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#'Collect and merge the computation results
#'
#'The final step of the startR workflow after the data operation. It is used when
#'the parameter 'wait' of Compute() is FALSE. It combines all the chunks of the
#'results as one data array when the execution is done. See more details on
#'\href{https://earth.bsc.es/gitlab/es/startR/-/blob/master/inst/doc/practical_guide.md}{practical guide}.
#'Collect() calls Collect_ecflow() or Collect_autosubmit() according to the
#'chosen workflow manager.
#'@param startr_exec An R object returned by Compute() when the parameter 'wait'
#' of Compute() is FALSE. It can be directly from a Compute() call or read from
#' the RDS file.
#'@param wait A logical value deciding whether the R session waits for the
#' Collect() call to finish (TRUE) or not (FALSE). If TRUE, it will be a
#' blocking call, in which Collect() will retrieve information from the HPC,
#' including signals and outputs, each polling_period seconds. The the status
#' can be monitored on the workflow manager GUI. Collect() will not return
#' until the results of all the chunks have been received. If FALSE, Collect()
#' return an error if the execution has not finished, otherwise it will return
#' the merged array. The default value is TRUE.
#'@param remove A logical value deciding whether to remove of all chunk results
#' received from the HPC after data being collected, as well as the local job
#' folder under 'ecflow_suite_dir' or 'autosubmit_suite_dir'. To preserve the
#' data and Collect() them as many times as desired, set remove to FALSE. The
#' default value is TRUE.
#' @param on_remote A logical value deciding to the function is run locally and
#' sync the outputs back from HPC (FALSE, default), or it is run on HPC
#' (TRUE).
#' data_path <- system.file('extdata', package = 'startR')
#' path_obs <- file.path(data_path, 'obs/monthly_mean/$var$/$var$_$sdate$.nc')
#' sdates <- c('200011', '200012')
#' data <- Start(dat = list(list(path = path_obs)),
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#' var = 'tos',
#' sdate = sdates,
#' time = 'all',
#' latitude = 'all',
#' longitude = 'all',
#' return_vars = list(latitude = 'dat',
#' longitude = 'dat',
#' time = 'sdate'),
#' retrieve = FALSE)
#' fun <- function(x) {
#' lat = attributes(x)$Variables$dat1$latitude
#' weight = sqrt(cos(lat * pi / 180))
#' corrected = Apply(list(x), target_dims = "latitude",
#' fun = function(x) {x * weight})
#' }
#' step <- Step(fun = fun,
#' target_dims = 'latitude',
#' output_dims = 'latitude',
#' use_libraries = c('multiApply'),
#' use_attributes = list(data = "Variables"))
#' wf <- AddStep(data, step)
#' \dontrun{
#' res <- Compute(wf, chunks = list(longitude = 2, sdate = 2),
#' threads_load = 1,
#' threads_compute = 4,
#' cluster = list(queue_host = 'nord3',
#' queue_type = 'lsf',
#' temp_dir = '/on_hpc/tmp_dir/',
#' cores_per_job = 2,
#' job_wallclock = '05:00',
#' max_jobs = 4,
#' extra_queue_params = list('#BSUB -q bsc_es'),
#' bidirectional = FALSE,
#' polling_period = 10
#' ),
#' ecflow_suite_dir = '/on_local_machine/username/ecflow_dir/',
#' wait = FALSE)
#' saveRDS(res, file = 'test_collect.Rds')
#' collect_info <- readRDS('test_collect.Rds')
#' result <- Collect(collect_info, wait = TRUE)
#' }
#'
#'@export
Collect <- function(startr_exec, wait = TRUE, remove = TRUE, on_remote = FALSE) {
stop("Parameter 'startr_exec' must be an object of the class ",
"'startR_exec', as returned by Compute(..., wait = FALSE).")
if (!tolower(startr_exec$workflow_manager) %in% c('ecflow', 'autosubmit')) {
stop("Cannot identify the workflow manager. Check the value of 'startr_exec$workflow_manager', which should be 'ecFlow' or 'Autosubmit'.")
}
if (!is.logical(wait)) {
stop("Parameter 'wait' must be logical.")
}
if (!is.logical(remove)) {
stop("Parameter 'remove' must be logical.")
}
if (!is.logical(on_remote)) {
stop("Parameter 'on_remote' must be logical.")
}
if (tolower(startr_exec$workflow_manager) == 'ecflow') {
res <- Collect_ecflow(startr_exec, wait = wait, remove = remove, on_remote = on_remote)
} else if (tolower(startr_exec$workflow_manager) == 'autosubmit') {
res <- Collect_autosubmit(startr_exec, wait = wait, remove = remove, on_remote = on_remote)
Collect_ecflow <- function(startr_exec, wait = TRUE, remove = TRUE, on_remote = FALSE) {
if (!on_remote && Sys.which('ecflow_client') == '') {
stop("ecFlow must be installed in order to collect results from a ",
"Compute() execution.")
