DAG job
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Submitting DAG job how-to
This is DAG job submiting example.
For demonstration use attached file. In this case job is split in 4 independent jobs. First A job will be executed, then B and C jobs, and finally job D
1.Extract file with:
[ngrkic@ui ~]$ tar xvzf DAG.tgz
2.Enter directory single with:
[ngrkic@ui ~]$ cd DAG
3.List directory:
[ngrkic@ui DAG]$ ll -rw-r--r-- 1 ngrkic ngrkic 1469 Oct 1 15:54 jobDAG.jdl -rwxr-xr-x 1 ngrkic ngrkic 92 Oct 1 15:54 job.sh
This is content of file jobDAG.jdl
[ Type = "dag"; InputSandbox = {"job.sh", "job2.sh"}; Nodes = [ nodeA = [ Description = [ JobType = "Normal"; Executable = "job.sh"; Arguments = "A"; StdOutput = "std.out"; StdError = "std.err"; InputSandbox = {root.InputSandbox[0]}; OutputSandbox = {"std.out","std.err"}; ]; ]; nodeB = [ Description = [ JobType = "Normal"; Executable = "job2.sh"; Arguments = "B"; StdOutput = "std.out"; StdError = "std.err"; InputSandbox = {root.InputSandbox[1]}; OutputSandbox = {"std.out","std.err"}; ]; ]; nodeC = [ Description = [ JobType = "Normal"; Executable = "job3.sh"; Arguments = "C"; StdOutput = "std.out"; StdError = "std.err"; InputSandbox = {"job3.sh"}; OutputSandbox = {"std.out","std.err"}; ]; ]; nodeD = [ Description = [ JobType = "Normal"; Executable = "job.sh"; Arguments = "D"; StdOutput = "std.out"; StdError = "std.err"; InputSandbox = {root.InputSandbox[0]}; OutputSandbox = {"std.out","std.err"}; ]; ]; ]; Dependencies = { {nodeA,nodeB},{nodeA,nodeC},{{nodeB,nodeC},nodeD} }; ]
This is content of file job.sh
#!/bin/bash echo "Job $1 - `date` - BEGIN" hostname sleep 100 echo "Job $1 - `date` - END"
4.Creating VOMS proxy:
[ngrkic@ui DAG]$ voms-proxy-init -voms aegis
Cannot find file or dir: /home/ngrkic/.glite/vomses Enter GRID pass phrase: Your identity: /C=RS/O=AEGIS/OU=Institute of Physics Belgrade/CN=Nikola Grkic Creating temporary proxy ......................... Done Contacting voms.ipb.ac.rs:15001 [/C=RS/O=AEGIS/OU=Institute of Physics Belgrade/CN=host/voms.ipb.ac.rs] "aegis" Done Creating proxy ..................................................... Done Your proxy is valid until Fri Oct 2 01:11:00 2009
5.Submiting DAG job:
[ngrkic@ui DAG]$ glite-wms-job-submit -a jobDAG.jdl
Connecting to the service https://wms-aegis.ipb.ac.rs:7443/glite_wms_wmproxy_server ====================== glite-wms-job-submit Success ====================== The job has been successfully submitted to the WMProxy Your job identifier is: https://wms-aegis.ipb.ac.rs:9000/O3Bxi2I9DoE2Lltmcoe0eQ ==========================================================================
Copy the job ID.Job is running now, and it should finish in few moments...
6.Requesting Job status:
[ngrkic@ui DAG]$ glite-wms-job-status https://wms-aegis.ipb.ac.rs:9000/O3Bxi2I9DoE2Lltmcoe0eQ ************************************************************* BOOKKEEPING INFORMATION: Status info for the Job : https://wms-aegis.ipb.ac.rs:9000/O3Bxi2I9DoE2Lltmcoe0eQ Current Status: Done (Success) Exit code: 0 Status Reason: Job terminated successfully Destination: dagman Submitted: Thu Oct 1 16:44:32 2009 CEST ************************************************************* - Nodes information for: Status info for the Job : https://wms-aegis.ipb.ac.rs:9000/4xL7Bu5cI6eaixg9y0oezg Current Status: Done (Success) Logged Reason(s): - - Job terminated successfully Exit code: 0 Status Reason: Job terminated successfully Destination: grid-ce.etf.bg.ac.rs:2119/jobmanager-pbs-aegis Submitted: Thu Oct 1 16:44:32 2009 CEST ************************************************************* Status info for the Job : https://wms-aegis.ipb.ac.rs:9000/LCE9ULBND3jYd2JUJPJ9wQ Current Status: Done (Success) Logged Reason(s): - - Job terminated successfully Exit code: 0 Status Reason: Job terminated successfully Destination: grid01.rcub.bg.ac.rs:2119/jobmanager-pbs-aegis Submitted: Thu Oct 1 16:44:32 2009 CEST ************************************************************* Status info for the Job : https://wms-aegis.ipb.ac.rs:9000/quIESEluISRrAXdcC7ELKQ Current Status: Done (Success) Exit code: 0 Status Reason: Job terminated successfully Destination: grid01.elfak.ni.ac.rs:2119/jobmanager-pbs-aegis Submitted: Thu Oct 1 16:44:32 2009 CEST ************************************************************* Status info for the Job : https://wms-aegis.ipb.ac.rs:9000/yNu3yqhSwf4sZ25bWuzKDg Current Status: Done (Success) Exit code: 0 Status Reason: Job terminated successfully Destination: grid01.elfak.ni.ac.rs:2119/jobmanager-pbs-aegis Submitted: Thu Oct 1 16:44:32 2009 CEST *************************************************************
7.Requesting Job output:
[ngrkic@ui DAG]$ glite-wms-job-output --dir /home/ngrkic/test https://wms-aegis.ipb.ac.rs:9000/O3Bxi2I9DoE2Lltmcoe0eQ
Connecting to the service https://wms-aegis.ipb.ac.rs:7443/glite_wms_wmproxy_server ================================================================================ JOB GET OUTPUT OUTCOME Output sandbox files for the DAG/Collection : https://wms-aegis.ipb.ac.rs:9000/O3Bxi2I9DoE2Lltmcoe0eQ have been successfully retrieved and stored in the directory: /home/ngrkic/test ================================================================================
8.Go to test directory and see output with commands:
[ngrkic@ui ~]$ cd [ngrkic@ui ~]$ cd test [ngrkic@ui test]$ ll drwxr-xr-x 2 ngrkic ngrkic 4096 Oct 1 17:31 nodeA drwxr-xr-x 2 ngrkic ngrkic 4096 Oct 1 17:31 nodeB drwxr-xr-x 2 ngrkic ngrkic 4096 Oct 1 17:31 nodeC drwxr-xr-x 2 ngrkic ngrkic 4096 Oct 1 17:31 nodeD
[ngrkic@ui test]$ cd nodeA [ngrkic@ui nodeA]$ ll -rw-rw-r-- 1 ngrkic ngrkic 0 Oct 12 17:31 std.err -rw-rw-r-- 1 ngrkic ngrkic 112 Oct 12 17:31 std.out [ngrkic@ui nodeA]$ cat std.out Job A - Thu Oct 1 17:14:14 CEST 2009 - BEGIN grid10.elfak.ni.ac.rs Job A - Thu Oct 1 17:14:54 CEST 2009 - END
For each node there is similar output.