Mercurial > repos > siwaa > redelac_stics_sim

annotate REDELACparallelSticsRsequence.R @ 0:21e91d3b7068 draft

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"planemo upload for repository https://forgemia.inra.fr/redelac"
author siwaa
date Thu, 01 Jun 2023 09:13:11 +0000
parents
children 50dd120308af
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0
21e91d3b7068 "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"),
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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))
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42
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43 no_cores <- detectCores() - 1
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44 cl <- makeCluster(no_cores)
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45 registerDoParallel(cl)
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46
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47 result <- foreach(i=1:nrow(successive_usms_tab),
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48 .packages = c("SticsRFiles", "SticsOnR") ) %dopar% {
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49
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50 nusms <- as.numeric(successive_usms_tab[i,2])
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51
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52 vec <- as.character(successive_usms_tab[i,c(3:(2+nusms))])
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53
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54 list_successive_usms <- list(vec)
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55
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56 sim_options <- stics_wrapper_options(javastics = javastics_path,
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57 stics_exe = paste0(javastics_path,"/bin/stics_modulo"),
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58 workspace = txt_path,
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59 verbose = TRUE,
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60 successive = list_successive_usms)
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61 list_usms <- vec
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62
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63 stics_wrapper(model_options = sim_options, situation = list_usms)
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64 }
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65
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66 stopCluster(cl)
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67
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68 for (i in 1:nrow(successive_usms_tab)) { #i=1
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69 if (i == 1) {
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70 simPCP <- result[[i]]
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71 } else {
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72 simPCP$sim_list <- c(simPCP$sim_list, result[[i]]$sim_list)
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73 }
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74
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75 }
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76
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77 save(simPCP, file = "results.RData")