}
cluster <- startr_exec[['cluster']]
ecflow_server <- startr_exec[['ecflow_server']]
suite_id <- startr_exec[['suite_id']]
chunks <- startr_exec[['chunks']]
num_outputs <- startr_exec[['num_outputs']]
ecflow_suite_dir <- startr_exec[['ecflow_suite_dir']]
timings <- startr_exec[['timings']]
ecflow_suite_dir_suite <- paste0(ecflow_suite_dir, '/STARTR_CHUNKING_',
suite_id, '/')
if (!is.null(cluster[['temp_dir']])) { #NOTE: Which case doesn't have temp_dir?
remote_ecflow_suite_dir <- cluster[['temp_dir']]
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remote_ecflow_suite_dir_suite <- paste0(cluster[['temp_dir']],
'/STARTR_CHUNKING_',
suite_id, '/')
}
find_task_name <- function(received_file) {
file_name <- received_file
parts <- strsplit(file_name, '__')[[1]]
parts <- parts[c(2:(length(parts) - 1))]
chunk_indices <- rev(sapply(parts, function(x) {
as.numeric(strsplit(x, '_')[[1]][2])
}))
task_pattern <- paste(paste0('*_', chunk_indices, '/'),
collapse = '')
task_glob <- paste0(ecflow_suite_dir_suite, '/*/*/',
task_pattern)
task_path <- Sys.glob(task_glob)
if (length(task_path) != 1) {
stop("Unexpected error while receiving results.")
}
task_name <- strsplit(task_path, 'computation')[[1]][2]
task_name <- paste0('/STARTR_CHUNKING_', suite_id,
'/computation', task_name)
task_name
}
done <- FALSE
attempt <- 1
list.files(ecflow_suite_dir_suite)))
}
if (cluster[['bidirectional']]) {
t_transfer_back <- NA
} else {
t_transfer_back <- 0
}
time_before_first_chunk <- startr_exec[['t_begin_first_chunk']]
first_chunk_received <- FALSE
rsync_petition_file_lines <- c('+ *.Rds', '+ *.timings', '+ *.crashed',
'+ *.running', '- *')
rsync_petition_file <- tempfile()
writeLines(rsync_petition_file_lines, rsync_petition_file)
Sys.sleep(2)
while (!done) {
if (cluster[['bidirectional']]) {
status <- system(paste0("ecflow_client --get_state=STARTR_CHUNKING_",
suite_id, " --host=",
ecflow_server[['host']], " --port=", ecflow_server[['port']]),
intern = TRUE)
if (any(grepl(paste0("suite STARTR_CHUNKING_", suite_id, " #.* state:complete"), status))) {
done <- TRUE
} else if (!wait) {
stop("Computation in progress...")
if (!first_chunk_received) {
if (any(grepl('state:complete', status))) {
if (!is.null(time_before_first_chunk)) {
time_after_first_chunk <- Sys.time()
estimate <- (time_after_first_chunk -
time_before_first_chunk) *
ceiling((prod(unlist(chunks)) - cluster[['max_jobs']]) /
cluster[['max_jobs']])
units(estimate) <- 'mins'
paste0('Remaining time estimate (neglecting queue and ',
'merge time) (at ', format(time_after_first_chunk),
time_before_first_chunk), ' per chunk)')
)
}
first_chunk_received <- TRUE
}
}
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Sys.sleep(min(sqrt(attempt), 5))
} else {
#if (sum_received_chunks == 0) {
# # Accounting for the fist chunk received in ByChunks and
# # setting it to complete
# # ByChunks needs the first chunk to calculate remaining time
# received_files <- list.files(ecflow_suite_dir_suite)
# received_chunks <- received_files[grepl('Rds$',
# received_files)]
#}
failed <- FALSE
t_begin_transfer_back <- Sys.time()
rsync_output <- tryCatch({
system(paste0("rsync -rav --include-from=", rsync_petition_file, " '",
cluster[['queue_host']], ":", remote_ecflow_suite_dir_suite, "' ",
ecflow_suite_dir_suite, "/"), intern = TRUE)
}, error = function(e) {
message("Warning: rsync from remote server to collect results failed. ",
"Retrying soon.")
