File: ClusterFuture-class.R

package info (click to toggle)
r-cran-future 1.11.1.1%2Bdfsg-1
  • links: PTS, VCS
  • area: main
  • in suites: buster
  • size: 1,380 kB
  • sloc: sh: 14; makefile: 2
file content (467 lines) | stat: -rw-r--r-- 16,923 bytes parent folder | download
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
#' A cluster future is a future whose value will be resolved asynchronously in a parallel process
#'
#' @inheritParams MultiprocessFuture-class
#' @inheritParams Future-class
#' 
#' @param persistent If FALSE, the evaluation environment is cleared
#' from objects prior to the evaluation of the future.
#' 
#' @param workers A \code{\link[parallel:makeCluster]{cluster}} object,
#' a character vector of host names, a positive numeric scalar,
#' or a function.
#' If a character vector or a numeric scalar, a \code{cluster} object
#' is created using \code{\link{makeClusterPSOCK}(workers)}.
#' If a function, it is called without arguments \emph{when the future
#' is created} and its value is used to configure the workers.
#' The function should return any of the above types.
#' 
#' @param revtunnel If TRUE, reverse SSH tunneling is used for the
#' PSOCK cluster nodes to connect back to the master \R process.  This
#' avoids the hassle of firewalls, port forwarding and having to know
#' the internal / public IP address of the master \R session.
#' 
#' @param user (optional) The user name to be used when communicating
#' with another host.
#' 
#' @param master (optional) The hostname or IP address of the master
#' machine running this node.
#' 
#' @param homogeneous If TRUE, all cluster nodes is assumed to use the
#' same path to \file{Rscript} as the main \R session.  If FALSE, the
#' it is assumed to be on the PATH for each node.
#'
#' @return
#' \code{ClusterFuture()} returns an object of class \code{ClusterFuture}.
#'
#' @seealso
#' To evaluate an expression using "cluster future", see function
#' \code{\link{cluster}()}.
#'
#' @aliases MultisessionFuture MultisessionFuture-class
#' @export
#' @export MultisessionFuture
#' @importFrom digest digest
#' @name ClusterFuture-class
#' @keywords internal
ClusterFuture <- function(expr = NULL, envir = parent.frame(), substitute = FALSE, globals = TRUE, packages = NULL, local = !persistent, gc = FALSE, persistent = FALSE, workers = NULL, user = NULL, master = NULL, revtunnel = TRUE, homogeneous = TRUE, ...) {
  if (substitute) expr <- substitute(expr)

  if (is.function(workers)) workers <- workers()
  if (is.null(workers)) {
    getDefaultCluster <- importParallel("getDefaultCluster")
    workers <- getDefaultCluster()
  } else if (is.character(workers) || is.numeric(workers)) {
    workers <- ClusterRegistry("start", workers = workers, user = user, master = master, revtunnel = revtunnel, homogeneous = homogeneous)
  } else {
    workers <- as.cluster(workers)
  }
  if (!inherits(workers, "cluster")) {
    stop("Argument 'workers' is not of class 'cluster': ", paste(sQuote(class(workers)), collapse = ", "))
  }
  stop_if_not(length(workers) > 0)

  ## Attached workers' session information, unless already done.
  ## FIXME: We cannot do this here, because it introduces a race condition
  ## where multiple similar requests may appear at the same time bringing
  ## the send/receive data to be out of sync and therefore corrupt the
  ## futures' values.
  ##  workers <- add_cluster_session_info(workers)
  
  ## Attach name to cluster?
  name <- attr(workers, "name", exact = TRUE)
  if (is.null(name)) {
    name <- digest(workers)
    stop_if_not(length(name) > 0, nzchar(name))
    attr(workers, "name") <- name
  }

  ## Global objects
  gp <- getGlobalsAndPackages(expr, envir = envir, persistent = persistent, globals = globals)
  globals <- gp$globals
  packages <- unique(c(packages, gp$packages))
  expr <- gp$expr
  gp <- NULL

  f <- MultiprocessFuture(expr = expr, envir = envir, substitute = FALSE, globals = globals, packages = packages, local = local, gc = gc, persistent = persistent, workers = workers, node = NA_integer_, version = "1.8", ...)
  f$.callResult <- TRUE
  structure(f, class = c("ClusterFuture", class(f)))
}



#' @importFrom parallel clusterCall clusterExport
#' @export
run.ClusterFuture <- function(future, ...) {
  debug <- getOption("future.debug", FALSE)
  
  if (future$state != 'created') {
    label <- future$label
    if (is.null(label)) label <- "<none>"
    stop(FutureError(sprintf("A future ('%s') can only be launched once.", label), future = future))
  }
  
