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Note

Note that this documentation applies to the OpenIFS/AC code extension for OpenIFS 43r3. This does not apply to users of OpenIFS 48r1 or later model releases.


...

Table of Contents

...


This page describes how OpenIFS/AC v1 (derived from OpenIFS 43r3v2) can be obtained, built and used for forecast experiments. The documentation shows examples of how to use the model on the ECMWF Atos Sequana XH2000 HPCF (hpc2020). Adjustments will need to be made for local installations. 

Info

Enquiries about OpenIFS/AC or technical questions should in the first instance be sent to openifs-support@ecmwf.int

OpenIFS/AC compared to the standard OpenIFS model

...

The standard OpenIFS model is described in detail in the OpenIFS 43r3 User Guide. The user guide introduces the model's components and supported model grids. It informs about additional required software packages and how to build the OpenIFS model. It further describes how to carry out an acceptance test after a successful model build in order to verify the model's functionality.

Info

Users who are new to OpenIFS should first read the OpenIFS 43r3 User Guide's sections 1 to 5 before proceeding with OpenIFS/AC, as the steps described therein are required for building OpenIFS/AC. The instructions in the user guide will not be repeated here.

...

No Format
ftp ftp.ecmwf.int
(login with username and password for OpenIFS users)
cd src/openifs-ac
get openifs-ac.43r3.v1.tgzgz
bye

Installing the OpenIFS/AC sources

...

  • Create a new home for the OpenIFS/AC installation. Here we call this location /home/openifs-ac. 
  • Change into your new directory and unpack therein the original OpenIFS model sources:   tar xvzf oifs43r3v2.tgz
  • In a second step, in the same folder unpack gunzip the OpenIFS/AC sources :  tar xvzf and patch the original OpenIFS:
    • gunzip openifs-ac.43r3.v1.
    tgz
    • gz
    • patch -p1 <openifs-ac.43r3.v1
Info

Note that some files of the original model will be replacedmodified. It is therefore essential to install the original OpenIFS 43r3v2 sources first before installing the OpenIFS/AC sources.

...

  • Change into your $OIFS_HOME directory where OpenIFS is installed:  cd $OIFS_HOME
  • In this directory extract the downloaded source package:   tar xvzf
    • gunzip openifs-ac.43r3.v1
    .tgz
    • .gz
    • patch -p1 <openifs-ac.43r3.v1
Info

Note that this unpacking will not only add new files to your existing $OIFS_HOME but it will also overwrite some of the existing files with updated versions required for OpenIFS/AC.

...

  • Unpack oifs-ac-43r3-initcond.tgz into /data/openifs-ac which results in a directory /data/openifs-ac/INITIAL-CONDITIONS.
    The files therein are initial data files for the first day of month for all 12 months of 2010.
  • Unpack ICMCL-2010.tgz into /data/openifs-ac which results in a directory /data/openifs-ac/ICMCL.
    This directory contains monthly files with surface boundary conditions (e.g. SSTs, soil temps, albedos, LAI etc).
  • In the tgz archives above, the data for the year 2013, provided on a Tl255L60 grid, is required for the T21 acceptance tests. The data for year 2010 is provided on a Tl255L91 grid and can be used for the example forecasts. 
  • From your conventional OpenIFS installation's OIFS_DATA_DIR copy the directories ifsdata and rtables to /data/openifs-ac/43r3 as they are also needed here. If this is your first model installation, these data directories are also available from the ftp server. 
  • Further, create a directory /data/openifs-ac/43r3/wam which needs to contain wave model initial data for 2010-01-01. 

Building the model

Info

Note:  In the reference forecast experiments discussed below the initial conditions files for the wave model (ocean surface waves) are added to the experiment separately from a central location in the OIFS_DATA_DIR. When initial experiment data is requested from ECMWF (e.g. through the OpenIFS Data Hub) the required files for the wave model are supplied together with the files for the atmospheric model. 



...

Building the model

This This section describes how to build the binary model executable for OpenIFS/AC. Most problems related to building the model executable are due to incorrect environment settings. Therefore we recommend that particular care should be given to the environment settings to ensure that they match the local hardware platform. 

...

  • To do this we run the standard t21test for experiment epc8 (T21L19) with the setup-exp.sh new script.
  • The name for the hardware platform needs to be set (l.89, e.g. platform=ecmwf-hpc2020)
  • The test experiment runs in the RUNDIR directory test experiment runs in the RUNDIR directory specified in setup-exp.sh (l.94, the default is $SCRATCH/43r3/epc8/).
  • We also need to use the command line option -x and give as argument the absolute full path to the master.exe binary executable.
  • In setup-exp.sh you should change the value for RUN_NUMBER otherwise any pre-existing model output from this test will be overwritten. 

