Merge pull request #721 from pvjeetze/f_mag-seals

Start script 'healthy landscapes paper' and output script for automatic submission of SEALS runs

CHANGELOG.md

@@ -23,6 +23,9 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 - **config** additional data update additional_data_rev4.53.tgz
 - **29_cropland** added option for linear and sigmoidal faders
 - **scripts** output/extra/highres.R use default 13_tc realization
+- **scripts** `.nc` files are no longer created by default after disaggregation
+- **config** `cfg$gms$land_snv`changed from "secdforest, forestry, past, other" to "secdforest, other"
+- **config** Submissions with high memory requirements now get 16 CPUs and 80GB of memory to account for the new specifications of PIK's new HPC 'Foote'. `maxMem` was renamed to `highMem`, because 80GB of memory does not correspond to the maximum available memory of a compute node.
 
 
 ### added
@@ -36,9 +39,12 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 - **cropland** added option for discarding initial treecover on cropland
 - **script** added output script for conversion of validation.mif file into validation.rds
 - **script** for downscaling to 0.25 deg using LUH2v2h as reference via mrdownscale
+- **config** added `scenario_config_year_fix.csv` for choosing until when parameters are fixed to SSP2 values
+- **scripts** added start script for 'Healthly Landscapes' paper `paper_healthyLscps.R`
+- **scripts** added script for automatic submission of SEALS allocation runs `./extra/runSEALSallocation.R`
 
 ### removed
--
+
 
 ### fixed
 - **scripts** fixing an error in start.R and output.R which occurred if more than one slurm job was submitted at the same time.
@@ -52,7 +58,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 ### changed
 - **29_ageclass** module 29_ageclass has been renamed to 28_ageclass to make space for `29_cropland` just before `30_croparea`
 - **30_crop** module `30_crop` renamed to `30_croparea`, which now only accounts for crop area.
-- **30_crop** Semi-Natural Vegetation (SNV) implementation has been moved from `30_crop` to `29_cropland` 
+- **30_crop** Semi-Natural Vegetation (SNV) implementation has been moved from `30_crop` to `29_cropland`
 - **30_crop** the previous `30_crop/endo_apr21` realization has been moved to `30_croparea/simple_apr24`
 - **30_crop** the two realizations `penalty_apr22` and `rotation_apr22` have been merged into a single `30_croparea/detail_apr24` realization
 - **default.cfg** update additional data to rev4.51

DESCRIPTION

@@ -21,7 +21,7 @@ Imports:
     m4fsdp,
     madrat,
     magclass (>= 6.14.0),
-    magpie4 (>= 2.11.0),
+    magpie4 (>= 2.12.0),
     MagpieNCGains,
     magpiesets,
     mip,

config/default.cfg

@@ -26,7 +26,7 @@ cfg$input <- c(regional    = "rev4.111_h12_magpie.tgz",
                cellular    = "rev4.111_h12_fd712c0b_cellularmagpie_c200_MRI-ESM2-0-ssp370_lpjml-8e6c5eb1.tgz",
                validation  = "rev4.111_h12_validation.tgz",
                additional  = "additional_data_rev4.53.tgz",
-               calibration = "calibration_H12_26Mar24.tgz")
+               calibration = "calibration_H12_26Mar24_fixed.tgz")
 
 # NOTE: It is recommended to recalibrate the model when changing cellular input data
 #       as well as for any other setting that would affect initial values in the model,
@@ -399,7 +399,7 @@ cfg$gms$kfo_rd <- "livst_rum"                             #def = livst_rum
 
 # * Switch for supplemental fat needed as ingredient for scp-based meat alternatives
 # *   options:  0 (=off), 1 (=on)
-cfg$gms$s15_scp_supplement_fat_meat <- 0    # def = 0 
+cfg$gms$s15_scp_supplement_fat_meat <- 0    # def = 0
 
