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

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The request information looks like this:
+
Do not use environmental variables like $SCRATCH, $USER to define LL keywords.
 +
 
 +
Then add your request information which might look like this:
 
  retrieve,
 
  retrieve,
−
   class    = od,
+
   class    = od,     ("Operational archive"
−
   stream  = enfo,
+
   stream  = oper,   ("operational Atmospheric model")
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   expver  = 1,
+
   expver  = 1,       ("Experiment version", always use 1)
−
   date    = $cdate,
+
   date    = 1,       ("Specifies the Analysis/Forecast base date",  n is the number of days before today)
−
   time    = 00:00,
+
   time    = 00:00,   ("Specifies the Analysis/Forecast base time"
 
   step    = 0/to/72/by/6,
 
   step    = 0/to/72/by/6,
 
   type    = cf,
 
   type    = cf,
Line 51: Line 53:
 
   grid    = 0.5/0.5,
 
   grid    = 0.5/0.5,
 
   area    = 65/0/55/20,
 
   area    = 65/0/55/20,
−
   target  = "ecmwf_ctl3d_$cdate.grib"
+
   target  = "ecmwf_data.grib" (Output file containing the data)
  
 
A summary of MARS keywords can be found here:
 
A summary of MARS keywords can be found here:
  
 
http://www.ecmwf.int/publications/manuals/mars/guide/MARS_keywords.html
 
http://www.ecmwf.int/publications/manuals/mars/guide/MARS_keywords.html
−
 
−
If retrieving fields for different times:
 
−
 
−
in a loop over dates:
 
−
 
−
- create a file “ct1ed” containing the request information for data for a  given date (need to specify keywords)
 
−
 
−
- execute this script on mars: mars ct1ed
 
−
 
−
- this script generates the specified file
 
−
 
−
- retrieve the file using ectrans command
 
  
  
 
To transfer files to zardoz add the following to your ksh script:
 
To transfer files to zardoz add the following to your ksh script:
 
  ectrans -remote my_ms_association@genericFtp \
 
  ectrans -remote my_ms_association@genericFtp \
−
  -source ecmwf_ctl3d_$cdate.grib \
+
  -source ecmwf_data.grib \
 
  -mailto user@nilu.no \
 
  -mailto user@nilu.no \
 
  -onfailure \
 
  -onfailure \
Line 78: Line 68:
 
  -verbose
 
  -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 ==
  
−
 
+
Submit your job as a batch job to LoadLeveler.
  
 
To submit your script:
 
To submit your script:
Line 89: Line 82:
 
  llcancel myscript
 
  llcancel myscript
  
−
To view where your job is in the queue:
 
−
llq
 
  
−
To append file2 to file1:
+
== MONITOR YOUR JOB ==
−
  cat file2 >> file1
+
 
−
To concatenate 2 files to make a new file:
+
  llq -u <UserId> To view where your job is in the queue
−
  cat file1 file2 > file3
+
 +
  llq -l <jobId> To get a detailed description for a job
  
 +
llq -s <jobId>  To determine why the job is not running
  
−
Working with files on the archive
+
See ''man llq'' for more options
−
els “ls” equivalent
 
−
ectrans “mv” equivalent
 
−
ecd “cd” equivalent
 
−
erm “rm” equivalent
 

Revision as of 15:19, 12 March 2013

Back to ECMWF overview[1]


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.

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

To cancel your script: 

llcancel 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

See man llq for more options

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