start_bundle_coupled.R

#!/usr/bin/env Rscript
# |  (C) 2006-2022 Potsdam Institute for Climate Impact Research (PIK)
# |  authors, and contributors see CITATION.cff file. This file is part
# |  of REMIND and licensed under AGPL-3.0-or-later. Under Section 7 of
# |  AGPL-3.0, you are granted additional permissions described in the
# |  REMIND License Exception, version 1.0 (see LICENSE file).
# |  Contact: remind@pik-potsdam.de
library(stringr)
require(lucode2)

########################################################################################################
#################################  U S E R   S E T T I N G S ###########################################
########################################################################################################

# Please provide all files and paths relative to the folder where start_coupled is executed
path_remind <- paste0(getwd(),"/")   # provide path to REMIND. Default: the actual path which the script is started from
path_magpie <- paste0(getwd(), "/../magpie/")

# Paths to the files where scenarios are defined
# path_settings_remind contains the detailed configuration of the REMIND scenarios
# path_settings_coupled defines which runs will be started, coupling infos, and optimal gdx and report information that overrides path_settings_remind
# these settings will be overwritten if you provide the path to the coupled file as first command line argument
path_settings_coupled <- paste0(path_remind, "config/scenario_config_coupled_NGFS_v3.csv")
path_settings_remind  <- sub("scenario_config_coupled", "scenario_config", path_settings_coupled)
                         # paste0(path_remind, "config/scenario_config.csv")

# You can put a prefix in front of the names of your runs, this will turn e.g. "SSP2-Base" into "prefix_SSP2-Base".
# This allows storing results of multiple coupled runs (which have the same scenario names) in the same MAgPIE and REMIND output folders.
# !Currently not working for prefixes different from "C_". "C_" is hard-coded elsewhere!
prefix_runname <- "C_"

# If there are existing runs you would like to take the gdxes (REMIND) or reportings (REMIND or MAgPIE) from, provide the path here and the name prefix below.
# Note: the scenario names of the old runs have to be identical to the runs that are to be started. If they differ please provide the names of the old scenarios in the
# file that you specified on path_settings_coupled (scenario_config_coupled_xxx.csv).
path_remind_oldruns <- paste0(path_remind, "output/")
path_magpie_oldruns <- paste0(path_magpie, "output/")

# If you want the script to find gdxs or reports of older runs as starting point for new runs please
# provide the prefix of the old run names so the script can find them.
prefix_oldruns <-  "C_"

# number of coupling iterations, can also be specified in path_settings_coupled
max_iterations <- 5

# Number of coupling iterations (before final iteration) in which MAgPIE uses higher n600 resolution.
# Until "max_iterations - n600_iterations" iteration MAgPIE runs with n200 resolution.
# Afterwards REMIND runs for "n600_iterations" iterations with results from higher resolution.
n600_iterations <- 0 # max_iterations

# run a compareScenario for each scenario comparing all rem-x: Choose qos (short, priority) or set to FALSE
run_compareScenarios <- "short"

########################################################################################################
#################################  load command line arguments  ########################################
########################################################################################################

require(magclass)
require(gms)
require(remind2)
require(gtools) # required for mixedsort()
require(dplyr) # for filter, secelt, %>%
require(stringr) # for str_sub

# Define colors for output
red   <- "\033[0;31m"
green <- "\033[0;32m"
blue  <- "\033[0;34m"
NC    <- "\033[0m"   # No Color

message("path_remind:           ", if (dir.exists(path_remind)) green else red, path_remind, NC)
message("path_magpie:           ", if (dir.exists(path_remind)) green else red, path_magpie, NC)
message("path_settings_coupled: ", if (file.exists(path_remind)) green else red, path_settings_coupled, NC)
message("path_settings_remind:  ", if (file.exists(path_remind)) green else red, path_settings_remind, NC)
message("path_remind_oldruns:   ", if (dir.exists(path_remind)) green else red, path_remind_oldruns, NC)
message("path_magpie_oldruns:   ", if (dir.exists(path_remind)) green else red, path_magpie_oldruns, NC)
message("prefix_runname:        ", prefix_runname)
message("max_iterations:        ", max_iterations)
message("n600_iterations:       ", n600_iterations)
message("run_compareScenarios:  ", run_compareScenarios)

# load arguments from command line
if (! exists("argv")) argv <- commandArgs(trailingOnly = TRUE)

readArgs("startnow")
if (! exists("startnow")) startnow <- "1" else argv <- setdiff(argv, paste0("startnow=", startnow))

