AR6 Climate assessment on reporting

DESCRIPTION

@@ -54,7 +54,7 @@ Imports:
     piamInterfaces (>= 0.12.18),
     plotly,
     purrr,
-    quitte (>= 0.3123.0),
+    quitte (>= 0.3128.4),
     R.utils,
     raster,
     readr,

config/default.cfg

@@ -49,6 +49,12 @@ cfg$runstatistics <- "/p/projects/rd3mod/models/statistics/remind"
 # copied into remind when starting a run and required to calculate climate responses (e.g. temperature).
 cfg$magicc_template <- "/p/projects/rd3mod/magicc/"
 
+#### Folder containing files for climate-assessment that cannot be published with REMIND
+# These files currently all have permissive licenses and can be easily found online
+cfg$climate_assessment_root       <- "/p/projects/rd3mod/python/climate-assessment/src/"
+cfg$climate_assessment_files_dir  <- "/p/projects/rd3mod/climate-assessment-files/"
+cfg$climate_assessment_magicc_bin <- "/p/projects/rd3mod/climate-assessment-files/magicc-v7.5.3/bin/magicc"
+
 #### Output folder of the modeltests generated by running config/scenario_config_AMT.csv
 # start.R searches in this folder for finished runs to be used as path_gdx...
 cfg$modeltests_folder <- "/p/projects/remind/modeltests/remind/output"
@@ -110,7 +116,7 @@ cfg$logoption <- 2
 
 # Just list the name of the output scripts that should be used by output.R
 # At the moment there are several R-scripts located in scripts/output/
-cfg$output <- c("reporting","reportCEScalib","rds_report","fixOnRef") #,"validation","emulator","reportCEScalib","validationSummary","dashboard")
+cfg$output <- c("reporting","reportCEScalib","rds_report","fixOnRef") #"ar6Climate","validation","emulator","reportCEScalib","validationSummary","dashboard")
 
 # Set the format for the results folder, type string :date: in order to use the current time stamp in the folder name (e.g. "results:date:") use :title: to use the current title in the folder name
 cfg$results_folder <- "output/:title::date:"

output.R

@@ -67,7 +67,8 @@ library(lucode2)
 library(gms)
 require(stringr, quietly = TRUE)
 
-source("scripts/start/isSlurmAvailable.R")
+# Import all functions from the scripts/start folder
+invisible(sapply(list.files("scripts/start", pattern = "\\.R$", full.names = TRUE), source))
 
 flags <- NULL
 ### Define arguments that can be read from command line
@@ -83,17 +84,19 @@ if ("--help" %in% flags) {
   q()
 }
 
-choose_slurmConfig_output <- function(slurmExceptions = NULL) {
+choose_slurmConfig_output <- function(output) {
   slurm_options <- c("--qos=priority", "--qos=short", "--qos=standby",
                      "--qos=priority --mem=16000", "--qos=short --mem=16000",
                      "--qos=standby --mem=16000", "--qos=priority --mem=32000")
 
   if (!isSlurmAvailable())
     return("direct")
 
-  if (!is.null(slurmExceptions)) {
-    slurm_options <- grep(slurmExceptions, slurm_options, value = TRUE)
-  }
+  # Modify slurm options for ar6 reporting, since we want to run MAGICC in parallel and we'll need a lot of memory
+  if ("ar6Climate" %in% output) slurm_options <- combine_slurmConfig(slurm_options[1:3], "--tasks-per-node=12 --mem=32000")
+  # reporting.R, in particular remind2::convGDX2MIF, requires at least --mem=8000 of memory
+  if ("reporting" %in% output) slurm_options <- grep("--mem=[0-9]*[0-9]{3}", slurm_options, value = TRUE)
+
   if (length(slurm_options) == 1) {
     return(slurm_options[[1]])
   }
@@ -176,7 +179,7 @@ if (comp %in% c("comparison", "export")) {
   # choose the slurm options. If you use command line arguments, use slurmConfig=priority or standby
   modules_using_slurmConfig <- c("compareScenarios2")
   if (!exists("slurmConfig") && any(modules_using_slurmConfig %in% output)) {
-    slurmConfig <- choose_slurmConfig_output()
+    slurmConfig <- choose_slurmConfig_output(output = output)
   }
   if (exists("slurmConfig")) {
     if (slurmConfig %in% c("priority", "short", "standby")) {
@@ -207,20 +210,18 @@ if (comp %in% c("comparison", "export")) {
     }
   }
 } else { # comp = single
-  # define slurm class or direct execution
+    # define slurm class or direct execution
   outputInteractive <- c("plotIterations", "fixOnRef", "integratedDamageCosts")
   if (! exists("source_include")) {
-    # for selected output scripts, only slurm configurations matching these regex are available
-    slurmExceptions <- if ("reporting" %in% output) "--mem=[0-9]*[0-9]{3}" else NULL
     if (any(output %in% outputInteractive)) {
       slurmConfig <- "direct"
       flags <- c(flags, "--interactive") # to tell scripts they can run in interactive mode
     }
     # if this script is not being sourced by another script but called from the command line via Rscript let the user
     # choose the slurm options
     if (!exists("slurmConfig")) {
-      slurmConfig <- choose_slurmConfig_output(slurmExceptions = slurmExceptions)
-      if (slurmConfig != "direct") slurmConfig <- paste(slurmConfig, "--nodes=1 --tasks-per-node=1")
+      slurmConfig <- choose_slurmConfig_output(output = output)
+      if (slurmConfig != "direct") slurmConfig <- combine_slurmConfig("--nodes=1 --tasks-per-node=1", slurmConfig)
     }
     if (slurmConfig %in% c("priority", "short", "standby")) {
       slurmConfig <- paste0("--qos=", slurmConfig, " --nodes=1 --tasks-per-node=1")

