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output.R
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output.R
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#!/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: [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()
}))
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=")))
source("scripts/utils/updateRenv.R")
} 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)
### 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
readArgs("outputdir", "output", "comp", "remind_dir", "slurmConfig", "filename_prefix")
}
# Setting relevant paths
if (file.exists("/iplex/01/landuse")) { # run is performed on the cluster
pythonpath <- "/iplex/01/landuse/bin/python/bin/"
latexpath <- "/iplex/01/sys/applications/texlive/bin/x86_64-linux/"
} else {
pythonpath <- ""
latexpath <- NA
}
choose_slurmConfig_output <- function(slurmExceptions = NULL) {
slurm_options <- c("--qos=priority", "--qos=short", "--qos=standby",
"--qos=priority --mem=8000", "--qos=short --mem=8000",
"--qos=standby --mem=8000", "--qos=priority --mem=32000", "direct")
if (!is.null(slurmExceptions)) {
slurm_options <- unique(c(grep(slurmExceptions, slurm_options, value = TRUE), "direct"))
}
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))]
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")) {
modules <- gsub("\\.R$", "", grep("\\.R$", list.files(paste0("./scripts/output/", if (isFALSE(comp)) "single" else comp)), value = TRUE))
output <- chooseFromList(modules, type = "modules to be used for output generation", addAllPattern = FALSE)
}
# Select output directories if not defined by readArgs
if (! exists("outputdir")) {
if ("policyCosts" %in% output) {
message("\nFor policyCosts, specify policy runs and reference runs alternatingly:")
message("3,1,4,1 compares runs 3 and 4 with 1.")
}
dir_folder <- if (exists("remind_dir")) remind_dir else "./output"
dirs <- basename(dirname(Sys.glob(file.path(dir_folder, "*", "fulldata.gdx"))))
names(dirs) <- stringr::str_extract(dirs, "rem-[0-9]+$")
names(dirs)[is.na(names(dirs))] <- ""
selectedDirs <- chooseFromList(dirs, type = "runs to be used for output generation", returnBoolean = FALSE,
multiple = TRUE)
outputdirs <- file.path("output", selectedDirs)
if (exists("remind_dir")) {
for (i in seq_along(selectedDirs)) {
last_iteration <-
max(as.numeric(sub("magpie_", "", grep("magpie_",
list.dirs(file.path(remind_dir, selectedDirs[i], "data", "results")),
value = TRUE))))
outputdirs[i] <- file.path(remind_dir, selectedDirs[i], "data", "results", paste0("magpie_", last_iteration))
}
}
} 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()
}
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))) {
print(paste("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
outputUsingDirect <- c("plotIterations")
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 (all(output %in% outputUsingDirect)) 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(slurmExceptions = slurmExceptions)
if (slurmConfig != "direct") slurmConfig <- paste(slurmConfig, "--nodes=1 --tasks-per-node=1")
}
if (slurmConfig %in% c("priority", "short", "standby")) {
slurmConfig <- paste0("--qos=", slurmConfig, " --nodes=1 --tasks-per-node=1")
}
} 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(is.na(output))) {
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")
for (rout in output) {
name <- paste(rout, ".R", sep = "")
if (file.exists(paste0("scripts/output/single/", name))) {
if (slurmConfig == "direct" | rout %in% outputUsingDirect) {
# execute output script directly (without sending it to slurm)
message("Executing ", name)
tmp.env <- new.env()
tmp.error <- try(sys.source(paste0("scripts/output/single/", name), envir = tmp.env))
# rm(list=ls(tmp.env),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 {
# send the output script to slurm
logfile <- paste0(outputdir, "/log_", rout, ".txt")
slurmcmd <- paste0("sbatch ", slurmConfig, " --job-name=", logfile, " --output=", logfile,
" --mail-type=END --comment=REMIND --wrap=\"Rscript scripts/output/single/", rout,
".R outputdir=", outputdir, "\"")
message("Sending to slurm: ", name, ". Find log in ", logfile)
system(slurmcmd)
Sys.sleep(1)
}
}
}
# finished
message("\nFinished ", ifelse(slurmConfig == "direct", "", "starting jobs for "), "output generation for ", outputdir, "!\n")
}
rm(source_include)
if (!is.null(warnings())) {
print(warnings())
}
}
}