Special Jobs

1
Special Jobs

• Paola Celio, Claudio Cherubino
• Universita Roma TRE
• INFN Sezione Roma TRE
• INFN Catania

2
Outline

• MPI jobs on gLite
• DAG
• Job Collection
• Parametric jobs

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.

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Requirements settings

• In order to guarantee that MPI job can run, the
  following requirements MUST BE satisfied
• the MPICH software must be installed and placed
  in the PATH environment variable on each WNs of
  the CE.
• Some MPIs applications require a shared
  filesystem among the WNs to run.
• The variable VO_ltname_of_VOgt_SW_DIR will contain
  the name of a directory in case of SHARED
  filesystem.
• The variable VO_ltname_of_VOgt_SW_DIR will contain
  . if there is NO SHARED filesystem.

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• From the users 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

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• 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.

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MPI exercise

• Create the file mpi-glite.jdl inside
  HOME/EXAMPLES/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

8
MPI submission

• sevilla25_at_glite-tutor specjob_exercise
  edg-job-submit -o id mpi-glite.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.it9000/bsrbbzbcXZWSzU
  3iUYlm6g
• The job identifier has been saved in the
  following file
• /home/sevilla25/Paola/specjob_exercise/id
• 
  

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MPI status and output

• Query the status of the job using the following
  command
• glite-tutor /home/claudio gt edg-job-status -i
  id
• .
• When the status of the job is DONE, you can
  retrieve output with the following command
• glite-tutor /home/claudio gt edg-job-get-output
  -i id

10
MPI on the web

• LCG-2 User Guide Manuals Series
• https//edms.cern.ch/file/454439/LCG-2-UserGuide.p
  df
• 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/

11
Workload Manager Proxy
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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

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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

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WMProxy submission monitoring

• In order to submit jobs with WMProxy, its
  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 gli
te-wms-job-status jobID glite-wms-job-output
\ https//glite-rb.ct.infn.it9000/LHIIGaCVdl7Olm
sz0jpI_g
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DAG job

• 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

16
JDL structure
17
Attribute Nodes
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Attribute Dependencies
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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
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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
• ltjob descr 1 gt,
• ltjob descr 2 gt,

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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.it2811/var/prg/sim.exe",
• "https//ghemon.cnaf.infn.it8443/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

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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
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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"
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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 gt 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 gt ls inputEARTH.txt
inputMARS.txt inputMOON.txt param2.jdl
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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/wmprox
  y_client_quickstart.shtml
• WMS user guides
• https//edms.cern.ch/document/572489/1

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Questions