Platform Configuration

Overview

This wiki page outlines the configuration files required by HARMONIE for successful compilation and running of the system.

All experiments require a valid host to "setup" an experiment using the Harmonie script. Recall from the quick start instructions that in order to setup a new experiment on your platform, called YOURHOST, using HARMONIE downloaded to PATH_TO_HARMONIE one must issue the following command:

cd hm_home/my_exp
PATH_TO_HARMONIE/config-sh/Harmonie setup -r PATH_TO_HARMONIE -h YOURHOST

hm_home/my_exp contains:

Env_submit -> config-sh/submit.YOURHOST           ## YOURHOST platform specific settings
Env_system -> config-sh/config.YOURHOST           ## YOURHOST task submission settings
./config-sh/hm_rev                                ## contains PATH_TO_HARMONIE
./config-sh/Main                                  ## The script used to run HARMONIE
./config-sh/submit.YOURHOST                       ## YOURHOST platform specific settings
./config-sh/config.YOURHOST                       ## YOURHOST task submission settings
./suites/harmonie.pm                              ## perl module to define ensemble settings
./ecf/config_exp.h                                ## your experiment definition (scientific type options)
./scr/include.ass                                 ## assimilation specific settings

But, what if your host configuration is not available in the HARMONIE system? Host specific configuration files in PATH_TO_HARMONIE/config-sh must be available for your host and configuration files for the compilation of the code must be available. This documentation attempts to describe what is required.

Host config files

`Env_system` -> `config-sh/config.YOURHOST`

The config.YOURHOST file defines host specific variables such as some input directory locations. If your YOURHOST is not already included in HARMONIE it may be work looking at config.* files in config-sh/ to see what other people have done. The table below outlines variables set in config-sh/config-sh.YOURHOST and what the variables do:

Variable name	Description
`COMPCENTRE`	controls special ECMWF solutions (such as MARS) where required. Set to LOCAL if you are unsure
`HARMONIE_CONFIG`	defines the config file used by Makeup compilation
`MAKEUP_BUILD_DIR`	location of where Makeup compiles the HARMONIE code
`MAKE_OWN_PRECOMPILED`	yes=>install pre-compiled code in `$PRECOMPILED`
`PRECOMPILED`	location of (optional) pre-compiled HARMONIE code
`E923_DATA_PATH`	location of input data for E923, climate generation
`PGD_DATA_PATH`	location of input data for PGD, surfex climate generation
`ECOSG_DATA_PATH`	location of input data for ECOCLIMAP2G
`GMTED2010_DATA_PATH`	location of HRES DEM
`SOILGRID_DATA_PATH`	location of SOILGRID data
`HM_SAT_CONST`	location of constants for satellite assimilation
`RTTOV_COEFDIR`	location of RTTOV coefficients
`HM_DATA`	location of top working directory for the experiment
`HM_LIB`	location of src/scripts and compiled code
`TASK_LIMIT`	Maximum number of jobs submitted by ECFLOW
`RSYNC_EXCLUDE`	used to exclude `.git*` sub-directories from copy of source code for compilation
`DR_HOOK_IGNORE_SIGNALS`	environment variable used by Dr Hook to ignore certain "signals"
`HOST0`	define primary host name
`HOSTN`	define other host name(s)
`HOST_INSTALL`	0=> install on HOST0, 0:...:N => install on HOST0,...,HOSTN
`MAKE`	`make` command may need to be explicity defined. Set to make for most platforms
`MKDIR`	`mkdir` command (default: `mkdir -p`)
`JOBOUTDIR`	where ECFLOW writes its log files
`ECCODES_DEFINITION_PATH`	location of local ecCodes definition files
`BUFR_TABLES`	location of local BUFR tables

`Env_submit` -> `config-sh/submit.YOURHOST`

The Env_submit file uses perl to tell the HARMONIE scheduler how to execute programs - which programs should be run on multiple processors and define batch submissions if required.

perl	description
`%backg_job`	defines variables for jobs run in the background on `HOST0`
`%scalar_job`	defines variables for single processor batch jobs
`%par_job`	defines variables for multi-processor batch jobs
`@backg_list`	list of tasks to be submitted as a background job
`@scalar_list`	list of tasks to be submitted as a scalar job
`@par_list`	list of tasks to be submitted as parallel job
`default`	"wildcard" task name to defined default type of job for unlisted tasks

Host summary

YOURHOST	Host type	batch	Contact	Notes
`AEMET.cirrus.gnu`
`AEMET.nimbus.ifort.mpi`
`bi`	SMHI
`centos8`
`cirrus`
`debian11`
`ecgb`				switched off
`ecgb-cca`	ECMWF HPC with MPI dual host	slurm/PBS		switched off
`ECMWF.atos`	ECMWF Atos HPC with MPI	slurm
`fedora33`
`fedora34`
`KNMI.bullx_b720`	KNMI Atos HPC with MPI	slurm	Bert van Ulft
`LinuxPC`	General Linux PC no MPI	none
`LinuxPC-MPI`	General Linux PC with MPI	none
`LinuxPC-MPI-KNMI`	KNMI Linux workstation (Fedora)	none
`LinuxPC-MPI-ubuntu`	Ubuntu Linux PC with MPI	none
`LinuxPC-serial`
`METIE.LinuxPC`	METIE CentOS 6 PC with MPI	none	Eoin Whelan
`METIE.LinuxPC8`
`METIE.LinuxRH7gnu`	METIE Redhat 7 server with MPI	none	Eoin Whelan
`METIE.LinuxRH7gnu-dev`
`METIE.reaserve8`
`METIE.reaserve8musc`
`nebula`
`nebula-gnu`
`opensuse`
`SMHI.Linda4`	SMHI
`SMHI.Linda5`	SMHI
`stratus`
`teho`
`ubuntu18`
`ubuntu20`
`ubuntu20_nompi`
`ubuntu2204.GNU`	podman container	none	Eoin Whelan	container
`ubuntu2304.GNU`	podman container	none	Eoin Whelan	container
`ubuntu2310.GNU`	podman container	none	Eoin Whelan	container
`ubuntu2404.GNU`	podman container	none	Eoin Whelan	container
`ubuntu2410.GNU`	podman container	none	Eoin Whelan	container
`voima`

Platform Configuration

Overview

Basic requirements

Host config files

`Env_system` -> `config-sh/config.YOURHOST`

`Env_submit` -> `config-sh/submit.YOURHOST`

Host summary

Compilation config files

Makeup

Obsmon