From 23ca6a72c58e8b6ecbcd636016f4a765f97e02ec Mon Sep 17 00:00:00 2001
From: pvjeetze <vjeetze@pik-potsdam.de>
Date: Wed, 18 Sep 2024 15:53:37 +0200
Subject: [PATCH 01/12] added SEALS allocation script

---
 DESCRIPTION                                 |   2 +-
 config/default.cfg                          |  21 +-
 scripts/output/extra/disaggregation.R       |   1 -
 scripts/output/extra/runSEALSallocation.R   | 231 ++++++++++++++++++++
 scripts/start/projects/paper_healthyLscps.R | 164 ++++++++++++++
 5 files changed, 408 insertions(+), 11 deletions(-)
 create mode 100644 scripts/output/extra/runSEALSallocation.R
 create mode 100644 scripts/start/projects/paper_healthyLscps.R

diff --git a/DESCRIPTION b/DESCRIPTION
index 779c99c49..3a199b5db 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -21,7 +21,7 @@ Imports:
     m4fsdp,
     madrat,
     magclass (>= 6.14.0),
-    magpie4 (>= 2.11.0),
+    magpie4 (>= 2.12.0),
     MagpieNCGains,
     magpiesets,
     mip,
diff --git a/config/default.cfg b/config/default.cfg
index 76facad41..c651b1aeb 100644
--- a/config/default.cfg
+++ b/config/default.cfg
@@ -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
diff --git a/scripts/output/extra/disaggregation.R b/scripts/output/extra/disaggregation.R
index 2592a29f1..e9e31f336 100644
--- a/scripts/output/extra/disaggregation.R
+++ b/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) {
diff --git a/scripts/output/extra/runSEALSallocation.R b/scripts/output/extra/runSEALSallocation.R
new file mode 100644
index 000000000..fe6b865d9
--- /dev/null
+++ b/scripts/output/extra/runSEALSallocation.R
@@ -0,0 +1,231 @@
+# |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
+# |  authors, and contributors see CITATION.cff file. This file is part
+# |  of MAgPIE and licensed under AGPL-3.0-or-later. Under Section 7 of
+# |  AGPL-3.0, you are granted additional permissions described in the
+# |  MAgPIE License Exception, version 1.0 (see LICENSE file).
+# |  Contact: magpie@pik-potsdam.de
+
+# --------------------------------------------------------------
+# description: Starts SEALS allocation run based on gridded MAgPIE land cover projections (SEALS)
+# comparison script: FALSE
+# ---------------------------------------------------------------
+
+# Version 1.00 - Patrick v. Jeetze, Pascal Sauer
+# 1.00: first working version
+
+library(gms)
+library(gdx)
+library(magpie4)
+library(filelock)
+
+message("Initialising SEALS allocation run")
+
+############################# BASIC CONFIGURATION #######################################
+if (!exists("source_include")) {
+  title <- NULL
+  outputdir <- NULL
+
+  # Define arguments that can be read from command line
+  readArgs("outputdir", "title")
+}
+#########################################################################################
+
+# ========================
+# User settings
+# ========================
+
+### SEALS python environment name
+# see https://justinandrewjohnson.com/earth_economy_devstack/installation.html
+# for instructions on how to set up a python environment for SEALS
+sealsEnv <- "seals_dev"
+
+### Path to miniforge installation
+# For instructions on how to install miniforge see https://github.com/conda-forge/miniforge
+miniforgePath <- "/home/vjeetze/miniforge3/bin/activate"
+
+### Path to SEALS base input file directory
+dirBaseFiles <- "/p/projects/magpie/users/vjeetze/seals/files"
+
+### Path to SEALS code base
+dirSEALS <- "/p/projects/magpie/users/vjeetze/seals/files/seals/seals_dev"
+
+
+# ========================
+# Prepare MAgPIE output
+# ========================
+
+message("Script started for output directory: ", outputdir)
+
+cfg <- gms::loadConfig(file.path(outputdir, "config.yml"))
+title <- cfg$title
+
+if (length(cfg$seals_years) != 0) {
+  rep_years <- cfg$seals_years[cfg$seals_years > 2020]
+  rep_years <- c(2020, rep_years)
+} else {
+  rep_years <- seq(2020, 2050, 5)
+}
+
+# Restructure data to conform to SEALS
+reportLandUseForSEALS(
+  magCellLand = "cell.land_0.5_share.mz",
+  outFile = paste0("cell.land_0.5_SEALS_", title, ".nc"),
+  dir = outputdir, selectyears = rep_years
+)
+
+
+# ========================
+# Setup SEALS run
+# ========================
+
+# --------------------------------
+# Prepare SEALS start script
+# --------------------------------
+
+.setupSEALSrun <- function(title, dir, dirProject, dirSEALS, dirBaseFiles) {
+  if (!dir.exists(file.path(dirProject, "scripts"))) {
+    dir.create(file.path(dirProject, "scripts"), recursive = TRUE)
+  }
+
+  file.copy(
+    from = list.files(file.path(dirSEALS, "seals"), full.names = TRUE),
+    to = file.path(dirProject, "scripts"),
+    overwrite = TRUE,
+    recursive = TRUE
+  )
+
+  if (!dir.exists(file.path(dirProject, "inputs"))) {
+    dir.create(file.path(dirProject, "inputs"), recursive = TRUE)
+  }
+
+  file.copy(
+    from = file.path(dir, paste0("seals_scenario_config_", title, ".csv")),
+    to = file.path(dirProject, "inputs", paste0("seals_scenario_config_", title, ".csv")),
+    overwrite = TRUE
+  )
+
+  main <- readLines(file.path(dirProject, "scripts/run_test_standard.py"))
+
+  main[min(which(grepl("    p.user_dir =", main)))] <- paste0("    p.user_dir = \'", dirBaseFiles, "\'")
+  main[min(which(grepl("    p.extra_dirs", main)))] <- paste0("    p.extra_dirs = '.'")
+  main[min(which(grepl("    p.project_name =", main)))] <- paste0("    p.project_name = \'", title, "\'")
+  main[min(which(grepl("    p.project_dir =", main)))] <- paste0(
+    "    p.project_dir = \'", normalizePath(dirProject), "\'"
+  )
+  main[min(which(grepl("hb.pretty_time()", main)))] <- " "
+  main[min(which(grepl("    p.base_data_dir =", main)))] <- paste0(
+    "    p.base_data_dir = \'", dirBaseFiles, "/base_data\'"
+  )
+  main[min(which(grepl("    p.scenario_definitions_filename =", main)))] <- paste0(
+    "    p.scenario_definitions_filename = \'", paste0("seals_scenario_config_", title, ".csv"), "\'"
+  )
+
+  writeLines(main, file.path(dirProject, "scripts", paste0("run_seals_", title, ".py")))
+
+
+  if (!dir.exists(file.path(dirProject, "run_submit"))) {
+    dir.create(file.path(dirProject, "run_submit"), recursive = TRUE)
+  }
+}
+
+# --------------------------------
+# Submit run
+# --------------------------------
+
+.submitSEALS <- function(title, dirProject, miniforgePath, sealsEnv, qos = "short",
+                         slurmID = FALSE, dependsID = NULL) {
+  submitFile <- file.path(dirProject, "run_submit", paste0("submit_seals_", title, ".sh"))
+
+  submit <- c(
+    "#!/bin/bash", "\n",
+    paste0("#SBATCH --qos=", qos),
+    ifelse(qos %in% c("priority", "standby"), "#SBATCH --partition=priority", "#SBATCH --partition=standard"),
+    "#SBATCH --job-name=seals_allocation",
+    paste0("#SBATCH --chdir=", normalizePath(file.path(dirProject, "scripts"))),
+    "#SBATCH --output=outfile_%j.out",
+    "#SBATCH --error=outfile_%j.err",
+    "#SBATCH --mail-type=END,FAIL",
+    "#SBATCH --time=3:00:00",
+    "#SBATCH --nodes=1",
+    "#SBATCH --ntasks=1",
