Error in "start_function.R"

[garpe]

Hi, I installed MAGPIE in Windows 11 via clone from github just today and I launched the default script for testing

The default run fails in the "start_function.R" script.
In this script, at a certain point the statement is executed
"setwd(cfg$results_folder)"
to set the directory where to save the "runstatistics.rda" file
Subsequently, the statement:
"system("Rscript submit.R", wait=cfg$sequential)"
is executed.
This fails because the file "submit.R" is not present in the current directory (the one set by setwd())
I solved it by removing the directory change and modififing the whole path of the "runstatistics.rda" file, in this way at least the script
ends without errors.
It seems to be an easily detectable problem but I don't think it has been reported before

Thanks in advance

[pascal-sauer]

Hi @garpe ,
submit.R should be present in the run folder, along with many other files it should be copied there as configured in default.cfg. On my local machine (Ubuntu) this works as intended. I'll try to reproduce this on a Windows computer.

[garpe]

Thanks for the answer. I try to explain better.

The installation is standard, so all the scripts are where they have to be.

As I wrote, the script "start_function.R" at a certain point change the working directory as

"setwd(cfg$results_folder)"

in the output directory (cfg$result_folder)

The error occurs in the else branch in the following code:

if(slurm && !cfg$sequential) {
  if(is.null(cfg$qos)) {
    # try to select best QOS based on available resources
    # and available information
    load <- lucode2::getClusterLoad()
    if(is.null(load)) {
      cfg$qos <- "standby"
    } else if(all(load > 80)) {
      cfg$qos <- "priority"
    } else if(all(c("priority", "standard") %in% names(load)) && load["priority"] < load["standard"]) {
      cfg$qos <- "standby"
    } else {
      cfg$qos <- "short"
    }
  }
  submitfile <- paste0("submit_",cfg$qos,".sh")
  if(!file.exists(submitfile)) stop("Submit script ",submitfile," not found!")
  system(paste("sbatch",submitfile))
  cat("Run submitted with ",submitfile,"!\n",sep="")
} else {
  system("Rscript submit.R", wait=cfg$sequential)
}

I think that the "else" is executed only in Windows.
In this case, the "system("Rscript submit.R", wait=cfg$sequential)" instruction, search the "submit.R" script file in the current working directory but, having changed before, this is no more the one where scripts are installed.

I fixed it just removing the directory change and adding the output directory explicitly where needed but there are several others way to do it

thank you very much

[pascal-sauer]

cfg$results_folder should be something like output/default_2024-08-07_16.30.11 which is what we refer to as a run folder. The submit.R script is located at scripts/run_submit/submit.R, but it is also copied to each run folder, so there should be a copy of it in the folder that setwd changes to. The copying happens here, the files which are copied are defined here. The question is, why is that copying not happening in your case, any ideas?

[pascal-sauer]

the "else" is executed only in Windows

No, it will run on any system which does not have slurm available, so it also runs on my local Ubuntu machine.

[garpe]

Thank you very much. So far I have tried to run the script from RStudio and, in this case, the statement
"system("Rscript submit.R", wait=cfg$sequential)" always fails.

I re-installed everything from scratch and ran the default script from a CMD shell. Now that error no longer appears and I was able to realize that there is a problem in my GAMS installation.

Many thanks for the information

[pascal-sauer]

Glad to hear that you got one step further :) How exactly are you running "the default script"? The intended way is to make sure you are in the main folder (the repository root) and then run Rscript start.R. From within RStudio you'd need to source the start.R script I guess, but that (running MAgPIE via RStudio) is not a workflow we typically use.

[garpe]

Yes, I opened a CMD shell (on Windows) in the main folder (the repository root) and run Rscript start.R. In this way works
Thanks