scripts/output/single/ar6Climate.R

@@ -0,0 +1,228 @@
+# |  (C) 2006-2023 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: [email protected]
+
+#' @title AR6 climate assessment
+#' @description Assessment of new emissions pathways consistent with the climate variable data from the working group
+#' III contribution to the IPCC Sixth Assessment (AR6) report. The script uses REMIND emissions data to perform
+#' harmonization and infilling based on the IIASA [climate-assessment](https://climate-assessment.readthedocs.io)
+#' package. The harmonized and infilled emissions are then used as input to the
+#' [MAGICC7 simple climate model](https://magicc.org/). Results are postprocessed and appended to the REMIND model
+#' intercomparison file (MIF).
+#'
+#' @author Gabriel Abrahao, Oliver Richters, Tonn Rüter
+#'
+#' @param outputdir Directory where REMIND MIF file is located. Output files generated in the process will be written
+#' to a subfolder "climate-assessment-data" in this directory. Defaults to "."
+#' @param gdxName Name of the REMIND GDX file. Defaults to "fulldata.gdx"
+
+library(madrat)
+library(remind2)
+library(quitte)
+library(piamInterfaces)
+library(lucode2)
+library(yaml)
+library(tidyverse)
+library(readr)
+library(stringr)
+
+############################# BASIC CONFIGURATION #############################
+
+gdxName <- "fulldata.gdx"             # name of the gdx
+cfgName <- "cfg.txt"                  # cfg file for getting file paths
+
+if (!exists("source_include")) {
+  # Define arguments that can be read from command line
+  outputdir <- "."
+  readArgs("outputdir", "gdxName", "gdx_ref_name", "gdx_refpolicycost_name")
+}
+
+cfgPath               <- file.path(outputdir, cfgName)
+logFile               <- file.path(outputdir, "log_climate.txt") # specific log for python steps
+scenario              <- getScenNames(outputdir)
+remindReportingFile   <- file.path(outputdir, paste0("REMIND_generic_", scenario, ".mif"))
+climateAssessmentEmi  <- normalizePath(file.path(outputdir, paste0("ar6_climate_assessment_", scenario, ".csv")),
+                                       mustWork = FALSE)
+climateAssessmentYaml <- file.path(system.file(package = "piamInterfaces"),
+                                   "iiasaTemplates", "climate_assessment_variables.yaml")
+
+############################# PREPARING EMISSIONS INPUT #############################
+
+logmsg <- paste0(
+  date(), " =================== CONFIGURATION STARTED ==================================\n",
+  "  outputdir = '",             outputdir,              "' exists? ", file.exists(outputdir), "\n",
+  "  cfgPath = '",               cfgPath,                "' exists? ", file.exists(cfgPath), "\n",
+  "  logFile = '",               logFile,                "' exists? ", file.exists(logFile), "\n",
+  "  scenario = '",              scenario, "'\n",
+  "  remindReportingFile = '",   remindReportingFile,   "' exists? ", file.exists(remindReportingFile), "\n",
+  "  climateAssessmentYaml = '", climateAssessmentYaml, "' exists? ", file.exists(climateAssessmentYaml), "\n",
+  "  climateAssessmentEmi = '",  climateAssessmentEmi,  "' exists? ", file.exists(climateAssessmentEmi), "\n",
+  date(), " =================== EXTRACT REMIND emission data ===========================\n",
+  "  ar6Climate.R: Extracting REMIND emission data\n"
+)
+cat(logmsg)
+capture.output(cat(logmsg), file = logFile, append = TRUE)
+
+climateAssessmentInputData <- as.quitte(remindReportingFile) %>%
+  # Consider only the global region
+  filter(region %in% c("GLO", "World")) %>%
+  # Extract only the variables needed for climate-assessment. These are provided from the iiasaTemplates in the