 # * Convergence of livestock food calorie supply towards a kcal/cap/day target with or w/o substitution.
 # * The functional form and the start and target years of the food substitution can be specified below.
@@ -695,7 +695,7 @@ cfg$gms$ageclass    <- "feb21"               # def = feb21
 # ***---------------------    29_cropland    -----------------------------------
 # * Cropland is defined as the sum of croparea, fallow land and tree cover
 # * Croparea is provided by 30_crop.
-# * Fallow land and tree cover are defined by 29_cropland, 
+# * Fallow land and tree cover are defined by 29_cropland,
 # * (simple_apr24): Fallow land and tree cover on cropland are fixed to zero
 # * (detail_apr24): Fallow land and tree cover based on rules or incentives
 # NOTE: It is recommended to recalibrate the model when changing this setting!
@@ -737,7 +737,7 @@ cfg$gms$s29_snv_scenario_target <- 2050       # def = 2050
 # * plausible options:  "secdforest, forestry, past, other",
 # *                     "secdforest, other",
 # *                     "secdforest, past, other" etc.
-cfg$gms$land_snv <- "secdforest, forestry, past, other"    #def = "secdforest, forestry, past, other"
+cfg$gms$land_snv <- "secdforest, other"    #def = "secdforest, other"
 
 # *** Options only available for `detail_apr24` realization ***
 
@@ -755,7 +755,7 @@ cfg$gms$s29_treecover_map <- 0    # def = 0
 # s29_treecover_target_noselect applies to all other countries.
 cfg$gms$s29_treecover_target <- 0   # def = 0
 cfg$gms$s29_treecover_target_noselect <- 0   # def = 0
-# * Avoid loss of existing treecover (1=yes 0=no). 
+# * Avoid loss of existing treecover (1=yes 0=no).
 # * If set to 1, `s29_treecover_target` will be adjusted based existing treecover area.
 cfg$gms$s29_treecover_keep <- 0   # def = 0
 # * Maximum share of treecover on total cropland (1)
@@ -808,12 +808,12 @@ cfg$gms$policy_countries30  <- all_iso_countries
 ## Agroforestry settings for bioenergy trees
 # * Sigmoid fader for minimum area share of bioenergy trees (betr) on total cropland at cluster level
 # * Minimum area share of bioenergy trees on total cropland in start year
-# Note: s30_betr_start applies to countries selected in policy_countries30, 
+# Note: s30_betr_start applies to countries selected in policy_countries30,
 # s30_betr_start_noselect applies to all other countries.
 cfg$gms$s30_betr_start <- 0   # def = 0
 cfg$gms$s30_betr_start_noselect <- 0   # def = 0
 # * Minimum area share of bioenergy trees on total cropland in target year
-# Note: s30_betr_target applies to countries selected in policy_countries30, 
+# Note: s30_betr_target applies to countries selected in policy_countries30,
 # s30_betr_target_noselect applies to all other countries.
 cfg$gms$s30_betr_target <- 0   # def = 0
 cfg$gms$s30_betr_target_noselect <- 0   # def = 0
@@ -841,14 +841,14 @@ cfg$gms$s30_implementation <- 1   # def = 1
 # * Rotation rules:
 # * min (minimal constraints), default (best guess), good (good practice),
 # * good_20div (good practice - 20% for other crops), setaside (default plus fallow),
-# * legumes (minimum share of legumes), sixfoldrotation (crops can only repeat after 6 years), 
+# * legumes (minimum share of legumes), sixfoldrotation (crops can only repeat after 6 years),
 # * agroecology (mix of previous scenarios), FSEC (similar to agroecology)
 # * betr0 (minimum share of short rotation agroforestry trees), betr10, betr20, betr25, betr30, betr40, betr50.
 cfg$gms$c30_rotation_rules <- "default"     # def = "default"
 
 # * Rotation incentives:
-# * none (no incentives), default (best guess), 
-# * legumes (increased incentives for legumes), agroecology (mix), 
+# * none (no incentives), default (best guess),
+# * legumes (increased incentives for legumes), agroecology (mix),
 # * betr500 and betr1000 (incentives for short rotation agroforestry trees)
 cfg$gms$c30_rotation_incentives <- "none"     # def = "none"
 
@@ -2072,6 +2072,9 @@ cfg$gms$s80_secondsolve <- 0 # def = 0
 #           bjoernAR6_C_SSP2-NPi.mif, bjoernAR6_C_SSP2-PkBudg900.mif
 cfg$magicc_emis_scen <- "bjoernAR6_C_SSP2-NDC.mif"
 
+# Years in which SEALS downscaling is applied
+cfg$seals_years <- c(2020, 2050)
+
 # Decide whether the runs should be run sequentially (TRUE),
 # or in parallel (FALSE)
 # NA means that this decision is taken automatically
@@ -2080,15 +2083,15 @@ cfg$sequential <- NA
 
