SERVIR West Africa Monthly Run Manual

This manual will outline the steps need to be performed to do the monthly run.

The directory structure is for NASA server: 10.5.5.37

Download data

1.1 Download CHIRPS data

Enter this directory: /home/Socrates/hjung/WA_025/MET_FORCING/
Open this script: get_CHIRPS_monthly.sh
Change chirpsdir to your directory where you would like to download the data
Run this script in the terminal: ./get_CHIRPS_monthly.sh
This will prompt you for 2 things:
- Year. Enter 2019, for example
- Month. Enter 4, for example
- Enter y for confirmation.
Download will commence

1.2 Download MERRA2 data

Enter this directory: /home/Socrates/hjung/WA_025/MET_FORCING/
Open this script: Get_merra2_ges_disc_ALLVARS.sh
Change WORKDIR to your directory where you would like to store the data
Run this script in the terminal: ./Get_merra2_ges_disc_ALLVARS.sh
This will prompt you for 3 things:
- Year. Enter 2019, for example
- Month. Enter 4, for example
- Enter y for confirmation.
Download will commence for 4 MERRA2 variables

GEOS 5 download

Enter this directory: /home/Socrates/hjung/WA_025/MODEL_RUN/BCSD_Scripts/

2.1 GEOS5 download

Activate the python environment: conda activate py2
Run this script: ./Download_GEOS5V2_all.F.sh
This will prompt you for 3 things:
- Forecast Year. Enter 2019, for example
- Forecast Month. Enter 4, for example
- Enter y for confirmation.

2.2 GEOS5 Bias correction

Run this script: ./TmpDisagg.F.sh
This will prompt you for 3 things:
- Year. Enter 2019, for example
- Month. Enter 4, for example
- Enter y for confirmation.
Download of bias-corrected daily and sub-daily forecasts will commence.

2.3 Merging

Run combine.F.sh
This will prompt you for 3 things:
- Forecast Year. Enter 2019, for example
- Forecast initialization Month. Enter 4, for example
- Enter y for confirmation.
Will combine all non-precip 6-hourly files into one file.

Retrospective run

`/home/Socrates/hjung/WA_025/MODEL_RUN/LDT_Files/ESPconv_RSTFILES/t2_upscale_01to07_grace_da.sh

2.1 LIS retro run

Go to /home/Socrates/hjung/WA_025/MODEL_RUN/OL_CLSM
Use mpirun with 32 processors.
Run LIS mpirun -np 32 ./LIS -f /home/Socrates/hjung/WA_025/MODEL_RUN/OL_CLSM/lis.config

2.2 Prepare LIS outputs for Tethys Viewer

The Land Surface Model and Routing model output files from Step 2.1 have to be merged and prepared for the Tethys Viewer

Go to netcdf_conversion
This will convert the data from start time (2019 5 20) to end time (2019 5 22): ./convertlisnetcdf 2019 5 20 2019 5 22 ./retrospective_directory /home/Socrates/hjung/tethyswa_lis_viewer/retrospective/ ./servirwa_nc_clsmf25_output.tbl.list.cf