# define arguments that are accepted (test for backward compatibility)
if ("test" %in% argv) argv <- unique(c(argv[! argv %in% c("test")], "--test"))
accepted <- c(p = "--parallel", t = "--test")

# search for strings that look like -i1asrR and transform them into long flags
onedashflags <- unlist(strsplit(paste0(argv[grepl("^-[a-zA-Z0-9]*$", argv)], collapse = ""), split = ""))
argv <- unique(c(argv[! grepl("^-[a-zA-Z0-9]*$", argv)], unlist(accepted[names(accepted) %in% onedashflags])))
message("\nAll command line arguments: ", paste(argv, collapse = ", "))
if (sum(! onedashflags %in% c(names(accepted), "-")) > 0) {
  stop("Unknown single character flags: ", onedashflags[! onedashflags %in% c(names(accepted), "-")],
  ". Only available: ", paste0("-", names(accepted), collapse = ", ") )
}

# check if user provided any unknown arguments or config files that do not exist
known <- argv %in% accepted
if (!all(known)) {
  file_exists <- file.exists(argv[!known])
  if (sum(file_exists) > 1) stop("Enter only a scenario_config_coupled* file via command line or set all files manually in start_bundle_coupled.R")
  if (!all(file_exists)) stop("Unknown parameter provided: ", paste(argv[!known][!file_exists], collapse = ", "),
  ".\nAccepted parameters: [config file], ", paste(accepted, collapse = ", "))
  # set config file to not known parameter where the file actually exists
  path_settings_coupled <- paste0(path_remind, argv[!known][[1]])
  if (! grep("scenario_config_coupled", path_settings_coupled))
    stop("Enter only a scenario_config_coupled* file via command line or set all files manually in start_bundle_coupled.R")
  path_settings_remind  <- sub("scenario_config_coupled", "scenario_config", path_settings_coupled)
}

if (! file.exists("output")) dir.create("output")

parallel <- ifelse("--parallel" %in% argv, TRUE, FALSE)
errorsfound <- 0
startedRuns <- 0
waitingRuns <- 0
deletedFolders <- 0

stamp <- format(Sys.time(), "_%Y-%m-%d_%H.%M.%S")

####################################################
############## F U N C T I O N S ###################
####################################################
.setgdxcopy <- function(needle, stack, new){
  # delete entries in stack that contain needle and append new
  matches <- grepl(needle, stack)
  out <- c(stack[!matches], new)
  return(out)
}

####################################################
##############  READ SCENARIO FILES ################
####################################################
# Read-in the switches table, use first column as row names

settings_coupled <- read.csv2(path_settings_coupled, stringsAsFactors = FALSE, row.names=1, na.strings="")
settings_remind  <- read.csv2(path_settings_remind, stringsAsFactors = FALSE, row.names=1, na.strings="")

# Choose which scenarios to start: select rows according to "subset" and columns according to "select" (not used in the moment)
scenarios_coupled  <- subset(settings_coupled, subset = (start == startnow))

# some checks for title
if (any(nchar(rownames(scenarios_coupled)) > 75)) stop(paste0("These titles are too long: ", paste0(rownames(scenarios_coupled)[nchar(rownames(scenarios_coupled)) > 75], collapse = ", "), " – GAMS would not tolerate this, and quit working at a point where you least expect it. Stopping now."))
if (length(grep("\\.", rownames(scenarios_coupled))) > 0) stop(paste0("These titles contain dots: ", paste0(rownames(scenarios_coupled)[grep("\\.", rownames(scenarios_coupled))], collapse = ", "), " – GAMS would not tolerate this, and quit working at a point where you least expect it. Stopping now."))
if (length(grep("_$", rownames(scenarios_coupled))) > 0) stop(paste0("These titles end with _: ", paste0(rownames(scenarios_coupled)[grep("_$", rownames(scenarios_coupled))], collapse = ", "), ". This may lead start_bundle_coupled.R to select wrong gdx files. Stopping now."))


missing <- setdiff(rownames(scenarios_coupled),rownames(settings_remind))
if (!identical(missing, character(0))) {
  message("The following scenarios are given in '", path_settings_coupled,
          "' but could not be found in '", path_settings_remind, "':")
  message("  ", paste(missing, collapse = ", "), "\n")
}

common <- intersect(rownames(settings_remind),rownames(scenarios_coupled))
knownRefRuns <- apply(expand.grid(prefix_runname , common, "-rem-", seq(max_iterations)), 1, paste, collapse="")
if (!identical(common,character(0))) {
  message("The following ", length(common), " scenarios will be started:")
  message("  ", paste(common, collapse = ", "))
} else {
  message("No scenario selected.")
}
message("")

