Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils Loading required package: utils > #!/usr/bin/env Rscript > > ############################################################################### > # script pour lancer calibration sur Datarmor avec PBS qsub > # toutes les variables d���environnement sont d��finies dans le script PBS > ############################################################################### > > # normalement 2 packages charg��s: {Rmpi} et {snow} qui mettent �� dispo: > # `makeCluster`, `clusterEvalQ`, `clusterExport`, `stopCluster` > sessionInfo() R version 3.6.3 (2020-02-29) Platform: x86_64-pc-linux-gnu (64-bit) Running under: SUSE Linux Enterprise Server 12 SP1 Matrix products: default BLAS/LAPACK: /appli/intel/parallel_studio/parallel_studio_xe_2017_update2/compilers_and_libraries_2017.2.174/linux/mkl/lib/intel64_lin/libmkl_rt.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] snow_0.4-3 Rmpi_0.6-9 loaded via a namespace (and not attached): [1] compiler_3.6.3 parallel_3.6.3 > > library(doParallel, include.only = c("registerDoParallel")) # pour ��viter d�����craser `makeCluster` > > # la fa��on dont {calibrar} utilise {foreach} perturbe {doParallel} > # il faut toujours charger tous les pkgs n��cessaires ici et dans `clusterEvalQ` dessous > # si vous le faites pas en double, erreur ���function not found��� directe! > #library(calibrar, lib.loc = Sys.getenv("NICO_REPO")) > library(calibrar, lib.loc = "/home1/datawork/nbarrier/libs/R/lib/") > library(dplyr, warn.conflicts = FALSE) > library(data.table, include.only = c("fread")) > library(stringi, include.only = c("stri_extract_last_regex", "stri_join")) > options(dplyr.summarise.inform = FALSE) > > cl <- makeCluster() > registerDoParallel(cl) > > clusterEvalQ(cl, { + # library(calibrar, lib.loc = Sys.getenv("NICO_REPO")) + library(calibrar, lib.loc = "/home1/datawork/nbarrier/libs/R/lib/") + + library(dplyr, warn.conflicts = FALSE) + library(data.table, include.only = c("fread")) + library(stringi, include.only = c("stri_extract_last_regex", "stri_join")) + options(dplyr.summarise.inform = FALSE) + }) %>% # cacher des messages encombrants + suppressMessages() %>% + suppressWarnings() %>% + capture.output() %>% + invisible() > > ############################################################################### > > runModel <- function(par) { # "par" provided by the calibrate function + + # run ISIS ====================================================== + # ATTENTION we are in RUN_*/i* folder + + # if necessary, manually save q of each generation + current_time <- format(Sys.time(), format = "%F %Hh%M", tz = "CET", usetz = TRUE) + current_gen <- 1L + length(list.files(pattern = "^params .+\\.csv$")) + info_suffix <- sprintf(" gen %03d start %s", current_gen, current_time) + + # get back the capturability parameters (par) and write them in the format the model is able to read (csv, semantic) + textLines <- readLines(Sys.getenv("PARAMS_FILE")) + for (i in seq_along(par)) { + id <- 2 + i + tmp <- strsplit(textLines[id], ";")[[1]] + textLines[id] <- paste0(tmp[1], ";", par[i]) + } + write(textLines, file = Sys.getenv("PARAMS_FILE")) + file.copy(from = Sys.getenv("PARAMS_FILE"), to = paste0("params", info_suffix, ".csv")) + + # launch ISIS from R, cf le script PBS + current_ind <- basename(getwd()) # current individual of the population + nomSimul_i <- Sys.getenv("SIMUL_BASENAME") %>% paste(., current_ind, sep = "_") + # debug_file <- paste0("debugISIS", info_suffix, ".log") + system2("myIsis", args = nomSimul_i, stdout = "debugISIS_octopus2017.log", stderr = "debugISIS_octopus2017.log") + + dossier_simul <- file.path(Sys.getenv("ISIS_BD"), "isis-database/simulations", nomSimul_i, "resultExports") + + # read the model outputs and tranform them into a list ========== + + # catch at age + export1 <- file.path(dossier_simul, "CapturesPoids.csv") %>% + fread(data.table = FALSE) %>% + mutate(names = paste0("gp",group,"_Octopus2017")) %>% + select(names, value) + + + # combine (if several inputs)======================================================= + # export <- rbind(export1, export2) + export <- export1 + output <- as.list(export$value) + names(output) <- export$names + return(output) + + + + # path_export <- file.path(ifelse(Mon_disk == "~", "~", "c:/Users/Dedah"), paste0("isis-fish-4/isis-database/simulations/", nomSimu, "/resultExports/")) + export1 <- read.table(paste(dossier_simul, "Captures_AgeStructure_pop.csv", sep = '/'), header = TRUE, sep = ';') + export2 <- read.table(paste(dossier_simul, "Captures_MoisStructure_pop.csv", sep = '/'), header = TRUE, sep = ';') + + + export2 = export2[-c(1:5, 11:12),] + df.output <- data.frame('step'=c(paste("gp", c(0, 1:2) ,"_" ,"2018" , sep =""), paste("Mois", c(6:10) ,"_" ,"2018" , sep ="")) + , 'value'=NA) + + for (i in 1:3) { + df.output[i,2] <- export1[i, 4] + } + + + for (i in 4:8) { + df.output[i,2] <- export2[i-3, 3] + } + + output <- list() + for (i in 1:dim(df.output)[1]) { + output[[i]] <- df.output[i,2] + } + + names(output) <- c(df.output[,1]) + + return(output) ## List of nb year X nb pop group elements : captures per age, per year + + + } > > ############################################################################### > > #' @title residual sum of squares function > #' @description name of this fx must match what is declared in calibrationInfo.csv > #' @param obs,sim numeric values of LENGTH 1 > userFunction <- function(obs, sim) { + # obs peut ��tre NA, c-a-d pas de valeurs observ��es mais valeurs simul��es existent dans les exports + # d�� �� des combinaisons irr��elles entre flottille avec GSA zone pop + res <- + if (is.na(obs)) 0 + else if (obs == 0) sim + else (obs - sim) / obs + return(res ^ 2) + } > > # calibrationInfo > calib_set <- calibration_setup( + file = "data_calib/data_calib_Octopus2017/calibrationInfo.csv", + control = list(col_skip = 1) # pour compatibilit�� avec ancienne version + ) Error in calibration_setup(file = "data_calib/data_calib_Octopus2017/calibrationInfo.csv", : could not find function "calibration_setup" Execution halted