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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
autosubmit_suite_dir <- "/home/Earth/aho/startR_local_autosubmit/"
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)
#========================================================
#========================================================
# CASE 1: return data directly
# library(startR)
source("~/aho-testtest/helper_script/load_local_package.R")
load_local_package("/esarchive/scratch/aho/git/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',
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/" # can be NULL
if (run_on == 'local') {
r_module_ver <- "R/4.1.2-foss-2015a-bare"
} else if (run_on == 'nord3') {
r_module_ver <- "R/4.1.2-foss-2019b"
}
# extra_queue_params = list('#SBATCH --constraint=medmem', '#SBATCH --exclusive'),
autosubmit_server = NULL, #'bscesautosubmit01',
#========================================================
# CASE 2: real calculation
#========================================================
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',
time = indices(1:3),
lat = values(list(20, 80)), lat_reorder = Sort(),
lon = values(list(-80, 40)), lon_reorder = CircularSort(-180, 180),
synonims = list(lat = c('lat', 'latitude'), lon = c('lon', 'longitude')),
return_vars = list(time = 'sdate', lon = NULL, lat = NULL),
retrieve = FALSE)
func <- function(x) {
res <- ClimProjDiags::WeightedMean(x, lon = attr(x, 'Variables')$common$lon, lat = attr(x, 'Variables')$common$lat)
return(res)
}
step <- Step(func, target_dims = c('lat', 'lon'), output_dims = NULL,
use_attributes = list("Variables"), use_libraries = "ClimProjDiags")
wf <- AddStep(data, step)
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#--------- Source stuff for testing -------------
setwd('/esarchive/scratch/aho/git/aho-testtest/startR/autosubmit')
source('Compute.R')
source('ByChunks_AS.R')
source("Collect_AS.R")
.message <- startR:::.message
.warning <- startR:::.warning
#-----------------------------------------------
run_on <- 'local'
if (run_on == 'local') {
r_module_ver <- "R/4.1.2-foss-2015a-bare"
} else if (run_on == 'nord3') {
r_module_ver <- "R/4.1.2-foss-2019b"
}
res <- Compute(wf, chunks = list(sdate = 2, ensemble = 2),
threads_compute = 4,
cluster = list(
queue_host = run_on, #'nord3', # name in platforms.yml
r_module = r_module_ver,
autosubmit_module = 'autosubmit/4.0.0b-foss-2015a-Python-3.7.3',
cores_per_job = 4,
job_wallclock = '01:00:00',
max_jobs = 4,
polling_period = 10,
extra_queue_params = list('#SBATCH --constraint=medmem', '#SBATCH --exclusive'),
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hpc_user = "bsc32734"
),
workflow_manager = 'autosubmit', # 'ecFlow'
autosubmit_suite_dir = autosubmit_suite_dir,
autosubmit_server = NULL, #'bscesautosubmit01',
wait = TRUE
)
#========================================================
# CASE 3: 2 dats
#========================================================
library(startR)
path1 <- "/esarchive/exp/ecmwf/system5c3s/monthly_mean/$var$_f6h/$var$_$sdate$.nc"
path2 <- "/esarchive/exp/ecmwf/system5_m1/monthly_mean/$var$_f6h/$var$_$sdate$.nc"
data <- Start(dat = list(list(name = 'system5c3s', path = path1),
list(name = 'system5_m1', path = path2)),
var = c('tas'),
sdate = paste0(2017:2018, '0501'),
ensemble = 'all',
time = indices(1:3),
lat = values(list(20, 80)), lat_reorder = Sort(),
lon = values(list(-80, 40)), lon_reorder = CircularSort(-180, 180),
transform = CDORemapper,
transform_extra_cells = 2,
transform_params = list(grid = 'r360x181',
method = 'conservative'),
transform_vars = c('lat', 'lon'),
synonims = list(lat = c('lat', 'latitude'), lon = c('lon', 'longitude')),
