Difference between revisions of "5. Retrieve larger data sets on MARS"

Revision as of 15:24, 12 March 2013

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BATCH JOBS

The retrieval of data is done through a submission of a shell-script.

When running a program on the UNIX system use the batch system (not interactive mode). That means you submit the job with explicit commands so that the job is run unattended under Unix.

nohup is similarly submission of jobs to run unattended on a Unix system, but there exists more sophisticated batch systems for handling jobs.

The batch system currently available on ECgate and HPCF is called LoadLeveler and jobs are submitted with the command llsubmit.

The default shell is either Korn (ksh) or C-shell (csh).

CREATING A SCRIPT

Log in to ECgate.

To retrieve large numbers of files from MARS create a ksh script on your home directory on ecgate.

For a script example see the script from Sam-Erik:

/nilu/home/sec/ecmwf/ecmwf_starg_all.ksh

In the beginning of the script, set the Batch System keywords:

#@ shell        = /usr/bin/ksh
#@ job_type     = serial
#@ job_name     = request_to_MARS
#@ output       = /scratch/ms/no/$user/MARS_out
#@ error        = /scratch/ms/no/$user/MARS_err
#@ initialdir   = /scratch/ms/no/$user/
#@ class        = normal
#@ notification = complete
#@ account_no   = spnoflex
#@ queue

Do not use environmental variables like $SCRATCH, $USER to define LL keywords.

Then add your request information which might look like this:

retrieve,
 class    = od,      ("Operational archive"
 stream   = oper,    ("operational Atmospheric model")
 expver   = 1,       ("Experiment version", always use 1)
 date     = 1,       ("Specifies the Analysis/Forecast base date",  n is the number of days before today)
 time     = 00:00,   ("Specifies the Analysis/Forecast base time"
 step     = 0/to/72/by/6,
 type     = cf,
 levtype  = pl,
 levelist = 100/150/200/250/300/400/500/700/850/925/1000,
 param    = 129.128/130.128/131.128/132.128/133.128,
 grid     = 0.5/0.5,
 area     = 65/0/55/20,
 target   = "ecmwf_data.grib"  (Output file containing the data)

A summary of MARS keywords can be found here:

http://www.ecmwf.int/publications/manuals/mars/guide/MARS_keywords.html

To transfer files to zardoz add the following to your ksh script:

ectrans -remote my_ms_association@genericFtp \
-source ecmwf_data.grib \
-mailto user@nilu.no \
-onfailure \
-remove \
-verbose

Instead of the "retrieve" keyword in the above script you can use other keywords to "read", "compute" or "write" data. As a rule - you should have as few retrieval routines as possible, but rather have each retrieval routine

SUBMIT YOUR JOB

Submit your job as a batch job to LoadLeveler.

To submit your script:

llsubmit myscript

MONITOR YOUR JOB

llq -u <UserId> To view where your job is in the queue.

llq -l <jobId>  To get a detailed description for a joc

llq -s <jobId>  To determine why the job is not running

llcancel <jobId>To cancel your script

See man llq for more options