+    ifelse(!is.null(dependsID), paste0(
+      "#SBATCH --dependency=afterok:", dependsID,
+      "\n#SBATCH --kill-on-invalid-dep=yes"
+    ),
+    "#SBATCH --dependency=singleton"
+    ), "\n",
+    ifelse(qos == "priority", "#SBATCH --cpus-per-task=64", "#SBATCH --cpus-per-task=128"), "\n",
+    paste("source", miniforgePath),
+    paste("conda activate", sealsEnv), "\n",
+    paste("python", paste0("run_seals_", title, ".py"))
+  )
+  writeLines(submit, submitFile)
+
+  id <- system(paste("sbatch --parsable", submitFile), intern = TRUE)
+  if (slurmID) {
+    return(id)
+  }
+}
+
+# create output directory
+dirProject <- "./output/seals"
+
+if (!dir.exists(file.path(dirProject))) {
+  dir.create(file.path(dirProject), recursive = TRUE)
+}
+
+iniLock <- file.path(dirProject, ".lock")
+lockOn <- filelock::lock(iniLock, exclusive = TRUE, timeout = Inf)
+Sys.chmod(iniLock, mode = "0664")
+
+# --------------------------------
+# Run SEALS allocation
+# --------------------------------
+
+if (!is.null(lockOn)) {
+  sealsLock <- file.path(dirProject, "seals.lock")
+
+  if (!file.exists(sealsLock) || file.size(sealsLock) == 0) {
+    message("Starting SEALS allocation with input data creation.")
+    .setupSEALSrun(
+      title = title,
+      dir = outputdir,
+      dirProject = dirProject,
+      dirSEALS = dirSEALS,
+      dirBaseFiles = dirBaseFiles
+    )
+
+    id <- .submitSEALS(
+      title = title,
+      dirProject = dirProject,
+      miniforgePath = miniforgePath,
+      sealsEnv = sealsEnv,
+      qos = "short",
+      slurmID = TRUE
+    )
+
+    writeLines(id, sealsLock)
+  } else {
+    message("Starting SEALS allocation using existing input data.")
+    id <- readLines(sealsLock)
+
+    .setupSEALSrun(
+      title = title,
+      dir = outputdir,
+      dirProject = dirProject,
+      dirSEALS = dirSEALS,
+      dirBaseFiles = dirBaseFiles
+    )
+
+    .submitSEALS(
+      title = title,
+      dirProject = dirProject,
+      miniforgePath = miniforgePath,
+      sealsEnv = sealsEnv,
+      qos = "short",
+      slurmID = FALSE,
+      dependsID = id
+    )
+  }
+  unlink(iniLock)
+}
diff --git a/scripts/start/projects/paper_healthyLscps.R b/scripts/start/projects/paper_healthyLscps.R
new file mode 100644
index 000000000..0ea21e921
--- /dev/null
+++ b/scripts/start/projects/paper_healthyLscps.R
@@ -0,0 +1,164 @@
+# |  (C) 2008-2021 Potsdam Institute for Climate Impact Research (PIK)
+# |  authors, and contributors see CITATION.cff file. This file is part
+# |  of MAgPIE and licensed under AGPL-3.0-or-later. Under Section 7 of
+# |  AGPL-3.0, you are granted additional permissions described in the
+# |  MAgPIE License Exception, version 1.0 (see LICENSE file).
+# |  Contact: magpie@pik-potsdam.de
+
+# ----------------------------------------------------------
+# description: Healthy Landscapes Paper
+# ----------------------------------------------------------
+
+rev <- "rev9"
+
+# Note: rev4 used MAgPIE 4.6.9
+# Note: rev6 used MAgPIE 4.6.10
+# Note: rev7 used MAgPIE 4.6.11
+# Note: rev8 used MAgPIE dev 16 Sep 2024
+# Note: rev9 used MAgPIE 4.8.2
+
+######################################
+#### Script to start a MAgPIE run ####
+######################################
+
+library(gms)
+library(lucode2)
+library(magclass)
+library(gdx2)
+
+# Load start functions
+source("scripts/start_functions.R")
+
+# ====================
+# Calibration
+# ====================
+
+source("config/default.cfg")
+
+cfg$title <- "calib_run"
+cfg$output <- c("rds_report", "validation_short")
+cfg$force_replace <- TRUE
+
+cfg$recalibrate <- TRUE
+cfg$recalibrate_landconversion_cost <- TRUE
+
+cfg$best_calib <- TRUE
+cfg$best_calib_landconversion_cost <- FALSE
+
+# cc is new default
+cfg <- setScenario(cfg, "nocc_hist")
+
+# New iso food realisation
+cfg$gms$food <- "anthro_iso_jun22"
+
+cfg$gms$s14_use_yield_calib <- 1
+
+# sticky
+cfg$gms$factor_costs <- "sticky_feb18"
+
+# marginal land scenario
+cfg$gms$c30_marginal_land <- "q33_marginal"
+
+start_run(cfg = cfg)
+calib_tgz <- magpie4::submitCalibration(paste(rev, "healthyLscps", sep = "_"))
+
+# ====================
+# Scenario runs
+# ====================
+
+prefix <- paste(rev, "healthyLscps", sep = "_")
+
+SSPs <- c("SSP2", "SSP1", "SSP3")
+
+scenarios <- c(
+  "REF", "DIET100", "DIET50",
+  "BIOS", "DIET100-BIOS", "DIET50-BIOS",
+  "landConservation", "DIET100-landConservation", "DIET50-landConservation",
+  "noNatureLoss2030", "DIET100-noNatureLoss2030", "DIET50-noNatureLoss2030",
+  "SNV20", "DIET100-SNV20", "DIET50-SNV20"
+)
+
+for (ssp in SSPs) {
+  for (scen in scenarios) {
+    actions <- unlist(strsplit(scen, "-"))
+
+    source("config/default.cfg")
+
+    cfg$qos <- "short_maxMem"
+
+    cfg$results_folder <- "output/:title::date:"
+
+    cfg$output <- c(
+      "output_check", "extra/disaggregation", "rds_report", "extra/runSEALSallocation"
+    )
+
+    cfg$input["calibration"] <- calib_tgz
+
+    # Climate change switched off for these runs
+    cfg <- setScenario(cfg, "nocc_hist")
+
+    # New iso food realisation
+    cfg$gms$food <- "anthro_iso_jun22"
+
+    cfg$gms$s14_use_yield_calib <- 1
+
+    # sticky
+    cfg$gms$factor_costs <- "sticky_feb18"
+
+    # SNV habitat defintion
+    cfg$gms$land_snv <- "secdforest, other"
+
+    cfg <- setScenario(cfg, c(ssp, "NPI"))
+    cfg$gms$c15_food_scenario <- ssp
+
+    cfg$seals_years <- c(2020, 2050)
+
+    # --- Dietary transitions ---
+
+    # 50 % convergence towards EAT lancet diet
+    if ("DIET50" %in% actions) {
+      cfg <- setScenario(cfg, "eat_lancet_diet_v1")
+      cfg$gms$s15_exo_foodscen_start <- 2020
+      cfg$gms$s15_exo_foodscen_target <- 2050
+      cfg$gms$s15_exo_foodscen_convergence <- 0.5
+      cfg$gms$s15_exo_waste <- 1
+    }
+
+    # 100% convergence towards EAT lancet diet
+    if ("DIET100" %in% actions) {
+      cfg <- setScenario(cfg, "eat_lancet_diet_v1")
+      cfg$gms$s15_exo_foodscen_start <- 2020
+      cfg$gms$s15_exo_foodscen_target <- 2050
+      cfg$gms$s15_exo_foodscen_convergence <- 1
+      cfg$gms$s15_exo_waste <- 1
+    }
+
+    # --- Ecosystem stewarship actions ---
+
+    # 30by30 land conservation
+    if (any(actions %in% c("BIOS", "landConservation"))) {
+      cfg$gms$c22_protect_scenario <- "30by30"
+      cfg$gms$s22_conservation_start <- 2020
+      cfg$gms$s22_conservation_target <- 2030
+    }
+
+    # no net nature loss
+    if (any(actions %in% c("BIOS", "noNatureLoss2030"))) {
+      cfg$gms$c44_bii_decrease <- 0
+      cfg$gms$s44_start_year <- 2030
+    }
+
+    # permanent habitats in agricultural landscapes
+    if (any(actions %in% c("BIOS", "SNV20"))) {
+      cfg$gms$s29_snv_shr <- 0.2
+      cfg$gms$s29_snv_scenario_start <- 2020
+      cfg$gms$s29_snv_scenario_target <- 2030
+    }
+
+    # parameters are fixed to SSP2 values until 2020
+    cfg <- setScenario(cfg, "fix_2020", scenario_config = "config/projects/scenario_config_year_fix.csv")
+
+    cfg$title <- paste0(prefix, "_", ssp, "-", scen)
+    start_run(cfg = cfg, codeCheck = FALSE)
+  }
+}

