainers – in conjunction with ISGC 19-23 March 2007 - TAIPEI. Preliminars. LCG middleware The workload is managed by the Resource Broker

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WMS tricks & tips – further scripting

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  1. WMS tricks & tips –further scripting Giuseppe La Rocca INFN – Catania giuseppe.larocca@ct.infn.it Training the Trainers – in conjunction with ISGC 19-23 March 2007 - TAIPEI

  2. Preliminars • LCG middleware • The workload is managed by the Resource Broker • Doesn’t support neither parametric jobs nor DAGs • Works fine • gLite • Support both the parametric and the DAG jobs • Under developing • Uses WMProxy to manage the workload • Will be available in a few months • Tips and tricks • Some ideas to use LCG RB to support parametric jobs and DAGs while waiting for WMProxy stable release Training the Trainers – in conjunction with ISGC 19-23 March 2007 - TAIPEI

  3. Exercise 1: Parametric jobs Training the Trainers – in conjunction with ISGC 19-23 March 2007 - TAIPEI

  4. About Parametric jobs • A Parametricjob is a job having one or more parametric attributes in the JDL. The parametric attributes change their values according to another attribute (named Parameters). • The submission of a Parametric job results in the submission of a set of jobs having the same descriptions apart from the values of the parametric attributes. • All jobs resulting from the submission of it are assigned by the WMS with an identifier so that it is possible to monitor and control each of them separately and as a single entity (through the parametric job handle). Training the Trainers – in conjunction with ISGC 19-23 March 2007 - TAIPEI

  5. An example [ JobType = "Parametric"; Executable = "cms_sim.exe"; StdOutput = "myoutput_PARAM_.txt"; StdError = "myerror_PARAM_.txt"; Parameters = 3; ParameterStart = 1; ParameterStep = 1; InputSandbox = {"cms_sim.exe","input_PARAM_.txt"}; OutputSandbox = {"myoutput_PARAM_.txt", "myerror_PARAM_.txt" }; Requirements = other.GlueCEInfoTotalCPUs > 2; Rank = other.GlueCEStateFreeCPUs; ] The future - WMProxy Training the Trainers – in conjunction with ISGC 19-23 March 2007 - TAIPEI

  6. The present: using scripts • Submitter script (submitter.sh) • Creates multiple JDL files and submits these • Inspect the status of each JDL files • Retrieve the output files produced by each JDL. Training the Trainers – in conjunction with ISGC 19-23 March 2007 - TAIPEI

  7. Exercise 1: The bash script (1/2) • A set of jobs differing for input files only • The bash script (submitter.sh) looks like this #!/bin/sh if [ "$2" = "" ]; then echo "Usage: $0 begin end [step]" echo " begin The first value of the sequence" echo " end The last value of the sequence" echo " step The step between two submissions" exit 0 fi joblist="jobs.list" begin_index=$1 // the first parameter of the script end_index=$2 // the second parameter of the script if [ "$3" = "" ]; then step=1; else step=$3 // the third parameter of the script fi . . . Training the Trainers – in conjunction with ISGC 19-23 March 2007 - TAIPEI

  8. Exercise 1: The bash script (2/2) # starts iterations for ((index=$begin_index; index<=$end_index; index=$index+$step)) do # we generate the input file automatically. Obviously it can be made by hand inputfile="input$index.txt" echo "creating input file $inputfile" echo "The name of this input file is $inputfile" > $inputfile # create the correspondent jdl file depending on the index jdlfile="job$index.jdl“# name of the jdl echo "creating JDL file $jdlfile" ( echo 'Type="Job";' echo 'JobType="Normal";' echo 'Executable=“/bin/cat";' echo "Arguments=\"$inputfile\";" echo "StdOutput=\"stdout$index.txt\";" echo "StdError=\"stderr$index.txt\";“ echo "InputSandbox={\"$inputfile\"};" echo "OutputSandbox={\"stdout$index.txt\", \"stderr$index.txt\"};" ) > $jdlfile glite-job-submit -o jobs.id $jdlfile # actual job submission done# end of iterations Training the Trainers – in conjunction with ISGC 19-23 March 2007 - TAIPEI

  9. $ ./submitter.sh 1 2 creating input file input1.txt; creating JDL file job1.jdl Selected Virtual Organisation name (from proxy certificate extension): gilda Connecting to host glite-rb2.ct.infn.it, port 7772 Logging to host glite-rb2.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-rb2.ct.infn.it:9000/xD7PgJBfdbyE-x5O9LhBWA The job identifier has been saved in the following file: /home/larocca/tips_and_tricks/parametric/jobs.id ============================================================================== creating input file input2.txt; creating JDL file job2.jdl Selected Virtual Organisation name (from proxy certificate extension): gilda Connecting to host glite-rb2.ct.infn.it, port 7772 Logging to host glite-rb2.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-rb2.ct.infn.it:9000/jF7Dz4nzzDrTywIgUijCYQ The job identifier has been saved in the following file: /home/larocca/tips_and_tricks/parametric/jobs.id ================================================================================ Training the Trainers – in conjunction with ISGC 19-23 March 2007 - TAIPEI

  10. $ glite-job-status --noint -i jobs.id ************************************************************* BOOKKEEPING INFORMATION: Status info for the Job : https://glite-rb2.ct.infn.it:9000/xD7PgJBfdbyE-x5O9LhBWA Current Status: Done (Success) Exit Code: 0 Status Reason: Job terminated successfully Destination: grid011f.cnaf.infn.it:2119/jobmanager-lcgpbs-long Submitted: Thu Mar 15 16:15:31 2007 CET ************************************************************* ************************************************************* BOOKKEEPING INFORMATION: Status info for the Job : https://glite-rb2.ct.infn.it:9000/jF7Dz4nzzDrTywIgUijCYQ Current Status: Done (Success) Exit Code: 0 Status Reason: Job terminated successfully Destination: ce-nano-37.to.infn.it:2119/jobmanager-lcgpbs-short Submitted: Thu Mar 15 16:15:35 2007 CET ************************************************************* Training the Trainers – in conjunction with ISGC 19-23 March 2007 - TAIPEI

  11. $ glite-job-output --dir . --noint -i jobs.id Retrieving files from host: glite-rb2.ct.infn.it ( for https://glite-rb2.ct.infn.it:9000/xD7PgJBfdbyE-x5O9LhBWA ) ************************************************************ JOB GET OUTPUT OUTCOME Output sandbox files for the job: - https://glite-rb2.ct.infn.it:9000/jF7Dz4nzzDrTywIgUijCYQ have been successfully retrieved and stored in the directory: /home/larocca/tips_and_tricks/parametric/larocca_jF7Dz4nzzDrTywIgUijCYQ ************************************************************ Retrieving files from host: glite-rb2.ct.infn.it ( for https://glite-rb2.ct.infn.it:9000/jF7Dz4nzzDrTywIgUijCYQ ) ************************************************************ JOB GET OUTPUT OUTCOME Output sandbox files for the job: - https://glite-rb2.ct.infn.it:9000/jF7Dz4nzzDrTywIgUijCYQ have been successfully retrieved and stored in the directory: /home/larocca/tips_and_tricks/parametric/larocca_jF7Dz4nzzDrTywIgUijCYQ ************************************************************ Training the Trainers – in conjunction with ISGC 19-23 March 2007 - TAIPEI

  12. Exercise 2: DAGs Training the Trainers – in conjunction with ISGC 19-23 March 2007 - TAIPEI

  13. 1 2 3 4 5 6 Exercise 2: DAG modelling • DAGs can be emulated with a simplified Petri net • A job is submitted only when activating jobs have terminated • Each transition bar corresponds to a bash script that • Waits for termination of activating job(s) by polling every minute • Collects the output • Submits next job(s) job Training the Trainers – in conjunction with ISGC 19-23 March 2007 - TAIPEI

  14. last ./last_job.sh: submits the last job and waits for its completion, downloading the output n 1 2 ./polling.sh: waits for jobs [1..n] completion, collect the output and creates the final input file ./submitter.sh: generates input[1..n].txt and submits jobs Exercise 2: An example • We emulate a simple split and merge DAG • Two states machine • Anyway, this example can be extended to any possible DAG input1.txt stdout input2.txt stdout final_output final_input stdout input(n).txt Training the Trainers – in conjunction with ISGC 19-23 March 2007 - TAIPEI

  15. Exercise 2: ./submitter.sh #!/bin/sh if [ "$1" = "" ]; then echo "Usage: $0 num-splits“ ; exit 0 fi for ((index=1; index<= $1; index++)); do# for each job echo "this is the content of input$index.txt" >> input$index.txt ( ## creates the jdl for this job echo "Type=\"Job\";" echo "JobType=\"Normal\";" echo "Executable=\"/bin/cat\";" echo "Arguments=\"input$index.txt\";" echo "InputSandbox={\"input$index.txt\"};" echo "StdOutput=\"stdout.txt\";" echo "StdError=\"stderr.txt\";" echo "OutputSandbox={\"stdout.txt\", \"stderr.txt\"};" ) > job$index.jdl; glite-job-submit -o jobs.id job$index.jdl done Training the Trainers – in conjunction with ISGC 19-23 March 2007 - TAIPEI

