Merge 0ac09f9 into 3c7a1a9

R/fit.R

@@ -322,6 +322,7 @@ CmdStanFit$set("public", name = "init", value = init)
 #' @param seed (integer) The random seed to use when initializing the model.
 #' @param verbose (logical) Whether to show verbose logging during compilation.
 #' @param hessian (logical) Whether to expose the (experimental) hessian method.
+#' @param force_recompile (logical) Whether to recompile cached model methods.
 #'
 #' @examples
 #' \dontrun{
@@ -332,25 +333,26 @@ CmdStanFit$set("public", name = "init", value = init)
 #'   [unconstrain_variables()], [unconstrain_draws()], [variable_skeleton()],
 #'   [hessian()]
 #'
-init_model_methods <- function(seed = 0, verbose = FALSE, hessian = FALSE) {
+init_model_methods <- function(seed = 0, verbose = FALSE, hessian = FALSE, force_recompile = FALSE) {
   if (os_is_wsl()) {
     stop("Additional model methods are not currently available with ",
           "WSL CmdStan and will not be compiled",
           call. = FALSE)
   }
   require_suggested_package("Rcpp")
-  if (length(private$model_methods_env_$hpp_code_) == 0) {
+  if (length(private$model_methods_env_$hpp_code_) == 0 && (
+        is.null(private$model_methods_env_$obj_file_) ||
+        !file.exists(private$model_methods_env_$obj_file_))) {
     stop("Model methods cannot be used with a pre-compiled Stan executable, ",
           "the model must be compiled again", call. = FALSE)
   }
   if (hessian) {
-    message("The hessian method relies on higher-order autodiff ",
-            "which is still experimental. Please report any compilation ",
-            "errors that you encounter")
+    warning("The hessian argument is deprecated and will be removed in a future release.\n",
+            "The hessian method is now exposed by default.")
   }
-  message("Compiling additional model methods...")
   if (is.null(private$model_methods_env_$model_ptr)) {
-    expose_model_methods(private$model_methods_env_, verbose, hessian)
+    expose_model_methods(private$model_methods_env_, verbose = verbose,
+                          force_recompile = force_recompile)
   }
   initialize_model_pointer(private$model_methods_env_, self$data_file(), seed)
   invisible(NULL)

R/install.R

@@ -475,6 +475,8 @@ build_cmdstan <- function(dir,
 clean_cmdstan <- function(dir = cmdstan_path(),
                           cores = getOption("mc.cores", 2),
                           quiet = FALSE) {
+  unlink(file.path(dir, "model_methods.o"))
+  unlink(file.path(dir, "model_methods.cpp"))
   withr::with_path(
     c(
       toolchain_PATH_env_var(),

R/model.R

@@ -405,8 +405,8 @@ CmdStanModel <- R6::R6Class(
 #' @param compile_model_methods (logical) Compile additional model methods
 #'   (`log_prob()`, `grad_log_prob()`, `constrain_variables()`,
 #'   `unconstrain_variables()`).
-#' @param compile_hessian_method (logical) Should the (experimental) `hessian()` method be
-#'   be compiled with the model methods?
+#' @param compile_hessian_method (logical) Deprecated and will be removed in a future release.
+#'   The hessian method is now compiled by default.
 #' @param compile_standalone (logical) Should functions in the Stan model be
 #'   compiled for use in R? If `TRUE` the functions will be available via the
 #'   `functions` field in the compiled model object. This can also be done after
@@ -504,6 +504,10 @@ compile <- function(quiet = TRUE,
     warning("'threads' is deprecated. Please use 'cpp_options = list(stan_threads = TRUE)' instead.")
     cpp_options[["stan_threads"]] <- TRUE
   }
+  if (isTRUE(compile_hessian_method)) {
+    warning("'compile_hessian_method' is deprecated. The hessian method is now compiled by default.")
+    compile_hessian_method <- FALSE
+  }
 
