Set the default number of cores to use as 2 unless otherwise specified

NEWS.md

@@ -214,3 +214,6 @@
 
 # Racmacs 1.2.5
 * Allow for shorthand description of shapes e.g. "C" for "CIRCLE" in map .ace files.
+
+# Racmacs 1.2.6
+* Set the default number of cores to use as 2 unless otherwise specified in either RacOptimizer.options, or by setting the global option 'RacOptimizer.num_cores' with e.g. `options(RacOptimizer.num_cores = parallel::detectCores())`.

R/map_optimize.R

@@ -243,7 +243,7 @@ make.acmap <- function(
 #' @param max_line_search_trials The maximum number of trials for the line search (before giving up).
 #' @param min_step The minimum step of the line search.
 #' @param max_step The maximum step of the line search.
-#' @param num_cores The number of cores to run in parallel
+#' @param num_cores The number of cores to run in parallel when running optimizations
 #' @param report_progress Should progress be reported
 #' @param ignore_disconnected Should the check for disconnected points be skipped
 #' @param progress_bar_length Progress bar length when progress is reported
@@ -270,7 +270,7 @@ RacOptimizer.options <- function(
   max_line_search_trials = 50,
   min_step = 1e-20,
   max_step = 1e20,
-  num_cores = parallel::detectCores(),
+  num_cores = getOption("RacOptimizer.num_cores"),
   report_progress = NULL,
   ignore_disconnected = FALSE,
   progress_bar_length = options()$width
@@ -281,9 +281,19 @@ RacOptimizer.options <- function(
   check.logical(ignore_disconnected)
   check.string(method)
   check.numeric(maxit)
-  check.numeric(num_cores)
   check.numeric(progress_bar_length)
   if (!is.null(report_progress)) check.logical(report_progress)
+  if (!is.null(num_cores)) check.integer(num_cores)
+
+  # Set default number of cores to 2
+  if (is.null(num_cores)) {
+    rlang::warn(
+      message = "Number of parallel cores to use for optimization was not specified, so using default of 2. You can set the number of cores to use explicitly by passing it as an argument to the optimizer function, or globally by setting the option 'RacOptimizer.num_cores', e.g. by adding the line `options(RacOptimizer.num_cores = parallel::detectCores())` to the top of your script.",
+      .frequency = "regularly",
+      .frequency_id = "RacOptimizer_num_cores_check"
+    )
+    num_cores <- 2
+  }
 
   # This is a hack to attempt to see if messages are currently suppressed
   if (is.null(report_progress)) {

src/ac_move_trapped_points.cpp

@@ -15,7 +15,8 @@ arma::mat check_ag_trapped_points(
     const AcOptimization &optimization,
     const arma::mat &tabledists,
     const arma::imat &titertypes,
-    const double &grid_spacing
+    const double &grid_spacing,
+    AcOptimizerOptions options
 ){
 
   // Variables
@@ -28,7 +29,7 @@ arma::mat check_ag_trapped_points(
   trapped_ag_improved_coords.fill(arma::datum::nan);
 
   // Check trapped antigens
-  #pragma omp parallel for schedule(dynamic)
+  #pragma omp parallel for schedule(dynamic) num_threads(options.num_cores)
   for(int ag=0; ag<num_ags; ag++){
 
     // Do a grid search
@@ -62,7 +63,8 @@ arma::mat check_sr_trapped_points(
     const AcOptimization &optimization,
     const arma::mat &tabledists,
     const arma::imat &titertypes,
-    const double &grid_spacing
+    const double &grid_spacing,
+    AcOptimizerOptions options
 ){
 
   // Variables
@@ -75,7 +77,7 @@ arma::mat check_sr_trapped_points(
   trapped_sr_improved_coords.fill(arma::datum::nan);
 
   // Check trapped sera
-  #pragma omp parallel for schedule(dynamic)
+  #pragma omp parallel for schedule(dynamic) num_threads(options.num_cores)
   for(int sr=0; sr<num_sr; sr++){
 
     // Do a grid search
@@ -134,8 +136,8 @@ AcOptimization ac_move_trapped_points(
     arma::mat sr_coords = optimization.get_sr_base_coords();
 
     // Check for any improved coordinates
-    arma::mat ag_trapped_improved_coords = check_ag_trapped_points(optimization, tabledists, titertypes, grid_spacing);
-    arma::mat sr_trapped_improved_coords = check_sr_trapped_points(optimization, tabledists, titertypes, grid_spacing);
+    arma::mat ag_trapped_improved_coords = check_ag_trapped_points(optimization, tabledists, titertypes, grid_spacing, options);
+    arma::mat sr_trapped_improved_coords = check_sr_trapped_points(optimization, tabledists, titertypes, grid_spacing, options);
 
     // Get any improved indices
     arma::uvec ag_trapped_coord_indices = arma::find_finite(ag_trapped_improved_coords);

src/ac_optim_map_stress.cpp

@@ -573,7 +573,7 @@ void ac_relaxOptimizations(
   }
 
   // Run and return optimization results
-  #pragma omp parallel for schedule(dynamic)
+  #pragma omp parallel for schedule(dynamic) num_threads(options.num_cores)
   for (int i=0; i<num_optimizations; i++) {
 
     // Run the optimization

tests/testthat/test-diagnostics_bootstrap.R

@@ -4,6 +4,7 @@ library(testthat)
 context("Bootstrapping maps")
 
 # Set variables
+options(RacOptimizer.num_cores = 2)
 num_bs_repeats <- 200
 map <- read.acmap(test_path("../testdata/testmap_h3subset.ace"))