3. Flexpart model¶
FLEXPART (FLEXible PARTicle dispersion model) is an Lagrangian transport and dispersion model and can be used to study a large range of atmospheric transport processes. The current version is FLEXPART V 10.4 and you can find more information and resources on FLEXPART in the reference paper reference paper or at flexpart.eu.
3.1. FLEXPART installation¶
FLEXPART is currently not available as a preloaded module on SAGA which means that you have to compile the source code yourself. First you need to download the FLEXPART source code by cloning the git repository.
$git clone https://github.com/flexpart/flexpart.git
After you have cloned the repository you need to edit the paths in the Makefile in flexpart/src/makefile. To compile on saga you would need change the following paths:
#Changes to be made in flexpart/src/makefile
F90 = ifort
MPIF90 = mpif90
INCPATH1 = /usr/include
INCPATH2 = /cluster/software/ecCodes/2.9.2-intel-2018b/include
LIBPATH1 = /cluster/software/ecCodes/2.9.2-intel-2018b/lib
Before you compile FLEXPART you need to load the necessary fortran modules:
module load ecCodes/2.9.2-intel-2018b
module load netCDF-Fortran/4.4.4-intel-2018b
When compiling FLEXPART, you can add ncf=yes to enable netCDF output.
$ cd flexpart/src
$ make ncf=yes
3.2. FLEXPART Setup¶
Setting up a FLEXPART is primarily done by editing the COMMAND, RELEASES, OUTGRID files in the flexpart/options folder. For a in depth explanation of the different settings in flexpart take a look at the reference paper . FLEXPART expect following files and folders to be present:
$ ls
options output pathnames
- options folder containing the flexpart setting files COMMAND, RELEASES, OUTGRID etc.
- output folder which should be empty
- pathnames a files containing the necessary paths, particularly the path to the atmospheric forcing
$ less pathnames
./options/
./output/
/
/path/to/AVAILABLE_WINDFIELDS
============================================
pathnames (END)
AVAILABLE_WINDFIELDS is a text file contains the paths to where the atmospheric forcing is stored and has to be formatted in a certain way. (A python script which makes the AVAILABLE_WINDFIELDS). The formatted AVAILABLE_WINDFIELDS file should look something like this.
DATE TIME FILENAME SPECIFICATIONS
YYYYMMDD HHMISS
________ ______ __________________ __________________
19990301 000000 /cluster/shared/flexpart/databases/flexpart/WIND_FIELDS/ECMWF/GLOBAL/ERA5/1999/03/EA99030100 ON DISC
19990301 030000 /cluster/shared/flexpart/databases/flexpart/WIND_FIELDS/ECMWF/GLOBAL/ERA5/1999/03/EA99030103 ON DISC
19990301 060000 /cluster/shared/flexpart/databases/flexpart/WIND_FIELDS/ECMWF/GLOBAL/ERA5/1999/03/EA99030106 ON DISC
19990301 090000 /cluster/shared/flexpart/databases/flexpart/WIND_FIELDS/ECMWF/GLOBAL/ERA5/1999/03/EA99030109 ON DISC
19990301 120000 /cluster/shared/flexpart/databases/flexpart/WIND_FIELDS/ECMWF/GLOBAL/ERA5/1999/03/EA99030112 ON DISC
...........................
On Saga atmospheric forcing for FLEXPART is stored in shared folder /cluster/shared/databases/flexpart and currently only ERA-INTERIM is globally available on Saga, from 1986 until 2016.
3.3. Running FLEXPART¶
To run FLEXPART Saga you would first need to make a job script:
#! /bin/bash
#SBATCH --account=nnXXXXk
#SBATCH --time=00:40:00
#SBATCH --ntasks=1
#SBATCH --mem-per-cpu=6G
#SBATCH --mail-user=example@student.geo.uio.no
#SBATCH --job-name=FLEXPART_TEST
#SBATCH --mail-type=FAIL
set -o errexit
set -o nounset
module --quiet purge
module load ecCodes/2.9.2-intel-2018b
module load netCDF-Fortran/4.4.4-intel-2018b
export PATH=/path/to/flexpart/src:$PATH
time FLEXPART
Make sure you have the jobscript in the folder where the FLEXPART simulation has been setup and then submit the job to the jobqueue.
$ sbatch flexpart_job.sh
FLEXPART simulations does not depend on each other, which means that FLEXPART can easily be parallelized by running many FLEXPART instances at the same time, through submitting multiple jobs to the job queue. Though be careful as there is a limit of 10000 jobs that can be in the queue at the same time.