This shell script uses a Fortran program calling ecCodes routines to decode GRIB data.
- fields are retrieved from MARS in GRIB format
- the GRIB decoding Fortran program is compiled and linked against the ecCodes library using gfortran
- the program is executed to decode and prints various sections of GRIB data using calls to the grib_api ecCodes functions
#!/bin/bash
#
# **************************** LICENSE START ***********************************
#
# Copyright 2021 ECMWF. This software is distributed under the terms
# of the Apache License version 2.0. In applying this license, ECMWF does not
# waive the privileges and immunities granted to it by virtue of its status as
# an Intergovernmental Organization or submit itself to any jurisdiction.
#
# ***************************** LICENSE END ************************************
#
# Retrieve_decode_grib_api USER SERVICES NOVEMBER 2021 - ECMWF
#
#
# This shell-script:
#
# - retrieves fields in GRIB format from MARS
# - compiles and links a Fortran90 decoding program using gfortran
# - decodes and prints various sections of GRIB data, using ecCodes
#
# This shell script produces the standard output file
#
# Retrieve_decode_grib.<JOB-ID>.out
#
# containing the log of job execution.
#
# For more information on ecCodes see
#
# https://confluence.ecmwf.int/display/ECC/ecCodes+Home
#
#
#-------------------------------
# setting options for SLURM
#-------------------------------
# Options that are specified within the script file should precede the
# first executable shell command in the file.
# All options, which are case sensitive, are preceded by #SBATCH.
# These lines become active only when the script is submitted
# using the "sbatch" command.
# All job output is written to the workdir directory, by default.
#SBATCH --qos=ef
# Specifies that your job will run in the queue (Quality Of
# Service) "ef".
#SBATCH --job-name=retrieve_decode_grib_api
# Assigns the specified name to the request
#SBATCH --output=retrieve_decode_grib_api.%j.out
# Specifies the name and location of STDOUT where %j is the job-id
# The file will be # written in the workdir directory if it is a
# relative path. If not given, the default is slurm-%j.out in the
# workdir.
#SBATCH --error=retrieve_decode_grib_api.%j.out
# Specifies the name and location of STDERR where %j is the job-id
# The file will be # written in the workdir directory if it is a
# relative path. If not given, the default is slurm-%j.outin the
# workdir.
#SBATCH --chdir=/scratch/...
# Sets the working directory of the batch script before it is
# executed.
#SBATCH --mail-type=FAIL
# Specifies that an email should be sent in case the job fails.
# Other options include BEGIN, END, REQUEUE and ALL (any state
# change).
#SBATCH --time=00:05:00
# Specifies that your job my run up to HH:MM:SS of wall clock
# time. The job will be killed if it exceeds this limit. If
# time is not defined, the default limit for the queue (qos)
# will be used.
#-------------------------------
# setting environment variables
#-------------------------------
export PATH=$PATH:. # Allows you to run any of your programs or
# scripts held in the current directory (not
# required if already done in your .user_profile
# or .user_kshrc)
set -ev
#-------------------------------
# commands to be executed
#-------------------------------
cd $SCRATCHDIR # All the files created in this directory will be
# deleted when the job terminates.
# cat is used to read the Fortran 90 program from the input stream
# and to write it to the file 'grib_api_demo.f90'.
# cat reads line by line until it reaches a line which starts with EOF.
#
cat>grib_api_demo.f90<<EOF
PROGRAM grib_api_demo
use grib_api
implicit none
!
INTEGER :: status, iret, rfile, gribid, i
CHARACTER(LEN=*), PARAMETER :: input_file='grib_file.grb'
CHARACTER(LEN=*), PARAMETER :: open_mode='r'
real, dimension(:), allocatable :: values
integer :: numberOfPoints
!
! Open data file for reading.
!
call grib_open_file (rfile, input_file, open_mode)
!
! Check return code.
!
call grib_new_from_file(rfile, gribid, status)
LOOP: DO WHILE (status /= GRIB_END_OF_FILE)
!**************************************************
! Start of User data processing
!**************************************************
!
! grib_dump should only be usd for diagnostic purposes.
!
! To process the data and grib headers, you will have to use
! grib_get and request the decoding of the keys you need,
! e.g. the date, the time, the parameter, the "level".
!
call grib_dump(gribid)
call grib_get_size(gribid,'values',numberOfPoints)
allocate(values(numberOfPoints), stat=iret)
if (iret /= 0) then
STOP 'grib_api_demo: allocate failed'
end if
call grib_get(gribid,'values',values)
print *, "First 20 values:"
write(*,'(f10.4)')(values(i),i=1,20)
!**************************************************
! End of User data processing
!**************************************************
!
! To access the next record in the grib file
!
call grib_release (gribid)
deallocate(values)
call grib_new_from_file(rfile, gribid, status)
!
! Loop back for next input field.
!
END DO LOOP
!
! End-of-file on input.
!
! release and close grib file
call grib_close_file (rfile)
!
!
END PROGRAM grib_api_demo
EOF
#--------------------
# MARS request
#--------------------
# Retrieve the data from MARS to the target data file "grib_file".
mars<<EOF
retrieve,
class = od,
stream = oper,
date = -2,
time = 00,
type = fc,
step = 12,
target = "grib_file.grb"
EOF
if [ $? != 0 ] # Check MARS exit code.
then
echo " The MARS request failed."
exit 1
fi
#-------------------------------
# compile and link libraries
#-------------------------------
module load prgenv/gnu
module load ecmwf-toolbox
gfortran -march=native -O3 -o grib_api_demo grib_api_demo.f90 $ECCODES_INCLUDE $ECCODES_LIB
# Use gfortran -o to create the grib_api_demo
# executable. The compiler options
# -arch=native -O3 provide
# some basic optimisation. The variables
# $ECCODES_INCLUDE and $ECCODES_LIB
# respectively contain the location of the
# ecCodes include files and libraries.
time ./grib_api_demo # timing the run of grib_api_demo
#-------------------------------
# tidy up by deleting unwanted files
#-------------------------------
# This is done automatically when using $SCRATCHDIR.
exit 0
# End of example job 'Retrieve_decode_grib_api'