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output.R
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output.R
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#!/usr/bin/env Rscript
# | (C) 2006-2024 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]
##########################################################
#### REMIND Output Generation ####
##########################################################
# Version 1.0
# Type "Rscript output.R" to start the script in the command line
# Based on the Version 2.2 of same file in the MAgPIE main folder
#########################################################################################
# Write dump file when error occurs, see help to dump.frames for more information
options(error = quote({
dump.frames(to.file = TRUE)
traceback()
q()
}))
helpText <- "
#' Rscript output.R [options]
#'
#' [options] can be the following flags:
#'
#' --help, -h: show this help text and exit
#' --test, -t: tests output.R without actually starting any run
#' --renv=<path> load the renv located at <path>, incompatible with --update
#' --update update packages in renv first, incompatible with --renv=<path>
#'
#' [options] can also specify the following variables. If they are not specified
#' but needed, the scripts will ask the user.
#'
#' comp= comp=single means output for single runs (reporting, …)
#' comp=comparison means scripts to compare runs (compareScenarios2, …)
#' comp=export means scripts to export runs (xlsx_IIASA, …)
#' filename_prefix= string to be added to filenames by some output scripts
#' (compareScenarios, xlsx_IIASA)
#' output= output=compareScenarios2 directly selects the specific script
#' outputdir= Can be used to specify the output directories to be used.
#' Example: outputdir=./output/SSP2-Base-rem-1,./output/NDC-rem-1
#' remind_dir= path to remind or output folder(s) where runs can be found.
#' Defaults to ./output but can also be used to specify multiple
#' folders, comma-separated, such as remind_dir=.,../otherremind
#' slurmConfig= use slurmConfig=priority, short or standby to specify slurm
#' selection. You may also pass complicated arguments such as
#' slurmConfig='--qos=priority --mem=8000'
"
argv <- get0("argv", ifnotfound = commandArgs(trailingOnly = TRUE))
# run updates before loading any packages
if ("--update" %in% argv) {
stopifnot(`--update must not be used together with --renv=...` = !any(startsWith(argv, "--renv=")))
installedUpdates <- piamenv::updateRenv()
piamenv::stopIfLoaded(names(installedUpdates))
} else if (any(startsWith(argv, "--renv="))) {
renvProject <- normalizePath(sub("^--renv=", "", grep("^--renv=", argv, value = TRUE)))
renv::load(renvProject)
}
# load landuse library
library(lucode2)
library(gms)
require(stringr, quietly = TRUE)
# 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
if (!exists("source_include")) {
# if this script is not being sourced by another script but called from the command line via Rscript read the command
# line arguments and let the user choose the slurm options
flags <- readArgs("outputdir", "output", "comp", "remind_dir", "slurmConfig", "filename_prefix",
.flags = c(t = "--test", h = "--help"))
}
if ("--help" %in% flags) {
message(gsub("#' ?", '', helpText))
q()
}
choose_slurmConfig_output <- function(output) {
slurm_options <- c("--qos=priority --partition=priority", "--qos=short", "--qos=standby",
"--qos=priority --partition=priority --mem=8000", "--qos=short --mem=8000",
"--qos=standby --mem=8000", "--qos=priority --partition=priority --mem=32000")
if (!isSlurmAvailable())
return("direct")
# Modify slurm options for reporting options that run in parallel (MAGICC) or need more memory
if ("MAGICC7_AR6" %in% output) {
slurm_options <- paste(slurm_options[1:3], "--tasks-per-node=12 --mem=32000")
} else if ("nashAnalysis" %in% output) {
slurm_options <- paste(slurm_options[1:3], "--mem=32000")
} else if ("reporting" %in% output) {
slurm_options <- grep("--mem=[0-9]*[0-9]{3}", slurm_options, value = TRUE)
} else if ("fixOnRef" %in% output && length(output) == 1) {
slurm_options <- c("direct", slurm_options)
}
if (length(slurm_options) == 1) {
return(slurm_options[[1]])
}
identifier <- chooseFromList(gsub("qos=", "", gsub("--", "", slurm_options)), multiple = FALSE, returnBoolean = TRUE,
type = "slurm mode", userinfo = "Uses the first option if empty.")
