From 8c5ba084ba66c72f936b02c264e86d88b261f742 Mon Sep 17 00:00:00 2001
From: vagudets <victoria.agudetse@bsc.es>
Date: Fri, 1 Aug 2025 12:38:41 +0200
Subject: [PATCH 1/9] Run Compute() with Autosubmit on MN5 and CTE-AMD (WIP)

---
 R/ByChunks_autosubmit.R                       | 67 +++++++++++++------
 R/Collect.R                                   | 42 +++++++++---
 R/Utils.R                                     |  6 +-
 inst/chunking/Autosubmit/startR_autosubmit.sh |  2 +-
 4 files changed, 85 insertions(+), 32 deletions(-)

diff --git a/R/ByChunks_autosubmit.R b/R/ByChunks_autosubmit.R
index bf63878d..795cd8ea 100644
--- a/R/ByChunks_autosubmit.R
+++ b/R/ByChunks_autosubmit.R
@@ -29,7 +29,7 @@
 #'  as autosubmit machine. The default value is NULL, and a temporary folder 
 #'  under the current working folder will be created.
 #'@param autosubmit_server A character vector indicating the login node of the 
-#'  autosubmit machine. It can be "bscesautosubmit01" or "bscesautosubmit02".
+#'  autosubmit machine. It can be "bscesautosubmit03" or "bscesautosubmit04".
 #'  If NULL, Autosubmit will be run locally on the current machine.
 #'  The default value is NULL.
 #'@param silent A logical value deciding whether to print the computation 
@@ -165,8 +165,9 @@ ByChunks_autosubmit <- function(step_fun, cube_headers, ..., chunks = 'auto',
 
   ## autosubmit_server
   if (!is.null(autosubmit_server)) {
-    if (!autosubmit_server %in% c('bscesautosubmit01', 'bscesautosubmit02')) {
-      stop("Parameter 'autosubmit_server' must be one existing Autosubmit machine login node, 'bscesautosubmit01' or 'bscesautosubmit02'.")
+    if (!autosubmit_server %in% c('bscesautosubmit03', 'bscesautosubmit04')) {
+      stop("Parameter 'autosubmit_server' must be one existing Autosubmit ",
+           "machine login node, 'bscesautosubmit03' or 'bscesautosubmit04'.")
     }
   }
 
@@ -192,7 +193,7 @@ ByChunks_autosubmit <- function(step_fun, cube_headers, ..., chunks = 'auto',
   default_cluster <- list(queue_host = NULL,
 #                          queue_type = 'slurm',
                           data_dir = NULL,
-#                          temp_dir = NULL,
+                          temp_dir = NULL,
                           lib_dir = NULL,
                           init_commands = list(''),
                           r_module = 'R',
@@ -236,7 +237,7 @@ ByChunks_autosubmit <- function(step_fun, cube_headers, ..., chunks = 'auto',
   cluster <- default_cluster
 
   ### queue_host 
-  support_hpcs <- c('local', 'nord3', 'nord4') # names in platforms.yml
+  support_hpcs <- c('local', 'nord3', 'nord4', 'amd', 'mn5') # names in platforms.yml
   if (is.null(cluster$queue_host) || !cluster$queue_host %in% support_hpcs) {
     stop("Cluster component 'queue_host' must be one of the following: ", 
          paste(support_hpcs, collapse = ','), '.')
@@ -353,7 +354,7 @@ ByChunks_autosubmit <- function(step_fun, cube_headers, ..., chunks = 'auto',
   if (is.null(cluster[['special_setup']])) {
     cluster[['special_setup']] <- 'none'
   }
-  if (!(cluster[['special_setup']] %in% c('none', 'marenostrum4', 'nord4'))) {
+  if (!(cluster[['special_setup']] %in% c('none', 'gpfs', 'nord4'))) {
     stop("The value provided for the component 'special_setup' of the parameter ",
          "'cluster' is not recognized.")
   }
@@ -387,12 +388,13 @@ ByChunks_autosubmit <- function(step_fun, cube_headers, ..., chunks = 'auto',
   if (!is.null(cluster$hpc_user) && (!is.character(cluster$hpc_user) | length(cluster$hpc_user) != 1)) {
     stop("Cluster component 'hpc_user' must be a character string.")
   }
+  ## TODO: Adjust
   ### run_dir
-  if (!is.null(cluster$run_dir)) {
-    if (!dir.exists(cluster$run_dir)) {
-      stop("Cluster component 'run_dir' ", cluster$run_dir," is not found.")
-    }
-  }
+  ## if (!is.null(cluster$run_dir)) {
+  ##   if (!dir.exists(cluster$run_dir)) {
+  ##     stop("Cluster component 'run_dir' ", cluster$run_dir," is not found.")
+  ##   }
+  ## }
 