# add lacking path_gdx columns
miss_refpolicycost <- NULL
if ("path_gdx_ref" %in% names(settings_remind) && ! "path_gdx_refpolicycost" %in% names(settings_remind)) {
  settings_remind$path_gdx_refpolicycost <- settings_remind$path_gdx_ref
  miss_refpolicycost <- c("settings_remind")
}
if ("path_gdx_ref" %in% names(scenarios_coupled) && ! "path_gdx_refpolicycost" %in% names(scenarios_coupled)) {
  scenarios_coupled$path_gdx_refpolicycost <- scenarios_coupled$path_gdx_ref
  miss_refpolicycost <- c(miss_refpolicycost, "settings_remind")
}
if (length(miss_refpolicycost) > 0) {
  message("In ", paste(miss_refpolicycost, collapse = " and "),
        ", no column path_gdx_refpolicycost for policy cost comparison found, using path_gdx_ref instead.")
}

path_gdx_list <- c("path_gdx" = "input.gdx",
                   "path_gdx_ref" = "input_ref.gdx",
                   "path_gdx_refpolicycost" = "input_refpolicycost.gdx",
                   "path_gdx_bau" = "input_bau.gdx",
                   "path_gdx_carbonprice" = "input_carbonprice.gdx")

settings_remind[, names(path_gdx_list)[! names(path_gdx_list) %in% names(settings_remind)]] <- NA
scenarios_coupled[, names(path_gdx_list)[! names(path_gdx_list) %in% names(scenarios_coupled)]] <- NA

# If provided replace gdx paths given in scenario_config with paths given in scenario_config_coupled
for (scen in common) {
  use_path_gdx <- names(path_gdx_list)[! is.na(scenarios_coupled[scen, names(path_gdx_list)])]
  if (length(use_path_gdx) > 0) {
    settings_remind[scen, use_path_gdx] <- scenarios_coupled[scen, use_path_gdx]
    message("For ", scen, ", use data specified in coupled config for: ", paste(use_path_gdx, collapse = ", "), ".")
  }
}

# check REMIND settings

source(paste0(path_remind,"config/default.cfg")) # retrieve REMIND default settings

knownColumnNames <- c(names(cfg$gms), names(path_gdx_list), "start", "output", "description", "model",
                      "regionmapping", "inputRevision", "slurmConfig")
unknownColumnNames <- names(settings_remind)[! names(settings_remind) %in% knownColumnNames]
if (length(unknownColumnNames) > 0) {
  message("\nAutomated checks did not find counterparts in default.cfg for these config file columns:")
  message("  ", paste(unknownColumnNames, collapse = ", "))
  message("The start script might simply ignore them. Please check if these switches are not deprecated.")
  message("This check was added Jan. 2022. If you find false positives, add them to knownColumnNames in start_bundle_coupled.R.\n")
  forbiddenColumnNames <- list(   # specify forbidden column name and what should be done with it
     "c_budgetCO2" = "Rename to c_budgetCO2from2020, adapt emission budgets, see https://github.com/remindmodel/remind/pull/640",
     "c_budgetCO2FFI" = "Rename to c_budgetCO2from2020FFI, adapt emission budgets, see https://github.com/remindmodel/remind/pull/640"
   )
  for (i in intersect(names(forbiddenColumnNames), unknownColumnNames)) {
    message("Column name ", i, " in remind settings is outdated. ", forbiddenColumnNames[i])
  }
  if (any(names(forbiddenColumnNames) %in% unknownColumnNames)) {
    stop("Outdated column names found that must not be used. Stopped.")
  }
}

if (parallel && file.exists("/p") && "qos" %in% names(scenarios_coupled)
    && sum(scenarios_coupled[common, "qos"] == "priority", na.rm = TRUE) > 4) {
      message("\nAttention, you want to start more than 4 runs with qos=priority mode.")
      message("They may not be able to run in parallel on the PIK cluster.")
}