return_vars = list(time = 'sdate', lon = 'dat', lat = 'dat'),
retrieve = FALSE)
func <- function(x) {
res <- ClimProjDiags::WeightedMean(x, lon = attr(x, 'Variables')$system5c3s$lon, lat = attr(x, 'Variables')$system5c3s$lat)
return(res)
}
step <- Step(func, target_dims = c('dat', 'lat', 'lon'), output_dims = 'dat',
use_attributes = list("Variables"), use_libraries = "ClimProjDiags")
step <- Step(func, target_dims = c('lat', 'lon'), output_dims = NULL,
use_attributes = list("Variables"), use_libraries = "ClimProjDiags")
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')
source("Collect_AS.R")
.message <- startR:::.message
.warning <- startR:::.warning
#-----------------------------------------------
run_on <- 'local'
if (run_on == 'local') {
r_module_ver <- "R/4.1.2-foss-2015a-bare"
cdo_module_ver <- "CDO/1.9.8-foss-2015a"
} else if (run_on == 'nord3') {
r_module_ver <- "R/4.1.2-foss-2019b"
cluster = list(
queue_host = run_on, #'nord3', # name in platforms.yml
r_module = r_module_ver,
autosubmit_module = 'autosubmit/4.0.0b-foss-2015a-Python-3.7.3',
CDO_module = cdo_module_ver,
cores_per_job = 4,
job_wallclock = '01:00:00',
max_jobs = 4,
polling_period = 10,
extra_queue_params = list('#SBATCH --constraint=medmem', '#SBATCH --exclusive'),
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expid = "a68e"
),
workflow_manager = 'autosubmit', # 'ecFlow'
autosubmit_suite_dir = autosubmit_suite_dir,
autosubmit_server = NULL, #'bscesautosubmit01',
wait = TRUE
)
#========================================================
# CASE 4: 2 outputs, named outputs
#========================================================
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',
time = indices(1:3),
lat = values(list(20, 80)), lat_reorder = Sort(),
lon = values(list(-80, 40)), lon_reorder = CircularSort(-180, 180),
synonims = list(lat = c('lat', 'latitude'), lon = c('lon', 'longitude')),
return_vars = list(time = 'sdate', lon = NULL, lat = NULL),
retrieve = FALSE)
func <- function(x) {
return(list(mean = mean(x, na.rm = T), min = min(x, na.rm = T)))
}
step <- Step(func, target_dims = c('lat', 'lon'), output_dims = list(mean = NULL, min = NULL))
wf <- AddStep(data, step)[[1]]
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')
source("Collect_AS.R")
.message <- startR:::.message
.warning <- startR:::.warning
#-----------------------------------------------
run_on <- 'local'
if (run_on == 'local') {
r_module_ver <- "R/4.1.2-foss-2015a-bare"
cdo_module_ver <- "CDO/1.9.8-foss-2015a"
} else if (run_on == 'nord3') {
r_module_ver <- "R/4.1.2-foss-2019b"
}
res <- Compute(wf, chunks = list(sdate = 2),
threads_compute = 4,
cluster = list(
queue_host = run_on, #'nord3', # name in platforms.yml
r_module = r_module_ver,
autosubmit_module = 'autosubmit/4.0.0b-foss-2015a-Python-3.7.3',
# CDO_module = cdo_module_ver,
cores_per_job = 4,
job_wallclock = '01:00:00',
max_jobs = 4,
polling_period = 10,
extra_queue_params = list('#SBATCH --constraint=medmem', '#SBATCH --exclusive'),
# hpc_user = "bsc32734",
expid = "a68e"
),
workflow_manager = 'autosubmit', # 'ecFlow'
autosubmit_suite_dir = autosubmit_suite_dir,
autosubmit_server = NULL, #'bscesautosubmit01',
wait = TRUE
)
# Minimal example, on AS VM
test_AS_error <- function () {
as_module <- "autosubmit/4.0.0b-foss-2015a-Python-3.7.3"
exp_id <- "a659" # minimum script
sys_commands <- paste0("module load ", as_module, "; ",
"autosubmit create ", exp_id, " -np; ",
"autosubmit refresh ", exp_id, "; ",
"autosubmit run ", exp_id)
system(sys_commands)
# It should stop here because autosubmit run xxxx jobs failed
# But now, it keeps running the following line.
print("You shouldn't see this message!!")
}