Mercurial > repos > siwaa > redelac_stics_s

comparison redelacSticsSimulator.R @ 6:41f652e6616f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/f8a7aebffe0c850bef03045efa3772aca6cd51c2/tools/REDELACSticsSimulator commit f8a7aebffe0c850bef03045efa3772aca6cd51c2-dirty"
author siwaa
date Tue, 26 Sep 2023 15:21:42 +0000
parents 70ae7516e925
children 2586f7dbcde1
comparison
equal deleted inserted replaced
5:fa8e742b197b 6:41f652e6616f
1 library(SticsRFiles) 1 library(SticsRFiles)
2 library(SticsOnR) 2 library(SticsOnR)
3 library(parallel) 3 library(parallel)
4 library(doParallel) 4 library(doParallel)
5 library(readxl) 5 library(readxl)
6
7 sessionInfo()
6 8
7 workspace <- paste0(getwd(), "/WS") 9 workspace <- paste0(getwd(), "/WS")
8 javastics_path <- getwd() 10 javastics_path <- getwd()
9 default_config_path <- paste0(javastics_path, "/config") 11 default_config_path <- paste0(javastics_path, "/config")
10 12
11 txt_path <- paste0(getwd(), "/WS/txt_files") 13 txt_path <- paste0(getwd(), "/WS/txt_files")
12 14
13 print("==================================")
14
15 print(paste0("Cores=", detectCores()))
16 print(paste0("javastics=", javastics_path))
17 print(paste0("ws=", workspace))
18 print(paste0("out_dir=", txt_path))
19
20 print("==================================")
21
22 # List of successive USMs 15 # List of successive USMs
23 successive_usms_file <- ("successionPlan.csv") 16 successive_usms_file <- ("successionPlan.csv")
24 successive_usms_tab <- read.csv(file = file.path(workspace, successive_usms_file), sep =";") 17 successive_usms_tab <- read.csv(file = file.path(workspace, successive_usms_file), sep =";")
25 18
26 #no_cores <- detectCores() - 1 19 args = commandArgs(trailingOnly = TRUE)
27 #no_cores <- 10
28 #cl <- makeCluster(no_cores)
29 #registerDoParallel(cl)
30 20
31 result <- list() 21 parallel <- (args[1] == "parallel")
22 nbSlots <- as.integer(args[2])
32 23
33 #result <- foreach(i=1:nrow(successive_usms_tab), 24 if (parallel) {
34 # .packages = c("SticsRFiles", "SticsOnR") ) %dopar% { 25 cl <- makeCluster(nbSlots)
35 for(i in 1:nrow(successive_usms_tab)) { 26 print(cl)
27 registerDoParallel(cl)
28 `%dordopar%` <- `%dopar%`
29 } else {
30 `%dordopar%` <- `%do%`
31 }
32
33 result <- foreach(i=1:nrow(successive_usms_tab),
34 .packages = c("foreach", "SticsRFiles", "SticsOnR") ) %dordopar% {
36 35
37 nusms <- as.numeric(successive_usms_tab[i,2]) 36 nusms <- as.numeric(successive_usms_tab[i,2])
38 37
39 vec <- as.character(successive_usms_tab[i,c(3:(2+nusms))]) 38 vec <- as.character(successive_usms_tab[i,c(3:(2+nusms))])
40 39
45 workspace = txt_path, 44 workspace = txt_path,
46 verbose = TRUE, 45 verbose = TRUE,
47 successive = list_successive_usms) 46 successive = list_successive_usms)
48 list_usms <- vec 47 list_usms <- vec
49 48
50 singleResult = stics_wrapper(model_options = sim_options, situation = list_usms) 49 return(stics_wrapper(model_options = sim_options, situation = list_usms))
51 50
52 result = append(result, list(singleResult)) 51 }
53 }
54 52
55 #stopCluster(cl) 53 if (parallel) stopCluster(cl)
56 54
57 for (i in 1:nrow(successive_usms_tab)) { #i=1 55 for (i in 1:nrow(successive_usms_tab)) { #i=1
58 if (i == 1) { 56 if (i == 1) {
59 simPCP <- result[[i]] 57 simPCP <- result[[i]]
60 } else { 58 } else {