...

Test result:  As before an error calculation file res_021_0072 is created in the run directory and the model output is found in the subfolder output1 (this name depends on the RUN_NUMBER variable). 

With chemistry:  Now repeat the test with enabled model chemistry. This is a short 1-day test run that uses the newly added source code of OpenIFS/AC. It has a very limited set of options and should not be used for forecast experiments. Note that you cannot increase the experiment duration beyond one day because the boundary conditions are only supplied from 2013-07-01 to 2013-07-03. 

This experiment is named oiac and uses a Tl255L60 grid and runs for 24 hours. The default run directory is $SCRATCH/43r3/oiac/. 

No Format
./setup-exp.sh -c -n 16 -t 2 -x /home/damk/oifs/model/openifs-ac/make/gnu-opt-chem-fftw/oifs/bin/master.exe

This test runs with a 30 min time step and due to the computational requirements for the added chemistry it will take much longer to complete. The variable CHEM_SCHEME offers the choice of two chemistry schemes, the AER aerosol scheme is always enabled. 

Note

Note:  If the XIOS server is to be used in the t21test experiments (option -i ) then the variables OIFS_XIOS and OIFS_XIOS_DIR need to be set appropriately in the configuration file in the platform directory. Also, the binary executable master.exe needs to have been built with XIOS support enabled.

Test result:  This experiment calculates budgets of atmospheric mass and ozone which are stored in the NODE.001_01 file and also in files $RUNDIR/output{$RUN_NUMBER}/massdia_chem_oiac.txt and ozonbud_chem_dia.txt.

These diagnostics can be compared with pre-calculated results in files massdia_chem__oiac_2013070100.txt and ozonbud_chem__oiac_2013070100.txt which are located in $OIFS_HOME/t21test_xois_t255ac/ctrl/. For example this could be done with a small shell script such as illustrated in the box below. 

No Format
EXPID=oiac; RUNDIR=${SCRATCH}/${OIFS_CYCLE}/${EXPID} ;  RUN_NUMBER=3  #checkoifs
fref1=${OIFS_HOME}/t21test_xios_ac/ctrl/massdia_chem__oiac_2013070100.txt
fref2=${OIFS_HOME}/t21test_xios_ac/ctrl/ozonbud_chem__oiac_2013070100.txt
fnew1=${RUNDIR}/output${RUN_NUMBER}/massdia_chem_oiac.txt
fnew2=${RUNDIR}/output${RUN_NUMBER}/ozonbud_chem_oiac.txt
diff $fref1 $fnew1
diff $fref2 $fnew2

Differences between the reference budgets and those from the t21test should be only small (below 5%). 

Single forecast experiments

This section describes the required steps to carry out a forecast experiment with chemistry. The essential three steps can be summarised as:

  1. Edit paths and variables in $OIFS_HOME/AC-experiments/config.h. This controls model switches and the chemistry scheme. 
  2. Prepare initial conditions using $OIFS_HOME/AC-epxeriments/prep-ic-icmcl-compo.sh.
  3. Customise a job wrapper script for the relevant hardware platform (a *.job file) in order to submit the oifs-run.sh script to the batch scheduler.

Overview of the AC-experiments directory

Info

Running on the ECMWF HPCF: 
This script requires more resources than are provided using the ecinteractive node.
One recommendation is to adapt an existing template from the platform subdirectory and submit this using the sbatch command.
Alternatively, the srun command could be used:
export NPROC=120 
export OMP_NUM_THREADS=4 
export OIFS_RUNCMD="srun --qos=np $OMP_NUM_THREADS -n $NPROC master.exe" 
./setup-exp.sh -n 120 -t 4 -x master.exe 


With chemistry:  Now repeat the test with enabled model chemistry. This is a short 1-day test run that uses the newly added source code of OpenIFS/AC. It has a very limited set of options and should not be used for forecast experiments. Note that you cannot increase the experiment duration beyond one day because the boundary conditions are only supplied from 2013-07-01 to 2013-07-03. 

This experiment is named oiac and uses a Tl255L60 grid and runs for 24 hours. The default run directory is $SCRATCH/43r3/oiac/. 

No Format
./setup-exp.sh -c -n 16 -t 2 -x /home/damk/oifs/model/openifs-ac/make/gnu-opt-chem-fftw/oifs/bin/master.exe

This test runs with a 30 min time step and due to the computational requirements for the added chemistry it will take much longer to complete. The variable CHEM_SCHEME offers the choice of two chemistry schemes, the AER aerosol scheme is always enabled. 