From 1f503af21495e9d9d4eb31f4d7a4c1c570a1381c Mon Sep 17 00:00:00 2001
From: pvjeetze <vjeetze@pik-potsdam.de>
Date: Wed, 18 Sep 2024 16:01:58 +0200
Subject: [PATCH 02/12] updated changelog

---
 CHANGELOG.md | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 95a5a39bd..e9b093e0e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -22,6 +22,7 @@ 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
 
 
 ### added
@@ -34,9 +35,12 @@ 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.
@@ -50,7 +54,7 @@ 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

From 40a442ab2590e9f427757830cf72102f742c09aa Mon Sep 17 00:00:00 2001
From: pvjeetze <vjeetze@pik-potsdam.de>
Date: Wed, 18 Sep 2024 16:13:45 +0200
Subject: [PATCH 03/12] added scenario config to set SSP2 fix

---
 config/projects/scenario_config_year_fix.csv | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)
 create mode 100644 config/projects/scenario_config_year_fix.csv

diff --git a/config/projects/scenario_config_year_fix.csv b/config/projects/scenario_config_year_fix.csv
new file mode 100644
index 000000000..282d61934
--- /dev/null
+++ b/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

From 98778a49a5cd7e93859ed1f0bfc3869c546fdb47 Mon Sep 17 00:00:00 2001
From: pvjeetze <vjeetze@pik-potsdam.de>
Date: Wed, 18 Sep 2024 17:03:06 +0200
Subject: [PATCH 04/12] updated copyright year

---
 scripts/start/projects/GENIE_0_default.R         |  2 +-
 scripts/start/projects/GENIE_1_tau-export.R      |  4 ++--
 scripts/start/projects/GENIE_2_bm-priced.R       |  6 +++---
 scripts/start/projects/GENIE_3_bm-demand.R       |  4 ++--
 scripts/start/projects/GENIE_4_feedback.R        | 10 +++++-----
 scripts/start/projects/paper_healthyLscps.R      |  2 +-
 scripts/start/projects/project_EAT2p0_DeepDive.R |  4 ++--
 7 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/scripts/start/projects/GENIE_0_default.R b/scripts/start/projects/GENIE_0_default.R
index 248e67bfa..74fde2c3c 100644
--- a/scripts/start/projects/GENIE_0_default.R
+++ b/scripts/start/projects/GENIE_0_default.R
@@ -1,4 +1,4 @@
-# |  (C) 2008-2021 Potsdam Institute for Climate Impact Research (PIK)
+# |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
 # |  authors, and contributors see CITATION.cff file. This file is part
 # |  of MAgPIE and licensed under AGPL-3.0-or-later. Under Section 7 of
 # |  AGPL-3.0, you are granted additional permissions described in the
diff --git a/scripts/start/projects/GENIE_1_tau-export.R b/scripts/start/projects/GENIE_1_tau-export.R
index 4859e7855..561266c5c 100644
--- a/scripts/start/projects/GENIE_1_tau-export.R
+++ b/scripts/start/projects/GENIE_1_tau-export.R
@@ -1,4 +1,4 @@
-# |  (C) 2008-2021 Potsdam Institute for Climate Impact Research (PIK)
+# |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
 # |  authors, and contributors see CITATION.cff file. This file is part
 # |  of MAgPIE and licensed under AGPL-3.0-or-later. Under Section 7 of
 # |  AGPL-3.0, you are granted additional permissions described in the
@@ -52,7 +52,7 @@ cfg$info$flag <- identifierFlag
 cfg$results_folder <- paste0("output/", identifierFlag, "/:title:")
 
 cfg$gms$c44_bii_decrease <- 0
-cfg$gms$c22_protect_scenario <- "BH" 
+cfg$gms$c22_protect_scenario <- "BH"
 
 cfg$gms$s60_2ndgen_bioenergy_dem_min_post_fix <- 0
 cfg$gms$c60_bioenergy_subsidy <- 0
diff --git a/scripts/start/projects/GENIE_2_bm-priced.R b/scripts/start/projects/GENIE_2_bm-priced.R
index e58c1b485..5cac56463 100644
--- a/scripts/start/projects/GENIE_2_bm-priced.R
+++ b/scripts/start/projects/GENIE_2_bm-priced.R
@@ -1,4 +1,4 @@
-# |  (C) 2008-2021 Potsdam Institute for Climate Impact Research (PIK)
+# |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
 # |  authors, and contributors see CITATION.cff file. This file is part
 # |  of MAgPIE and licensed under AGPL-3.0-or-later. Under Section 7 of
 # |  AGPL-3.0, you are granted additional permissions described in the
@@ -52,7 +52,7 @@ cfg$info$flag <- identifierFlag
 cfg$results_folder <- paste0("output/", identifierFlag, "/:title:")
 
