Mercurial > repos > siwaa > redelac_stics_s

annotate parallelSticsRRotation.R @ 1:be10e3fb6e64 draft

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"planemo upload for repository https://forgemia.inra.fr/redelac"
author siwaa
date Mon, 12 Jun 2023 16:22:04 +0000
parents ca96540c23cd
children
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0
ca96540c23cd "planemo upload for repository https://forgemia.inra.fr/redelac"
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1 library(SticsRFiles)
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2 library(SticsOnR)
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3 library(parallel)
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4 library(doParallel)
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5 library(readxl)
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6
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7 workspace <- paste0(getwd(), "/WS")
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8 javastics_path <- getwd()
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9 default_config_path <- paste0(javastics_path, "/config")
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10
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11 # copy of the var.mod and rap.mod into the config folder
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12 # generalizing maybe should be inside a config folder
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13
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14 #file.copy(from = file.path(workspace, "var.mod"),
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15 # to = file.path(default_config_path, "var.mod"),
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16 # overwrite = TRUE)
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17 #file.copy(from = file.path(workspace, "rap.mod"),
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18 # to = file.path(default_config_path, "rap.mod"),
ca96540c23cd "planemo upload for repository https://forgemia.inra.fr/redelac"
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19 # overwrite = TRUE)
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20
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21 txt_path <- paste0(getwd(), "/WS/txt_files")
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22 #dir.create(txt_path,recursive = T)
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23
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24 #gen_usms_xml2txt(javastics = javastics_path,
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25 # workspace = workspace,
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26 # out_dir = txt_path,
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27 # check = FALSE)
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28
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29 print("==================================")
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30
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31 print(paste0("Cores=", detectCores()))
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32 print(paste0("javastics=", javastics_path))
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33 print(paste0("ws=", workspace))
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34 print(paste0("out_dir=", txt_path))
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35
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36 print("==================================")
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37
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38
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39 # List of successive USMs
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40 successive_usms_file <- ("successionPlan.csv")
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41 successive_usms_tab <- read.csv(file = file.path(workspace, successive_usms_file), sep =";")
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42
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43 no_cores <- detectCores() - 1
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44 no_cores <- 10
0
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45 cl <- makeCluster(no_cores)
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46 registerDoParallel(cl)
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47
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48 result <- foreach(i=1:nrow(successive_usms_tab),
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49 .packages = c("SticsRFiles", "SticsOnR") ) %dopar% {
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50
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51
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52 print(paste("coucou ", i))
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53 nusms <- as.numeric(successive_usms_tab[i,2])
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54 print(paste0("coco ", nusms))
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55
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56 vec <- as.character(successive_usms_tab[i,c(3:(2+nusms))])
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57
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58 list_successive_usms <- list(vec)
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59
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60 sim_options <- stics_wrapper_options(javastics = javastics_path,
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61 stics_exe = paste0(javastics_path,"/bin/stics_modulo"),
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62 workspace = txt_path,
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63 verbose = TRUE,
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64 successive = list_successive_usms)
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65 list_usms <- vec
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66
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67 stics_wrapper(model_options = sim_options, situation = list_usms)
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68 }
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69
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70 stopCluster(cl)
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71
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72 for (i in 1:nrow(successive_usms_tab)) { #i=1
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73 if (i == 1) {
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74 simPCP <- result[[i]]
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75 } else {
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76 simPCP$sim_list <- c(simPCP$sim_list, result[[i]]$sim_list)
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77 }
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78
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79 }
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80
1
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81 save(simPCP, file = "results.RData")