Local mode - dependencies

The installation is the same for the access modes member and public.

The environment on your local system has to provide the following software packages and libraries, since the preparation of the extraction and the post-processing is done on the local machine:

Preparing the local environment

The easiest way to install all required packages is to use the package management system of your Linux distribution which requires admin rights. The installation was tested on a Debian GNU/Linux buster and an Ubuntu 18.04 Bionic Beaver system.

# On a Debian or Debian-derived (e. g. Ubuntu) system,
# you may use the following commands (or equivalent commands of your preferred package manager):
# (if respective packages are not already available):
 apt-get install python3 (usually already available on GNU/Linux systems)
 apt-get install python3-eccodes
 apt-get install python3-genshi
 apt-get install python3-numpy
 apt-get install gfortran
 apt-get install fftw3-dev
 apt-get install libeccodes-dev
 apt-get install libemos-dev
# Some of these packages will pull in further packages as dependencies.
# This is fine, and some are even needed by ``flex_extract''.

# As currently the CDS and ECMWF API packages are not available as Debian packages,
# they need to be installed outside of the Debian (Ubuntu etc.) package management system.
# The recommended way is:
 apt-get install pip
 pip install cdsapi
 pip install ecmwf-api-client

conda install conda-forge::python-eccodes

The CDS API (cdsapi) is required for ERA5 data and the ECMWF Web API (ecmwf-api-client) for all other public datasets.

Both user groups have to provide keys with their credentials for the Web APIs in their home directory, following these instructions:

ECMWF Web API:

Go to the MARS access website and log in with your credentials. Afterwards, go to the section "Install ECMWF KEY", where the key for the ECMWF Web API should be listed. Please follow the instructions in this section under 1 (save the key in a file .ecmwfapirc in your home directory).

CDS API:

Go to CDS API registration and register there, too. Log in on the cdsapi website and follow the instructions in the section "Install the CDS API key" to save your credentials in file .cdsapirc.

Testing the local environment

Check the availability of the python packages by typing python3 in a terminal window and run the import commands in the python shell: .. code-block:: python

# check in python3 console import eccodes import genshi import numpy import cdsapi import ecmwfapi

If there are no error messages, you succeeded in setting up the environment.

from ecmwfapi import ECMWFService
server = ECMWFService('mars')
server.retrieve({
    'stream'    : "oper",
    'levtype'   : "sfc",
    'param'     : "165.128/166.128/167.128",
    'dataset'   : "interim",
    'step'      : "0",
    'grid'      : "0.75/0.75",
    'time'      : "00/06/12/18",
    'date'      : "2014-07-01/to/2014-07-31",
    'type'      : "an",
    'class'     : "ei",
    'target'    : "download_erainterim_ecmwfapi.grib"
})

from ecmwfapi import ECMWFDataServer
server = ECMWFDataServer()
server.retrieve({
    'stream'    : "enda",
    'levtype'   : "sfc",
    'param'     : "165.128/166.128/167.128",
    'dataset'   : "cera20c",
    'step'      : "0",
    'grid'      : "1./1.",
    'time'      : "00/06/12/18",
    'date'      : "2000-07-01/to/2000-07-31",
    'type'      : "an",
    'class'     : "ep",
    'target'    : "download_cera20c_ecmwfapi.grib"
})

import cdsapi
c = cdsapi.Client()
c.retrieve("reanalysis-era5-pressure-levels",
{
"variable": "temperature",
"pressure_level": "1000",
"product_type": "reanalysis",
"year": "2008",
"month": "01",
"day": "01",
"time": "12:00",
"format": "grib"
},
"download_cdsapi.grib")

import cdsapi
c = cdsapi.Client()
c.retrieve('reanalysis-era5-complete',
{
    'class'   : 'ea',
    'expver'  : '1',
    'stream'  : 'oper',
    'type'    : 'fc',
    'step'    : '3/to/12/by/3',
    'param'   : '130.128',
    'levtype' : 'ml',
    'levelist': '135/to/137',
    'date'    : '2013-01-01',
    'time'    : '06/18',
    'area'    : '50/-5/40/5',
    'grid'    : '1.0/1.0',
    'format'  : 'grib',
}, 'download_era5_cdsapi.grib')

Local installation

First, adapt the Fortran makefile for your environment (if necessary) and insert it into setup.sh script (see :ref:`Fortran Makefile <ref-convert>` for more information). They can be found at flex_extract_vX.X/Source/Fortran/, where vX.X should be substituted by the current flex_extract version number.