 
-### BE 
+### BE
 cfg$gms$s60_2ndgen_bioenergy_dem_min_post_fix <- 0
 cfg$gms$c60_bioenergy_subsidy <- 0
 beV <- c(0, 5, 7, 10, 15, 25, 45)
@@ -83,7 +83,7 @@ for (bl in blV) {
     preflag <- paste0("MP", str_pad(mp, 2, pad = "0"), "BI", str_pad(bl * 100, 2, pad = "0"))
     cfg$results_folder <- paste("output", identifierFlag, preflag, ":title:", sep = "/")
     cfg$info$flag2 <- preflag
-    
+
     cfg$gms$s15_rumdairy_scp_substitution <- mp / 100
 
     for (be in beV) {
diff --git a/scripts/start/projects/GENIE_3_bm-demand.R b/scripts/start/projects/GENIE_3_bm-demand.R
index 5bca4b022..715ecb4e8 100644
--- a/scripts/start/projects/GENIE_3_bm-demand.R
+++ b/scripts/start/projects/GENIE_3_bm-demand.R
@@ -1,4 +1,4 @@
-# |  (C) 2008-2021 Potsdam Institute for Climate Impact Research (PIK)
+# |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
 # |  authors, and contributors see CITATION.cff file. This file is part
 # |  of MAgPIE and licensed under AGPL-3.0-or-later. Under Section 7 of
 # |  AGPL-3.0, you are granted additional permissions described in the
@@ -51,7 +51,7 @@ cfg$info$flag <- identifierFlag
 cfg$results_folder <- paste0("output/", identifierFlag, "/:title:")
 
 
-### BE 
+### BE
 cfg$gms$s60_2ndgen_bioenergy_dem_min_post_fix <- 0
 cfg$gms$c60_bioenergy_subsidy <- 0
 beV <- c(0, 5, 7, 10, 15, 25, 45)
diff --git a/scripts/start/projects/GENIE_4_feedback.R b/scripts/start/projects/GENIE_4_feedback.R
index 1fa097a56..2f2ced23b 100644
--- a/scripts/start/projects/GENIE_4_feedback.R
+++ b/scripts/start/projects/GENIE_4_feedback.R
@@ -1,4 +1,4 @@
-# |  (C) 2008-2021 Potsdam Institute for Climate Impact Research (PIK)
+# |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
 # |  authors, and contributors see CITATION.cff file. This file is part
 # |  of MAgPIE and licensed under AGPL-3.0-or-later. Under Section 7 of
 # |  AGPL-3.0, you are granted additional permissions described in the
@@ -50,12 +50,12 @@ cfg$info$flag <- identifierFlag
 cfg$results_folder <- paste0("output/", identifierFlag, "/:title:")
 
 
-### BE 
+### BE
 cfg$gms$s60_2ndgen_bioenergy_dem_min_post_fix <- 0
 cfg$gms$c60_bioenergy_subsidy <- 0
 
 ### Tau / Yield
-cfg$gms$tc <- "exo" 
+cfg$gms$tc <- "exo"
 
 ### Biodiv
 blV <- c(0) #BII lower bound (0-1), default 0
@@ -87,7 +87,7 @@ for (bl in blV) {
   # "output", identifierFlag, preflag, ":title:", sep = "/"
   "output", identifierFlag, ":title:", sep = "/"
   )
-  
+
   n <- "Feedback_step13_400f"
   m <- n
   cfg$gms$c60_2ndgen_biodem <- n
@@ -96,7 +96,7 @@ for (bl in blV) {
 
   ##############################################
   #runflag <- paste("feedback", f_flag, sep = "_")
-  runflag <- paste0(m, "") 
+  runflag <- paste0(m, "")
 
   cfg$title <- paste0(preflag, runflag)
 
diff --git a/scripts/start/projects/paper_healthyLscps.R b/scripts/start/projects/paper_healthyLscps.R
index 0ea21e921..d1d3e39eb 100644
--- a/scripts/start/projects/paper_healthyLscps.R
+++ b/scripts/start/projects/paper_healthyLscps.R
@@ -1,4 +1,4 @@
-# |  (C) 2008-2021 Potsdam Institute for Climate Impact Research (PIK)
+# |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
 # |  authors, and contributors see CITATION.cff file. This file is part
 # |  of MAgPIE and licensed under AGPL-3.0-or-later. Under Section 7 of
 # |  AGPL-3.0, you are granted additional permissions described in the
diff --git a/scripts/start/projects/project_EAT2p0_DeepDive.R b/scripts/start/projects/project_EAT2p0_DeepDive.R
index 3dd9e4bf2..40fbb9d8a 100644
--- a/scripts/start/projects/project_EAT2p0_DeepDive.R
+++ b/scripts/start/projects/project_EAT2p0_DeepDive.R
@@ -1,4 +1,4 @@
-# |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
+# |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
 # |  authors, and contributors see CITATION.cff file. This file is part
 # |  of MAgPIE and licensed under AGPL-3.0-or-later. Under Section 7 of
 # |  AGPL-3.0, you are granted additional permissions described in the
@@ -240,7 +240,7 @@ cfg <- setScenario(cfg, c("EL2_default"), scenario_config = "config/projects/sce
 cfg <- bau(cfg = cfg)
 # Mitigation
 cfg <- miti(cfg = cfg)
-# ecoSysProtAll_agMgmtOff: 
+# ecoSysProtAll_agMgmtOff:
 # (Above ground CO2 emis from LUC in forest, forestry, natveg; All types of emis from peatland; No further CH4/N2O/other emis related to ag. management)
 cfg$gms$c56_emis_policy <- "ecoSysProtAll_agMgmtOff"
 start_run(cfg, codeCheck = FALSE)

From eaadd8c395648d26adde064d34055e3af1a744bc Mon Sep 17 00:00:00 2001
From: pvjeetze <vjeetze@pik-potsdam.de>
Date: Thu, 19 Sep 2024 10:49:38 +0200
Subject: [PATCH 05/12] update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e9b093e0e..ac433147c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -23,6 +23,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 - **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"
 
 
 ### added

From 6aef8ede403b36302ceba22e06c49c310698860a Mon Sep 17 00:00:00 2001
From: pvjeetze <50408549+pvjeetze@users.noreply.github.com>
Date: Thu, 19 Sep 2024 11:38:52 +0200
Subject: [PATCH 06/12] Update scripts/output/extra/runSEALSallocation.R

Co-authored-by: Pascal Sauer <156898545+pascal-sauer@users.noreply.github.com>
---
 scripts/output/extra/runSEALSallocation.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/output/extra/runSEALSallocation.R b/scripts/output/extra/runSEALSallocation.R
index fe6b865d9..fa8184ad4 100644
--- a/scripts/output/extra/runSEALSallocation.R
+++ b/scripts/output/extra/runSEALSallocation.R
@@ -6,7 +6,7 @@
 # |  Contact: magpie@pik-potsdam.de
 
 # --------------------------------------------------------------
-# description: Starts SEALS allocation run based on gridded MAgPIE land cover projections (SEALS)
+# description: Starts SEALS allocation run based on gridded MAgPIE land cover projections
 # comparison script: FALSE
 # ---------------------------------------------------------------
 

From e859db92c918138d9202f7a23b955f78f1e2a2c3 Mon Sep 17 00:00:00 2001
From: pvjeetze <50408549+pvjeetze@users.noreply.github.com>
Date: Thu, 19 Sep 2024 11:46:09 +0200
Subject: [PATCH 07/12] Update scripts/output/extra/runSEALSallocation.R

Co-authored-by: Pascal Sauer <156898545+pascal-sauer@users.noreply.github.com>
---
 scripts/output/extra/runSEALSallocation.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/output/extra/runSEALSallocation.R b/scripts/output/extra/runSEALSallocation.R
index fa8184ad4..07ebf324a 100644
--- a/scripts/output/extra/runSEALSallocation.R
+++ b/scripts/output/extra/runSEALSallocation.R
@@ -104,7 +104,7 @@ reportLandUseForSEALS(
     overwrite = TRUE
   )
 
-  main <- readLines(file.path(dirProject, "scripts/run_test_standard.py"))
+  main <- readLines(file.path(dirProject, "scripts", "run_test_standard.py"))
 
   main[min(which(grepl("    p.user_dir =", main)))] <- paste0("    p.user_dir = \'", dirBaseFiles, "\'")
   main[min(which(grepl("    p.extra_dirs", main)))] <- paste0("    p.extra_dirs = '.'")

