Subsequent runs: do not save the timestamp to cfg$results_folder in RData...

Subsequent runs: do not save the timestamp to cfg$results_folder in RData files that are stored on REMIND's main folder. These files might be used to restart subsequent runs by hand. In this case the timestamp would cause the script to stop because the results folder already exists.

scripts/start/prepare_and_run.R

@@ -776,7 +776,7 @@ prepare_and_run <- function() {
     for(run in seq(1,length(cfg$subsequentruns))){
       filetext <- paste0(filetext,"\n")
       filetext <- paste0(filetext,"load('",cfg$subsequentruns[run],".RData')\n")
-      filetext <- paste0(filetext,"cfg$results_folder <- 'output/:title::date:'\n")
+      #filetext <- paste0(filetext,"cfg$results_folder <- 'output/:title::date:'\n")
       filetext <- paste0(filetext,"cat('",cfg$subsequentruns[run],"')\n")
       filetext <- paste0(filetext,"submit(cfg)\n")
     }

scripts/start/submit.R

@@ -15,7 +15,7 @@
 
 submit <- function(cfg) {
   
-  # Create name of output folder and output folder itself
+  # Generate name of output folder and create the folder
   date <- format(Sys.time(), "_%Y-%m-%d_%H.%M.%S")
   cfg$results_folder <- gsub(":date:", date, cfg$results_folder, fixed = TRUE)
   cfg$results_folder <- gsub(":title:", cfg$title, cfg$results_folder, fixed = TRUE)
@@ -30,26 +30,25 @@ submit <- function(cfg) {
     dir.create(cfg$results_folder, recursive = TRUE, showWarnings = FALSE)
   }
   
-  # save main folder
-  cfg$remind_folder <- getwd()
- 
-  # save the cfg data before moving it into the results folder
+  # Save the cfg (with the updated name of the result folder) into the results folder. 
+  # Do not save the new name of the results folder to the .RData file in REMINDs main folder, because it 
+  # might be needed to restart subsequent runs manually and should not contain the time stamp in this case.
   cat("Writing cfg to file\n")
-  save(cfg,file=paste0(cfg$title,".RData"))
+  save(cfg,file=paste0(cfg$results_folder,"/config.RData"))
   
   # Copy files required to confiugre and start a run
-  filelist <- c("config.Rdata" = paste0(cfg$title,".RData"),
-                "prepare_and_run.R" = "scripts/start/prepare_and_run.R")
+  filelist <- c("prepare_and_run.R" = "scripts/start/prepare_and_run.R")
   .copy.fromlist(filelist,cfg$results_folder)
   
-  # Do not remove .RData files from REMIND main folder because they are needed in case you need to manually restart subsequent runs
+  # Do not remove .RData files from REMIND main folder because they are needed in case you need to manually restart subsequent runs.
 
-  # change to run folder
+  # remember main folder and change to run folder
+  cfg$remind_folder <- getwd()
   setwd(cfg$results_folder)
   on.exit(setwd(cfg$remind_folder))
 
   # send prepare_and_run.R to cluster 
-  cat("Executing prepare_and_run.R for",cfg$title,"\n")
+  cat("Executing prepare_and_run.R with",cfg$title,"\n")
   if(cfg$slurmConfig=="direct") {
     log <- format(Sys.time(), paste0(cfg$title,"-%Y-%H-%M-%S-%OS3.log"))
     system("Rscript prepare_and_run.R")