####################################################
######## PREPARE AND START COUPLED RUNS ############
####################################################


for(scen in common){
  message("\n################################\nPreparing run ", scen, "\n")

  start_now <- FALSE # initalize, will be overwritten if all conditions are satisfied
  runname      <- paste0(prefix_runname, scen)           # name of the run that is used for the folder names
  path_report  <- NULL                                   # sets the path to the report REMIND is started with in the first loop
  qos          <- scenarios_coupled[scen, "qos"]         # set the SLURM quality of service (priority/short/medium/...)
  if(is.null(qos) | is.na(qos)) qos <- if (parallel) "short" else "medium" # if qos could not be found in scenarios_coupled use short/medium
  start_iter_first <- 1                                  # iteration to start the coupling with

  # look whether there is already a REMIND run (check for old name if provided)
  # Check for existing REMIND and MAgPIE runs and whether iteration can be continued from those (at least one REMIND iteration has to exist!)
  path_report_found <- NULL
  start_magpie <- FALSE
  iter_rem <- 0
  needle <- scen
  suche <- paste0(path_remind, "output/", prefix_runname, needle, "-rem-*/REMIND_generic_", prefix_runname, needle, "-rem-*.mif")
  possibleRemindReport <- mixedsort(Sys.glob(suche))[1]
  already_rem <- sub(paste0("REMIND_generic_", prefix_runname, needle, "-rem-.*\\.mif"), "fulldata.gdx", possibleRemindReport)
  if (! is.na(already_rem)) {
    if (! file.exists(already_rem)) stop(possibleRemindReport, " exists, but ", already_rem, " not!")
    iter_rem <- as.integer(sub(".*rem-(\\d.*)/.*","\\1", already_rem))
  } else if (! is.na(scenarios_coupled[scen, "oldrun"])) {
    message("Nothing found for ", suche, ", continue with oldrun.")
    if (isTRUE(str_sub(scenarios_coupled[scen, "oldrun"], -14, -1) == "/fulldata.gdx") &&
        file.exists(scenarios_coupled[scen, "oldrun"])) {
          already_rem <- c(scenarios_coupled[scen, "oldrun"])
    } else {
      needle <- scenarios_coupled[scen, "oldrun"]
      suche <- paste0(path_remind_oldruns, prefix_oldruns, needle, "-rem-*/fulldata.gdx")
      already_rem <- mixedsort(Sys.glob(suche))[1]
    }
  }
  if (is.na(already_rem)) {
    message("Nothing found for ", suche, ", starting with ", runname, "-rem-1.")
  } else {
    # if there is an existing REMIND run, use its gdx for the run to be started
    settings_remind[scen, "path_gdx"] <- normalizePath(already_rem)
    message("Found REMIND gdx here: ", normalizePath(already_rem))
  }
  # is there already a MAgPIE run with this name?
  iter_mag <- 0
  needle <- scen
  suche <- paste0(path_magpie, "output/", prefix_runname, needle,"-mag-*/report.mif")
  already_mag <- mixedsort(Sys.glob(suche))[1]
  if (! is.na(already_mag)) {
    iter_mag <- as.integer(sub(".*mag-(\\d.*)/.*","\\1",already_mag))
  } else if (! is.na(scenarios_coupled[scen, "oldrun"])) {
    message("Nothing found for ", suche, ", continue with oldrun")
    if (isTRUE(str_sub(scenarios_coupled[scen, "oldrun"], -14, -1) == "/report.mif") &&
        file.exists(scenarios_coupled[scen, "oldrun"])) {
          already_mag <- c(scenarios_coupled[scen, "oldrun"])
    } else {
      needle <- scenarios_coupled[scen, "oldrun"]
      suche <- paste0(path_magpie_oldruns, prefix_oldruns, needle, "-mag-*/report.mif")
      already_mag <- mixedsort(Sys.glob(suche))[1]
    }
  }
  if (is.na(already_mag)) {
    message("Nothing found for ", suche, ", starting REMIND standalone.")
  } else {
    path_report_found <- normalizePath(already_mag)
    message("Found MAgPIE report here: ", path_report_found)
  }
  # decide whether to continue with REMIND or MAgPIE
  if (iter_rem == iter_mag + 1 & iter_rem < max_iterations) {
    # if only remind has finished an iteration -> start with magpie in this iteration using a REMIND report
    start_iter_first  <- iter_rem
    path_run    <- gsub("/fulldata.gdx","",already_rem)
    path_report_found <- Sys.glob(paste0(path_run,"/REMIND_generic_*"))[1] # take the first entry to ignore REMIND_generic_*_withoutPlus.mif
    if (is.na(path_report_found)) stop("There is a fulldata.gdx but no REMIND_generic_.mif in ",path_run,".\nPlease use Rscript output.R to produce it.")
    message("Found REMIND report here: ", path_report_found)
    message("Continuing with MAgPIE with mag-", start_iter_first)
    start_magpie <- TRUE
  } else if (iter_rem == iter_mag) {
    # if remind and magpie iteration is the same -> start next iteration with REMIND with or without MAgPIE report
    start_iter_first <- iter_rem + 1
    message("REMIND and MAgPIE each finished run ", iter_rem, ", proceeding with REMIND run rem-", start_iter_first)
  } else if (iter_rem >= max_iterations & iter_mag >= max_iterations - 1) {
    message("This scenario is already completed with rem-", iter_rem, " and mag-", iter_mag, " and max_iterations=", max_iterations, ".")
    next
  } else {
    stop("REMIND has finished ", iter_rem, " runs, but MAgPIE ", iter_mag, " runs. Something is wrong!")
  }