  ## Assert that the process that created the future is
  ## also the one that evaluates/resolves/queries it.
  assertOwner(future)

  sendCall <- importParallel("sendCall")
  workers <- future$workers
  expr <- getExpression(future)
  persistent <- future$persistent

  ## FutureRegistry to use
  reg <- sprintf("workers-%s", attr(workers, "name", exact = TRUE))


  ## Next available cluster node
  node_idx <- requestNode(await = function() {
    FutureRegistry(reg, action = "collect-first", earlySignal = TRUE)
  }, workers = workers)
  future$node <- node_idx

  ## Cluster node to use
  cl <- workers[node_idx]


  ## WORKAROUND: When running covr::package_coverage(), the
  ## package being tested may actually not be installed in
  ## library path used by covr.  We here add that path iff
  ## covr is being used. /HB 2016-01-15
  if (is.element("covr", loadedNamespaces())) {
    if (debug) mdebug("covr::package_coverage() workaround ...")
    libPath <- .libPaths()[1]
    clusterCall(cl, fun = function() .libPaths(c(libPath, .libPaths())))
    if (debug) mdebug("covr::package_coverage() workaround ... DONE")
  }


  ## (i) Reset global environment of cluster node such that
  ##     previous futures are not affecting this one, which
  ##     may happen even if the future is evaluated inside a
  ##     local, e.g. local({ a <<- 1 }).
  if (!persistent) {
    clusterCall(cl, fun = grmall)
  }


  ## (ii) Attach packages that needs to be attached
  ##      NOTE: Already take care of by getExpression() of the Future class.
  ##      However, if we need to get an early error about missing packages,
  ##      we can get the error here before launching the future.
  packages <- packages(future)
  if (future$earlySignal && length(packages) > 0) {
    if (debug) mdebug("Attaching %d packages (%s) on cluster node #%d ...",
                      length(packages), hpaste(sQuote(packages)), node_idx)

    clusterCall(cl, fun = requirePackages, packages)

    if (debug) mdebug("Attaching %d packages (%s) on cluster node #%d ... DONE",
                      length(packages), hpaste(sQuote(packages)), node_idx)
  }
  

  ## (iii) Export globals
  globals <- globals(future)
  if (length(globals) > 0) {
    if (debug) {
      total_size <- asIEC(objectSize(globals))
      mdebug("Exporting %d global objects (%s) to cluster node #%d ...", length(globals), total_size, node_idx)
    }
    for (name in names(globals)) {
      ## For instance sendData.SOCKnode(...) may generate warnings
      ## on packages not being available after serialization, e.g.
      ##  In serialize(data, node$con) :
      ## package:future' may not be available when loading
      ## Here we'll suppress any such warnings.
      value <- globals[[name]]
      if (debug) {
        size <- asIEC(objectSize(value))
        mdebug("Exporting %s (%s) to cluster node #%d ...", sQuote(name), size, node_idx)
      }
      suppressWarnings({
        clusterCall(cl, fun = gassign, name, value)
      })
      if (debug) mdebug("Exporting %s (%s) to cluster node #%d ... DONE", sQuote(name), size, node_idx)
      value <- NULL
    }
    if (debug) mdebug("Exporting %d global objects (%s) to cluster node #%d ... DONE", length(globals), total_size, node_idx)
  }
  ## Not needed anymore
  globals <- NULL


  ## Add to registry
  FutureRegistry(reg, action = "add", future = future, earlySignal = FALSE)

  ## (iv) Launch future
  sendCall(cl[[1L]], fun = geval, args = list(expr))

  future$state <- 'running'

  if (debug) mdebug("%s started", class(future)[1])
  
  invisible(future)
}

#' @export
resolved.ClusterFuture <- function(x, timeout = 0.2, ...) {
  ## Is future even launched?
  if (x$state == 'created') return(FALSE)

  ## Is value already collected?
  if (!is.null(x$result)) return(TRUE)

  ## Assert that the process that created the future is
  ## also the one that evaluates/resolves/queries it.
  assertOwner(x)

  workers <- x$workers
  node_idx <- x$node
  cl <- workers[node_idx]

  ## Check if workers socket connection is available for reading
  node <- cl[[1]]

  if (!is.null(con <- node$con)) {
    ## AD HOC/SPECIAL CASE: Skip if connection has been serialized and lacks internal representation. /HB 2018-10-27
    if (connectionId(con) < 0) return(FALSE)

    isValid <- isValidConnection(con)
    if (!isValid) {
      label <- x$label
      if (is.null(label)) label <- "<none>"
      stop(FutureError(sprintf("Cannot resolve %s (%s), because the connection to the worker is corrupt: %s", class(x)[1], label, attr(isValid, "reason", exact = TRUE)), future = future))
    }