Note

Note:  If the XIOS server is to be used in the t21test experiments (option -i ) then the variables OIFS_XIOS and OIFS_XIOS_DIR need to be set appropriately in the configuration file in the platform directory. Also, the binary executable master.exe needs to have been built with XIOS support enabled.

Test result:  This experiment calculates budgets of atmospheric mass, along with overall production and loss tendencies, as well as more detailed reaction budget terms relevant for the ozone production and loss tendency. These are printed in the NODE.001_01 file and afterwards extracted to the files $RUNDIR/output{$RUN_NUMBER}/massdia_chem_oiac.txt and ozonbud_chem_dia.txt.

These diagnostics can be compared with pre-calculated results in files massdia_chem__oiac_2013070100.txt and ozonbud_chem__oiac_2013070100.txt which are located in $OIFS_HOME/t21test_xois_t255ac/ctrl/. For example this could be done with a small shell script such as illustrated in the box below. 

No Format
EXPID=oiac; RUNDIR=${SCRATCH}/${OIFS_CYCLE}/${EXPID} ;  RUN_NUMBER=3  #checkoifs
fref1=${OIFS_HOME}/t21test_xios_ac/ctrl/massdia_chem__oiac_2013070100.txt
fref2=${OIFS_HOME}/t21test_xios_ac/ctrl/ozonbud_chem__oiac_2013070100.txt
fnew1=${RUNDIR}/output${RUN_NUMBER}/massdia_chem_oiac.txt
fnew2=${RUNDIR}/output${RUN_NUMBER}/ozonbud_chem_oiac.txt
diff $fref1 $fnew1
diff $fref2 $fnew2

As a rule of thumb, differences between the reference budget numbers and those from the t21test should be only small (below 5%), although this depends on the exact variable that is assessed. 


...

Single forecast experiments

This section describes the required steps to carry out a single forecast experiment (no restarts) with chemistry. The essential three steps can be summarised as:

  1. Edit paths and variables in $OIFS_HOME/AC-experiments/config.h. This controls model switches and the chemistry scheme. 
  2. Prepare initial conditions using $OIFS_HOME/AC-epxeriments/prep-ic-icmcl-compo.sh.
  3. Customise a job wrapper script for the relevant hardware platform (a *.job file) in order to submit the oifs-run.sh script to the batch scheduler.

Overview of the AC-experiments directory

No Format
AC-experiments/
├── config.h                   # MAIN experiment config file
├── ctrl/
│   ├── context_ifs.xml
No Format
AC-experiments/
├── config.h                   # MAIN experiment config file
├── ctrl/
│   ├── context_ifs.xml        # xios resource
│   ├── ifs_xml/               # xios resource
│   ├── iodef.xml              # xios resource
│   ├── namelistfc 
│   ├── namelist.ifs-epc8.sh   # namelist for t21test
│   ├── namelist.ifs-oiac.sh   # namelist for t21test
│   ├── namelist.ifs.sh        # namelist template for forecast experiments
│   ├── Table/                 # dir with AC tracersxios resource
│   └──├── wam_namelist
├── ecmwf-atos.jobifs_xml/               # job wrapper script for oifs-run.sh
├── oifs-run.shxios resource
│   ├── iodef.xml                # MAINxios runresource
│   script
├── platform/namelistfc 
│   ├── namelist.ifs-epc8.sh   # namelist for t21test without chemistry
│   ├── namelist.ifs-oiac.sh   # namelist #for dirt21test with platform-specific templates
├── prep_emischemistry
│   ├── namelist.ifs.sh        # namelist template for forecast experiments
│   ├── Table/                 # dir with emission utilitiesAC tracers
│   └── wam_namelist
├── prep-ic-icmcl-compo.shecmwf-hpc2020.job      # MAIN script to prepare# initial/boundary conditions
└── scripts/   job wrapper script for oifs-run.sh
├── oifs-run.sh                # dirMAIN with low-level scripts
 run script
├── platform/   ├── add_nrt_fire_chem
    ├── gaussgr
    ├── get_alb_lai_intLimits
    ├── get_tablecol
    ├── grib_def.h
# dir with platform-specific templates
├── prep_emis/    ├── lib_chem_setup.sh
    ├── lib_general.sh       # dir   # lib ofwith emission utilities
    ├── lib_icmcl_climaprep-ic-icmcl-compo.sh     # MAIN #script libto ofprepare functs to create ICMCL boundary cond. files
initial/boundary conditions
└── scripts/        ├── lib_icmcl_compo.sh       # lib of functs# todir createwith ICMCLlow-COMPOlevel filesscripts
    ├── libadd_nrt_initcondfire_offline.shchem
    ├── └── lib_initcond.shgaussgr
    ├── get_alb_lai_intLimits
    ├── get_tablecol
 # lib of functs to create initial conditions files

The experiment controls are in $OIFS_HOME/AC-experiments/. 

