R/coresWrapper.R

Defines functions .close_cores .eval_Sobs_densities .set_cluster_type .inRstudio

.inRstudio <- function(silent=FALSE, bool=TRUE) {
  trygetfn <- try(get("getActiveProject",envir = asNamespace("rstudioapi")), silent=silent) # fails if rstudioapi not installed
  if ( tryres <- ( ! inherits(trygetfn,"try-error"))) {
    tryres <- try(trygetfn(), silent=silent) # fails if rstudioapi not running ie not an Rstudio session
    # otherwise NULL if no active project, or the path if there is an active project.
  }
  if (bool) tryres <- ! inherits(tryres,"try-error") # to return a boolean : whether we are in an Rstudio session or not
  # otherwise retuen value is (try-error, or NULL, or path).
  tryres 
}

projpath <- local({
  pp <- NULL
  function() {
    if (is.null(ppp <- .Infusion.data$options$projpath)) {
      if (is.null(pp)) {
        projpathinRstudio <- .inRstudio(silent=FALSE, bool=FALSE)
        if (inherits(projpathinRstudio,"try-error") || is.null(projpathinRstudio)) { # not an Rstudio session || no active project
          if (interactive()) {
            message('Need to give the project path, say "~/travail/stats/Infusionplus/Infusion":')
            pp <<- readline(prompt="Enter path: ")
          } else {
            message('Need to start in the projpath, say "~/travail/stats/Infusionplus/Infusion", so that getwd() finds it.')
            pp <<- getwd()
          }
        } else pp <<- projpathinRstudio
      }
      return(pp)
    } else return(ppp)
  }
})


.check_nb_cores <- local({
  nb_cores_warned <- FALSE
  cores_avail_warned <- FALSE
  parallel_Rstudio_warned <- FALSE
  function(nb_cores=NULL) {
    if (is.null(nb_cores)) nb_cores <- Infusion.getOption("nb_cores") ## may be NULL
    machine_cores <- parallel::detectCores()
    if (is.null(nb_cores)) {
      nb_cores <- 1L ## default
      if (machine_cores>1L && interactive()) {
        if (! cores_avail_warned) {
          message(paste(machine_cores,"cores are available for parallel computation\n(you may be allowed to fewer of them on a shared cluster).\n"))
          message("Change 'nb_cores' argument to use some of them.\nUse Infusion.options(nb_cores=<n>) to control nb_cores globally.")
          cores_avail_warned <<- TRUE
        }
      }
    } else {
      if (nb_cores>1L && .inRstudio(silent=TRUE,bool = TRUE) && ! parallel_Rstudio_warned) {
        warning("Parallel tasks have failed in some past versions of Rstudio... good luck!", immediate. = TRUE)
        parallel_Rstudio_warned <<- TRUE
      }
      if (nb_cores>machine_cores) {
        if (! nb_cores_warned) {
          warning("More cores were requested than found by parallel::detectCores(). Check Infusion.getOption(\"nb_cores\") argument.
                Number of availlable cores automatically downsized to the number of cores found by parallel::detectCores(). I continue.")
          nb_cores_warned <<- TRUE
        }
        nb_cores <- machine_cores
      }
    }
    return(nb_cores)
  }
})

.set_cluster_type <- function(cluster_args, nb_cores) {
  if (is.null(cluster_args$spec)) cluster_args$spec <- nb_cores # else... => which means that non-null cluster_args$spec overrides nb_cores
  cluster_args$spec <- .check_nb_cores(nb_cores=cluster_args$spec)
  if (cluster_args$spec>1L) {
    type_user <- cluster_args$type
    if (.Platform$OS.type == "windows") {
      if (is.null(type_user)) {
        cluster_args$type <- "PSOCK" # default, but explicit => can be tested # On windows, or on linux if explicitly requested
      } else if (type_user=="FORK") {
        message('cluster_args$type=="FORK" not feasible under Windows')
        cluster_args$type <- "PSOCK"
      }
    } else { # linux alikes
      if (is.null(type_user)) {
        if (.inRstudio(silent=TRUE)) {
          cluster_args$type <- "PSOCK"
        } else cluster_args$type <- "PSOCK" # finally decide to use PSOCK as default under linux too
      } else if (type_user=="FORK" && .inRstudio(silent=TRUE)) {
        message('cluster_args$type=="FORK" not feasible when R is called from an Rstudio session.')
        cluster_args$type <- "PSOCK"
      }
    }
  }
  cluster_args
}
  