    ## WORKAROUND: Non-integer timeouts (at least < 2.0 seconds) may result in
    ## infinite waiting (PR17203).  Fixed in R devel r73470 (2017-10-05)
    ## and R 3.4.3 (https://github.com/HenrikBengtsson/Wishlist-for-R/issues/35)
    if (.Platform$OS.type != "windows" && getRversion() < "3.4.3") {
      timeout <- round(timeout, digits = 0L)
    }
    res <- socketSelect(list(con), write = FALSE, timeout = timeout)
  } else if (inherits(node, "MPInode")) {
    res <- resolveMPI(x)
  } else {
    ## stop("Not yet implemented: ", paste(sQuote(class(node)), collapse = ", "))
    warning(sprintf("resolved() is not yet implemented for workers of class %s. Will use value() instead and return TRUE", sQuote(class(node)[1])))
    value(x, stdout = FALSE, signal = FALSE)
    res <- TRUE
  }

  ## Signal conditions early? (happens only iff requested)
  if (res) signalEarly(x, ...)

  res
}

#' @export
result.ClusterFuture <- function(future, ...) {
  debug <- getOption("future.debug", FALSE)
  if (debug) mdebug("result() for ClusterFuture ...")
  
  ## Has the result already been collected?
  result <- future$result
  if (!is.null(result)) {
    if (debug) mdebug("- result already collected: %s", class(result)[1])
    if (inherits(result, "FutureError")) stop(result)
    if (debug) mdebug("result() for ClusterFuture ... done")
    return(result)
  }

  if (future$state == "created") {
    if (debug) mdebug("- starting non-launched future")
    future <- run(future)
  }

  ## Assert that the process that created the future is
  ## also the one that evaluates/resolves/queries it.
  assertOwner(future)

  recvResult <- importParallel("recvResult")

  workers <- future$workers
  node_idx <- future$node
  cl <- workers[node_idx]
  node <- cl[[1]]

  if (!is.null(con <- node$con)) {
    if (debug) mdebug("- Validating connection of %s", class(future)[1])
    isValid <- isValidConnection(con)
    if (!isValid) {
      label <- future$label
      if (is.null(label)) label <- "<none>"
      stop(FutureError(sprintf("Cannot receive results for %s (%s), because the connection to the worker is corrupt: %s", class(future)[1], label, attr(isValid, "reason", exact = TRUE)), future = future))
    }
  }

  ## If not, wait for process to finish, and
  ## then collect and record the value
  ack <- tryCatch({
    result <- recvResult(node)
    TRUE
  }, simpleError = function(ex) ex)

  if (debug) mdebug("- class(result): %s", class(result)[1])

  if (inherits(ack, "simpleError")) {
    if (debug) mdebug("- parallel:::recvResult() produced an error: %s", conditionMessage(ack))
    label <- future$label
    if (is.null(label)) label <- "<none>"
    
    pid <- node$session_info$process$pid
    pid_info <- if (is.numeric(pid)) sprintf("PID %g", pid) else NULL

    ## AD HOC: This assumes that the worker has a hostname, which is not
    ## the case for MPI workers. /HB 2017-03-07
    host <- node$host
    localhost <- isTRUE(attr(host, "localhost", exact = TRUE))
    host_info <- if (!is.null(host)) {
      sprintf("on %s%s", if (localhost) "localhost " else "", sQuote(host))
    } else NULL
    
    info <- paste(c(pid_info, host_info), collapse = " ")
    msg <- sprintf("Failed to retrieve the value of %s (%s) from cluster %s #%d (%s).",
                   class(future)[1], label, class(node)[1], node_idx, info)
    msg <- sprintf("%s The reason reported was %s", msg, sQuote(ack$message))
    
    ## POST-MORTEM ANALYSIS:
    postmortem <- list()
    
    ## (a) Did the worker use a connection that changed?
    if (inherits(node$con, "connection")) {
      postmortem$connection <- check_connection_details(node, future = future)
    }