There the following essential files can be found:

  • prep-ic-icmcl-compo.sh  - a script to generate initial conditions for chemical fields for the selected run time. Begin and end date need to be given as an argument.
  • config.h  - settings for model installation, paths, and experiment configuration.
  • oifs-run.sh  - this script controls the workflow for the experiment: reads experiment config, sets up run directories (in $SCRATCH), loads platform configuration, edits namelists, links to initial conditions and executes OIFS_RUNCMD
  • ecmwf-atos.job  wrapper script for oifs-run.sh, required settings for the batch scheduler
├── grib_def.h
    ├── lib_chem_setup.sh
    ├── lib_general.sh           # lib of utilities
    ├── lib_icmcl_clima.sh       # lib of functs to create ICMCL boundary cond. files
    ├── lib_icmcl_compo.sh       # lib of functs to create ICMCL-COMPO files
    ├── lib_initcond_offline.sh
    └── lib_initcond.sh          # lib of functs to create initial conditions files

The experiment controls are in In $OIFS_HOME/AC-experiments/platform:

  • it is necessary to create a platform-specific machine config file:  oifs-config.ecmwf-atos.sh

The above ecmwf-atos.job wrapper script to submit the batch job is based on templates in the platform directory; a number of templates exist and for the ECMWF HPCF the following templates are relevant:

  • ecmwf-hpc2020.job.tmpl    –    run oifs without XIOS
  • oifs-config.ecmwf-hpc2020.sh  –  template for the machine config file

Editing the experiment configuration file

For the forecast experiment to succeed and in order to generate the initial data correctly, you will need to edit variables inside the file config.h to correspond with the chosen settings for your experiment.

In config.h you should edit the following variables. The example is for a single forecast (without restarts or multiple forecast legs), starting from 1st January 2010 having 48 hours duration. 

. 

There the following essential files can be found:

  • prep-ic-icmcl-compo.sh  - a script to generate initial conditions for chemical fields for the selected run time. Begin and end date need to be given as an argument.
  • config.h  - settings for model installation, paths, and experiment configuration.
  • oifs-run.sh  - this script controls the workflow for the experiment: reads experiment config, sets up run directories (in $SCRATCH), loads platform configuration, edits namelists, links to initial conditions and executes OIFS_RUNCMD
  • ecmwf-hpc2020.job  wrapper script for oifs-run.sh, required settings for the batch scheduler

In $OIFS_HOME/AC-experiments/platform:

  • it is necessary to create a platform-specific machine config file:  oifs-config.ecmwf-hpc2020.sh

The above ecmwf-hpcs2020.job wrapper script to submit the batch job is based on templates in the platform directory; a number of templates exist and for the ECMWF HPCF the following templates are relevant:

  • ecmwf-hpc2020.job.tmpl    –    run oifs without XIOS
  • oifs-config.ecmwf-hpc2020.sh  –  template for the machine config file

Editing the experiment configuration file

For the forecast experiment to succeed and in order to generate the initial data correctly, you will need to edit variables inside the file config.h to correspond with the chosen settings for your experiment.

In config.h you should edit the following variables. The example is for a single forecast (without restarts or multiple forecast legs), starting from 1st January 2010 having 48 hours duration. 

No Format
PLATFORM='ecmwf-hpc2020' # this needs to match the name of the platform configuration file
EXP=abcd                 # you should select here an experiment ID (4-letter alphanumeric word, must not start with '0')

RUNDIR
No Format
PLATFORM='ecmwf-atos'   # this needs to match the name of the platform configuration file
EXP=abcd                # you should select here an experiment ID (4-letter alphanumeric word, must not start with '0')

RUNDIR=${SCRATCH}/43r3/experiments/${EXP}/runs         # this is the experiment directory
AC_IC_DIR=${SCRATCH}/43r3/experiments/${EXP}/chem_icruns   # this is the stageing directory for# initialthis andis boundarythe conditions data experiment directory
AC_IC_DIR=${SCRATCH}/43r3/experiments/${EXP}/chem_ic   # this is the staging directory for initial and boundary conditions data files

# Simulation start and end date. If setting time (not mandatory), **put it before** the date
run_start_date="00:00 2010-01-01"
run_end_date="${run_start_date} + 2 days"
 
rst_freq='6 day'        # Run for 6 days without restarts. Our experiment will finish after 2 days, so this will be ignored. 
USE_RESTART=false       # Do not write restart files.