  source(paste0(path_remind,"config/default.cfg")) # retrieve REMIND settings
  cfg_rem <- cfg
  rm(cfg)
  cfg_rem$title <- scen
  rem_filesstart <- cfg_rem$files2export$start     # save to reset it to that later

  source(paste0(path_magpie,"config/default.cfg")) # retrieve MAgPIE settings
  cfg_mag <- cfg
  rm(cfg)
  cfg_mag$title <- scen

  # configure MAgPIE according to magpie_scen (scenario needs to be available in scenario_config.cfg)
  if(!is.null(scenarios_coupled[scen, "magpie_scen"])) {
    cfg_mag <- setScenario(cfg_mag, c(trimws(unlist(strsplit(scenarios_coupled[scen, "magpie_scen"], split = ",|\\|"))), "coupling"),
                           scenario_config = paste0(path_magpie,"config/scenario_config.csv"))
  }
  cfg_mag <- check_config(cfg_mag, reference_file=paste0(path_magpie,"config/default.cfg"), modulepath = paste0(path_magpie,"modules/"))
  
  # GHG prices will be set to zero (in start_run() of MAgPIE) until and including the year specified here
  cfg_mag$mute_ghgprices_until <- scenarios_coupled[scen, "no_ghgprices_land_until"] 
  
  # How to provide the exogenous TC to MAgPIE:
  # Running MAgPIE with exogenous TC requires a path with exogenous TC. Using exo_indc_MAR17 the path is chosen via c13_tau_scen.
  # Using exo_JUN13 the path is given in the file modules/13_tc/exo_JUN13/input/tau_scenario.csv
  # This file can be generated (prior to all runs that use exogenous TC) using the following lines of code:
  #  require(magpie) # for tau function
  #  write.magpie(tau("/p/projects/htc/MagpieEmulator/r11356/magmaster/output/SSP2-SSP2-Ref-SPA0-endo-73-lessts/fulldata.gdx"),"modules/13_tc/exo_JUN13/input/tau_scenario.csv")
  #  Useful in case years mismatch:
  #  t  <- tau("/p/projects/htc/MagpieEmulator/r11356/magmaster/output/SSP2-SSP2-Ref-SPA0-endo-73/fulldata.gdx")
  #  y  <- c(seq(2005,2060,5),seq(2070,2110,10),2130,2150)
  #  tn <- time_interpolate(t,y,integrate_interpolated_years=TRUE,extrapolation_type = "constant")
  #  write.magpie(tn,"modules/13_tc/exo_JUN13/input/tau_scenario.csv")

  # Switch REMIND and MAgPIE to endogenous TC
  #message("Setting MAgPIE to endogenous TC")
  #cfg_mag$gms$tc      <- "inputlib"
  #cfg_rem$gms$biomass <- "magpie_linear"

  # Configure Afforestation in MAgPIE
  # if (grepl("-aff760",scen)) {
  #    message("Setting MAgPIE max_aff_area to 760")
  #    cfg_mag$gms$s32_max_aff_area <- 760
  #} else if (grepl("-aff900",scen)) {
  #    message("Setting MAgPIE max_aff_area to 900")
  #    cfg_mag$gms$s32_max_aff_area <- 900
  #} else if (grepl("-affInf",scen)) {
  #    message("Setting MAgPIE max_aff_area to Inf")
  #    cfg_mag$gms$s32_max_aff_area <- Inf
  #} else if (grepl("-cost2",scen)) {
  #    message("Setting MAgPIE cprice_red_factor to 0.2")
  #    cfg_mag$gms$s56_cprice_red_factor <- 0.2
  #    cfg_mag$gms$s32_max_aff_area <- Inf
  #} else if (grepl("-cost3",scen)) {
  #    message("Setting MAgPIE cprice_red_factor to 0.3")
  #    cfg_mag$gms$s56_cprice_red_factor <- 0.3
  #    cfg_mag$gms$s32_max_aff_area <- Inf
  #}

