chunks <- list(lat = 2, lon = 3) cluster <- list(queue_host = "local", #"nord3", #'local', #Q: What is the name? The ones recognized by autosubmit? #temp_dir = '/esarchive/autosubmit/', #Q: Do we need a dir for autosubmit? NO. r_module = 'R/4.1.2-foss-2019b', cores_per_job = 4, job_wallclock = '01:00:00', max_jobs = 4, expid = "a659", # different from now hpc_user = "bsc32734") # different from now autosubmit_suite_dir <- "/home/Earth/aho/startR_local_autosubmit/" # These two functions should be called by ByChunks source("/esarchive/scratch/aho/git/aho-testtest/startR/autosubmit/write_autosubmit_conf.R") source("/esarchive/scratch/aho/git/aho-testtest/startR/autosubmit/write_bash.R") write_autosubmit_conf(chunks, cluster, autosubmit_suite_dir) write_bash(chunks, cluster, autosubmit_suite_dir) #======================================================== library(startR) data <- Start(dat = "/esarchive/exp/ecmwf/system5c3s/monthly_mean/$var$_f6h/$var$_$sdate$.nc", var = c('tas'), sdate = paste0(2017:2018, '0501'), ensemble = 'all', ftime = indices(1:3), lat = values(list(20, 80)), lat_reorder = Sort(), lon = values(list(-80, 40)), lon_reorder = CircularSort(-180, 180), synonims = list(ftime = c('ftime', 'time'), lat = c('lat', 'latitude'), lon = c('lon', 'longitude')), return_vars = list(ftime = 'sdate', lon = NULL, lat = NULL), retrieve = FALSE) func <- function(x) { return(x) } step <- Step(func, target_dims = c('lat', 'lon'), output_dims = c('lat', 'lon'), use_attributes = list("Variables")) wf <- AddStep(data, step) autosubmit_suite_dir <- "/home/Earth/aho/startR_local_autosubmit/" #--------- Source stuff for testing ------------- setwd('/esarchive/scratch/aho/git/aho-testtest/startR/autosubmit') source('Compute.R') source('ByChunks_AS.R') .message <- startR:::.message .warning <- startR:::.warning #----------------------------------------------- res <- Compute(wf, chunks = list(sdate = 2), threads_compute = 4, cluster = list( queue_host = 'nord3', # queue_type = 'slurm', # temp_dir = temp_dir, r_module = 'R/4.1.2-foss-2019b', cores_per_job = 4, job_wallclock = '01:00:00', max_jobs = 4, # bidirectional = FALSE, # polling_period = 10, extra_queue_params = list('#SBATCH --constraint=medmem', '#SBATCH --exclusive'), expid = "a68h", hpc_user = "bsc32734" ), workflow_manager = 'autosubmit', # 'ecFlow' autosubmit_suite_dir = autosubmit_suite_dir, wait = TRUE )