From b13da8f7ad53d52cf799f17023a7bdeb69416b6a Mon Sep 17 00:00:00 2001
From: pvjeetze <50408549+pvjeetze@users.noreply.github.com>
Date: Thu, 19 Sep 2024 11:47:48 +0200
Subject: [PATCH 08/12] Update scripts/output/extra/runSEALSallocation.R

Co-authored-by: Pascal Sauer <156898545+pascal-sauer@users.noreply.github.com>
---
 scripts/output/extra/runSEALSallocation.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/output/extra/runSEALSallocation.R b/scripts/output/extra/runSEALSallocation.R
index 07ebf324a..8f71ad912 100644
--- a/scripts/output/extra/runSEALSallocation.R
+++ b/scripts/output/extra/runSEALSallocation.R
@@ -139,7 +139,7 @@ reportLandUseForSEALS(
   submit <- c(
     "#!/bin/bash", "\n",
     paste0("#SBATCH --qos=", qos),
-    ifelse(qos %in% c("priority", "standby"), "#SBATCH --partition=priority", "#SBATCH --partition=standard"),
+    if (qos %in% c("priority", "standby")) "#SBATCH --partition=priority" else "#SBATCH --partition=standard",
     "#SBATCH --job-name=seals_allocation",
     paste0("#SBATCH --chdir=", normalizePath(file.path(dirProject, "scripts"))),
     "#SBATCH --output=outfile_%j.out",

From c04f45ba666708497d0341c4f8824840c2cae240 Mon Sep 17 00:00:00 2001
From: pvjeetze <vjeetze@pik-potsdam.de>
Date: Thu, 19 Sep 2024 14:15:02 +0200
Subject: [PATCH 09/12] changed source path of miniforge3

---
 scripts/output/extra/runSEALSallocation.R | 45 +++++++++++++++--------
 1 file changed, 30 insertions(+), 15 deletions(-)

diff --git a/scripts/output/extra/runSEALSallocation.R b/scripts/output/extra/runSEALSallocation.R
index fe6b865d9..93914f2bc 100644
--- a/scripts/output/extra/runSEALSallocation.R
+++ b/scripts/output/extra/runSEALSallocation.R
@@ -39,10 +39,6 @@ if (!exists("source_include")) {
 # for instructions on how to set up a python environment for SEALS
 sealsEnv <- "seals_dev"
 
-### Path to miniforge installation
-# For instructions on how to install miniforge see https://github.com/conda-forge/miniforge
-miniforgePath <- "/home/vjeetze/miniforge3/bin/activate"
-
 ### Path to SEALS base input file directory
 dirBaseFiles <- "/p/projects/magpie/users/vjeetze/seals/files"
 
@@ -78,6 +74,36 @@ reportLandUseForSEALS(
 # Setup SEALS run
 # ========================
 
+# Check whether base data and local SEALS code repo exist
+if (length(list.files(dirBaseFiles)) == 0) {
+  stop(paste(
+    "Please set the path to the SEALS base data",
+    "directory under 'User settings' of the",
+    "extra/runSEALSallocation.R script."
+  ))
+} else if (length(list.files(dirBaseFiles)) == 0) {
+  stop(paste(
+    "Please set the path to your local clone",
+    "of the SEALS code under 'User settings' of the",
+    "extra/runSEALSallocation.R script."
+  ))
+}
+
+### Path to miniforge installation
+miniforgePath <- "/p/projects/rd3mod/miniforge3/bin/activate"
+
+# create output directory
+dirProject <- "./output/seals"
+
+if (!dir.exists(file.path(dirProject))) {
+  dir.create(file.path(dirProject), recursive = TRUE)
+}
+
+iniLock <- file.path(dirProject, ".lock")
+lockOn <- filelock::lock(iniLock, exclusive = TRUE, timeout = Inf)
+Sys.chmod(iniLock, mode = "0664")
+
+
 # --------------------------------
 # Prepare SEALS start script
 # --------------------------------
@@ -167,17 +193,6 @@ reportLandUseForSEALS(
   }
 }
 
-# create output directory
-dirProject <- "./output/seals"
-
-if (!dir.exists(file.path(dirProject))) {
-  dir.create(file.path(dirProject), recursive = TRUE)
-}
-
-iniLock <- file.path(dirProject, ".lock")
-lockOn <- filelock::lock(iniLock, exclusive = TRUE, timeout = Inf)
-Sys.chmod(iniLock, mode = "0664")
-
 # --------------------------------
 # Run SEALS allocation
 # --------------------------------

From 5e8f173589a7db42c99e294cbd6e8cf3438ca740 Mon Sep 17 00:00:00 2001
From: pvjeetze <vjeetze@pik-potsdam.de>
Date: Thu, 19 Sep 2024 14:18:03 +0200
Subject: [PATCH 10/12] bugfix

---
 scripts/output/extra/runSEALSallocation.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/output/extra/runSEALSallocation.R b/scripts/output/extra/runSEALSallocation.R
index 5823fcda4..0b9f2eafa 100644
--- a/scripts/output/extra/runSEALSallocation.R
+++ b/scripts/output/extra/runSEALSallocation.R
@@ -81,7 +81,7 @@ if (length(list.files(dirBaseFiles)) == 0) {
     "directory under 'User settings' of the",
     "extra/runSEALSallocation.R script."
   ))
-} else if (length(list.files(dirBaseFiles)) == 0) {
+} else if (length(list.files(dirSEALS)) == 0) {
   stop(paste(
     "Please set the path to your local clone",
     "of the SEALS code under 'User settings' of the",

From ff6244b0a20a168e16e616c185e489dd8c66cf22 Mon Sep 17 00:00:00 2001
From: pvjeetze <50408549+pvjeetze@users.noreply.github.com>
Date: Thu, 19 Sep 2024 15:58:05 +0200
Subject: [PATCH 11/12] Update scripts/output/extra/runSEALSallocation.R

Co-authored-by: Pascal Sauer <156898545+pascal-sauer@users.noreply.github.com>
---
 scripts/output/extra/runSEALSallocation.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/scripts/output/extra/runSEALSallocation.R b/scripts/output/extra/runSEALSallocation.R
index 0b9f2eafa..21b289f02 100644
--- a/scripts/output/extra/runSEALSallocation.R
+++ b/scripts/output/extra/runSEALSallocation.R
@@ -94,6 +94,8 @@ miniforgePath <- "/p/projects/rd3mod/miniforge3/bin/activate"
 