failed <- TRUE
})
t_end_transfer_back <- Sys.time()
t_transfer_back <- t_transfer_back + as.numeric(difftime(t_end_transfer_back,
t_begin_transfer_back, units = 'secs'))
if (!failed) {
#if (sum_received_chunks == 0) {
# rsync_output <- c(rsync_output, received_chunks)
#}
received_running <- grepl('running$', rsync_output)
for (received_chunk_index in which(received_running)) {
file_name <- rsync_output[received_chunk_index]
task_name <- find_task_name(file_name)
system(paste0('ecflow_client --force=active recursive ',
task_name,
" --host=", ecflow_server[['host']],
" --port=", ecflow_server[['port']]))
}
received_crashed <- grepl('crashed$', rsync_output)
for (received_chunk_index in which(received_crashed)) {
file_name <- rsync_output[received_chunk_index]
task_name <- find_task_name(file_name)
system(paste0('ecflow_client --force=aborted recursive ',
task_name,
" --host=", ecflow_server[['host']],
" --port=", ecflow_server[['port']]))
}
received_chunks <- grepl('Rds$', rsync_output)
for (received_chunk_index in which(received_chunks)) {
file_name <- rsync_output[received_chunk_index]
task_name <- find_task_name(file_name)
system(paste0('ecflow_client --force=complete recursive ',
task_name,
" --host=", ecflow_server[['host']],
" --port=", ecflow_server[['port']]))
sum_received_chunks <- sum_received_chunks + 1
if (!first_chunk_received) {
if (!is.null(time_before_first_chunk)) {
time_after_first_chunk <- Sys.time()
estimate <- (time_after_first_chunk -
time_before_first_chunk) *
ceiling((prod(unlist(chunks)) - cluster[['max_jobs']]) /
cluster[['max_jobs']])
units(estimate) <- 'mins'
.message(
paste0('Remaining time estimate (neglecting queue and ',
'merge time) (at ', format(time_after_first_chunk),
'): ', format(estimate), ' (',
format(time_after_first_chunk -
time_before_first_chunk), ' per chunk)')
)
}
first_chunk_received <- TRUE
}
}
if (sum_received_chunks / num_outputs == prod(unlist(chunks))) {
done <- TRUE
} else if (!wait) {
stop("Computation in progress...")
}
} else { # on_remote
sum_received_chunks <- sum(grepl('.*\\.Rds$', list.files(remote_ecflow_suite_dir_suite )))
if (sum_received_chunks / num_outputs == prod(unlist(chunks))) {
done <- TRUE
} else if (!wait) {
stop("Computation in progress...")
} else {
message("Computation in progress, ", sum_received_chunks, " of ", prod(unlist(chunks)), " chunks are done.")
message("Will try again after polling_period...")
Sys.sleep(cluster[['polling_period']])
}
}
attempt <- attempt + 1
}
file.remove(rsync_petition_file)
timings[['transfer_back']] <- t_transfer_back
if (!on_remote && !is.null(cluster[['temp_dir']])) {
system(paste0('ssh ', cluster[['queue_host']], ' "rm -rf ',
remote_ecflow_suite_dir_suite, '"'))
}
if (remove) {
.warning("ATTENTION: The source chunks will be removed from the ",
"system. Store the result after Collect() ends if needed.")
}
if (!on_remote) {
target_folder <- ecflow_suite_dir
target_folder_suite <- ecflow_suite_dir_suite
} else {
target_folder <- remote_ecflow_suite_dir
target_folder_suite <- remote_ecflow_suite_dir_suite
}
result <- .MergeChunks(target_folder, suite_id, remove)
t_end_merge <- Sys.time()
timings[['merge']] <- as.numeric(difftime(t_end_merge, t_begin_merge, units = 'secs'))
received_files <- list.files(target_folder_suite, full.names = TRUE)
received_timings_files <- received_files[grepl('timings$', received_files)]
for (timings_file in received_timings_files) {
times <- readRDS(timings_file)
timings[['queue']] <- c(timings[['queue']], times['queue'])
timings[['job_setup']] <- c(timings[['job_setup']], times['job_setup'])
timings[['load']] <- c(timings[['load']], times['load'])
timings[['compute']] <- c(timings[['compute']], times['compute'])
}
if (remove) {
if (!on_remote) {
system(paste0("ecflow_client --delete=force yes /STARTR_CHUNKING_",
suite_id, " --host=", ecflow_server[['host']],
" --port=", ecflow_server[['port']]))
}
unlink(target_folder_suite, recursive = TRUE)
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}
if (attempt > 2) {
t_end_total <- Sys.time()
timings[['total']] <- as.numeric(difftime(t_end_total, timings[['total']], units = 'secs'))
} else {
# When attempt <= 2, it means all results were ready possibly from
# long ago, so is not straightfowrard to work out total time.
timings[['total']] <- NA
}
message(paste0("* Computation ended successfully."))