 # Selection of QOS to be used for submitted runs on cluster.
 # Will be ignored for all other runs.
-# *   options:   short  (24h max, no preemption)
-# *              short_maxMem (same as short but with 16 CPUs and max Memory)
-# *              medium (1 week max, no preemption)
-# *              priority (immediate start, but slots limited to 5 in parallel)
-# *              priority_maxMem (same as priority but with 16 CPUs and max Memory)
-# *              standby (1 week max, preemption possible)
-# *              standby_dayMax (24h max, preemption possible)
-# *              standby_maxMem_dayMax (same as standby_dayMax but with 16 CPUs and max Memory)
-# *              standby_maxMem (same as standby but with 16 CPUs and max Memory)
+# *   options:   short  (24h max, 3 CPUs, no preemption)
+# *              short_highMem (same as short but with 16 CPUs and 80GB of memory)
+# *              medium (1 week max, 3 CPUs, no preemption)
+# *              priority (immediate start, 3 CPUs, but slots limited to 5 in parallel)
+# *              priority_highMem (same as priority but with 16 CPUs and 80GB of memory)
+# *              standby (1 week max, 3 CPUs, preemption possible)
+# *              standby_dayMax (24h max, 3 CPUs, preemption possible)
+# *              standby_highMem_dayMax (same as standby_dayMax but with 16 CPUs and 80GB of memory)
+# *              standby_highMem (same as standby but with 16 CPUs and 80GB of memory)
 # *              NULL (educated guess of best option based
 # *                    available resources)
 cfg$qos <- NULL               # def = NULL

config/projects/scenario_config_year_fix.csv

@@ -0,0 +1,16 @@
+;fix_2020;fix_2025
+gms$sm_fix_SSP2;2020;2025
+gms$sm_fix_cc;2020;2025
+gms$s15_food_substitution_start;2020;2025
+gms$s15_exo_foodscen_start;2020;2025
+gms$s21_trade_tariff_startyear;2020;2025
+gms$s22_conservation_start;2020;2025
+gms$s29_snv_scenario_start;2020;2025
+gms$s29_treecover_scenario_start;2020;2025
+gms$s29_fallow_scenario_start;2020;2025
+gms$s30_betr_scenario_start;2020;2025
+gms$s30_rotation_scenario_start;2020;2025
+gms$s38_startyear_labor_substitution;2020;2025
+gms$s42_efp_startyear;2020;2025
+gms$s44_start_year;2020;2025
+gms$s70_feed_substitution_start;2020;2025

scripts/output/extra/disaggregation.R

@@ -68,7 +68,6 @@ if (length(map_file) > 1) {
   base::message(message)
   x <- .fixCoords(x)
   write.magpie(x, file, comment = comment)
-  write.magpie(x, sub(".mz", ".nc", file), comment = comment)
 }
 
 .dissagcrop <- function(gdx, land_hr, map_file) {

scripts/output/extra/highres.R

@@ -104,7 +104,7 @@ highres <- function(cfg = cfg, res = "c1000", tc = NULL) {
   cfg$gms$s_use_gdx   <- 2
 
   #max resources for parallel runs
-  cfg$qos <- "standby_maxMem_dayMax"
+  cfg$qos <- "standby_highMem_dayMax"
 
   # set force download to FALSE
   # otherwise data is download again when calling start_run(), which overwrites
@@ -156,7 +156,7 @@ highres <- function(cfg = cfg, res = "c1000", tc = NULL) {
   write.magpie(readGDX(gdx,"f56_pollutant_prices_emulator"),"modules/56_ghg_policy/input/f56_pollutant_prices_emulator.cs3")
   write.magpie(readGDX(gdx,"f60_bioenergy_dem_coupling"),"modules/60_bioenergy/input/reg.2ndgen_bioenergy_demand.csv")
   write.magpie(readGDX(gdx,"f60_bioenergy_dem_emulator"),"modules/60_bioenergy/input/glo.2ndgen_bioenergy_demand.csv")
-  
+
   #get regional afforestation patterns from low resolution run with c200
   aff <- dimSums(landForestry(gdx)[,,c("aff","ndc")],dim=3)
   #Take away initial NDC area for consistency with global afforestation limit