  
.init_cores <- local({
  doSNOW_warned <- FALSE
  function(cluster_args=list()) { 
    cluster_args$spec <- .check_nb_cores(nb_cores=cluster_args$spec) # if cluster_args was NULL it is converted to list here => no need for special handling code.
    cores_info <- list(nb_cores=cluster_args$spec)
    #
    if (cluster_args$spec > 1L) {
      cores_info$cl <- do.call(parallel::makeCluster, cluster_args) 
      #dotenv <- list2env(list(...))
      #parallel::clusterExport(cl=cores_info$cl, as.list(ls(dotenv)),envir=dotenv) 
      ## foreach is NOT a parallel backend so there is no point using it if doSNOW is not available
      if (cluster_args$type!="FORK") {
        if (cores_info$has_doSNOW <- (isNamespaceLoaded("doSNOW"))) {
          R.seed <- get(".Random.seed", envir = .GlobalEnv)
          ## allows progressbar but then requires foreach
          assign(".Random.seed", R.seed, envir = .GlobalEnv) # loading (?) the namespace of 'snow' changes the global RNG state!
          fn <- get("registerDoSNOW", asNamespace("doSNOW"))
          do.call(fn,list(cl=cores_info$cl)) 
        } else {
          if ( ! doSNOW_warned) {
            message("If the 'doSNOW' package were attached, better load-balancing might be possible (at the expense of control of RNG).")
            doSNOW_warned <<- TRUE
          } 
        }
      } else cores_info$has_doSNOW <- FALSE
    }
    return(cores_info)
  }
})

.eval_Sobs_densities <- function(method, object, cores_info, packages=NULL, stat.obs,logLname,
                                 verbose # list
                                 ) {
  #prevmsglength <- 0 ## no longer used ?
  if (cores_info$nb_cores > 1L) {
    #blackboxOptions <- blackbox.options() ## FIXME: none of the package options are passed to the child processed
    #InfusionOptions <- Infusion.options()
    packages <- c("Infusion","blackbox",packages)
    parallel::clusterExport(cores_info$cl, method,envir=environment()) ## passes useks
    parallel::clusterExport(cores_info$cl, "packages",envir=environment()) ## passes the list of packages to load
    abyss <- parallel::clusterEvalQ(cores_info$cl, {sapply(packages,library,character.only=TRUE)}) ## snif
    if (cores_info$has_doSNOW) {
      show_pb <- (verbose$most && ! isTRUE(getOption('knitr.in.progress')))
      if (show_pb) {
        pb <- txtProgressBar(max = length(object), style = 3, char="P")
        progress <- function(n) setTxtProgressBar(pb, n)
        parallel::clusterExport(cl=cores_info$cl, "progress",envir=environment()) ## slow! why?
        .options.snow = list(progress = progress)
      } else .options.snow = NULL
      ii <- NULL ## otherwise R CMD check complains that no visible binding for global variable 'ii'
      foreach_args <- list(
        ii = seq_len(length(object)), 
        .packages= packages,
        .options.snow = .options.snow,
        .inorder = TRUE, .errorhandling = "remove"
        #                                 "pass"## "pass" to see error messages
      )
      foreach_blob <- do.call(foreach::foreach,foreach_args)
      Sobs.densities <- foreach::`%dopar%`(foreach_blob,
                                     do.call(method,c(list(object[[ii]]),
                                                      list(stat.obs=stat.obs,logLname=logLname,verbose=verbose) )))
      if (show_pb) close(pb)
    } else {
      pbopt <- pboptions(nout=min(100,2*length(object)),type="timer", char="p")
      Sobs.densities <- pblapply(X=object, FUN = method, cl=cores_info$cl, stat.obs=stat.obs,logLname=logLname,verbose=verbose)
      pboptions(pbopt)
    }
  } else { 
    pbopt <- pboptions(nout=min(100,2*length(object)),type="timer", char="s")
    Sobs.densities <- pblapply(X=object, FUN = method, cl=NULL, stat.obs=stat.obs,logLname=logLname,verbose=verbose)
    pboptions(pbopt)
  }
  if (verbose$final) {
    areValid <- sapply(Sobs.densities,`[`,name="isValid")
    nInvalid <- sum(! areValid)
    if (nInvalid>0L) message(paste(nInvalid,"distributions tagged as 'outlier'(s))"))
  }
  return(Sobs.densities)
}

.close_cores <- function(cores_info) {
  if ( cores_info$nb_cores > 1L) {
    if (cores_info$has_doSNOW) foreach::registerDoSEQ() ## https://stackoverflow.com/questions/25097729/un-register-a-doparallel-cluster
    parallel::stopCluster(cores_info$cl)
  }
}

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Infusion documentation built on Sept. 29, 2022, 1:05 a.m.