...

No Format
OIFS_INIDATA_DIR=${OIFS_DATA_DIR}/INITIAL-CONDITIONS/T255L91-tm5-aer   # Initialinitial and boundary conditions for the chemistry scheme used
ICMCLDIR=${OIFS_DATA_DIR}/ICMCL                                        # physical/meteorological boundary conditions
MET_IC_DIR=${OIFS_DATA_DIR}/ICMCL/aabg/2010010100                      # path for meteorological initial data in case it needs to be generated
AC_IC_ONCE=${OIFS_DATA_DIR}/INITIAL-CONDITIONS/T255L91-tm5-aer/ICMUAoiac.ac_rst    # initial conditions for chemical tracers

...

Code Block
PLATFORM='ecmwf-atoshpc2020'

RUNDIR='${SCRATCH}/43r3/experiments/${EXP}/runs'        # where your experiment will run
AC_IC_DIR='${SCRATCH}/43r3/experiments/${EXP}/chem_ic'  # where your chemical initial conditions will be created
run_end_date="2010-01-03"
rst_freq='6 day'
USE_RESTART=false

LCHEM=true
CHEM_SCHEME="tm5"
CHEM_VER="ver15"
OIFS_INIDATA_DIR='${OIFS_DATA_DIR}/INITIAL-CONDITIONS/T255L91-tm5-none'
AC_IC_ONCE='${OIFS_INIDATA_DIR}/ICMUAoiac.ac_rst'
MET_IC_DIR='${OIFS_DATA_DIR}/ICMCL/aabg/2010010100'

LAERO=false
LAERCHEM=false
LCHEM_AEROI=false
LINJ_CHEM=false
LINJ_AER=false
LAEROSFC=false

LWAM=true
LRLXG=false
LAC4IC=true

Using TM5 chemistry with AER aerosol

...

Code Block
PLATFORM='ecmwf-atoshpc2020'

RUNDIR='${SCRATCH}/43r3/experiments/${EXP}/runs'        # where your experiment will run
AC_IC_DIR='${SCRATCH}/43r3/experiments/${EXP}/chem_ic'  # where your chemical initial conditions will be created
run_end_date="2010-01-03"
rst_freq='6 day'
USE_RESTART=false

LCHEM=true
CHEM_SCHEME="tm5"
CHEM_VER="ver15"
OIFS_INIDATA_DIR='${OIFS_DATA_DIR}/INITIAL-CONDITIONS/T255L91-tm5-aer'
AC_IC_ONCE='${OIFS_INIDATA_DIR}/ICMUAoiac.ac_rst'
MET_IC_DIR='${OIFS_DATA_DIR}/ICMCL/aabg/2010010100'

LAERO=true
LAERCHEM=true
LCHEM_AEROI=true
LINJ_CHEM=true
LINJ_

LAERO=true
LAERCHEM=true
LCHEM_AEROI=true
LINJ_CHEM=true
LINJ_AER=true
LAEROSFC=true

LWAM=true
LRLXG=false
LAC4IC=true

Using BASCOE-TM5 chemistry without aerosol

...

Code Block
PLATFORM='ecmwf-atoshpc2020'

RUNDIR='${SCRATCH}/43r3/experiments/${EXP}/runs'        # where your experiment will run
AC_IC_DIR='${SCRATCH}/43r3/experiments/${EXP}/chem_ic'  # where your chemical initial conditions will be created
run_end_date="2010-01-03"
rst_freq='6 day'
USE_RESTART=false

LCHEM=true
CHEM_SCHEME="bascoetm5"
CHEM_VER="ver2f"
OIFS_INIDATA_DIR='${OIFS_DATA_DIR}/INITIAL-CONDITIONS/T255L91-bascoetm5-none'
AC_IC_ONCE='${OIFS_INIDATA_DIR}/ICMUAoiac.ac_rst'
MET_IC_DIR='${OIFS_DATA_DIR}/ICMCL/aabg/2010010100'

LAERO=false
LAERCHEM=false
LCHEM_AEROI=false
LINJ_CHEM=false
LINJ_AER=false
LAEROSFC=false

LWAM=true
LRLXG=false
LAC4IC=true

Using BASCOE-TM5 chemistry with AER aerosol

Example:  Run a-2 day forecast starting from 2010-01-01 with combined BASCOE and TM5 chemistry without aerosol.