 # create output directory
 dirProject <- "./output/seals"
+message(paste("Stitched SEALS allocation outputs are written to", 
+  "'./output/seals/intermediate/stitched_lulc_simplified_scenarios'"))
 
 if (!dir.exists(file.path(dirProject))) {
   dir.create(file.path(dirProject), recursive = TRUE)

From 759ff44df1f4cdc64b489731b7133a543f98ab8b Mon Sep 17 00:00:00 2001
From: pvjeetze <vjeetze@pik-potsdam.de>
Date: Fri, 20 Sep 2024 12:03:15 +0200
Subject: [PATCH 12/12] additional fixes, including run submissions of Foote

---
 CHANGELOG.md                                  |  1 +
 config/default.cfg                            | 20 +++++++++----------
 scripts/output/extra/highres.R                |  4 ++--
 scripts/output/extra/runSEALSallocation.R     | 15 ++++++++++----
 scripts/projects/fsec.R                       |  2 +-
 scripts/run_submit/submit_priority.sh         |  1 +
 ...y_maxMem.sh => submit_priority_highMem.sh} |  2 +-
 scripts/run_submit/submit_short.sh            |  1 +
 ...hort_maxMem.sh => submit_short_highMem.sh} |  2 +-
 scripts/run_submit/submit_standby.sh          |  1 +
 scripts/run_submit/submit_standby_dayMax.sh   |  1 +
 ...by_maxMem.sh => submit_standby_highMem.sh} |  2 +-
 ...ax.sh => submit_standby_highMem_dayMax.sh} |  2 +-
 scripts/slurmOutput.yml                       |  8 ++++----
 scripts/start/projects/paper_healthyLscps.R   |  2 +-
 scripts/start/projects/paper_peatlandTax.R    | 20 +++++++++----------
 scripts/start/projects/project_ABCDR.R        |  2 +-
 scripts/start/projects/project_EAT2p0.R       |  2 +-
 .../start/projects/project_EAT2p0_DeepDive.R  |  2 +-
 .../start/projects/project_LAMACLIMA_WP4.R    |  2 +-
 20 files changed, 52 insertions(+), 40 deletions(-)
 rename scripts/run_submit/{submit_priority_maxMem.sh => submit_priority_highMem.sh} (86%)
 rename scripts/run_submit/{submit_short_maxMem.sh => submit_short_highMem.sh} (86%)
 rename scripts/run_submit/{submit_standby_maxMem.sh => submit_standby_highMem.sh} (86%)
 rename scripts/run_submit/{submit_standby_maxMem_dayMax.sh => submit_standby_highMem_dayMax.sh} (88%)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ac433147c..7fbdc8f34 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -24,6 +24,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 - **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
diff --git a/config/default.cfg b/config/default.cfg
index c651b1aeb..57b6d0970 100644
--- a/config/default.cfg
+++ b/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,
@@ -2083,15 +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$qos <- NULL               # def = NULL
diff --git a/scripts/output/extra/highres.R b/scripts/output/extra/highres.R
index 3d93842c7..c1768e03d 100644
--- a/scripts/output/extra/highres.R
+++ b/scripts/output/extra/highres.R
@@ -104,7 +104,7 @@ highres <- function(cfg = cfg, res = "c1000", tc = NULL) {
   cfg$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
diff --git a/scripts/output/extra/runSEALSallocation.R b/scripts/output/extra/runSEALSallocation.R
index 21b289f02..26b8fcfdf 100644
--- a/scripts/output/extra/runSEALSallocation.R
+++ b/scripts/output/extra/runSEALSallocation.R
@@ -94,8 +94,6 @@ miniforgePath <- "/p/projects/rd3mod/miniforge3/bin/activate"
 
 # create output directory
 dirProject <- "./output/seals"
-message(paste("Stitched SEALS allocation outputs are written to", 
-  "'./output/seals/intermediate/stitched_lulc_simplified_scenarios'"))
 
 if (!dir.exists(file.path(dirProject))) {
   dir.create(file.path(dirProject), recursive = TRUE)
@@ -203,7 +201,11 @@ if (!is.null(lockOn)) {
   sealsLock <- file.path(dirProject, "seals.lock")
 
   if (!file.exists(sealsLock) || file.size(sealsLock) == 0) {
-    message("Starting SEALS allocation with input data creation.")
+    message(paste(
+      "Starting SEALS allocation with input data creation.\n",
+      "Stitched SEALS allocation outputs will be written to",
+      "'./output/seals/intermediate/stitched_lulc_simplified_scenarios'"
+    ))
     .setupSEALSrun(
       title = title,
       dir = outputdir,
@@ -223,7 +225,12 @@ if (!is.null(lockOn)) {
 
     writeLines(id, sealsLock)
   } else {
-    message("Starting SEALS allocation using existing input data.")
+    message(paste(
+      "Starting SEALS allocation using existing input data.\n",
+      "Stitched SEALS allocation outputs will be written to",
+      "'./output/seals/intermediate/stitched_lulc_simplified_scenarios'"
+    ))
+
     id <- readLines(sealsLock)
 
     .setupSEALSrun(
diff --git a/scripts/projects/fsec.R b/scripts/projects/fsec.R
index 0449a6028..f7f3302ba 100644
--- a/scripts/projects/fsec.R
+++ b/scripts/projects/fsec.R
@@ -214,7 +214,7 @@ fsecScenario <- function(scenario) {
   # general
   cfg$title       <- paste(v, scenario, sep = "")
   cfg$recalibrate <- FALSE
-  cfg$qos         <- "standby_maxMem_dayMax"
+  cfg$qos         <- "standby_highMem_dayMax"
   cfg$output      <- c("extra/highres",
                        "extra/disaggregation",
                        "projects/FSEC_nitrogenPollution",
diff --git a/scripts/run_submit/submit_priority.sh b/scripts/run_submit/submit_priority.sh
index 33c8496d5..b23c5bd67 100644
--- a/scripts/run_submit/submit_priority.sh
+++ b/scripts/run_submit/submit_priority.sh
@@ -5,5 +5,6 @@
 #SBATCH --output=slurm.log
 #SBATCH --mail-type=END,FAIL
 #SBATCH --cpus-per-task=3
+#SBATCH --mem-per-cpu=5G
 
 Rscript submit.R
diff --git a/scripts/run_submit/submit_priority_maxMem.sh b/scripts/run_submit/submit_priority_highMem.sh
similarity index 86%
rename from scripts/run_submit/submit_priority_maxMem.sh
rename to scripts/run_submit/submit_priority_highMem.sh
index ae58b9695..feae97160 100644
--- a/scripts/run_submit/submit_priority_maxMem.sh
+++ b/scripts/run_submit/submit_priority_highMem.sh
@@ -5,6 +5,6 @@
 #SBATCH --output=slurm.log
 #SBATCH --mail-type=END,FAIL
 #SBATCH --cpus-per-task=16
-#SBATCH --mem-per-cpu=0
+#SBATCH --mem-per-cpu=5G
 