 #==============================================
 
@@ -404,9 +406,15 @@ ByChunks_autosubmit <- function(step_fun, cube_headers, ..., chunks = 'auto',
     stop("Could not find or create the directory in  parameter 'autosubmit_suite_dir'.")
   }
 
-  remote_autosubmit_suite_dir <- file.path("/esarchive/autosubmit/", suite_id, 'proj')
+  ## TODO: Order
+  is_autosubmit_suite_dir_shared <- TRUE
+  if (!is.null(cluster[['run_dir']])) {
+    remote_autosubmit_suite_dir <- cluster[['run_dir']]
+    is_autosubmit_suite_dir_shared <- FALSE
+  } else {
+    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, '/')
-
   
   # Work out chunked dimensions and target dimensions
   all_dims <- lapply(cube_headers, attr, 'Dimensions')
@@ -502,8 +510,10 @@ ByChunks_autosubmit <- function(step_fun, cube_headers, ..., chunks = 'auto',
   }
 
   # Copy load_process_save_chunk_autosubmit.R into local folder
-  chunk_script <- file(system.file('chunking/Autosubmit/load_process_save_chunk_autosubmit.R', 
-                                   package = 'startR'))
+  ## TODO: Change for testing
+  chunk_script <- file("/esarchive/scratch/vagudets/repos/startR/inst/chunking/Autosubmit/load_process_save_chunk_autosubmit.R")
+  ##  chunk_script <- file(system.file('chunking/Autosubmit/load_process_save_chunk_autosubmit.R', 
+  ##                                  package = 'startR'))
   chunk_script_lines <- readLines(chunk_script)
   close(chunk_script)
   chunk_script_lines <- gsub('^lib_dir <- *', paste0('lib_dir <- ', 
@@ -516,7 +526,7 @@ ByChunks_autosubmit <- function(step_fun, cube_headers, ..., chunks = 'auto',
                              chunk_script_lines)
   deparsed_calls <- paste0('start_calls <- list(')
   extra_path <- ''
-  if (cluster[['special_setup']] == 'marenostrum4') {
+  if (cluster[['special_setup']] == 'gpfs') {
     extra_path <- '/gpfs/archive/bsc32/'
   }
   for (cube_header in 1:length(cube_headers)) {
@@ -565,6 +575,20 @@ ByChunks_autosubmit <- function(step_fun, cube_headers, ..., chunks = 'auto',
 
   # Modify conf files from template and rewrite to /esarchive/autosubmit/expid/conf/
   write_autosubmit_confs(chunks, cluster, autosubmit_suite_dir)
+
+  ## TODO: Copy files HERE?
+  command <- paste0("ssh ", cluster[['hpc_user']], "@transfer1.bsc.es 'mkdir -p ",
+                  remote_autosubmit_suite_dir,
+                  ' ; cp -r ', '/gpfs/archive/bsc32/', autosubmit_suite_dir, '/. ', remote_autosubmit_suite_dir,
+                  " ; sleep 10 '")
+  if (!is_autosubmit_suite_dir_shared) {
+    system(command)
+    # system(paste0("ssh ", cluster[['hpc_user']], "@transfer1.bsc.es 'mkdir -p ",
+    #               remote_autosubmit_suite_dir,
+    #               # rsync -Rrav
+    #               ' ; cp -r ', '\'', '/gpfs/archive/bsc32/', autosubmit_suite_dir, '/. \' "', remote_autosubmit_suite_dir, '/"',
+    #               " ; sleep 10 '"))
+  }
   
