Submitting Grid Job at Hallasan cluster (hallasan.kisti.re.kr)

Obtaining personal cert

  • Personal cert is necessary to submit jobs in Grid env.
  • User needs to get the cert from the Certificate Authority (i.e. NCSA, KISTI)
  • Personal cert consists of two files: private key and public key
  • Please follow the steps below to use your cert:
  1. Copy your cert files at $HOME/.globus/ at a machine (userkey.pem, usercert.pem)
  2. Change the permission to 400 (userkey.pem), 644 (usercert.pem)
-rw-r{-}{-}r-\- 1 eairs eairs 1833 Oct 14 14:19 usercert.pem
-r-\------\- 1 eairs eairs 1995 Oct 14 14:19 userkey.pem

Creating Grid Proxy

grid-proxy-init

$ grid-proxy-init
Your identity: [your cert info]
Enter GRID pass phrase for this identity:
Creating proxy .................................................................................................. Done
Your proxy is valid until: Wed Apr  7 04:10:14 2010

grid-proxy-info

$ grid-proxy-info
subject  : [subject info]
issuer   : [issuer info]
identity : [identity info]
type     : Proxy draft (pre-RFC) compliant impersonation proxy
strength : 512 bits
path     : /tmp/x509up_u699
timeleft : 17:55:43

General info about submitting Grid Job

  • Command for submitting Grid Job
    • GT2: globusrun, globus-job-run, globus-job-submit
    • GT4: globusrun-ws
    • refer to globus web site
  • Simple Example (by using fork) 
    $ globus-job-run hallasan.kisti.re.kr/jobmanager-fork /bin/hostname
hallasan.kisti.re.kr
  • SGE example 
    $ globus-job-run hallasan.kisti.re.kr/jobmanager-sge /bin/hostname
hallasan.kisti.re.kr

How to submit a job for 2D, 3D Solver (CFD)

An example for 2D solver

Creating a RSL file (script for job)
$ cat  hallasan.gt2.rsl
&
(directory=/home/eairs/2D_Comp-2.0)
(executable=/home/eairs/2D_Comp-2.0/2D_Comp-2.0)
(arguments= -mesh eAIRS_naca15.msh -param endowed.inp )
(stdout=2D_Comp-2.0.out)
(stderr=2D_Comp-2.0.err)
  • The example above executes /home/eairs/2D_Comp-2.0/2D_Comp-2.0 under the directory, /home/eairs/2D_Comp-2.0
  • The parameters are -mesh eAIRS_naca15.msh -param endowed.inp
    • Two files above needs to reside at the working directory, /home/eairs/2D_Comp-2.0
  • The outputs are stored at 2D_Comp-2.0.out under the working directory
  • The errors are stored at 2D_Comp-2.0.err under the working directory
  • Note: If the working directory and files do not exist, the directory must be created and the files must be placed at the directory before submitting the job
  • Tip: when there are many users and many jobs with different parameters, the output and error files will be overwritten. So, each job file (RSL) should have different working folder such as 
    (directory=/home/eairs/JOB/20100309)  /JOB/20100406 ...
Submitting the job
globusrun  -r  hallasan.kisti.re.kr  -f  hallasan.gt2.rsl

An example for 3D Solver (MPI code)

Creating a RSL file (script for job)
  • cat gt4.rsl.xml 
    <?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<ns2:job xmlns="http://schemas.xmlsoap.org/ws/2004/03/addressing" xmlns:ns2="http://www.globus.org/namespaces/2004/10/gram/job/description" xmlns:ns3="http://www.globus.org/namespaces/2004/10/gram/job/types" xmlns:ns4="http://www.globus.org/namespaces/2004/10/rft" xmlns:ns5="urn:abc" xmlns:ns6="urn:def">
<ns2:executable>/home/eairs/eAIRS_3DP_Wing2.0/eAIRS_3DP_Wing2</ns2:executable>
    <ns2:directory>/home/eairs/eAIRS_3DP_Wing2.0/</ns2:directory>
    <ns2:argument>-mesh</ns2:argument>
    <ns2:argument>eAIRS_RectangWing_P.msh</ns2:argument>
    <ns2:stdout>Wing.out</ns2:stdout>
    <ns2:stderr>Wing.err</ns2:stderr>
    <ns2:count>4</ns2:count>
    <ns2:jobType>mpi</ns2:jobType>
</ns2:job>
  • The MPI job, jobType must be mpi
  • count is the number of processors (in the example, it uses 4 processors)
Submitting the job
globusrun-ws  -submit  -b  -F hallasan.kisti.re.kr -Ft SGE -f gt4.rsl.xml
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