 Rscript submit.R
diff --git a/scripts/run_submit/submit_short.sh b/scripts/run_submit/submit_short.sh
index 4e7b6edfc..433ed3308 100644
--- a/scripts/run_submit/submit_short.sh
+++ b/scripts/run_submit/submit_short.sh
@@ -5,5 +5,6 @@
 #SBATCH --output=slurm.log
 #SBATCH --mail-type=END,FAIL
 #SBATCH --cpus-per-task=3
+#SBATCH --mem-per-cpu=5G
 
 Rscript submit.R
diff --git a/scripts/run_submit/submit_short_maxMem.sh b/scripts/run_submit/submit_short_highMem.sh
similarity index 86%
rename from scripts/run_submit/submit_short_maxMem.sh
rename to scripts/run_submit/submit_short_highMem.sh
index 2016794e7..cf8f9669a 100644
--- a/scripts/run_submit/submit_short_maxMem.sh
+++ b/scripts/run_submit/submit_short_highMem.sh
@@ -5,7 +5,7 @@
 #SBATCH --output=slurm.log
 #SBATCH --mail-type=END,FAIL
 #SBATCH --cpus-per-task=16
-#SBATCH --mem-per-cpu=0
+#SBATCH --mem-per-cpu=5G
 
 Rscript submit.R
 
diff --git a/scripts/run_submit/submit_standby.sh b/scripts/run_submit/submit_standby.sh
index f0bff3233..e3ab2dd5b 100644
--- a/scripts/run_submit/submit_standby.sh
+++ b/scripts/run_submit/submit_standby.sh
@@ -5,5 +5,6 @@
 #SBATCH --output=slurm.log
 #SBATCH --mail-type=END,FAIL
 #SBATCH --cpus-per-task=3
+#SBATCH --mem-per-cpu=5G
 
 Rscript submit.R
diff --git a/scripts/run_submit/submit_standby_dayMax.sh b/scripts/run_submit/submit_standby_dayMax.sh
index d7836390d..aa6b3673d 100644
--- a/scripts/run_submit/submit_standby_dayMax.sh
+++ b/scripts/run_submit/submit_standby_dayMax.sh
@@ -5,6 +5,7 @@
 #SBATCH --output=slurm.log
 #SBATCH --mail-type=END,FAIL
 #SBATCH --cpus-per-task=3
+#SBATCH --mem-per-cpu=5G
 #SBATCH --time=24:00:00
 
 Rscript submit.R
diff --git a/scripts/run_submit/submit_standby_maxMem.sh b/scripts/run_submit/submit_standby_highMem.sh
similarity index 86%
rename from scripts/run_submit/submit_standby_maxMem.sh
rename to scripts/run_submit/submit_standby_highMem.sh
index 23b099943..4791ed844 100644
--- a/scripts/run_submit/submit_standby_maxMem.sh
+++ b/scripts/run_submit/submit_standby_highMem.sh
@@ -5,6 +5,6 @@
 #SBATCH --output=slurm.log
 #SBATCH --mail-type=END,FAIL
 #SBATCH --cpus-per-task=16
-#SBATCH --mem-per-cpu=0
+#SBATCH --mem-per-cpu=5G
 
 Rscript submit.R
diff --git a/scripts/run_submit/submit_standby_maxMem_dayMax.sh b/scripts/run_submit/submit_standby_highMem_dayMax.sh
similarity index 88%
rename from scripts/run_submit/submit_standby_maxMem_dayMax.sh
rename to scripts/run_submit/submit_standby_highMem_dayMax.sh
index ac3ba4d30..674bc10f5 100644
--- a/scripts/run_submit/submit_standby_maxMem_dayMax.sh
+++ b/scripts/run_submit/submit_standby_highMem_dayMax.sh
@@ -5,7 +5,7 @@
 #SBATCH --output=slurm.log
 #SBATCH --mail-type=END,FAIL
 #SBATCH --cpus-per-task=16
-#SBATCH --mem-per-cpu=0
+#SBATCH --mem-per-cpu=5G
 #SBATCH --time=24:00:00
 
 Rscript submit.R
diff --git a/scripts/slurmOutput.yml b/scripts/slurmOutput.yml
index f493010be..d3e35abe5 100644
--- a/scripts/slurmOutput.yml
+++ b/scripts/slurmOutput.yml
@@ -1,5 +1,5 @@
 slurmjobs:
-  SLURM standby: "sbatch --job-name=scripts-output --output=logs/out-%NAME-%j.out --error=logs/out-%NAME-%j.err --mail-type=END,FAIL --time=200 --mem-per-cpu=8000 --wrap=\"Rscript %SCRIPT\" --qos=standby --time=24:00:00"
-  SLURM standby maxMem: "sbatch --job-name=scripts-output --output=logs/out-%NAME-%j.out --error=logs/out-%NAME-%j.err --mail-type=END,FAIL --time=200 --mem-per-cpu=8000 --wrap=\"Rscript %SCRIPT\" --qos=standby --time=24:00:00 --mem-per-cpu=0 --cpus-per-task=16"
-  SLURM priority: "sbatch --job-name=scripts-output --output=logs/out-%NAME-%j.out --error=logs/out-%NAME-%j.err --mail-type=END,FAIL --time=200 --mem-per-cpu=8000 --wrap=\"Rscript %SCRIPT\" --qos=priority"
-  SLURM priority maxMem: "sbatch --job-name=scripts-output --output=logs/out-%NAME-%j.out --error=logs/out-%NAME-%j.err --mail-type=END,FAIL --time=200 --mem-per-cpu=8000 --wrap=\"Rscript %SCRIPT\" --qos=priority --mem-per-cpu=0 --cpus-per-task=16"
+  SLURM standby: "sbatch --job-name=scripts-output --output=logs/out-%NAME-%j.out --error=logs/out-%NAME-%j.err --mail-type=END,FAIL --time=200 --wrap=\"Rscript %SCRIPT\" --qos=standby --mem-per-cpu=5G --cpus-per-task=3"
+  SLURM standby highMem: "sbatch --job-name=scripts-output --output=logs/out-%NAME-%j.out --error=logs/out-%NAME-%j.err --mail-type=END,FAIL --wrap=\"Rscript %SCRIPT\" --qos=standby --time=24:00:00 --mem-per-cpu=5G --cpus-per-task=16"
+  SLURM priority: "sbatch --job-name=scripts-output --output=logs/out-%NAME-%j.out --error=logs/out-%NAME-%j.err --mail-type=END,FAIL --time=200 --wrap=\"Rscript %SCRIPT\" --qos=priority --mem-per-cpu=5G --cpus-per-task=3"
+  SLURM priority highMem: "sbatch --job-name=scripts-output --output=logs/out-%NAME-%j.out --error=logs/out-%NAME-%j.err --mail-type=END,FAIL --wrap=\"Rscript %SCRIPT\" --qos=priority --time=24:00:00  --mem-per-cpu=5G --cpus-per-task=16"
diff --git a/scripts/start/projects/paper_healthyLscps.R b/scripts/start/projects/paper_healthyLscps.R
index d1d3e39eb..9e5ff9776 100644
--- a/scripts/start/projects/paper_healthyLscps.R
+++ b/scripts/start/projects/paper_healthyLscps.R
@@ -84,7 +84,7 @@ for (ssp in SSPs) {
 
     source("config/default.cfg")
 