   # Iterate through chunks
   chunk_array <- array(1:prod(unlist(chunks)), dim = (unlist(chunks)))
@@ -596,7 +620,7 @@ ByChunks_autosubmit <- function(step_fun, cube_headers, ..., chunks = 'auto',
     for (cube_header in 1:length(cube_headers)) {
       expected_files <- attr(cube_headers[[cube_header]], 'ExpectedFiles')
       #files_to_check <- c(files_to_check, expected_files)
-      #if (cluster[['special_setup']] == 'marenostrum4') {
+      #if (cluster[['special_setup']] == 'gpfs') {
       #  expected_files <- paste0('/gpfs/archive/bsc32/', expected_files)
       #}
       files_to_send <- c(files_to_send, expected_files)
@@ -653,7 +677,6 @@ ByChunks_autosubmit <- function(step_fun, cube_headers, ..., chunks = 'auto',
   if ((is.null(autosubmit_server)) || 
       (gsub('[[:digit:]]', "", Sys.getenv('HOSTNAME')) == 'bscesautosubmit')) {
     # If autosubmit_server is NULL or we are already on bscesautosubmit0x
-    #NOTE: If we ssh to AS VM and run everything there, we don't need to ssh here
     system(sys_commands)
 
    } else {
@@ -668,6 +691,7 @@ ByChunks_autosubmit <- function(step_fun, cube_headers, ..., chunks = 'auto',
   if (substr(failed_file_size, 1, 1) != 0) {
     # Remove bigmemory objects (e.g., a68h_1_1 and a68h_1_1.desc) if they exist
     # If run_dir is specified, the files are under run_dir; if not, files are under proj/STARTR_CHUNKING_xxxx/
+    ## TODO: If run_dir is not in esarchive this will not work
     if (!is.null(cluster[['run_dir']])) {
       file.remove(
         file.path(cluster[['run_dir']],
@@ -692,8 +716,11 @@ ByChunks_autosubmit <- function(step_fun, cube_headers, ..., chunks = 'auto',
   class(startr_exec) <- 'startR_exec'
 
   if (wait) {
-    result <- Collect(startr_exec, wait = TRUE, remove = T)
-   .message("Computation ended successfully.")
+    result <- Collect(startr_exec,
+                      wait = TRUE,
+                      remove = TRUE,
+                      on_remote = !is_autosubmit_suite_dir_shared)
+    .message("Computation ended successfully.")
     return(result)
 
   } else {
diff --git a/R/Collect.R b/R/Collect.R
index 5ae8b150..6dd58165 100644
--- a/R/Collect.R
+++ b/R/Collect.R
@@ -417,22 +417,46 @@ Collect_autosubmit <- function(startr_exec, wait = TRUE, remove = TRUE, on_remot
   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, '/')
   run_dir <- startr_exec$cluster[['run_dir']]
+  hpc_user <- startr_exec$cluster[['hpc_user']]
 
   done <- FALSE
 
   while (!done) { # If wait, try until it is done
-    sum_received_chunks <- sum(grepl('.*\\.Rds$', list.files(remote_autosubmit_suite_dir_suite)))
-    if (sum_received_chunks / num_outputs == prod(unlist(chunks))) {
-      done <- TRUE
+    if (!on_remote) {
+      sum_received_chunks <- sum(grepl('.*\\.Rds$', 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 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)
+        Sys.sleep(startr_exec$cluster[['polling_period']])
+      }
     } else {
-      message("Computation in progress,  ", sum_received_chunks, "  of ", prod(unlist(chunks)), " chunks are done...\n",
-              "Check status on Autosubmit GUI: https://earth.bsc.es/autosubmitapp/experiment/", suite_id)
-      Sys.sleep(startr_exec$cluster[['polling_period']])
+      # Execution on remote server
+      ## TODO: Not use transfer machine
+      files_in_remote_dir <- system(paste0("ssh ", hpc_user, "@transfer1.bsc.es 'ls ",
+                                           run_dir, "'"),
+                                    intern = TRUE)
+      sum_received_chunks <- sum(grepl('.*\\.Rds$', files_in_remote_dir))
+      if (sum_received_chunks / num_outputs == prod(unlist(chunks))) {
+        done <- TRUE
+        # Transfer files back
+        message("Computation finished on cluster, retrieving files...")
+        files_to_retrieve <- paste0(run_dir, files_in_remote_dir[grepl('.*\\.Rds$', files_in_remote_dir)])
+        ## TODO: Not use transfer machine
+        system(paste0("ssh ", hpc_user, "@transfer1.bsc.es 'mv ",
+                      run_dir, "/* /gpfs/archive/bsc32/", remote_autosubmit_suite_dir_suite, "'"))
+      } 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)
+        Sys.sleep(startr_exec$cluster[['polling_period']])
+      }
     }
-
   } # while !done
 
