inst/estimation/kcde/submit-cluster-job-kcde-estimation-step.R

In reichlab/2017-2018-cdc-flu-contest: code for cdc flu contest 2017-2018

options(warn = 2, error = recover)

all_data_sets <- c("X", paste0("Region-", 1:10))
all_prediction_horizons <- as.character(seq_len(52))
all_max_lags <- as.character(c(6L))
all_seasonality_values <- c("FALSE")
all_first_test_seasons <- paste0(2010:2016, "/", 2011:2017)

cores_req <- "1"
mem_req <- "10000"
time_req <- "48:00"
queue_req <- "long"

for(data_set in all_data_sets) {
  for(prediction_horizon in all_prediction_horizons) {
    for(max_lag in all_max_lags) {
      for(seasonality in all_seasonality_values) {
        for(first_test_season in all_first_test_seasons) {
          for(season_left_out in all_seasons_left_out) {
            save_path <- "/home/er71a/adaptively-weighted-ensemble/inst/estimation/kcde/fits"
            output_path <- "/home/er71a/adaptively-weighted-ensemble/inst/estimation/kcde/cluster-estimation-output"
            lsfoutfilename <- "adaptively-weighted-ensemble-kcde-est-scott-rule-start.out"

            system_cmd <- paste0("R --vanilla --args ",
              " < inst/estimation/kcde/kcde-estimation-step.R")

            case_descriptor <- paste0(
              data_set,
              "-prediction_horizon_", prediction_horizon,
              "-max_lag_", max_lag,
              "-seasonality_", seasonality,
              "-season_left_out_", gsub("/", "-", season_left_out),
              "-first_test_season_", gsub("/", "-", first_test_season)
            )
            filename <- paste0(output_path, "/submit-kcde-estimation-step-", case_descriptor, ".sh")

            requestCmds <- "#!/bin/bash\n"
            requestCmds <- paste0(requestCmds, "#BSUB -n ", cores_req, " # how many cores we want for our job\n",
              "#BSUB -R span[hosts=1] # ask for all the cores on a single machine\n",
              "#BSUB -R rusage[mem=", mem_req, "] # ask for memory\n",
              "#BSUB -o ", lsfoutfilename, " # log LSF output to a file\n",
              "#BSUB -W ", time_req, " # run time\n",
              "#BSUB -q ", queue_req, " # which queue we want to run in\n")

            cat(requestCmds, file = filename)
            cat("module load R/3.2.2\n", file = filename, append = TRUE)
            cat(paste0("R CMD BATCH --vanilla \'--args ",
                       data_set, " ",
                       prediction_horizon, " ",
                       max_lag, " ",
                       seasonality, " ",
                       season_left_out, " ",
                       first_test_season, " ",
                       save_path,
                       "\'  /home/er71a/adaptively-weighted-ensemble/inst/estimation/kcde/kcde-estimation-step.R ",
                       output_path, "/output-kde-estimation-step-", case_descriptor, ".Rout"),
                file = filename, append = TRUE)

            bsubCmd <- paste0("bsub < ", filename)

            system(bsubCmd)
          } # season_left_out
        } # first_test_season
      } # seasonality
    } # max_lag
  } # prediction_horizon
} # data_set