-    cfg$qos <- "short_maxMem"
+    cfg$qos <- "short_highMem"
 
     cfg$results_folder <- "output/:title::date:"
 
diff --git a/scripts/start/projects/paper_peatlandTax.R b/scripts/start/projects/paper_peatlandTax.R
index 2ed3cdbbe..91824915f 100644
--- a/scripts/start/projects/paper_peatlandTax.R
+++ b/scripts/start/projects/paper_peatlandTax.R
@@ -30,7 +30,7 @@ cfg$results_folder_highres <- "output"
 cfg$output <- c(cfg$output, "extra/highres")
 cfg$force_replace <- TRUE
 cfg$force_download <- FALSE
-cfg$qos <- "standby_maxMem_dayMax"
+cfg$qos <- "standby_highMem_dayMax"
 
 # support function to create standardized title
 .title <- function(cfg, ...)
@@ -55,7 +55,7 @@ calc_ghgprice <- function() {
   T0 <- read.magpie("modules/56_ghg_policy/input/f56_pollutant_prices.cs3")
   T0 <- collapseNames(T0[, , getNames(T0, dim = 2)[1]])
   T0[, , ] <- 0
-  
+
   #T200 200 USD/tCO2 in 2050
   T200 <- new.magpie(getRegions(T0), c(seq(1995, 2025, by = 5), 2050, 2100, 2150), getNames(T0), fill = 0)
   T200[, "y2025", "co2_c"] <- 0
@@ -68,12 +68,12 @@ calc_ghgprice <- function() {
   T200[, , "n2o_n_direct"] <- T200[, , "co2_c"] * 265 * 44 / 28
   T200[, , "n2o_n_indirect"] <- T200[, , "co2_c"] * 265 * 44 / 28
   T200[, , "co2_c"] <- T200[, , "co2_c"] * 44 / 12
-  
+
   T50 <- T200 * 0.25
   T100 <- T200 * 0.5
   T400 <- T200 * 2
   T800 <- T200 * 4
-  
+
   GHG <- mbind(
     add_dimension(T0, dim = 3.2, add = "scen", nm = "T0-GHG"),
     add_dimension(
@@ -107,16 +107,16 @@ calc_ghgprice <- function() {
       nm = "T800-GHG"
     )
   )
-  
+
   CO2 <- GHG
   CO2[, , c("ch4", "n2o_n_direct", "n2o_n_indirect")] <- 0
   getNames(CO2, dim = 2) <- gsub("GHG", "CO2", getNames(CO2, dim = 2))
-  
+
   GHGCH4GWP20 <- GHG
   GHGCH4GWP20[, , "ch4"] <- GHGCH4GWP20[, , "ch4"] / 28 * 84
   getNames(GHGCH4GWP20, dim = 2) <- gsub("GHG", "GHG-GWP20", getNames(GHGCH4GWP20, dim =
                                                                         2))
-  
+
   GHG <- mbind(CO2, GHG, GHGCH4GWP20)
   if (!dir.exists("./patch_inputdata"))
     dir.create("./patch_inputdata")
@@ -126,7 +126,7 @@ calc_ghgprice <- function() {
   write.magpie(GHG, file_name = "patch_inputdata/patchGHGprices/f56_pollutant_prices.cs3")
   tardir("patch_inputdata/patchGHGprices",
          "patch_inputdata/patchGHGprices.tgz")
-  
+
   unlink("patch_inputdata/patchGHGprices", recursive = TRUE)
   return(getNames(GHG, dim = 2))
 }
@@ -146,7 +146,7 @@ cfg$gms$s56_c_price_induced_aff <- 0
 
 ## Start scenarios
 for (res in c("c400")) {
-  if (res == "c400") 
+  if (res == "c400")
     cfg$input['cellular'] <- "rev4.111_36f73207_44a213b6_cellularmagpie_c400_MRI-ESM2-0-ssp370_lpjml-8e6c5eb1_clusterweight-ba4466a8.tgz"
   else if (res == "c1000") {
     cfg$input['cellular'] <- "rev4.111_36f73207_10f98ac1_cellularmagpie_c1000_MRI-ESM2-0-ssp370_lpjml-8e6c5eb1_clusterweight-ba4466a8.tgz"
@@ -156,7 +156,7 @@ for (res in c("c400")) {
   cfg$gms$c56_mute_ghgprices_until <- "y2150"
   cfg$gms$c56_pollutant_prices <- "T0-CO2"
   start_run(cfg, codeCheck = FALSE)
-  
+
   ## Policy scenarios
   for (tax in c("T50-CO2",
                 "T100-CO2",
diff --git a/scripts/start/projects/project_ABCDR.R b/scripts/start/projects/project_ABCDR.R
index 981fb823e..8b1480c53 100644
--- a/scripts/start/projects/project_ABCDR.R
+++ b/scripts/start/projects/project_ABCDR.R
@@ -25,7 +25,7 @@ cfg$results_folder <- "output/:title:"
 cfg$force_replace <- TRUE
 cfg$force_download <- FALSE
 
-cfg$qos <- "standby_maxMem_dayMax"
+cfg$qos <- "standby_highMem_dayMax"
 
 # support function to create standardized title
 .title <- function(cfg, ...) return(paste(cfg$info$flag, sep="_",...))
diff --git a/scripts/start/projects/project_EAT2p0.R b/scripts/start/projects/project_EAT2p0.R
index 9b1c073d2..83c759c07 100644
--- a/scripts/start/projects/project_EAT2p0.R
+++ b/scripts/start/projects/project_EAT2p0.R
@@ -27,7 +27,7 @@ cfg$results_folder <- "output/:title::date:"
 cfg$force_download <- TRUE
 
 # Special outputs required for Deep Dive
-cfg$qos <- "standby_maxMem_dayMax"
+cfg$qos <- "standby_highMem_dayMax"
 cfg$output <- c(
   "output_check",
   # "extra/highres", # do manually on last magpie run
diff --git a/scripts/start/projects/project_EAT2p0_DeepDive.R b/scripts/start/projects/project_EAT2p0_DeepDive.R
index 40fbb9d8a..704e05d09 100644
--- a/scripts/start/projects/project_EAT2p0_DeepDive.R
+++ b/scripts/start/projects/project_EAT2p0_DeepDive.R
@@ -27,7 +27,7 @@ cfg$results_folder <- "output/:title::date:"
 cfg$force_download <- TRUE
 
 # Special outputs required for Deep Dive
-cfg$qos <- "standby_maxMem_dayMax"
+cfg$qos <- "standby_highMem_dayMax"
 cfg$output <- c(
   "output_check",
   "extra/highres",
diff --git a/scripts/start/projects/project_LAMACLIMA_WP4.R b/scripts/start/projects/project_LAMACLIMA_WP4.R
index 709d58052..a8b1ac6f1 100644
--- a/scripts/start/projects/project_LAMACLIMA_WP4.R
+++ b/scripts/start/projects/project_LAMACLIMA_WP4.R
@@ -39,7 +39,7 @@ cfg$gms$c37_labor_uncertainty <- "ensmean"
 
 cfg$results_folder <- "output/:title:"
 cfg$output <- c("rds_report","extra/disaggregation","extra/disaggregation_LUH2","extra/highres")
-cfg$qos <- "priority_maxMem"
+cfg$qos <- "priority_highMem"
 
 #### Main scenarios