+  # piamInterfaces package. See also:
+  # https://github.com/pik-piam/piamInterfaces/blob/master/inst/iiasaTemplates/climate_assessment_variables.yaml
+  generateIIASASubmission(
+    mapping = "AR6",
+    outputFilename = NULL,
+    iiasatemplate = climateAssessmentYaml,
+    logFile = logFile
+  ) %>%
+  mutate(region = factor("World")) %>%
+  # Rename the columns using str_to_title which capitalizes the first letter of each word
+  rename_with(str_to_title) %>%
+  # Transforms the yearly values for each variable from a long to a wide format. The resulting data frame then has
+  # one column for each year and one row for each variable
+  pivot_wider(names_from = "Period", values_from = "Value") %>%
+  write_csv(climateAssessmentEmi, quote = "none")
+
+logmsg <- paste0(
+  date(), "  ar6Climate.R: Wrote REMIND emission data to '", climateAssessmentEmi, "' for climate-assessment\n"
+)
+cat(logmsg)
+capture.output(cat(logmsg), file = logFile, append = TRUE)
+
+############################# PYTHON/MAGICC SETUP #############################
+
+# Read the cfg to get the location of MAGICC-related files
+cfg <- read_yaml(cfgPath)
+
+# All climate-assessment files will be written to this folder
+climateAssessmentFolder <- normalizePath(file.path(outputdir, "climate-assessment-data"))
+dir.create(climateAssessmentFolder, showWarnings = FALSE)
+
+# The base name, that climate-assessment uses to derive it's output names
+baseFileName <- sub("\\.csv$", "", basename(climateAssessmentEmi))
+
+# These files are supposed to be all inside cfg$climate_assessment_files_dir in a certain structure
+probabilisticFile <- normalizePath(file.path(
+  cfg$climate_assessment_files_dir,
+  "parsets", "0fd0f62-derived-metrics-id-f023edb-drawnset.json"
+))
+infillingDatabaseFile <- normalizePath(file.path(
+  cfg$climate_assessment_files_dir,
+  "1652361598937-ar6_emissions_vetted_infillerdatabase_10.5281-zenodo.6390768.csv"
+))
+
+# Extract the location of the climate-assessment scripts and the MAGICC binary from cfg.txt
+scriptsFolder       <- normalizePath(file.path(cfg$climate_assessment_root, "scripts"))
+magiccBinFile       <- normalizePath(file.path(cfg$climate_assessment_magicc_bin))
+magiccWorkersFolder <- file.path(normalizePath(climateAssessmentFolder), "workers")
+
+# Read parameter sets file to ascertain how many parsets there are
+allparsets <- read_yaml(probabilisticFile)
+nparsets <- length(allparsets$configurations)
+
+logmsg <- paste0(date(), " =================== SET UP climate-assessment scripts environment ===================\n")
+cat(logmsg)
+capture.output(cat(logmsg), file = logFile, append = TRUE)
+
+# Create working folder for climate-assessment files
+dir.create(magiccWorkersFolder, recursive = TRUE, showWarnings = FALSE)
+
+# Set relevant environment variables and create a MAGICC worker directory
+Sys.setenv(MAGICC_EXECUTABLE_7 = magiccBinFile)
+Sys.setenv(MAGICC_WORKER_ROOT_DIR = magiccWorkersFolder) # Has to be an absolute path
+Sys.setenv(MAGICC_WORKER_NUMBER = 1) # TODO: Get this from slurm or nproc
+
+# Specify the commands to (de-)activate the venv & run the harmonization/infilling/model scripts
+# TODO: This makes assumptions about the users climate-assessment installation. There are a couple of options:
+# A) Remove entirely and assume that the user has set up their environment correctly
+# B) Make this more flexible by explictly setting them in default.cfg
+#activate_venv_cmd <- paste("source", normalizePath(file.path(cfg$climate_assessment_root, "..", "venv", "bin", "activate")))
+#deactivate_venv_cmd <- "deactivate"
+
+run_harm_inf_cmd <- paste(
