From c8fb7fbdbba269252c028696ccf9d66dc8f41917 Mon Sep 17 00:00:00 2001
From: David Klein <dklein@pik-potsdam.de>
Date: Wed, 29 Jan 2020 10:50:00 +0100
Subject: [PATCH] Subsequent runs: do not save the timestamp to
cfg$results_folder in RData files that are stored on REMIND's main folder.
These files might be used to restart subsequent runs by hand. In this case
the timestamp would cause the script to stop because the results folder
already exists.
---
scripts/start/prepare_and_run.R | 2 +-
scripts/start/submit.R | 21 ++++++++++-----------
2 files changed, 11 insertions(+), 12 deletions(-)
diff --git a/scripts/start/prepare_and_run.R b/scripts/start/prepare_and_run.R
index 6f729e1..320e62e 100644
--- a/scripts/start/prepare_and_run.R
+++ b/scripts/start/prepare_and_run.R
@@ -776,7 +776,7 @@ prepare_and_run <- function() {
for(run in seq(1,length(cfg$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")
}
diff --git a/scripts/start/submit.R b/scripts/start/submit.R
index e8be0fb..8d358b9 100644
--- a/scripts/start/submit.R
+++ b/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")
--
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