5. Retrieve larger data sets from MARS

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Revision as of 14:31, 12 March 2013 by Nik (talk | contribs) (BATCH JOBS)

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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.


OBS OBS! From June 2013 the batch system on ECgate will change from Loadleveler to SLURM and jobs are submitted with the command sbatch.

This page should be updated to contain the commands for the new batch system when it is up running.

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.

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


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 job
llq -s <jobId>  To determine why the job is not running
llcancel <jobId>To cancel your script


See man llq for more options