Commit 2c3534bb authored by Jan Philipp Dietrich's avatar Jan Philipp Dietrich
Browse files

bugfix and test submit script

parent 67bcc0a7
......@@ -12,7 +12,7 @@ runsubmit <- function(runscripts, submit) {
}
cat("Executing",name,"\n")
sbatch_command <- paste0("sbatch --job-name=",rout," --output=",rout,"-%j.out --mail-type=END --wrap=\"Rscript ",name,"\"")
sbatch_command <- paste0("sbatch --job-name=",basename(rout)," --output=",basename(rout),"-%j.out --mail-type=END --wrap=\"Rscript ",name,"\"")
if(submit=="direct") {
tmp.env <- new.env()
tmp.error <- try(sys.source(name,envir=tmp.env))
......
......@@ -12,5 +12,5 @@ config <- "default.cfg"
#defaults are overwritten if specified as argument
readArgs("config")
#start MAgPIE run
#start MAgPIE preprocessing
start_preprocessing(cfg=config)
#################################################
#### Script to start a MAgPIE preprocessing ####
#################################################
library(lucode2)
source("preprocessing.R")
#set defaults
config <- "default.cfg"
#defaults are overwritten if specified as argument
readArgs("config")
#start preprocessing
start_preprocessing(cfg=config, submit="slurmstandard")
# start another preprocessing in parallel
start_preprocessing(cfg=config, submit="slurmstandard")
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment