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David Klein
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############## Define function: .copy.fromlist #########################
.copy.fromlist <- function(filelist,destfolder) {
if(is.null(names(filelist))) names(filelist) <- rep("",length(filelist))
for(i in 1:length(filelist)) {
if(!is.na(filelist[i])) {
to <- paste0(destfolder,"/",names(filelist)[i])
if(!file.copy(filelist[i],to=to,recursive=dir.exists(to),overwrite=T))
cat(paste0("Could not copy ",filelist[i]," to ",to,"\n"))
}
}
}
############## Define function: runsubmit #########################
submit_run <- function(cfg) {
# Create name of output folder and output folder itself
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$results_folder, fixed = TRUE)
# Create output folder
if (!file.exists(cfg$results_folder)) {
dir.create(cfg$results_folder, recursive = TRUE, showWarnings = FALSE)
} else if (!cfg$force_replace) {
stop(paste0("Results folder ",cfg$results_folder," could not be created because it already exists."))
} else {
cat("Deleting results folder because it alreay exists:",cfg$results_folder,"\n")
unlink(cfg$results_folder, recursive = TRUE)
dir.create(cfg$results_folder, recursive = TRUE, showWarnings = FALSE)
}
# save main folder
cfg$remind_folder <- getwd()
# save the cfg data before moving it into the results folder
cat("Writing cfg to file\n")
save(cfg,file=paste0(cfg$title,".RData"))
# Copy files required to confiugre and start a run
filelist <- c(paste0(cfg$title,".Rdata") = "config.Rdata",
"scripts/run_submit/prepare_and_run.R" = "prepare_and_run.R")
.copy.fromlist(filelist,cfg$results_folder)
# remove config in main folder (after copying into results folder)
if(!file.remove(paste0(cfg$title,".Rdata"))
# change to run folder
setwd(cfg$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")
sbatch_command <- paste0("sbatch --job-name=",cfg$title," --output=",cfg$title,"-%j.out --mail-type=END --comment=REMIND --wrap=\"Rscript prepare_and_run.R ",cfg$title,"\"")
if(cfg$slurmConfig=="direct") {
log <- format(Sys.time(), paste0(cfg$title,"-%Y-%H-%M-%S-%OS3.log"))
system("Rscript prepare_and_run.R ",cfg$title, stderr = log, stdout = log, wait=FALSE)
} else if(cfg$slurmConfig=="priority") {
system(paste(sbatch_command,"--qos=priority"))
Sys.sleep(1)
} else if(cfg$slurmConfig=="standby") {
#tmp <- paste(sbatch_command,"--qos=standby")
#print(tmp)
system(paste(sbatch_command,"--qos=standby"))
Sys.sleep(1)
} else if(cfg$slurmConfig=="short") {
system(paste(sbatch_command,"--qos=short"))
Sys.sleep(1)
} else if(cfg$slurmConfig=="medium") {
system(paste(sbatch_command,"--qos=medium"))
Sys.sleep(1)
} else if(cfg$slurmConfig=="long") {
system(paste(sbatch_command,"--qos=long"))
Sys.sleep(1)
} else {
stop("Unknown submission type")
}
# Gedchtnissttze fr die slurm-Varianten
## Replace load leveler-script with appropriate version
#if (cfg$gms$optimization == "nash" && cfg$gms$cm_nash_mode == "parallel") {
# if(length(unique(map$RegionCode)) <= 12) {
# cfg$files2export$start[cfg$files2export$start == "scripts/run_submit/submit.cmd"] <-
# "scripts/run_submit/submit_par.cmd"
# } else { # use max amount of cores if regions number is greater than 12
# cfg$files2export$start[cfg$files2export$start == "scripts/run_submit/submit.cmd"] <-
# "scripts/run_submit/submit_par16.cmd"
# }
#} else if (cfg$gms$optimization == "testOneRegi") {
# cfg$files2export$start[cfg$files2export$start == "scripts/run_submit/submit.cmd"] <-
# "scripts/run_submit/submit_short.cmd"
#}
# Call appropriate submit script
#if (cfg$sendToSlurm) {
# # send to slurm
# if(cfg$gms$optimization == "nash" && cfg$gms$cm_nash_mode == "parallel") {
# if(length(unique(map$RegionCode)) <= 12) {
# system(paste0("sed -i 's/__JOB_NAME__/pREMIND_", cfg$title,"/g' submit_par.cmd"))
# system("sbatch submit_par.cmd")
# } else { # use max amount of cores if regions number is greater than 12
# system(paste0("sed -i 's/__JOB_NAME__/pREMIND_", cfg$title,"/g' submit_par16.cmd"))
# system("sbatch submit_par16.cmd")
# }
# } else if (cfg$gms$optimization == "testOneRegi") {
# system(paste0("sed -i 's/__JOB_NAME__/REMIND_", cfg$title,"/g' submit_short.cmd"))
# system("sbatch submit_short.cmd")
# } else {
# system(paste0("sed -i 's/__JOB_NAME__/REMIND_", cfg$title,"/g' submit.cmd"))
# if (cfg$gms$cm_startyear > 2030) {
# system("sbatch --partition=ram_gpu submit.cmd")
# } else {
# system("sbatch submit.cmd")
# }
return(cfg$results_folder)
}