   result <- .MergeChunks(remote_autosubmit_suite_dir, suite_id, remove = remove)
diff --git a/R/Utils.R b/R/Utils.R
index 28840e19..84a6be49 100644
--- a/R/Utils.R
+++ b/R/Utils.R
@@ -885,8 +885,10 @@ write_autosubmit_bash <- function(chunks, cluster, autosubmit_suite_dir) {
     chunk_args[2, ] <- paste0('%JOBS.CHUNK_', n_chunk, '.', chunk_names, '_N%')
     chunk_args <- paste0('(', paste(c(chunk_args), collapse = ' '), ')')
 
-    bash_script_template <- file(system.file('chunking/Autosubmit/startR_autosubmit.sh',
-                                 package = 'startR'))
+    ## TODO: Change back
+    bash_script_template <- file("/esarchive/scratch/vagudets/repos/startR/inst/chunking/Autosubmit/startR_autosubmit.sh")
+    ## bash_script_template <- file(system.file('chunking/Autosubmit/startR_autosubmit.sh',
+    ##                              package = 'startR'))
     bash_script_lines <- readLines(bash_script_template)
     close(bash_script_template)
 
diff --git a/inst/chunking/Autosubmit/startR_autosubmit.sh b/inst/chunking/Autosubmit/startR_autosubmit.sh
index be8ce1d5..14931eed 100644
--- a/inst/chunking/Autosubmit/startR_autosubmit.sh
+++ b/inst/chunking/Autosubmit/startR_autosubmit.sh
@@ -22,5 +22,5 @@ include_module_load
 cd_run_dir
 
 #e.g., Rscript load_process_save_chunk_autosubmit.R --args $task_path 1 1 1 1 2 2 1 1 1 2 1 2
-Rscript ${proj_dir}/load_process_save_chunk_autosubmit.R --args ${task_path} ${chunk_args[@]}
+Rscript load_process_save_chunk_autosubmit.R --args ${task_path} ${chunk_args[@]}
 
-- 
GitLab


From 453c901c0f47acd7225d5aed032ad923f2db47aa Mon Sep 17 00:00:00 2001
From: vagudets <victoria.agudetse@bsc.es>
Date: Thu, 7 Aug 2025 15:27:52 +0200
Subject: [PATCH 2/9] Clean code

---
 R/ByChunks_autosubmit.R | 46 +++++++++++++++++++++++++----------------
 R/Collect.R             | 11 ++++++----
 R/Utils.R               |  1 +
 3 files changed, 36 insertions(+), 22 deletions(-)

diff --git a/R/ByChunks_autosubmit.R b/R/ByChunks_autosubmit.R
index 795cd8ea..4f6767f1 100644
--- a/R/ByChunks_autosubmit.R
+++ b/R/ByChunks_autosubmit.R
@@ -238,10 +238,21 @@ ByChunks_autosubmit <- function(step_fun, cube_headers, ..., chunks = 'auto',
 
   ### queue_host 
   support_hpcs <- c('local', 'nord3', 'nord4', 'amd', 'mn5') # names in platforms.yml
+  hostnames <- list(local = "",
+                    nord3 = "nord4.bsc.es",
+                    nord4 = "n4login1.bsc.es",
+                    amd = "amdlogin1.bsc.es",
+                    mn5 = "glogin1.bsc.es")
   if (is.null(cluster$queue_host) || !cluster$queue_host %in% support_hpcs) {
     stop("Cluster component 'queue_host' must be one of the following: ", 
          paste(support_hpcs, collapse = ','), '.')
   }
+  ### hostname
+  if (is.null(cluster$hostname) {
+    hostname <- hostnames[[cluster$queue_host]]
+  } else {
+    warning("Taking user-defined hostname for HPC platform.")
+  }
 
