Merge pull request #215 from mrc-ide/mrc-3349

Allow workers to parallelise non-package models

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: mcstate
 Title: Monte Carlo Methods for State Space Models
-Version: 0.9.5
+Version: 0.9.6
 Authors@R: c(person("Rich", "FitzJohn", role = c("aut", "cre"),
                     email = "rich.fitzjohn@gmail.com"),
              person("Marc", "Baguelin", role = "aut"),
@@ -22,7 +22,7 @@ BugReports: https://github.com/mrc-ide/mcstate/issues
 Imports:
     R6,
     callr (>= 3.7.0),
-    dust (>= 0.11.26),
+    dust (>= 0.11.28),
     processx,
     progress (>= 1.2.0)
 Suggests:
@@ -40,6 +40,6 @@ Suggests:
 RoxygenNote: 7.2.0
 Roxygen: list(markdown = TRUE)
 Remotes:
-    mrc-ide/dust@mrc-3157,
+    mrc-ide/dust,
     mrc-ide/odin.dust
 VignetteBuilder: knitr

R/pmcmc_chains.R

@@ -75,6 +75,8 @@ pmcmc_chains_run <- function(chain_id, path, n_threads = NULL) {
   inputs <- readRDS(path$inputs)
   assert_is(inputs, "pmcmc_inputs")
 
+  dust::dust_repair_environment(inputs$filter$model)
+
   control <- inputs$control
   if (chain_id < 1 || chain_id > control$n_chains) {
     stop(sprintf("'chain_id' must be an integer in 1..%d",

tests/testthat/test-pmcmc-parallel.R

@@ -188,3 +188,23 @@ test_that("thread allocation", {
 
   expect_equal(pmcmc_parallel_threads(21, 3, 8), c(rep(7, 6), 10, 11))
 })
+
+
+test_that("Can use workers on non-package models", {
+  path <- system.file("examples/sir.cpp", package = "dust", mustWork = TRUE)
+  tmp <- tempfile()
+  writeLines(c("// [[dust::name(walk2)]]", readLines(path)), tmp)
+  model <- dust::dust(tmp, quiet = TRUE)
+
+  dat <- example_sir()
+
+  control <- pmcmc_control(10, n_chains = 2,
+                           n_workers = 2, n_threads_total = 2,
+                           progress = FALSE, use_parallel_seed = TRUE)
+  filter <- particle_filter$new(dat$data, model, 42, dat$compare,
+                                n_threads = 1, index = dat$index, seed = 1L)
+  ans <- pmcmc(dat$pars, filter, control = control)
+  ## It's sufficient to check that this does not error, previously we
+  ## failed to load the model.
+  expect_s3_class(ans, "mcstate_pmcmc")
+})