add testOneRegi option to refactored start scripts

- testOneRegi runs are useful for fast development iterations ("do these
  changes break the model, or does it still run"), so setting them up
  should be fast as well

- supplying the parameter "--testOneRegi" to start.R will ignore any
  scenario_config file provided and modify the default configuration to
  start a testOneRegi run in the directory output/testOneRegi with no
  output processing
- the old oneRegi.R script and oneRegi.cfg configuration are deleted

- existing output/testOneRegi directories are overwritten

oneRegi.R

-# |  (C) 2006-2019 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
-#! /usr/bin/Rscript
-
-##########################################################
-#### Script to start a REMIND run ####
-##########################################################
-
-library(lucode, quietly = TRUE, warn.conflicts = FALSE)
-library(magclass, quietly = TRUE, warn.conflicts = FALSE)
-
-#Here the function start_run(cfg) is loaded which is needed to start REMIND runs
-#The function needs information about the configuration of the run. This can be either supplied as a list of settings or as a file name of a config file
-source("scripts/start_functions.R")
-
-if (file.exists("./output/testOneRegi/"))
-    unlink("./output/testOneRegi/", recursive = TRUE)
-
-#Load config-file
-cfg_REMIND <- "oneRegi.cfg"
-readArgs("cfg")
-
-# start REMIND run
-start_run(cfg_REMIND)
-#rep = read.report("coupling.mif")
-#start_reportrun(rep)

start.R

@@ -6,7 +6,7 @@ source("scripts/start/choose_slurmConfig.R")
 ############## Define function: configure_cfg #########################
 
 configure_cfg <- function(icfg, iscen, iscenarios, isettings) {
-    
+
     .setgdxcopy <- function(needle, stack, new) {
       # delete entries in stack that contain needle and append new
       out <- c(stack[-grep(needle, stack)], new)
@@ -16,20 +16,20 @@ configure_cfg <- function(icfg, iscen, iscenarios, isettings) {
     # Edit run title
     icfg$title <- iscen
     cat("\n", iscen, "\n")
-  
+
     # Edit main file of model
     if( "model" %in% names(iscenarios)){
-      icfg$model <- iscenarios[iscen,"model"] 
+      icfg$model <- iscenarios[iscen,"model"]
     }
 
     # Edit regional aggregation
     if( "regionmapping" %in% names(iscenarios)){
-      icfg$regionmapping <- iscenarios[iscen,"regionmapping"] 
+      icfg$regionmapping <- iscenarios[iscen,"regionmapping"]
     }
-    
+
     # Edit input data revision
     if( "revision" %in% names(iscenarios)){
-      icfg$revision <- iscenarios[iscen,"revision"] 
+      icfg$revision <- iscenarios[iscen,"revision"]
     }
 
     # Edit switches in default.cfg according to the values given in the scenarios table
@@ -41,13 +41,13 @@ configure_cfg <- function(icfg, iscen, iscenarios, isettings) {
     if( "output" %in% names(iscenarios)){
       icfg$output <- paste0("c(\"",gsub(",","\",\"",gsub(", ",",",iscenarios[iscen,"output"])),"\")")
     }
-    
+
     # check if full input.gdx path is provided and, if not, search for correct path
     if (!substr(isettings[iscen,"path_gdx"], nchar(isettings[iscen,"path_gdx"])-3, nchar(isettings[iscen,"path_gdx"])) == ".gdx"){
       #if there is no correct scenario folder within the output folder path provided, take the config/input.gdx
       if(length(grep(iscen,list.files(path=isettings[iscen,"path_gdx"]),value=T))==0){
         isettings[iscen,"path_gdx"] <- "config/input.gdx"
-      #if there is only one instance of an output folder with that name, take the fulldata.gdx from this 
+      #if there is only one instance of an output folder with that name, take the fulldata.gdx from this
       } else if (length(grep(iscen,list.files(path=isettings[iscen,"path_gdx"]),value=T))==1){
         isettings[iscen,"path_gdx"] <- paste0(isettings[iscen,"path_gdx"],"/",
                                             grep(iscen,list.files(path=isettings[iscen,"path_gdx"]),value=T),"/fulldata.gdx")
@@ -55,13 +55,13 @@ configure_cfg <- function(icfg, iscen, iscenarios, isettings) {
         #if there are multiple instances, take the newest one
         isettings[iscen,"path_gdx"] <- paste0(isettings[iscen,"path_gdx"],"/",
                                             substr(grep(iscen,list.files(path=isettings[iscen,"path_gdx"]),value=T),1,
-                                                   nchar(grep(iscen,list.files(path=isettings[iscen,"path_gdx"]),value=T))-19)[1],      
+                                                   nchar(grep(iscen,list.files(path=isettings[iscen,"path_gdx"]),value=T))-19)[1],
         max(substr(grep(iscen,list.files(path=isettings[iscen,"path_gdx"]),value=T),
                                  nchar(grep(iscen,list.files(path=isettings[iscen,"path_gdx"]),value=T))-18,
                                  nchar(grep(iscen,list.files(path=isettings[iscen,"path_gdx"]),value=T)))),"/fulldata.gdx")
       }
     }
-    
+
     # if the above has not created a path to a valid gdx, take config/input.gdx
     if (!file.exists(isettings[iscen,"path_gdx"])){
       isettings[iscen,"path_gdx"] <- "config/input.gdx"
@@ -70,7 +70,7 @@ configure_cfg <- function(icfg, iscen, iscenarios, isettings) {
       stop("Cant find a gdx under path_gdx, please specify full path to gdx or else location of output folder that contains previous run")
       }
     }
-   
+
     # Define path where the GDXs will be taken from
     gdxlist <- c(input.gdx     = isettings[iscen, "path_gdx"],
                  input_ref.gdx = isettings[iscen, "path_gdx_ref"],
@@ -82,7 +82,7 @@ configure_cfg <- function(icfg, iscen, iscenarios, isettings) {
     # add gdx information for subsequent runs
     icfg$subsequentruns        <- rownames(isettings[isettings$path_gdx_ref == iscen & !is.na(isettings$path_gdx_ref) & isettings$start == 1,])
     icfg$RunsUsingTHISgdxAsBAU <- rownames(isettings[isettings$path_gdx_bau == iscen & !is.na(isettings$path_gdx_bau) & isettings$start == 1,])
-    
+
     return(icfg)
 }
 