  16. Exercise 2: ./submitter.sh [fscibi@glite-tutor dag]$ ./submitter.sh 2 . . . . 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-rb2.ct.infn.it:9000/Od68j9IBOuJHGlUq-EfWTg The job identifier has been saved in the following file: /home/fscibi/tips_and_tricks/dag/jobs.id . . . . 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-rb2.ct.infn.it:9000/-suh1wmmo1VvYJd_4AiLhA The job identifier has been saved in the following file: /home/fscibi/tips_and_tricks/dag/jobs.id Training the Trainers – in conjunction with ISGC 19-23 March 2007 - TAIPEI

  17. Exercise 2: ./polling.sh (1/4) #!/bin/sh while read line; do if [ "$line" != "###Submitted Job Ids###" ]; then joblist="$joblist $line" fi done < jobs.id for job in $joblist; do status="unknown" finished="false" while [ "$finished" = "false" ]; do# loops waiting for job completion ## Gets the status of the job echo echo "getting status of job $job" output=`glite-job-status $job` status=`echo "$output" | grep "Current Status" | awk '{print $3 }'` echo "status = $status" Training the Trainers – in conjunction with ISGC 19-23 March 2007 - TAIPEI

  18. Exercise 2: ./polling.sh (2/4) ## depens on the status, decides what to do case $status in "Aborted“ ) echo "The job has been aborted on the CE" finished="true" ;; "Cleared“ ) echo "The job output sandbox has been already retrieved. I don't know where!" finished="true" ;; "Done“ ) echo "Job $job Done!!! Downloading the output" ## executes and parses the output of glite-job-output ## to understand where the output has been stored Training the Trainers – in conjunction with ISGC 19-23 March 2007 - TAIPEI

  19. Exercise 2: ./polling.sh (3/4) glite-job-output --dir . $job | ( ## pipes the glite-job-output to llok for job status found="false" while read line; do if"$found" = "true“ ; then## this line contains the dir path dirpath=$line echo "output sandbox stored at $dirpath" break fi if echo "$line" | grep -q "have been successfully retrieved and stored“ ; then found= "true"## next line contains the dir path fi done if"$found" = "true“; then filename=$dirpath/stdout.txt echo "appending $filename to final_input" cat $filename >> final_input fi ) finished="true" ;; Training the Trainers – in conjunction with ISGC 19-23 March 2007 - TAIPEI

  20. Exercise 2: ./polling.sh (4/4) *) echo "sleeping 1 minute" sleep 1m ;; esac done# while done# for [fscibi@glite-tutor dag]$ ./polling.sh . . . (after a while) getting status of job https://glite-rb2.ct.infn . . . Od68j9IBOuJHGlUq-EfWTg status = Done Job https://glite-rb2.ct.infn . . . Done!!! Downloading the output output sandbox stored at . . . /dag/fscibi_Od68j9IBOuJHGlUq-EfWTg appending . . .dag/fscibi_Od68j9IBOuJHGlUq-EfWTg/stdout.txt to final_input getting status of job https://glite-rb2.ct.infn . . . _-suh1wmmo1VvYJd_4AiLhA status = Done Job https://glite-rb2.ct.infn . . . Done!!! Downloading the output output sandbox stored at . . . /dag/fscibi_-suh1wmmo1VvYJd_4AiLhA appending . . . dag/fscibi_-suh1wmmo1VvYJd_4AiLhA/stdout.txt to final_input Training the Trainers – in conjunction with ISGC 19-23 March 2007 - TAIPEI

  21. Exercise 2: Submitting last job [fscibi@. . . ] cat last_job.sh #!/bin/sh ## submits the last job glite-job-submit -o last_job.id last_job.jdl status=unknown while [ "$status" != "Done" ]; do echo "sleeping 30 seconds“ sleep 30s output=`edg-job-status -i last_job.id` status=`echo "$output" | grep "Current Status" | awk '{print $3 }'` echo "status = $status" done glite-job-output -i last_job.id --dir . echo "Everything is Done !!! " [fscibi@. . . ] cat last_job.jdl Type="Job"; JobType="Normal"; Executable="/bin/cat"; Arguments="-n final_input"; StdOutput="final_output"; StdError="stderr.txt"; InputSandBox={"final_input"}; OutputSandbox={"stderr.txt", "final_output"}; Training the Trainers – in conjunction with ISGC 19-23 March 2007 - TAIPEI