return(if (any(identifier)) slurm_options[as.numeric(which(identifier))] else slurm_options[1])
}
choose_filename_prefix <- function(modules, title = "") {
cat(paste0("\n\n ", title, "Please choose a prefix for filenames of ", paste(modules, collapse=", "), ".\n"))
cat(" For example compareScenarios2 uses it for the filenames: compScen-yourprefix-2022-….pdf.\n Use only A-Za-z0-9_-, or leave empty:\n\n")
filename_prefix <- gms::getLine()
if(grepl("[^A-Za-z0-9_-]", filename_prefix)) {
filename_prefix <- choose_filename_prefix(modules, title = paste("No, this contained special characters, try again.\n",title))
}
return(filename_prefix)
}
if (exists("source_include")) {
comp <- "single"
} else if (! exists("comp")) {
modes <- c("single" = "Output for single run", "comparison" = "Comparison across runs", "export" = "Export", "exit" = "Exit")
comp <- names(modes)[which(chooseFromList(unname(modes), type = "output mode", multiple = FALSE, returnBoolean = TRUE, userinfo = "Leave empty for 'single'."))]
if (length(comp) == 0) comp <- names(modes)[[1]]
if (comp == "exit") q()
}
if (isFALSE(comp)) comp <- "single" # legacy from times only two comp modes existed
if (isTRUE(comp)) comp <- "comparison"
if (! exists("output")) {
# search for R scripts in scripts/output subfolders
modules <- gsub("\\.R$", "", grep("\\.R$", list.files(paste0("./scripts/output/", comp)), value = TRUE))
# if more than one option exists, let user choose
defaultoutput <- switch(comp, "single" = gms::readDefaultConfig(".")$output, "comparison" = "compareScenarios2", "export" = "xlsx_IIASA")
userinfo <- paste("Leave empty for", paste(defaultoutput, collapse = ", "))
output <- if (length(modules) == 1) modules else chooseFromList(modules, type = "modules to be used for output generation", addAllPattern = FALSE, userinfo = userinfo)
if (length(output) == 0) output <- defaultoutput
# move "reporting" to first position, if it exists
output <- c(if ("reporting" %in% output) "reporting", output[! output %in% "reporting"])
}
# Select output directories if not defined by readArgs
if (! exists("outputdir")) {
modulesNeedingMif <- c("compareScenarios2", "xlsx_IIASA", "policyCosts", "Ariadne_output",
"plot_compare_iterations", "varListHtml", "fixOnRef", "MAGICC7_AR6")
needingMif <- any(modulesNeedingMif %in% output) && ! "reporting" %in% output[[1]]
if (exists("remind_dir")) {
dir_folder <- c(file.path(remind_dir, "output"), remind_dir)
} else {
defaultcfg <- readDefaultConfig(".")
dir_folder <- unique(c("output", dirname(defaultcfg$results_folder)))
}
dirs <- dirname(Sys.glob(file.path(dir_folder, "*", "fulldata.gdx")))
if (needingMif) dirs <- intersect(dirs, unique(dirname(Sys.glob(file.path(dir_folder, "*", "REMIND_generic_*.mif")))))
dirnames <- if (length(dir_folder) == 1) basename(dirs) else dirs
names(dirnames) <- stringr::str_extract(dirnames, "rem-[0-9]+$")
names(dirnames)[is.na(names(dirnames))] <- ""
if (length(dirnames) == 0) {
stop("No directories found containing gdx", if (needingMif) " and mif", " files. Aborting.")
}
selectedDirs <- chooseFromList(dirnames, type = "runs to be used for output generation",
userinfo = paste0(if ("policyCosts" %in% output) "The reference run will be selected separately! " else NULL,
if (needingMif) "Do you miss a run? Check if .mif exists and rerun reporting. " else NULL),
returnBoolean = FALSE, multiple = TRUE)
outputdirs <- if (length(dir_folder) == 1) file.path(dir_folder, selectedDirs) else selectedDirs
if ("policyCosts" %in% output) {
policyrun <- chooseFromList(c("--- only here to avoid that folder numbers change ---", dirnames),
type = "reference run to which policy run will be compared",
userinfo = "Select a single reference run.",
returnBoolean = TRUE, multiple = FALSE)
outputdirs <- c(rbind(outputdirs, dirs[policyrun[-1]])) # generate 3,1,4,1,5,1 out of 3,4,5 and policyrun 1
}
} else {
outputdirs <- outputdir
}
if (comp %in% c("comparison", "export")) {
# ask for filename_prefix, if one of the modules that use it is selected
modules_using_filename_prefix <- c("compareScenarios2", "xlsx_IIASA", "varListHtml")
if (!exists("filename_prefix")) {
if (any(modules_using_filename_prefix %in% output)) {
filename_prefix <- choose_filename_prefix(modules = intersect(modules_using_filename_prefix, output))
} else {
filename_prefix <- ""
}
}
# 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(output = output)
}
if (exists("slurmConfig")) {
if (slurmConfig %in% c("priority", "short", "standby")) {
slurmConfig <- paste0("--qos=", slurmConfig)
}
}
# Set value source_include so that loaded scripts know, that they are
# included as source (instead of a load from command line)
source_include <- TRUE
# Execute output scripts over all chosen folders
for (rout in output) {
name <- paste(rout, ".R", sep = "")
if (file.exists(paste0("scripts/output/", comp, "/", name))) {
if ("--test" %in% flags) {
message("Test mode, not executing ", paste0("scripts/output/", comp, "/", name))
} else {
message("\n\n## Executing ", name)
tmp.env <- new.env()
tmp.error <- try(sys.source(paste0("scripts/output/", comp, "/", name), envir = tmp.env))
rm(tmp.env)
gc()
if (!is.null(tmp.error)) {
warning("Script ", name, " was stopped by an error and not executed properly!")