   if (length(self$exe_file()) == 0) {
     if (is.null(dir)) {
@@ -655,9 +659,10 @@ compile <- function(quiet = TRUE,
       run_log <- wsl_compatible_run(
         command = make_cmd(),
         args = c(wsl_safe_path(tmp_exe),
-                cpp_options_to_compile_flags(cpp_options),
+                cpp_options_to_compile_flags(c(cpp_options, list("KEEP_OBJECT"="true"))),
                 stancflags_val),
         wd = cmdstan_path(),
+        env = c("current", "CXXFLAGS" = "-fPIC"),
         echo = !quiet || is_verbose_mode(),
         echo_cmd = is_verbose_mode(),
         spinner = quiet && rlang::is_interactive() && !identical(Sys.getenv("IN_PKGDOWN"), "true"),
@@ -708,6 +713,7 @@ compile <- function(quiet = TRUE,
       file.remove(exe)
     }
     file.copy(tmp_exe, exe, overwrite = TRUE)
+    private$model_methods_env_$obj_file_ <- paste0(temp_file_no_ext, ".o")
     if (os_is_wsl()) {
       res <- processx::run(
         command = "wsl",
@@ -726,11 +732,9 @@ compile <- function(quiet = TRUE,
   private$precompile_stanc_options_ <- NULL
   private$precompile_include_paths_ <- NULL
 
-  if(!dry_run) {
+  if (!dry_run) {
     if (compile_model_methods) {
-      expose_model_methods(env = private$model_methods_env_,
-                            verbose = !quiet,
-                            hessian = compile_hessian_method)
+      expose_model_methods(private$model_methods_env_, verbose = !quiet)
     }
   }
   invisible(self)

R/utils.R

@@ -728,45 +728,116 @@ get_cmdstan_flags <- function(flag_name) {
   paste(flags, collapse = " ")
 }
 
-rcpp_source_stan <- function(code, env, verbose = FALSE) {
+with_cmdstan_flags <- function(expr, model_methods = FALSE) {
   cxxflags <- get_cmdstan_flags("CXXFLAGS")
   cmdstanr_includes <- system.file("include", package = "cmdstanr", mustWork = TRUE)
-  cmdstanr_includes <- paste0(" -I\"", cmdstanr_includes,"\"")
+  cmdstanr_includes <- paste0("-I", shQuote(cmdstanr_includes))
+
+  r_includes <- paste(
+    paste0("-I", shQuote(system.file("include", package = "Rcpp", mustWork = TRUE))),
+    paste0("-I", shQuote(R.home(component = "include")))
+  )
+
   libs <- c("LDLIBS", "LIBSUNDIALS", "TBB_TARGETS", "LDFLAGS_TBB")
   libs <- paste(sapply(libs, get_cmdstan_flags), collapse = " ")
-  if (.Platform$OS.type == "windows") {
+  if (os_is_windows()) {
     libs <- paste(libs, "-fopenmp")
   }
   lib_paths <- c("/stan/lib/stan_math/lib/tbb/",
                  "/stan/lib/stan_math/lib/sundials_6.1.1/lib/")
-  withr::with_path(paste0(cmdstan_path(), lib_paths),
-    withr::with_makevars(
-      c(
-        USE_CXX14 = 1,
-        PKG_CPPFLAGS = ifelse(cmdstan_version() <= "2.30.1", "-DCMDSTAN_JSON", ""),
-        PKG_CXXFLAGS = paste0(cxxflags, cmdstanr_includes, collapse = " "),
-        PKG_LIBS = libs
-      ),
-      Rcpp::sourceCpp(code = code, env = env, verbose = verbose)
+  new_makevars <- c(
+    PKG_CPPFLAGS = ifelse(cmdstan_version() <= "2.30.1", "-DCMDSTAN_JSON", ""),
+    PKG_CXXFLAGS = paste(cxxflags, cmdstanr_includes, r_includes, collapse = " "),
+    PKG_LIBS = libs
+  )
+  if (os_is_windows() && model_methods) {
+    new_makevars <- c(
+      new_makevars,
+      SHLIB_LD = paste0(rtools4x_toolchain_path(),"/gcc"),
+      LOCAL_CPPFLAGS = paste0("-I'",rtools4x_toolchain_path(),"/../include'"),
+      LOCAL_LIBS = paste0("-L'",rtools4x_toolchain_path(),"/../lib' -lstdc++"),
+      BINPREF = paste0(rtools4x_toolchain_path(), "/")
     )
+  }
+  withr::with_path(
+    c(
+      paste0(cmdstan_path(), lib_paths),
+      toolchain_PATH_env_var()
+    ),
+    withr::with_makevars(new_makevars, expr)
   )
+}
+
+rcpp_source_stan <- function(code, env, verbose = FALSE) {
+  with_cmdstan_flags(Rcpp::sourceCpp(code = code, env = env, verbose = verbose))
   invisible(NULL)
 }
 