  #cfg$logoption  <- 2  # Have the log output written in a file (not on the screen)

  # Edit remind main model file, region settings and input data revision based on scenarios table, if cell non-empty
  for (switchname in intersect(c("model", "regionmapping", "inputRevision"), names(settings_remind))) {
    if ( ! is.na(settings_remind[scen, switchname] )) {
      cfg_rem[[switchname]] <- settings_remind[scen, switchname]
    }
  }

  # Edit switches in default.cfg based on scenarios table, if cell non-empty
  for (switchname in intersect(names(cfg_rem$gms), names(settings_remind))) {
    if ( ! is.na(settings_remind[scen, switchname] )) {
      cfg_rem$gms[[switchname]] <- settings_remind[scen, switchname]
    }
  }

  # Set description
  if ("description" %in% names(settings_remind) && ! is.na(settings_remind[scen, "description"])) {
    cfg_rem$description <- gsub('"', '', settings_remind[scen, "description"])
  } else {
    cfg_rem$description <- paste0("Coupled REMIND and MAgPIE run ", scen, " started by ", path_settings_remind, " and ", path_settings_coupled, ".")
  }

  # save cm_nash_autoconverge to be used for last REMIND run
  if ("cm_nash_autoconverge_lastrun" %in% names(scenarios_coupled)) {
    cfg_rem$cm_nash_autoconverge_lastrun <- scenarios_coupled[scen, "cm_nash_autoconverge_lastrun"]
  }
  configureIterations <- if(parallel) max_iterations:start_iter_first else c(start_iter_first)

  for (i in configureIterations) {
    fullrunname <- paste0(runname, ifelse(parallel, paste0("-rem-", i), ""))
    start_iter <- i

    # If provided replace the path to the MAgPIE report found automatically with path given in scenario_config_coupled.csv
    if (i == start_iter_first) {
      if (! is.na(scenarios_coupled[scen, "path_report"]) & i == 1) {
        path_report <- scenarios_coupled[scen, "path_report"] # sets the path to the report REMIND is started with in the first loop
        message("Replacing path to MAgPIE report with that one specified in\n  ", path_settings_coupled, "\n  ", scenarios_coupled[scen, "path_report"], "\n")
      } else {
        path_report <- path_report_found
      }
    } else {
      path_report <- runname
    }

    # if provided use ghg prices for land (MAgPIE) from a different REMIND run than the one MAgPIE runs coupled to
    path_mif_ghgprice_land <- NULL
    if (i == 1 && "path_mif_ghgprice_land" %in% names(scenarios_coupled)) {
      if (! is.na(scenarios_coupled[scen, "path_mif_ghgprice_land"])) {
        if (str_sub(scenarios_coupled[scen, "path_mif_ghgprice_land"], -4, -1) == ".mif") {
            # if real file is given (has ".mif" at the end) take it for path_mif_ghgprice_land
            path_mif_ghgprice_land <- scenarios_coupled[scen, "path_mif_ghgprice_land"]
        } else {
            # if no real file is given but a reference to another scenario (that has to run first) create path to the reference scenario
            ghgprice_remindrun <- paste0(prefix_runname, scenarios_coupled[scen, "path_mif_ghgprice_land"], "-rem-", ifelse(parallel, i, max_iterations))
            path_mif_ghgprice_land <- paste0(path_remind,"output/", ghgprice_remindrun ,"/REMIND_generic_", ghgprice_remindrun ,".mif")
        }
        cfg_mag$path_to_report_ghgprices <- path_mif_ghgprice_land
      }
    }