Use the following settings in config.h:

Code Block
PLATFORM='ecmwf-atos'

RUNDIR='${SCRATCH}/43r3/experiments/${EXP}/runs'        # where your experiment will run
AC_IC_DIR='${SCRATCH}/43r3/experiments/${EXP}/chem_ic'  # where your chemical initial conditions will be created
run_end_date="2010-01-03"
rst_freq='6 day'
USE_RESTART=false

LCHEM=true
CHEM_SCHEME="bascoetm5"
CHEM_VER="ver2f"
OIFS_INIDATA_DIR='${OIFS_DATA_DIR}/INITIAL-CONDITIONS/T255L91-bascoetm5-none'
AC_IC_ONCE='${OIFS_INIDATA_DIR}/ICMUAoiac.ac_rst'
MET_IC_DIR='${OIFS_DATA_DIR}/ICMCL/aabg/2010010100'

LAERO=true
LAERCHEM=true
LCHEM_AEROI=true
LINJ_CHEM=true
LINJ_AER=true
LAEROSFC=true

LWAM=true
LRLXG=false
LAC4IC=true

Generating initial data

Initial conditions for the standard OpenIFS model can be generated using the OpenIFS Data Hub or alternatively they can be requested from the ECMWF OpenIFS support by email openifs-support@ecmwf.int. This provides initial experiment data and surface boundary conditions for the physical/meteorological NWP forecast model.

In order to simulate atmospheric composition with OpenIFS/AC additional initial and boundary conditions are needed. These can be created using the prep-ic-icmcl-compo.sh script. 

Info

Note:  The prep-ic-icmcl-compo.sh script requires external software: the CDO command line operators to manipulate and analyse climate and NWP model data which are available here: https://code.mpimet.mpg.de/projects/cdo/. If these utilities are not available on your computer system then they need to be installed before using the script. 

The prep-ic-icmcl-compo.sh script (henceforth: prep script) carries out 4 tasks:

  • Creates a destination directory $AC_IC_DIR which serves as a staging area for all initial and boundary conditions required for the forecast experiment. Symbolic links will point later from inside the experiment run directory to these files.
  • Copies the physical/meteorological initial conditions files that must be specific to the experiment start date from $OIFS_INIDATA_DIR to the new $AC_IC_DIR. If these files cannot be found then an attempt is made to create them from files found in the $MET_IC_DIR directory. 
  • Copies the physical boundary conditions file ICMCL{exp}INIT (SSTs, albedos, etc) from $OIFS_INIDATA_DIR to $AC_IC_DIR and if necessary truncate to length of experiment duration. 
  • Copies the chemistry initial and boundary conditions file (emission fluxes, deposition velocities) ICMCL-INIT-COMPO from $OIFS_INIDATA_DIR to $AC_IC_DIR. If this file cannot be found it will be created. 

The syntax to run the prep script is:

No Format
nopaneltrue
./prep-ic-icmcl-compo.sh <start_date> <end_date>

with start_date and end_date having the format YYYY-MM-DD.

In the examples above for a 2-day forecast, the syntax should be  ./prep-ic-icmcl-compo.sh 2010-01-01 2010-01-03  to generate the data for 48 hours from 1st January 2010. 

Running the prep script will take a few minutes and will result in new data that will be written to $AC_IC_DIR, by default this location is $SCRATCH/43r3/experiments/{exp}/chem_ic.

This folder serves as a staging area for the initial and boundary conditions data and if the target files in $AC_IC_DIR already exist then they they will not be overwritten. 

Creating initial conditions at the end of an experiment run

When setting  LAC4IC=true an AC-for-IC grib file is created at the end of a run. It is a snapshot of all chemical/atmospheric composition tracers. This file can be used by the pre-processing script (prep script) to create new initial conditions. 

With the AC-for-IC file, initial conditions for a new experiment can be generated which will provide a continuation of the chemical evolution of the tracer fields from the previous experiment. The meteorological fields to complement the initial conditions can originate from an archived experiment or can be generated with the OpenIFS Data Hub. This workflow is desirable when aiming to reinitialise the model integration with an updated weather forecast or analysis data (which does not provide AC tracers).  

In order to restart with atmospheric composition tracers from the AC-for-IC grib file select the following settings in config.h:

  • Set OIFS_INIDATA_DIR to nothing or comment it out.
  • Set the variable AC_IC_ONCE to the generated AC-for-IC grib file from the previous experiment. This is typically found in this location in the previous experiment:
    ${RUNDIR}/output/001/ICMUA${EXP}.ac_rst
  • Set the MET_IC_DIR to the relevant path or modify the "variables to retrieve METEO initial conditions from an archived experiment" section as appropriate.