  22. Exercise 2: ./last_job.sh output [fscibi@glite-tutor dag]$ ./last_job.sh . . . The job has been successfully submitted to the Network Server. . . . - https://glite-rb2.ct.infn.it:9000/q_rqVQpNFt0GshDn5MZHEw . . . sleeping 30 seconds (many times) status = Scheduled (waiting for status Done) . . . sleeping 30 seconds status = Done Retrieving files from host: . . . Output sandbox files for the job: - https://glite-rb2.ct.infn.it:9000/q_rqVQpNFt0GshDn5MZHEw have been successfully retrieved and stored in the directory: /home/fscibi/tips_and_tricks/dag/fscibi_q_rqVQpNFt0GshDn5MZHEw "Everything is Done !!! [fscibi@glite-tutor dag]$ cat fscibi_q_rqVQpNFt0GshDn5MZHEw/final_output 1 this is the content of input1.txt 2 this is the content of input2.txt Training the Trainers – in conjunction with ISGC 19-23 March 2007 - TAIPEI

  23. Jobs + Data Training the Trainers – in conjunction with ISGC 19-23 March 2007 - TAIPEI

  24. Overview • User can stage input files from the UI to the WN using the InputSandbox attribute InputSandbox = {"codesa.i686", "start_root.sh", "./Korba/atmbc.const", "./Korba/bctran-window.3", "./Korba/codesa3d.fnames", ".rootrc", "convert.C", "GraphCODESA3D.C"}; The upper limit for InputSandbox is 10Mbyte!

  25. ..the question What can I do if my job requires huge data to be processed ? Training the Trainers – in conjunction with ISGC 19-23 March 2007 - TAIPEI

  26. ..the answer /1 • InputData(optional) • This is a string or a list of strings representing the Logical File Name (LFN) or Grid Unique Identifier (GUID)needed by the job as input. • The list is used by the RB to find the close CE (from which the specified files can be better accessed) and schedules the job to run there. InputData = {“lfn:cmstestfile”, “guid:135b7b23-4a6a-11d7-87e7-9d101f8c8b70”}; Training the Trainers – in conjunction with ISGC 19-23 March 2007 - TAIPEI

  27. ..the answer /2 • DataAccessProtocol(mandatory if InputData has been specified) • The protocol or the list of protocols which the application is able to “speak” with for accessing files listed in InputData on a given SE. • Supported protocols in gLite are currentlygsiftp, and file. DataAccessProtocol = {“file”,“gsiftp”}; Training the Trainers – in conjunction with ISGC 19-23 March 2007 - TAIPEI

  28. pds2jpg-MERIS-Etna.jdl [ JobType = "normal"; Type = "Job"; Executable = "/bin/bash"; Arguments = "pds2jpg_install.sh \ MER_FR__2PNUPA20030504_092534_000000502016_00079_06145_0033"; StdOutput = "pds2jpg.out"; StdError = "pds2jpg.err"; InputSandbox = {"./pds2jpg_install.sh","./beam20.tar.gz"}; InputData = {"lfn:/grid/gilda/MER_FR__2PNUPA20030504_092534_000000502016_00079_06145_0033.N1"}; DataAccessProtocol = {"gridftp","rfio","gsiftp"}; OutputSandbox = { "MER_FR__2PNUPA20030504_092534_000000502016_00079_06145_0033.jpg", "ENVISAT_Product_courtesy_of_European_Space_Agency", "pds2jpg.out", "pds2jpg.err" }; RetryCount = 3; ] Training the Trainers – in conjunction with ISGC 19-23 March 2007 - TAIPEI

  29. pds2jpg_install.sh #!/bin/sh echo Staging Input Data \(Courtesy of European Space Agency\); #Skip the "/" from the argument. file=`echo $1 | awk -F '/' '{print $2}'` echo lcg-cp --vo gilda lfn:/grid/gilda/MER_FR__2PNUPA20030504_092534_000000502016_00079_06145_0033.N1 file:`pwd`/${file}.N1 lcg-cp --vo gilda lfn:/grid/gilda/MER_FR__2PNUPA20030504_092534_000000502016_00079_06145_0033.N1 file:`pwd`/${file}.N1 echo Staging Application; ls -al gunzip beam20.tar.gz; tar xvf beam20.tar; cd beam-2.0/bin; echo Starting Application; echo "./pds2jpg-run.sh $file;" ./pds2jpg-run.sh $file; echo "mv $file.jpg ../.." mv $file.jpg ../.. touch ../../ENVISAT_Product_courtesy_of_European_Space_Agency echo "Input ENVISAT Product courtesy of European Space Agency">../../ENVISAT_Product_courtesy_of_European_Space_Agency echo No Output Packaging; Training the Trainers – in conjunction with ISGC 19-23 March 2007 - TAIPEI

  30. the output.. Input ENVISAT Product courtesy of European Space Agency Training the Trainers – in conjunction with ISGC 19-23 March 2007 - TAIPEI

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