Updating README for ggcmi_ph3; including all GCMs and scenarios in ba…

…sh files por sdate_hdate and phu.

README_ggcmi_ph3.md

@@ -1,38 +1,42 @@
-README (28.04.2021)
-------
+# README (28.04.2021)
+--------------------
 Author: Sara Minoli
 Affiliation: Potsdam Institute for Climate Impact Research, Germany
 Contact: sara.minoli@pik-potsdam.de
 
 This folder includes R-coded scripts for computing sowing and harvest dates following the approaches from Waha et al. (2012) and Minoli et al. (2019).
 
-Running the code:
+## Running the code:
 
-1) Create a configuration file: `./compute_sdate_hdate/configuration/configuration_ggcmi_ph3.R`
+### Crop calendars (sdate & hdate)
+
+1. Adjust crop parameters in `./compute_sdate_hdate/parameters/crop_parameters.csv` (default are taken from Waha 2012 & Minoli 2019)
+
+2. Create a configuration file: `./compute_sdate_hdate/configuration/configuration_ggcmi_ph3.R`
 - Define I/O paths (make sure automatically created directories are correct)
 - Define crops to simulate
 - Grid coordinates (by default LPJmL grid.bin is used, which is converted into a dataframe)
 
-2) Prepare monthly climate files: `./preprocessing/ prepare_monthly_climate_isimip3b.R` and `./preprocessing/ prepare_monthly_climate_isimip3b.sh`
+3. Prepare monthly climate files: `./preprocessing/ prepare_monthly_climate_isimip3b.R` and `./preprocessing/ prepare_monthly_climate_isimip3b.sh`
 - Compute long-term monthly average of temperature (degC), precipitation (mm), potential evapotranspiration (mm), P/PET ratio (frac), stored in a datatable with header: lon, lat, month, tas, pr, pet, ppet
 - pass arguments and submit job via bash script
 
-3) Set up main script: `./compute_sdate_hdate/main_ggcmi_ph3.R`
+4.  Set up main script: `./compute_sdate_hdate/main_ggcmi_ph3.R`
 - Choose if On Cluster TRUE/FALSE
 - Define Working directory
 
-4) `./compute_sdate_hdate/main_ggcmi_ph3.R`
+5. `./compute_sdate_hdate/main_ggcmi_ph3.R`
 - Define loops for running scenarios and crops in batch
 - To run it type: `bash main_ggcmi_ph3.sh` (note: module purge might be needed beforehand, if need to open old Rdata files)
 
-5) `./postprocessing/create_ncdf_sdate_hdate_multiyear_ggcmi_ph3.sh`
+6. `./postprocessing/create_ncdf_sdate_hdate_multiyear_ggcmi_ph3.sh`
+
+### Phenological Heat Units (PHU)
 
-6) `./compute_phu/main_ggcmi_ph3.sh`
+1. `./compute_phu/main_ggcmi_ph3.sh`
 
-7) `./compute_phu/postprocessing/create_lpjml_sdate_hdate_phu_input.sh`
+2. `./compute_phu/postprocessing/create_lpjml_sdate_hdate_phu_input.sh`
 
-Parameters:
-- Adjust crop parameters in crop_parameters.txt (default are taken from Waha 2012 & Minoli 2019)
+### Accessories
 
-Debugging:
-- ./compute_sdate_hdate/src/debugging.R can help troubleshooting
+1. Debugging `./compute_sdate_hdate/src/debugging.R` can help troubleshooting

compute_phu/main_ggcmi_ph3.sh

@@ -1,8 +1,10 @@
 #!/bin/bash
 
+# Run time per job about 30 min
+
 wd=/home/minoli/crop_calendars_gitlab/ggcmi_ph3/compute_phu
 
-gcms=('UKESM1-0-LL')
+gcms=('GFDL-ESM4' 'IPSL-CM6A-LR' 'MPI-ESM1-2-HR' 'MRI-ESM2-0') #('GFDL-ESM4' 'IPSL-CM6A-LR' 'MPI-ESM1-2-HR' 'MRI-ESM2-0' 'UKESM1-0-LL')
 scens=('historical' 'ssp585' 'ssp370' 'ssp126')
 crops=('wwh' 'swh' 'mai' 'ri1' 'ri2' 'soy' 'mil' 'sor' 'pea' 'sgb' 'cas' 'rap' 'sun' 'nut' 'sgc')
 irrigs=('rf' 'ir')
@@ -16,7 +18,7 @@ for gc in "${!gcms[@]}";do
         echo "GCM: ${gcms[gc]} --- SCENARIO: ${scens[sc]} --- CROP: ${crops[cr]}"
         echo "------------------------------------------------------------------"
 