Running a forecast experiment on the ECMWF HPCF

The actual forecast experiment will be carried out inside the run directory. By default this is set to $SCRATCH/43r3/experiments/${exp}/runs/.

Multiple forecasts with restarts

Info

This option is at an experimental development stage and it is therefore currently not supported for general users.

Its implementation depends on scripting that is dependant on the hardware platform. Suggestions for script templates that are used on the ECMWF HPCF can be provided on request.

...



LAERO=false
LAERCHEM=false
LCHEM_AEROI=false
LINJ_CHEM=false
LINJ_AER=false
LAEROSFC=false

LWAM=true
LRLXG=false

Using BASCOE-TM5 chemistry with AER aerosol

Example:  Run a-2 day forecast starting from 2010-01-01 with combined BASCOE and TM5 chemistry without aerosol.

Use the following settings in config.h:

Code Block
PLATFORM='ecmwf-hpc2020'

RUNDIR='${SCRATCH}/43r3/experiments/${EXP}/runs'        # where your experiment will run
AC_IC_DIR='${SCRATCH}/43r3/experiments/${EXP}/chem_ic'  # where your chemical initial conditions will be created
run_end_date="2010-01-03"
rst_freq='6 day'
USE_RESTART=false

LCHEM=true
CHEM_SCHEME="bascoetm5"
CHEM_VER="ver2f"
OIFS_INIDATA_DIR='${OIFS_DATA_DIR}/INITIAL-CONDITIONS/T255L91-bascoetm5-none'

LAERO=true
LAERCHEM=true
LCHEM_AEROI=true
LINJ_CHEM=true
LINJ_AER=true
LAEROSFC=true

LWAM=true
LRLXG=false

Generating initial data

Initial conditions for the standard OpenIFS model can be generated using the OpenIFS Data Hub or alternatively they can be requested from the ECMWF OpenIFS support by email openifs-support@ecmwf.int. This provides initial experiment data and surface boundary conditions for the physical/meteorological NWP forecast model.

In order to simulate atmospheric composition with OpenIFS/AC additional initial and boundary conditions are needed. These can be created using the prep-ic-icmcl-compo.sh script. 

Info

Note:  The prep-ic-icmcl-compo.sh script requires external software: the CDO command line operators to manipulate and analyse climate and NWP model data which are available here: https://code.mpimet.mpg.de/projects/cdo/. If these utilities are not available on your computer system then they need to be installed before using the script. 

The prep-ic-icmcl-compo.sh script (henceforth: prep script) carries out 4 tasks:

  • Creates a destination directory $AC_IC_DIR which serves as a staging area for all initial and boundary conditions required for the forecast experiment. Symbolic links will point later from inside the experiment run directory to these files.
  • Copies the physical/meteorological initial conditions files that must be specific to the experiment start date from $OIFS_INIDATA_DIR to the new $AC_IC_DIR. If these files cannot be found then an attempt is made to create them from files found in the $MET_IC_DIR directory. 
  • Copies the physical boundary conditions file ICMCL{exp}INIT (SSTs, albedos, etc) from $OIFS_INIDATA_DIR to $AC_IC_DIR and if necessary truncate to length of experiment duration. 
  • Copies the chemistry initial and boundary conditions file (emission fluxes, deposition velocities) ICMCL-INIT-COMPO from $OIFS_INIDATA_DIR to $AC_IC_DIR. If this file cannot be found it will be created. 

The syntax to run the prep script is:

No Format
./prep-ic-icmcl-compo.sh <start_date> <end_date>

with start_date and end_date having the format YYYY-MM-DD.

In the examples above for a 2-day forecast, the syntax should be  ./prep-ic-icmcl-compo.sh 2010-01-01 2010-01-03  to generate the data for 48 hours from 1st January 2010. 

Running the prep script will take a few minutes and will result in new data that will be written to $AC_IC_DIR, by default this location is $SCRATCH/43r3/experiments/{exp}/chem_ic.

This folder serves as a staging area for the initial and boundary conditions data and if the target files in $AC_IC_DIR already exist then they they will not be overwritten. 

Creating initial conditions at the end of an experiment run

When setting  LAC4IC=true an AC-for-IC grib file is created at the end of a run. It is a snapshot of all chemical/atmospheric composition tracers. This file can be used by the pre-processing script (prep script) to create new initial conditions. 