+  "python", file.path(scriptsFolder, "run_harm_inf.py"),
+  climateAssessmentEmi,
+  climateAssessmentFolder,
+  "--no-inputcheck",
+  "--infilling-database", infillingDatabaseFile
+)
+
+run_clim_cmd <- paste(
+  "python", file.path(scriptsFolder, "run_clim.py"),
+  normalizePath(file.path(climateAssessmentFolder, paste0(baseFileName, "_harmonized_infilled.csv"))),
+  climateAssessmentFolder,
+  "--num-cfgs", nparsets,
+  "--scenario-batch-size", 1,
+  "--probabilistic-file", probabilisticFile
+)
+
+logmsg <- paste0(
+  "  climateAssessmentFolder = '", climateAssessmentFolder, "' exists? ", dir.exists(climateAssessmentFolder), "\n",
+  "  baseFileName = '",            baseFileName, "'\n",
+  "  probabilisticFile = '",       probabilisticFile,       "' exists? ", file.exists(probabilisticFile), "\n",
+  "  infillingDatabaseFile = '",   infillingDatabaseFile,   "' exists? ", file.exists(infillingDatabaseFile), "\n",
+  "  scriptsFolder = '",           scriptsFolder,           "' exists? ", dir.exists(scriptsFolder), "\n",
+  "  magiccBinFile = '",           magiccBinFile,           "' exists? ", file.exists(magiccBinFile), "\n",
+  "  magiccWorkersFolder = '",     magiccWorkersFolder,     "' exists? ", dir.exists(magiccWorkersFolder), "\n\n",
+  "  ENVIRONMENT VARIABLES:\n",
+  "  MAGICC_EXECUTABLE_7    = ", Sys.getenv("MAGICC_EXECUTABLE_7") ,"\n",
+  "  MAGICC_WORKER_ROOT_DIR = ", Sys.getenv("MAGICC_WORKER_ROOT_DIR") ,"\n",
+  "  MAGICC_WORKER_NUMBER   = ", Sys.getenv("MAGICC_WORKER_NUMBER") ,"\n",
+  date(), " =================== RUN climate-assessment infilling & harmonization ===================\n",
+  run_harm_inf_cmd, "'\n"
+)
+cat(logmsg)
+capture.output(cat(logmsg), file = logFile, append = TRUE)
+
+############################# HARMONIZATION/INFILLING #############################
+
+system(run_harm_inf_cmd)
+
+logmsg <- paste0(date(), "  Done with harmonization & infilling\n")
+cat(logmsg)
+capture.output(cat(logmsg), file = logFile, append = TRUE)
+
+############################# RUNNING MODEL #############################
+
+logmsg <- paste0(
+  date(), "  Found ", nparsets, " nparsets, start climate-assessment model runs\n", run_harm_inf_cmd, "\n",
+  date(), " =================== RUN climate-assessment model ============================\n",
+  run_clim_cmd, "'\n"
+)
+cat(logmsg)
+capture.output(cat(logmsg), file = logFile, append = TRUE)
+
+system(run_clim_cmd)
+
+############################# POSTPROCESS CLIMATE OUTPUT #############################
+climateAssessmentOutput <- file.path(
+  climateAssessmentFolder,
+  paste0(baseFileName, "_harmonized_infilled_IAMC_climateassessment.xlsx")
+)
+
+logmsg <- paste0(
+  date(), "  climate-assessment finished\n",
+  date(), " =================== POSTPROCESS climate-assessment output ==================\n",
+  "  climateAssessmentOutput = '", climateAssessmentOutput, "'\n"
+)
+cat(logmsg)
+capture.output(cat(logmsg), file = logFile, append = TRUE)
+
+############################# APPEND TO REMIND MIF #############################
+# Filter only periods used in REMIND, so that it doesn't expand the original mif
+usePeriods <- as.numeric(grep("[0-9]+", quitte::read_mif_header(remindReportingFile)$header, value = TRUE))
+
+climateAssessmentData <- read.quitte(climateAssessmentOutput) %>%
+  filter(period %in% usePeriods) %>%
+  interpolate_missing_periods(usePeriods, expand.values = FALSE) %>%
+  write.mif(remindReportingFile, append = TRUE)
+
+logmsg <- paste0(
+  date(), " postprocessing done! Results appended to REMIND mif '", remindReportingFile, "'\n",
+  "ar6Climate.R finished\n"
+)
+cat(logmsg)
+capture.output(cat(logmsg), file = logFile, append = TRUE)