message(paste0("* Number of chunks: ",
timings[['nchunks']]))
message(paste0("* Max. number of concurrent chunks (jobs): ",
timings[['concurrent_chunks']]))
message(paste0("* Requested cores per job: ",
timings[['cores_per_job']]))
message(paste0("* Load threads per chunk: ",
timings[['threads_load']]))
message(paste0("* Compute threads per chunk: ",
timings[['threads_compute']]))
message(paste0("* Total time (s): ",
timings[['total']]))
message(paste0("* Chunking setup: ",
timings[['bychunks_setup']]))
message(paste0("* Data upload to cluster: ",
timings[['transfer']]))
message(paste0("* All chunks: ",
timings[['total']] -
timings[['bychunks_setup']] -
timings[['transfer']] -
timings[['transfer_back']] -
timings[['merge']]))
message(paste0("* Transfer results from cluster: ",
timings[['transfer_back']]))
message(paste0("* Merge: ",
timings[['merge']]))
message(paste0("* Each chunk: "))
message(paste0("* queue: "))
message(paste0("* mean: ",
mean(timings[['queue']])))
message(paste0("* min: ",
min(timings[['queue']])))
message(paste0("* max: ",
max(timings[['queue']])))
message(paste0("* job setup: "))
message(paste0("* mean: ",
mean(timings[['job_setup']])))
message(paste0("* min: ",
min(timings[['job_setup']])))
message(paste0("* max: ",
max(timings[['job_setup']])))
message(paste0("* load: "))
message(paste0("* mean: ",
mean(timings[['load']])))
message(paste0("* min: ",
min(timings[['load']])))
message(paste0("* max: ",
max(timings[['load']])))
message(paste0("* compute: "))
message(paste0("* mean: ",
mean(timings[['compute']])))
message(paste0("* min: ",
min(timings[['compute']])))
message(paste0("* max: ",
max(timings[['compute']])))
#system("ecflow_client --shutdown --port=5678")
#system("ecflow_stop.sh -p 5678")
#result <- readRDS(paste0(ecflow_output_dir, '/result.Rds'))
#file.remove(paste0(ecflow_output_dir, '/result.Rds'))
attr(result, 'startR_compute_profiling') <- timings
result
}
Collect_autosubmit <- function(startr_exec, wait = TRUE, remove = TRUE, on_remote = FALSE) {
suite_id <- startr_exec[['suite_id']]
chunks <- startr_exec[['chunks']]
num_outputs <- startr_exec[['num_outputs']]
autosubmit_suite_dir <- startr_exec[['autosubmit_suite_dir']]
autosubmit_suite_dir_suite <- paste0(autosubmit_suite_dir, '/STARTR_CHUNKING_', suite_id, '/')
remote_autosubmit_suite_dir <- file.path("/esarchive/autosubmit/", suite_id, 'proj')
remote_autosubmit_suite_dir_suite <- paste0(remote_autosubmit_suite_dir, '/STARTR_CHUNKING_', suite_id, '/')
done <- FALSE
while (!done) { # If wait, try until it is done
sum_received_chunks <- sum(grepl('.*\\.Rds$', list.files(remote_autosubmit_suite_dir_suite)))
if (sum_received_chunks / num_outputs == prod(unlist(chunks))) {
done <- TRUE
} else if (!wait) {
stop("Computation in progress...")
} else {
message("Computation in progress, ", sum_received_chunks, " of ", prod(unlist(chunks)), " chunks are done...\n",
"Check status on Autosubmit GUI: https://earth.bsc.es/autosubmitapp/experiment/", suite_id)
}
} # while !done
result <- .MergeChunks(remote_autosubmit_suite_dir, suite_id, remove = remove)
if (remove) {
.warning("ATTENTION: The source chunks will be removed from the ",
"system. Store the result after Collect() ends if needed.")
unlink(paste0(autosubmit_suite_dir_suite),
recursive = TRUE)
}
# Remove bigmemory objects (e.g., a68h_1_1_1_1_1 and a68h_1_1_1_1_1.desc)
# If run_dir is specified, the files are under run_dir; if not, files are under proj/STARTR_CHUNKING_xxxx/
if (!is.null(run_dir)) {
file.remove(
file.path(run_dir,
list.files(run_dir)[grepl(paste0("^", suite_id, "_.*"), list.files(run_dir))])
)
} else {
file.remove(
file.path(remote_autosubmit_suite_dir_suite,
list.files(remote_autosubmit_suite_dir_suite)[grepl(paste0("^", suite_id, "_.*"), list.files(remote_autosubmit_suite_dir_suite))])
)
}