-sbatch --qos=standby --ntasks=1 --cpus-per-task=4 -J nc_${gc}_${sc}_${cr}_${ir} -A macmit -t 01:00:00 --workdir=${wd} -o out_err/nc_${gc}_${sc}_${crops[cr]}_${ir}.out -e out_err/nc_${gc}_${sc}_${crops[cr]}_${cr}.err R -f main_ggcmi_ph3.R --args "${gcms[gc]}" "${scens[sc]}" "${crops[cr]}" "${irrigs[ir]}"
+sbatch --ntasks=1 --cpus-per-task=4 -J nc_${gc}_${sc}_${crops[cr]}_${irrigs[ir]} -A macmit -t 01:00:00 --workdir=${wd} -o out_err/nc_${gc}_${sc}_${crops[cr]}_${irrigs[ir]}.out -e out_err/nc_${gc}_${sc}_${crops[cr]}_${irrigs[ir]}.err R -f main_ggcmi_ph3.R --args "${gcms[gc]}" "${scens[sc]}" "${crops[cr]}" "${irrigs[ir]}"
 
       done
     done

compute_sdate_hdate/main_ggcmi_ph3.sh

@@ -4,7 +4,7 @@ module load piam
 
 wd=/home/minoli/crop_calendars_gitlab/ggcmi_ph3/compute_sdate_hdate
 
-gcms=('GFDL-ESM4') #('GFDL-ESM4' 'IPSL-CM6A-LR' 'MPI-ESM1-2-HR' 'MRI-ESM2-0' 'UKESM1-0-LL')
+gcms=('GFDL-ESM4' 'IPSL-CM6A-LR' 'MPI-ESM1-2-HR' 'MRI-ESM2-0' 'UKESM1-0-LL')
 scens=('ssp585' 'ssp370' 'ssp126')
 syears=('1961' '1971' '1981' '1991' '2001' '2011' '2021' '2031' '2041' '2051' '2061' '2071')
 eyears=('1990' '2000' '2010' '2020' '2030' '2040' '2050' '2060' '2070' '2080' '2090' '2100')
@@ -27,13 +27,3 @@ done
 
 
 #------
-
-# R -f ./postprocessing/merge_winter_spring_wheat.R --args $SLURM_ARRAY_TASK_ID
-
-
-
-
-# R -f ./postprocessing/mirca2000.R
-
-# Array 1-12 or 13
-# R -f ./postprocessing/create_lpjml_sdate_hdate_input.R --args  $SLURM_ARRAY_TASK_ID

compute_sdate_hdate/postprocessing/create_ncdf_sdate_hdate_multiyear_ggcmi_ph3.sh

@@ -1,8 +1,10 @@
 #!/bin/bash
 
+# Run time per each job 15 min 
+
 wd=/home/minoli/crop_calendars_gitlab/ggcmi_ph3/compute_sdate_hdate
 
-gcms=('UKESM1-0-LL')
+gcms=('GFDL-ESM4' 'IPSL-CM6A-LR' 'MPI-ESM1-2-HR' 'MRI-ESM2-0' 'UKESM1-0-LL')
 scens=('historical' 'ssp585' 'ssp370' 'ssp126')
 #crops=('Maize' 'Rice' 'Sorghum' 'Soybean' 'Spring_Wheat' 'Winter_Wheat')
 #irrigs=('Rainfed' 'Irrigated')
@@ -20,7 +22,7 @@ for gc in "${!gcms[@]}";do
         echo "GCM: ${gcms[gc]} --- SCENARIO: ${scens[sc]} --- CROP: ${crops[cr]}"
         echo "------------------------------------------------------------------"
 
-sbatch --ntasks=1 --cpus-per-task=4 -J nc_${gc}_${sc}_${cr}_${ir} -A macmit -t 03:00:00 --workdir=${wd} -o out_err/nc_${gc}_${sc}_${crops[cr]}_${ir}.out -e out_err/nc_${gc}_${sc}_${crops[cr]}_${cr}.err R -f postprocessing/create_ncdf_sdate_hdate_multiyear_ggcmi_ph3.R --args "${crops[cr]}" "${irrigs[ir]}" "${gcms[gc]}" "${scens[sc]}"
+sbatch --ntasks=1 --cpus-per-task=4 -J nc_${gc}_${sc}_${cr}_${ir} -A macmit -t 00:30:00 --workdir=${wd} -o out_err/nc_${gc}_${sc}_${crops[cr]}_${ir}.out -e out_err/nc_${gc}_${sc}_${crops[cr]}_${cr}.err R -f postprocessing/create_ncdf_sdate_hdate_multiyear_ggcmi_ph3.R --args "${crops[cr]}" "${irrigs[ir]}" "${gcms[gc]}" "${scens[sc]}"
 
       done
     done