    # Create list of previously defined paths to gdxs
    gdxlist <- unlist(settings_remind[scen, names(path_gdx_list)])
    names(gdxlist) <- path_gdx_list
    if (parallel) {
      gdxlist[gdxlist %in% rownames(settings_coupled)] <- paste0(prefix_runname, gdxlist[gdxlist %in% rownames(settings_coupled)], "-rem-", i)
      possibleFulldata <- paste0(path_remind, "output/", gdxlist, "/fulldata.gdx")
      possibleRemindReport <- paste0(path_remind, "output/", gdxlist, "/REMIND_generic_", gdxlist, ".mif")
      # if file fulldata.gdx and report already exists because run was already finished, use it directly as input
      replaceByFulldata <- file.exists(possibleFulldata) & file.exists(possibleRemindReport)
      gdxlist[replaceByFulldata] <- possibleFulldata[replaceByFulldata]
    }

    if (i == start_iter_first) {
      gdx_specified <- grepl(".gdx", gdxlist, fixed = TRUE)
      gdx_na <- is.na(gdxlist)
      start_now <- all(gdx_specified | gdx_na)
    }

    # in parallel mode, remove gdxlist generated by earlier i
    if (parallel) cfg_rem$files2export$start <- rem_filesstart
    # Remove potential elements that contain ".gdx" and append gdxlist
    cfg_rem$files2export$start <- .setgdxcopy(".gdx", cfg_rem$files2export$start, gdxlist)

    # add table with information about runs that need the fulldata.gdx of the current run as input (will be further processed in start_coupled.R)
    cfg_rem$RunsUsingTHISgdxAsInput <- settings_remind[common, ] %>% select(contains("path_gdx")) %>%    # select columns that have "path_gdx" in their name
                                                 filter(rowSums(. == scen, na.rm = TRUE) > 0)           # select rows that have the current scenario in any column
    if (parallel && length(cfg_rem$RunsUsingTHISgdxAsInput[[1]]) > 0) {
      cfg_rem$RunsUsingTHISgdxAsInput[! is.na(cfg_rem$RunsUsingTHISgdxAsInput)] <- paste0(prefix_runname,
                    cfg_rem$RunsUsingTHISgdxAsInput[! is.na(cfg_rem$RunsUsingTHISgdxAsInput)], "-rem-", i)
      rownames(cfg_rem$RunsUsingTHISgdxAsInput) <- paste0(prefix_runname, rownames(cfg_rem$RunsUsingTHISgdxAsInput), "-rem-", i)
    }
    # add the next remind run
    if (parallel && i < max_iterations) {
      cfg_rem$RunsUsingTHISgdxAsInput[paste0(runname, "-rem-", (i+1)), "path_gdx"] <- fullrunname
    }

    if (i > start_iter_first || ! start_now) {
      # if no real file is given but a reference to another scenario (that has to run first) create path for input_ref and input_bau
      # using the scenario names given in the columns path_gdx_ref and path_gdx_ref in the REMIND standalone scenario config
      for (path_gdx in names(path_gdx_list)) {
        if (! is.na(cfg_rem$files2export$start[path_gdx_list[path_gdx]]) && ! grepl(".gdx", cfg_rem$files2export$start[path_gdx_list[path_gdx]], fixed = TRUE)) {
          cfg_rem$files2export$start[path_gdx_list[path_gdx]] <- paste0(prefix_runname, settings_remind[scen, path_gdx],
                                                                        "-rem-", ifelse(parallel, i, max_iterations))
        }
      }
      if (parallel & i > start_iter_first) {
        cfg_rem$files2export$start["input.gdx"] <- paste0(runname, "-rem-", i-1)
      }
      # If the preceding run has already finished (= its gdx file exist) start 
      # the current run immediately. This might be the case e.g. if you started
      # the NDC run in a first batch and now want to start the subsequent policy
      # runs by hand after the NDC has finished.
    }
    if (i == start_iter_first && ! start_now && all(file.exists(cfg_rem$files2export$start[path_gdx_list]) | unlist(gdx_na))) {
        start_now <- TRUE
    }
    foldername <- file.path("output", fullrunname)
    if (parallel && (i > start_iter_first | !start_magpie) && file.exists(foldername)) {
      if (! "--test" %in% argv) unlink(foldername, recursive = TRUE, force = TRUE)
      message("Delete ", foldername, if ("--test" %in% argv) " if not in test mode", ". ", appendLF = FALSE)
      deletedFolders <- deletedFolders + 1
    }
    Rdatafile <- paste0(fullrunname, ".RData")
    message("Save settings to ", Rdatafile)
    save(path_remind, path_magpie, cfg_rem, cfg_mag, runname, fullrunname, max_iterations, start_iter,
         n600_iterations, path_report, qos, parallel, prefix_runname, run_compareScenarios, file = Rdatafile)

  } # end for (i %in% configureIterations)