@@ -91,13 +91,21 @@ slurmConfig <- choose_slurmConfig()
 
 ###################### Load csv if provided  ##########################
 
-# If scenario_config.csv was provided from command line, set cfg according to it (copy from start_bundle)
-# check for config file parameter
-config.file <- commandArgs(trailingOnly = TRUE)[1]
-if (!is.na(config.file)) {
+# If testOneRegi was selected, set up a testOneRegi run.  IF a
+# scenario_config.csv file was provided, set cfg according to it (copy from
+# start_bundle).
 
+# check command-line arguments for testOneRegi and scenario_config file
+argv <- commandArgs(trailingOnly = TRUE)
+config.file <- argv[1]
+if ('--testOneRegi' %in% argv) {
+  testOneRegi <- TRUE
+  config.file <- NA
+}
+
+if (!is.na(config.file)) {
   cat(paste("reading config file", config.file, "\n"))
-    
+
   # Read-in the switches table, use first column as row names
   settings <- read.csv2(config.file, stringsAsFactors = FALSE, row.names = 1, comment.char = "#", na.strings = "")
 
@@ -115,26 +123,37 @@ if (!is.na(config.file)) {
 for (scen in rownames(scenarios)) {
   #source cfg file for each scenario to avoid duplication of gdx entries in files2export
   source("config/default.cfg")
-  
+
   # Have the log output written in a file (not on the screen)
   cfg$slurmConfig <- slurmConfig
   cfg$logoption   <- 2
   start_now       <- TRUE
-  
+
+  # testOneRegi settings
+  if (testOneRegi) {
+    cfg$title            <- 'testOneRegi'
+    cfg$gms$optimization <- 'testOneRegi'
+    cfg$output           <- NA
+    cfg$results_folder   <- 'output/testOneRegi'
+
+    # delete existing Results directory
+    unlink('output/testOneRegi', recursive = TRUE)
+  }
+
   # configure cfg based on settings from csv if provided
   if (!is.na(config.file)) {
-  
+
   cfg <- configure_cfg(cfg, scen, scenarios, settings)
-  
+
   # Directly start runs that have a gdx file location given as path_gdx_ref or where this field is empty
-  start_now <- (substr(scenarios[scen,"path_gdx_ref"], nchar(scenarios[scen,"path_gdx_ref"])-3, nchar(scenarios[scen,"path_gdx_ref"])) == ".gdx" 
+  start_now <- (substr(scenarios[scen,"path_gdx_ref"], nchar(scenarios[scen,"path_gdx_ref"])-3, nchar(scenarios[scen,"path_gdx_ref"])) == ".gdx"
                | is.na(scenarios[scen,"path_gdx_ref"]))
   }
-  
+
   # save the cfg data for later start of subsequent runs (after preceding run finished)
   cat("Writing cfg to file\n")
   save(cfg,file=paste0(scen,".RData"))
-  
+
   if (start_now){
    cat("Creating and starting: ",cfg$title,"\n")
    submit(cfg)