Add starter and collector scripts. Adjust sbatch script

Grendel/ALMaSS_q28_goose_scenario_02

@@ -4,7 +4,7 @@
 #SBATCH --ntasks=1
 #SBATCH --mem=240G
 #SBATCH --ntasks-per-node=1
-#SBATCH --cpus-per-task=4
+#SBATCH --cpus-per-task=8
 #SBATCH --time=06:00:00
 #SBATCH --exclusive
 #SBATCH --mem-per-cpu=60G
@@ -12,6 +12,6 @@
 #SBATCH --mail-user=lars@bios.au.dk
 
 echo "========= Job started at `date` =========="
-sh /home/ldalby/ALMaSS/almass/Grendel/start-scenario_01.sh
+sh /home/ldalby/ALMaSS/almass/Grendel/start-scenario_02.sh
 echo "========= Job finished at `date` =========="
 #
\ No newline at end of file

Grendel/collect-results-scenario_02.R

+# Collect results from parameter fitting
+# Author: Lars Dalby
+# Date: 12 Aug 2018
+# Short script to combine the results form mulitple runs into one file and 
+# write that to a safe place on Grendel.
+
+# Set the local R package library (if not done already)
+if (!"/home/ldalby/R/packages" %in% .libPaths()) {
+  .libPaths("/home/ldalby/R/packages")
+}
+suppressMessages(library(furrr))
+library(fs)
+library(magrittr)
+# Get the slurm job-id (is being passed in from the shell script calling this R script)
+args <- commandArgs(trailingOnly = TRUE)
+
+# The parent directory of all the work directories
+path_to_dirs <- path("/scratch", args)
+file_name <- "scenario-results.txt"
+npar = 4  # Specifies the number of run directories that was being used
+
+plan(multiprocess)  # to run in parallel future_map in parallel.
+
+suffix <- stringr::str_pad(as.character(1:npar), width = 2, pad = "0")
+path(path_to_dirs, glue::glue("WD{suffix}"), "Results", file_name) %>% 
+  future_map(data.table::fread) %>%
+  data.table::rbindlist() %>% 
+  data.table::setnames(c("season", "day", "pinkfoot", "pinkfoot_dist",
+                         "barnacle", "barnacle_dist", "greylag", "greylag_dist",
+                         "grain", "maize", "polyref", "param", "value")) -> all_res
+
+grain_file_name <- "scenario-grain-distributions.txt"
+path(path_to_dirs, glue::glue("WD{suffix}"), "Results", grain_file_name) %>% 
+  future_map(data.table::fread) %>%
+  data.table::rbindlist() %>% 
+  data.table::setnames(c("season", "grain_dist", "param", "value")) -> all_grain
+
+numbers_file_name <- "scenario-goose-numbers.txt"
+path(path_to_dirs, glue::glue("WD{suffix}"), "Results", numbers_file_name) %>% 
+  future_map(data.table::fread) %>%
+  data.table::rbindlist() %>% 
+  data.table::setnames(c("season", "day", "pf_families", "pf_non_breeders", "bn_families",
+                         "bn_non_breeders", "gl_families", "gl_non_breeders", "snow_depth",
+                         "param", "value")) -> all_numbers
+
+dest_dir <- "/home/ldalby/workspace/Goose/Scenarios/Results/"
+
+res_file_name <- glue::glue("{args}_scenario-results_{Sys.Date()}.fst")
+fst::write_fst(all_res, path = path(dest_dir, res_file_name))
+
+grain_file_name <-  glue::glue("{args}_scenario-grain-distributions_{Sys.Date()}.fst")
+fst::write_fst(all_grain, path = path(dest_dir, grain_file_name))
+
+numbers_file_name <-  glue::glue("{args}_scenario-goose-numbers_{Sys.Date()}.fst")
+fst::write_fst(all_numbers, path = path(dest_dir, numbers_file_name))
+
+vers_path <- path("/scratch", args, "WD01", "almass-version.txt")
+file_copy(vers_path, path(dest_dir, glue::glue("{args}_almass-version.txt")))

Grendel/start-scenario_02.sh

+#!/bin/bash
+cd /home/ldalby/workspace/Goose/Scenarios
+chmod +x scenario_01_goose-numbers_file-dist.R
+/home/com/R/3.4.1/bin/Rscript scenario_01_goose-numbers_file-dist.R $SLURM_JOB_ID
+
+for i in {01..4}; do
+	cd /scratch/$SLURM_JOB_ID/WD"$i"
+	chmod +x _01_BatchLoop.sh
+	./_01_BatchLoop.sh > out &
+	sleep 5
+done
+
+wait
+
+cd /home/ldalby/workspace/Goose/Scenarios
+chmod +x collect-results-scenario_01.R
+/home/com/R/3.4.1/bin/Rscript collect-results-scenario_01.R $SLURM_JOB_ID