Thus, go to the Fortran source directory and open the makefile of your choice, and check / modify with an editor of your choice:

cd flex_extract_vX.X/Source/Fortran
nedit makefile_fast

Set the paths to the eccodes library on your local machine, if necessary.

# for the ECCODES_INCLUDE_DIR path do:
$ dpkg -L libeccodes-dev | grep eccodes.mod
# for the ECCODES_LIB path do:
$ dpkg -L libeccodes-dev | grep libeccodes.so

Assign these paths to the parameters ECCODES_INCLUDE_DIR and ECCODES_LIB in the makefile, and save it.

# these are the paths on Debian Buster:
ECCODES_INCLUDE_DIR=/usr/lib/x86_64-linux-gnu/fortran/gfortran-mod-15/
ECCODES_LIB= -L/usr/lib -leccodes_f90 -leccodes -lm

The Fortran program called calc_etadot will be compiled during the installation process. Therefore, the name of the makefile to be used needs to be given in setup.sh.

In the root directory of flex_extract, open the setup.sh script with an editor and adapt the installation parameters in the section labelled with "AVAILABLE COMMANDLINE ARGUMENTS TO SET" as shown below:

.. code-block:: bash
   :caption: 'Example settings for a local installation.'
   :name: setup.sh
   ...
   # -----------------------------------------------------------------
   # AVAILABLE COMMANDLINE ARGUMENTS TO SET
   #
   # THE USER HAS TO SPECIFY THESE PARAMETER
   #
   TARGET='local'
   MAKEFILE='makefile_fast'
   ECUID=None
   ECGID=None
   GATEWAY=None
   DESTINATION=None
   INSTALLDIR=None
   JOB_TEMPLATE='job.template'
   CONTROLFILE='CONTROL_EA5'
   ...

Afterwards, type:

$ ./setup.sh

to start the installation. You should see the following standard output.

# Output of setup.sh
    WARNING: installdir has not been specified
    flex_extract will be installed in here by compiling the Fortran source in <path-to-flex_extract>/flex_extract_v7.1/Source/Fortran
    Install flex_extract_v7.1 software at local in directory <path-to-flex_extract>/flex_extract_v7.1
    Using makefile: makefile_fast
    gfortran   -O3 -march=native -Bstatic -leccodes_f90 -leccodes -Bdynamic -lm -ljasper -lemosR64 -I. -I/usr/local/include -fdefault-real-8 -fopenmp -fconvert=big-endian   -c     ./rwgrib2.f90
    gfortran   -O3 -march=native -Bstatic -leccodes_f90 -leccodes -Bdynamic -lm -ljasper -lemosR64 -I. -I/usr/local/include -fdefault-real-8 -fopenmp -fconvert=big-endian   -c     ./phgrreal.f90
    gfortran   -O3 -march=native -Bstatic -leccodes_f90 -leccodes -Bdynamic -lm -ljasper -lemosR64 -I. -I/usr/local/include -fdefault-real-8 -fopenmp -fconvert=big-endian   -c     ./grphreal.f90
    gfortran   -O3 -march=native -Bstatic -leccodes_f90 -leccodes -Bdynamic -lm -ljasper -lemosR64 -I. -I/usr/local/include -fdefault-real-8 -fopenmp -fconvert=big-endian   -c     ./ftrafo.f90
    gfortran   -O3 -march=native -Bstatic -leccodes_f90 -leccodes -Bdynamic -lm -ljasper -lemosR64 -I. -I/usr/local/include -fdefault-real-8 -fopenmp -fconvert=big-endian   -c     ./calc_etadot.f90
    gfortran   -O3 -march=native -Bstatic -leccodes_f90 -leccodes -Bdynamic -lm -ljasper -lemosR64 -I. -I/usr/local/include -fdefault-real-8 -fopenmp -fconvert=big-endian   -c     ./posnam.f90
    gfortran  rwgrib2.o calc_etadot.o ftrafo.o grphreal.o posnam.o phgrreal.o -o calc_etadot_fast.out  -O3 -march=native -Bstatic -leccodes_f90 -leccodes -Bdynamic -lm -ljasper -lemosR64 -fopenmp
    ln -sf calc_etadot_fast.out calc_etadot
    lrwxrwxrwx. 1 <username> tmc 20 15. Mär 13:31 ./calc_etadot -> calc_etadot_fast.out