With the AC-for-IC file, initial conditions for a new experiment can be generated which will provide a continuation of the chemical evolution of the tracer fields from the previous experiment. The meteorological fields to complement the initial conditions can originate from an archived experiment or can be generated with the OpenIFS Data Hub. This workflow is desirable when aiming to reinitialise the model integration with an updated weather forecast or analysis data (which does not provide AC tracers).  

In order to restart with atmospheric composition tracers from the AC-for-IC grib file select the following settings in config.h:

  • Either leave the variable OIFS_INIDATA_DIR empty, delete it or comment it out.
  • Set the variable AC_IC_ONCE to point to the generated AC-for-IC grib file from the previous experiment. This file is typically found in this location in the previous experiment:
    ${RUNDIR}/output/${RUN_NUMBER}/ICMUA${EXP}.ac_rst
  • Set the variable MET_IC_DIR to the relevant path for the new experiment's initial conditions or modify the "variables to retrieve METEO initial conditions from an archived experiment" section as appropriate.

Running the forecast experiment

Now the actual forecast experiment can be submitted to the batch scheduler using the platform-specific job wrapper script. Examples for this are found in $OIFS_HOME/AC-experiments/platform. An example template for the ECMWF HPCF Atos Sequana XH2000 is the file ecmwf-hpc2020.job.tmpl. 

The actual forecast experiment will be carried out inside the run directory which is defined in config.h with variable RUNDIR. The default on the ECMWF HPCF is $SCRATCH/43r3/experiments/${exp}/runs/.

Due to the much increased computational requirements for simulating atmospheric composition, forecast experiments are often broken into individual parts (sometimes referred to as "legs"). For each leg a restart of the forecast experiment needs to be carried out. 

Model Output
The oifs-run.sh script for OpenIFS/AC has been designed to be able to cope with restarts or "legs", and the model output from each experiment leg is stored in individual subfolders named by leg number. In the case of a single forecast experiment without restarts the output will be written to $RUNDIR/output/001.

Log files
Log file and experiment-related configuration data (namelist, NODE file, ifs.stat), as well as text files with diagnostic model outuput (e.g. mass and ozone budgets) are copied to $RUNDIR/log/001.

Restart Data
Model data relevant for restarts (not discussed here on this page) will be stored in $RUNDIR/restart/${next_leg_number}.

XIOS output
Files relevant to XIOS server output are stored in $RUNDIR/ifs_xml (not discussed here on this page). 


...

Multiple forecasts with restarts

Info

Note:  This option is at an experimental development stage and it is therefore currently not supported for general users.

Its implementation depends on scripting that is dependant on the hardware platform. Suggestions for script templates that are used on the ECMWF HPCF can be provided on request.

There are several reasons why a user may wish to restart a forecast experiment. The increase in computational costs for simulating atmospheric composition may require to break a longer forecast experiment into individual sections ("legs"). Also, a restart will allow to initialise the meteorology in the model with data taken from an analysis of the current modelled time. 

Due to the time scales associated with the different chemical processes and the lifetime of chemical tracers with respect to their loss processes, it is often convenient to retain the chemical tracer fields in the model simulation and update only the driving meteorology at the time of the restart. In some applications, the model could even be initialised every single day with an up-to-date meteorological analysis field while the chemical fields are left to evolve.  The previous section described how chemical initial conditions can be created at the end of an experiment run, thus retaining the chemical tracer information from the previous experiment leg. 

We will here provide some examples of the principle steps required for restarting experiments.

Example 1:  Longer experiment with manual stop and restart

The experiment parameters need to be defined by editing config.h. The following settings are used for a 2-month experiment with a stop-and-restart after the first month. This will result in two experiment legs of 1 month duration each.

No Format
run_start_date="2010-01-01"
run_end_date="${run_start_date} + 2 months"
rst_freq="1 month"
USE_RESTART=true

The initial conditions for each leg need to be either created or gathered from a prepared repository.

No Format
prep-ic-icmcl-compo.sh  2010-01-01 2010-02-01
prep-ic-icmcl-compo.sh  2010-02-01 2010-03-01

These processes can be run simultaneously. The meteorological fields and initial conditions can be requested from the OpenIFS Data Hub. The wrapper script needs to be submitted for the first experiment leg. Once the experiment has completed, config.h needs to be edited to use the initial experiment data from the date and time when the first leg has stopped. Then the wrapper script for the second month should be submitted.

Example 2: Using a workflow script

The 4 jobs in the previous example, can be all triggered automatically and in a timely fashion with a single script. The  $OIFS_HOME/AC-experiments/platform/<platform-name>-workflow.sh templates provide examples that need to be adjusted for the local hardware and file paths. In this case the config.h file only needs editing once and instead of the batch job wrapper script the workflow script is submitted.