-expose_model_methods <- function(env, verbose = FALSE, hessian = FALSE) {
-  code <- c(env$hpp_code_,
-            readLines(system.file("include", "model_methods.cpp",
-                                  package = "cmdstanr", mustWork = TRUE)))
+initialize_method_functions <- function(env, so_name) {
+  env$model_ptr <-
+    function(...) { .Call("model_ptr_", ..., PACKAGE = so_name) }
+  env$log_prob <-
+    function(...) { .Call("log_prob_", ..., PACKAGE = so_name) }
+  env$grad_log_prob <-
+    function(...) { .Call("grad_log_prob_", ..., PACKAGE = so_name) }
+  env$hessian <-
+    function(...) { .Call("hessian_", ..., PACKAGE = so_name) }
+  env$get_num_upars <-
+    function(...) { .Call("get_num_upars_", ..., PACKAGE = so_name) }
+  env$get_param_metadata <-
+    function(...) { .Call("get_param_metadata_", ..., PACKAGE = so_name) }
+  env$unconstrain_variables <-
+    function(...) { .Call("unconstrain_variables_", ..., PACKAGE = so_name) }
+  env$constrain_variables <-
+    function(...) { .Call("constrain_variables_", ..., PACKAGE = so_name) }
+  env$unconstrained_param_names <-
+    function(...) { .Call("unconstrained_param_names_", ..., PACKAGE = so_name) }
+  env$constrained_param_names <-
+    function(...) { .Call("constrained_param_names_", ..., PACKAGE = so_name) }
+}
 
-  if (hessian) {
-    code <- c("#include <stan/math/mix.hpp>",
-            code,
-            readLines(system.file("include", "hessian.cpp",
-                                  package = "cmdstanr", mustWork = TRUE)))
+expose_model_methods <- function(env, force_recompile = FALSE, verbose = FALSE) {
+  precomp_methods_file <- file.path(cmdstan_path(), "model_methods.o")
+  if (file.exists(precomp_methods_file) && force_recompile) {
+    unlink(precomp_methods_file)
   }
+  model_methods_cpp <- system.file("include", "model_methods.cpp",
+                                  package = "cmdstanr", mustWork = TRUE)
+  source_file <- paste0(strip_ext(precomp_methods_file), ".cpp")
+  file.copy(model_methods_cpp, source_file, overwrite = FALSE)
+
+  model_obj_file <- env$obj_file_
+  if (!file.exists(model_obj_file)) {
+    if (rlang::is_interactive()) {
+      message("Model object file not found, recompiling model...")
+    }
+    temp_hpp_file <- tempfile()
+    writeLines(env$hpp_code_, con = paste0(temp_hpp_file, ".cpp"))
+    model_obj_file <- paste0(temp_hpp_file, ".o")
+  }
+
+  if (!file.exists(precomp_methods_file) && rlang::is_interactive()) {
+    message("Compiling and caching additional model methods...")
+  }
+  if (rlang::is_interactive()) {
+    message("Linking precompiled model methods to model object file...")
+  }
+
+  methods_dll <- tempfile(fileext = .Platform$dynlib.ext)
+  with_cmdstan_flags(
+    processx::run(
+      command = file.path(R.home(component = "bin"), "R"),
+      args = c("CMD", "SHLIB", repair_path(model_obj_file), repair_path(precomp_methods_file),
+                "-o", repair_path(methods_dll)),
+      echo = verbose || is_verbose_mode(),
+      echo_cmd = is_verbose_mode(),
+      error_on_status = FALSE
+    ),
+    model_methods = TRUE
+  )
 
-  code <- paste(code, collapse = "\n")
-  rcpp_source_stan(code, env, verbose)
+  env$methods_dll_info <- with_cmdstan_flags(dyn.load(methods_dll, local = TRUE, now = TRUE))
+  initialize_method_functions(env, strip_ext(basename(methods_dll)))
   invisible(NULL)
 }