From b69f943c55bd0011288fb40994a2c0f1e0fb3b2a Mon Sep 17 00:00:00 2001
From: David Klein <dklein@pik-potsdam.de>
Date: Thu, 23 Apr 2020 12:44:04 +0200
Subject: [PATCH] Allow providing additional SLURM parameters via
cfg$slurmConfig. Parameters that are later provided interactively via start.R
overwrite the cfg values. Closing #139
---
scripts/start/choose_slurmConfig.R | 41 ++++++++++++++++++++++++++++++
start.R | 4 +--
2 files changed, 43 insertions(+), 2 deletions(-)
diff --git a/scripts/start/choose_slurmConfig.R b/scripts/start/choose_slurmConfig.R
index d3db0cd..8bf3934 100644
--- a/scripts/start/choose_slurmConfig.R
+++ b/scripts/start/choose_slurmConfig.R
@@ -69,3 +69,44 @@ choose_slurmConfig <- function() {
return(comp)
}
+
+# combine_slurmconfig takes two strings with SLURM parameters (e.g. "--qos=priority --time=40000")
+# and combines them into one sting of SLURM parameters overwriting the parameters in "original"
+# if they also exist in "update_with".
+
+combine_slurmConfig <- function (original, update_with) {
+
+ # trim whitespaces
+ original <- trimws(original)
+ update_with <- trimws(update_with)
+
+ # remove double whitespaces
+ original <- gsub("\\s+"," ",original)
+ update_with <- gsub("\\s+"," ",update_with)
+
+ # if user chose "direct" dont update any slurm commands
+ if(update_with == "direct") return(update_with)
+
+ # ignore original if it is "direct"
+ if (original == "direct") original <- ""
+
+ # put RHS strings into vector
+ v_update_with <- gsub("--.*=(.*)","\\1",unlist(strsplit(update_with,split=" ")))
+ # name the vector using LHS strings
+ names(v_update_with) <- gsub("--(.*)=.*","\\1",unlist(strsplit(update_with,split=" ")))
+
+ # put RHS strings into vector
+ v_original <- gsub("--.*=(.*)","\\1",unlist(strsplit(original,split=" ")))
+ # name the vector using LHS strings
+ names(v_original) <- gsub("--(.*)=.*","\\1",unlist(strsplit(original,split=" ")))
+
+ # remove elements from "original" that are existing in "update_with"
+ v_original <- v_original[!names(v_original) %in% "qos"]
+
+ combined <- c(v_update_with,v_original)
+
+ # concatenate SLURM command (insert "--" and "=")
+ res <- paste(paste0("--",names(combined),"=",combined),collapse = " ")
+
+ return(res)
+}
diff --git a/start.R b/start.R
index e295ce8..f8b44aa 100755
--- a/start.R
+++ b/start.R
@@ -196,7 +196,7 @@ if ('--restart' %in% argv) {
for (outputdir in outputdirs) {
cat("Restarting",outputdir,"\n")
load(paste0("output/",outputdir,"/config.Rdata")) # read config.Rdata from results folder
- cfg$slurmConfig <- slurmConfig # update the slurmConfig setting to what the user just chose (it was being ignored before)
+ cfg$slurmConfig <- combine_slurmConfig(cfg$slurmConfig,slurmConfig) # update the slurmConfig setting to what the user just chose (it was being ignored before)
submit(cfg, restart = TRUE)
#cat(paste0("output/",outputdir,"/config.Rdata"),"\n")
}
@@ -238,7 +238,7 @@ if ('--restart' %in% argv) {
source("config/default.cfg")
# Have the log output written in a file (not on the screen)
- cfg$slurmConfig <- slurmConfig
+ cfg$slurmConfig <- combine_slurmConfig(cfg$slurmConfig,slurmConfig)
cfg$logoption <- 2
start_now <- TRUE
--
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