    ## (b) Did a localhost worker process terminate?
    if (!is.null(host)) {
      if (localhost && is.numeric(pid)) {
        alive <- pid_exists(pid)
        if (is.na(alive)) {
          msg2 <- "Failed to determined whether a process with this PID exists or not, i.e. cannot infer whether localhost worker is alive or not."
        } else if (alive) {
          msg2 <- "A process with this PID exists, which suggests that the localhost worker is still alive."
        } else {
          msg2 <- "No process exists with this PID, i.e. the localhost worker is no longer alive."
        }
        postmortem$alive <- msg2
      }
    }

    postmortem <- unlist(postmortem, use.names = FALSE)
    if (!is.null(postmortem)) {
       postmortem <- sprintf("Post-mortem diagnostic: %s",
                             paste(postmortem, collapse = ". "))
       msg <- paste0(msg, ". ", postmortem)
    }

    ex <- FutureError(msg, call = ack$call, future = future)
    future$result <- ex
    stop(ex)          
  }
  stop_if_not(isTRUE(ack))

  future$result <- result
  
  if (!inherits(result, "FutureResult")) {
    str(list(node_idx = node_idx, node = node))
    hint <- sprintf("This suggests that the communication with %s worker (%s #%d) is out of sync.",
                    class(future)[1], sQuote(class(node)[1]), node_idx)
    ex <- UnexpectedFutureResultError(future, hint = hint)
    future$result <- ex
    stop(ex)
  }

  ## BACKWARD COMPATIBILITY
  future$state <- if (inherits(result$condition, "error")) "failed" else "finished"

  ## FutureRegistry to use
  reg <- sprintf("workers-%s", attr(workers, "name", exact = TRUE))

  ## Remove from registry
  FutureRegistry(reg, action = "remove", future = future, earlySignal = FALSE)

  ## Garbage collect cluster worker?
  if (future$gc) {
    ## Cleanup global environment while at it
    if (!future$persistent) clusterCall(cl[1], fun = grmall)
    
    ## WORKAROUND: Need to clear cluster worker before garbage collection,
    ## cf. https://github.com/HenrikBengtsson/Wishlist-for-R/issues/27
    ## UPDATE: This has been fixed in R (>= 3.3.2) /HB 2016-10-13
    ## Return a value identifiable for troubleshooting purposes
    clusterCall(cl[1], function() "future-clearing-cluster-worker")
    
    clusterCall(cl[1], gc, verbose = FALSE, reset = FALSE)
  }

  result
}


requestNode <- function(await, workers, timeout = getOption("future.wait.timeout", as.numeric(Sys.getenv("R_FUTURE_WAIT_TIMEOUT", 30 * 24 * 60 * 60))), delta = getOption("future.wait.interval", as.numeric(Sys.getenv("R_FUTURE_WAIT_INTERVAL", 0.2))), alpha = getOption("future.wait.alpha", as.numeric(Sys.getenv("R_FUTURE_WAIT_ALPHA", 1.01)))) {
  debug <- getOption("future.debug", FALSE)
  
  stop_if_not(inherits(workers, "cluster"))
  stop_if_not(is.function(await))
  stop_if_not(is.finite(timeout), timeout >= 0)
  stop_if_not(is.finite(alpha), alpha > 0)

  ## Maximum number of nodes available
  total <- length(workers)

  ## FutureRegistry to use
  name <- attr(workers, "name", exact = TRUE)
  stop_if_not(is.character(name), length(name) == 1L)
  reg <- sprintf("workers-%s", name)
  
  usedNodes <- function() {
    ## Number of unresolved cluster futures
    length(FutureRegistry(reg, action = "list", earlySignal = FALSE))
  }


  t0 <- Sys.time()
  dt <- 0
  iter <- 1L
  interval <- delta
  finished <- FALSE
  while (dt <= timeout) {
    ## Check for available nodes
    used <- usedNodes()
    finished <- (used < total)
    if (finished) break

    if (debug) mdebug("Poll #%d (%s): usedNodes() = %d, workers = %d", iter, format(round(dt, digits = 2L)), used, total)

    ## Wait
    Sys.sleep(interval)
    interval <- alpha * interval
    
    ## Finish/close workers, iff possible
    await()

    iter <- iter + 1L
    dt <- difftime(Sys.time(), t0)
  }

  if (!finished) {
    msg <- sprintf("TIMEOUT: All %d cluster nodes are still occupied after %s (polled %d times)", total, format(round(dt, digits = 2L)), iter)
    if (debug) mdebug(msg)
    stop(msg)
  }

  ## Find which node is available
  avail <- rep(TRUE, times = length(workers))
  futures <- FutureRegistry(reg, action = "list", earlySignal = FALSE)
  nodes <- unlist(lapply(futures, FUN = function(f) f$node), use.names = FALSE)
  avail[nodes] <- FALSE

  ## Sanity check
  stop_if_not(any(avail))

  node_idx <- which(avail)[1L]
  stop_if_not(is.numeric(node_idx), is.finite(node_idx), node_idx >= 1)

  node_idx
}