Local mode installation¶

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:

Python code	Fortran code
Python3 numpy genshi eccodes for python ecmwf-api-client (everything except ERA5) cdsapi (just for ERA5 and member user)	gfortran fftw3 eccodes emoslib

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

Note

If you are using Anaconda Python, we recommend to follow the installation instructions of Anaconda Python Installation for Linux and then install the eccodes package from conda with:

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.

Note

Since public users currently don’t have access to the full ERA5 dataset, they can skip the installation of the CDS API.

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:

# 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.

Testing the Web APIs¶

You can start very simple test retrievals for both Web APIs to be sure that everything works. This is recommended to minimise the range of possible errors using flex_extract later on.

ECMWF Web API¶

Please use this Python code snippet as a Member user:

Please use this Python code snippet as a Public user:

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"
})

CDS API¶

Extraction of ERA5 data via CDS API might take time as currently there is a high demand for ERA5 data. Therefore, as a simple test for the API just retrieve pressure-level data (even if that is NOT what we need for FLEXPART), as they are stored on disk and don’t need to be retrieved from MARS (which is the time-consuming action):

Please use the following Python code snippet to retrieve a small sample of ERA5 pressure level data:

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")

If you know that your CDS API works, you can try to extract some data from MARS.

Please use the following Python code snippet to retrieve a small ERA5 data sample as a member-state user! The Public user do not have access to the full ERA5 dataset!

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¶

The Fortran program called calc_etadot will be compiled during the installation process. A suitable makefile (makefile_local_gfortran) for the compilation is set by default. This may be overwritten by the MAKEFILE parameter in setup.sh.

However, you may have to adapt the makefile for your environment (the current default makefile works on Debian stretch and similar GNU/Linux distributions). If you use a new name for it, you will have to insert it into setup.sh For details on the makefile and how to adapt them, see Fortran Makefile.

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:

‘Example settings for a local installation.’¶

...
# -----------------------------------------------------------------
# AVAILABLE COMMANDLINE ARGUMENTS TO SET
#
# THE USER HAS TO SPECIFY THESE PARAMETER
#
TARGET='local'
MAKEFILE=<name_of_your_makefile>
ECUID=None
ECGID=None
GATEWAY=None
DESTINATION=None
INSTALLDIR=None
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_local_gfortran
gfortran   -O3 -march=native -Bstatic -leccodes_f90 -leccodes -Bdynamic -lm -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 -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 -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 -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 -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 -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 -lemosR64 -fopenmp
ln -sf calc_etadot_fast.out calc_etadot

lrwxrwxrwx. 1 <username> tmc 20 Aug 12  10:59 ./calc_etadot -> calc_etadot_fast.out