  # convert from logi to character so file.exists does not throw an error
  path_report <- as.character(path_report)

  message("\nSUMMARY")
  message("runname       : ", runname)
  message("Start iter    : ", if (start_magpie) "mag-" else "rem-", start_iter_first)
  message("QOS           : ", qos)
  message("remind gdxes  :")
  for (path_gdx in names(path_gdx_list)) {
      gdxname <- cfg_rem$files2export$start[path_gdx_list[path_gdx]]
      gdxfound <- (is.na(gdxname) || file.exists(gdxname))
      usecolor <- if (gdxfound) green else if (gdxname %in% knownRefRuns) blue else red
      message("  ", str_pad(path_gdx, 23, "right"), ": ", usecolor, gdxname, NC)
  }
  if(!is.null(path_mif_ghgprice_land)) message("ghg_price_mag : ",ifelse(file.exists(path_mif_ghgprice_land), green,red), path_mif_ghgprice_land, NC, "\n",sep="")
  message("path_report   : ",ifelse(file.exists(path_report),green,red), path_report, NC)
  message("no_ghgprices_land_until: ", cfg_mag$mute_ghgprices_until)

  if (cfg_rem$gms$optimization == "nash" && cfg_rem$gms$cm_nash_mode == "parallel") {
    # for nash: set the number of CPUs per node to number of regions + 1
    nr_of_regions <- length(unique(read.csv2(cfg_rem$regionmapping)$RegionCode)) + 1
  } else {
    # for negishi: use only one CPU
    nr_of_regions <- 1
  }

  if (start_now){
      startedRuns <- startedRuns + 1
      if (! "--test" %in% argv) {
        logfile <- if (parallel) file.path("output", fullrunname, paste0("log", if (start_magpie) "-mag", ".txt"))
                   else file.path("output", paste0("log_", sub("-rem-", if(start_magpie) "-mag-" else "-rem-", fullrunname), stamp, ".txt"))
        if (! file.exists(dirname(logfile))) dir.create(dirname(logfile))
        message("Find logging in ", logfile)
        system(paste0("sbatch --qos=", qos, " --job-name=", if (parallel) fullrunname else runname,
        " --output=", logfile, " --mail-type=END --comment=REMIND-MAgPIE --tasks-per-node=", nr_of_regions,
        " --wrap=\"Rscript start_coupled.R coupled_config=", Rdatafile, "\""))
      } else {
        message("Test mode: run ", fullrunname, " NOT submitted to the cluster.")
      }
  } else {
      missingRefRuns <- unique(cfg_rem$files2export$start[path_gdx_list][! gdx_specified & ! gdx_na])
      message("Waiting for: ", blue, paste(intersect(knownRefRuns, missingRefRuns), collapse = ", "), NC)
      if (length(setdiff(missingRefRuns, knownRefRuns)) > 0) {
        message("Cannot start because ", paste(setdiff(missingRefRuns, knownRefRuns), collapse = ", "), " not found!")
        errorsfound <- errorsfound + length(setdiff(missingRefRuns, knownRefRuns))
      } else {
        waitingRuns <- waitingRuns + 1
      }
  }
}

if (! "--test" %in% argv) {
 system(paste0("cp ", path_remind, ".Rprofile ", path_magpie, ".Rprofile"))
 message("\nCopied REMIND .Rprofile to MAgPIE folder.")
  cs_runs <- paste0("output/", common, "-rem-", max_iterations, collapse = ",")
  cs_name <- paste0("compScen-all-rem-", max_iterations)
  cs_qos <- if (! isFALSE(run_compareScenarios)) run_compareScenarios else "short"
  cs_command <- paste0("sbatch --qos=", cs_qos, " --job-name=", cs_name, " --output=", cs_name, ".out --error=",
    cs_name, ".out --mail-type=END --time=60 --wrap='Rscript scripts/utils/run_compareScenarios2.R outputdirs=",
    cs_runs, " shortTerm=FALSE outfilename=", cs_name,
    " regionList=World,LAM,OAS,SSA,EUR,NEU,MEA,REF,CAZ,CHA,IND,JPN,USA mainRegName=World'")
  message("\n### To start a compareScenario once everything is finished, run:")
  message(cs_command)
}

message("\nFinished: ", deletedFolders, " folders deleted. ", startedRuns, " runs started. ", waitingRuns, " runs are waiting. Number of problems: ",
        errorsfound, ".", ifelse("--test" %in% argv, " You are in TEST mode, only RData files were written.", ""))