}
}
}
}
} else { # comp = single
# define slurm class or direct execution
outputInteractive <- c("plotIterations", "integratedDamageCosts")
if (! exists("source_include")) {
if (any(output %in% outputInteractive)) {
slurmConfig <- "direct"
}
# 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(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")
}
if (isTRUE(slurmConfig %in% "direct")) {
flags <- c(flags, "--interactive") # to tell scripts they can run in interactive mode
}
} else {
# if being sourced by another script execute the output scripts directly without sending them to the cluster
slurmConfig <- "direct"
}
# Execute outputscripts for all choosen folders
for (outputdir in outputdirs) {
if (exists("cfg")) {
title <- cfg$title
gms <- cfg$gms
revision <- cfg$inputRevision
magpie_folder <- cfg$magpie_folder
}
# Get values of config if output.R is called standalone
if (!exists("source_include")) {
magpie_folder <- getwd()
message("Load data from ", file.path(outputdir, "config.Rdata"))
if (file.exists(file.path(outputdir, "config.Rdata"))) {
load(file.path(outputdir, "config.Rdata"))
title <- cfg$title
gms <- cfg$gms
revision <- cfg$inputRevision
} else {
config <- grep("\\.cfg$", list.files(outputdir), value = TRUE)
l <- readLines(file.path(outputdir, config))
title <- strsplit(grep("(cfg\\$|)title +<-", l, value = TRUE), "\"")[[1]][2]
gms <- list()
gms$scenarios <- strsplit(grep("(cfg\\$|)gms\\$scenarios +<-", l, value = TRUE), "\"")[[1]][2]
revision <- as.numeric(unlist(strsplit(grep("(cfg\\$|)inputRevision +<-", l, value = TRUE), "<-[ \t]*"))[2])
}
}
# Set value source_include so that loaded scripts know, that they are
# included as source (instead of a load from command line)
source_include <- TRUE
###################################################################################
# Execute R scripts
###################################################################################
# output creation for --testOneRegi was switched off in start.R in this commit:
# https://github.com/remindmodel/remind/commit/5905d9dd814b4e4a62738d282bf1815e6029c965
if (all(output %in% c(NA, "NA"))) {
message("\nNo output generation, as output was set to NA, as for example for --testOneRegi or --quick.")
} else {
message("\nStarting output generation for ", outputdir, "\n")
name <- paste0(output, ".R")
scriptsfound <- file.exists(paste0("scripts/output/single/", name))
if ("--test" %in% flags) {
message("Test mode, not executing scripts/output/single/", paste(name, collapse = ", "))
} else {
if (slurmConfig == "direct") {
# execute output script directly (without sending it to slurm)
for (n in name[scriptsfound]) {
message("Executing ", n)
tmp.env <- new.env()
tmp.error <- try(sys.source(paste0("scripts/output/single/", n), envir = tmp.env))
# rm(list=ls(tmp.env),envir=tmp.env)
rm(tmp.env)
gc()
if (!is.null(tmp.error)) {
warning("Script ", n, " was stopped by an error and not executed properly!")
}
}
} else {
# send the output script to slurm
logfile <- file.path(outputdir, "log_output.txt")
Rscripts <- paste0("Rscript scripts/output/single/", name, " outputdir=", outputdir, collapse = "; ")
slurmcmd <- paste0("sbatch ", slurmConfig, " --job-name=", logfile, " --output=", logfile,
" --mail-type=END,FAIL --comment=output.R --wrap='", Rscripts, "'")
message("Sending to slurm: ", paste(name, collapse = ", "), ". Find log in ", logfile)
system(slurmcmd)
}
# finished
message("\nFinished ", ifelse(slurmConfig == "direct", "", "starting job for "), "output generation for ", outputdir, "!\n")
}
if (any(! scriptsfound)) {
warning("Skipping those output script selected that could not be found in scripts/output/single: ",
name[! scriptsfound])
}
}
rm(source_include)
if (!is.null(warnings())) {
print(warnings())
}
}
}