   ### data_dir
   is_data_dir_shared <- FALSE
@@ -388,13 +399,17 @@ ByChunks_autosubmit <- function(step_fun, cube_headers, ..., chunks = 'auto',
   if (!is.null(cluster$hpc_user) && (!is.character(cluster$hpc_user) | length(cluster$hpc_user) != 1)) {
     stop("Cluster component 'hpc_user' must be a character string.")
   }
-  ## TODO: Adjust
   ### run_dir
-  ## if (!is.null(cluster$run_dir)) {
-  ##   if (!dir.exists(cluster$run_dir)) {
-  ##     stop("Cluster component 'run_dir' ", cluster$run_dir," is not found.")
-  ##   }
-  ## }
+  is_autosubmit_suite_dir_shared <- TRUE
+  if (!is.null(cluster$run_dir)) {
+    if (!dir.exists(cluster$run_dir)) {
+      warning("Cluster component 'run_dir' ", cluster$run_dir" not found.",
+              " It will be created in the remote cluster.")
+    is_autosubmit_suite_dir_shared <- FALSE
+    }
+  }
+
+
 
 #==============================================
 
@@ -406,11 +421,8 @@ ByChunks_autosubmit <- function(step_fun, cube_headers, ..., chunks = 'auto',
     stop("Could not find or create the directory in  parameter 'autosubmit_suite_dir'.")
   }
 
-  ## TODO: Order
-  is_autosubmit_suite_dir_shared <- TRUE
   if (!is.null(cluster[['run_dir']])) {
     remote_autosubmit_suite_dir <- cluster[['run_dir']]
-    is_autosubmit_suite_dir_shared <- FALSE
   } else {
     remote_autosubmit_suite_dir <- file.path("/esarchive/autosubmit/", suite_id, 'proj')
   }
@@ -526,7 +538,7 @@ ByChunks_autosubmit <- function(step_fun, cube_headers, ..., chunks = 'auto',
                              chunk_script_lines)
   deparsed_calls <- paste0('start_calls <- list(')
   extra_path <- ''
-  if (cluster[['special_setup']] == 'gpfs') {
+  if (cluster[['special_setup']] == 'marenostrum4') {
     extra_path <- '/gpfs/archive/bsc32/'
   }
   for (cube_header in 1:length(cube_headers)) {
@@ -576,17 +588,15 @@ ByChunks_autosubmit <- function(step_fun, cube_headers, ..., chunks = 'auto',
   # Modify conf files from template and rewrite to /esarchive/autosubmit/expid/conf/
   write_autosubmit_confs(chunks, cluster, autosubmit_suite_dir)
 
-  ## TODO: Copy files HERE?
-  command <- paste0("ssh ", cluster[['hpc_user']], "@transfer1.bsc.es 'mkdir -p ",
-                  remote_autosubmit_suite_dir,
-                  ' ; cp -r ', '/gpfs/archive/bsc32/', autosubmit_suite_dir, '/. ', remote_autosubmit_suite_dir,
-                  " ; sleep 10 '")
+  ## TODO: Avoid using transfer machine
   if (!is_autosubmit_suite_dir_shared) {
-    system(command)
+    system(paste0("ssh ", cluster[['hpc_user']], "@", cluster[['hostname']], 
+                  " 'mkdir -p remote_autosubmit_suite_dir'; rsync -r",
+                  autosubmit_suite_dir, "/.", " " cluster[['hostname']], ":", remote_autosubmit_suite_dir,
+                  " ; sleep 10"))
     # system(paste0("ssh ", cluster[['hpc_user']], "@transfer1.bsc.es 'mkdir -p ",
     #               remote_autosubmit_suite_dir,
-    #               # rsync -Rrav
-    #               ' ; cp -r ', '\'', '/gpfs/archive/bsc32/', autosubmit_suite_dir, '/. \' "', remote_autosubmit_suite_dir, '/"',
+    #               ' ; cp -r ', '/gpfs/archive/bsc32/', autosubmit_suite_dir, '/. ', remote_autosubmit_suite_dir,
     #               " ; sleep 10 '"))
   }
   
diff --git a/R/Collect.R b/R/Collect.R
index 6dd58165..61216c96 100644
--- a/R/Collect.R
+++ b/R/Collect.R
@@ -418,6 +418,7 @@ Collect_autosubmit <- function(startr_exec, wait = TRUE, remove = TRUE, on_remot
   remote_autosubmit_suite_dir_suite <- paste0(remote_autosubmit_suite_dir, '/STARTR_CHUNKING_', suite_id, '/')
   run_dir <- startr_exec$cluster[['run_dir']]
   hpc_user <- startr_exec$cluster[['hpc_user']]
+  hostname <- startr_exec$cluster[['hostname']]
 
   done <- FALSE
 
@@ -436,8 +437,7 @@ Collect_autosubmit <- function(startr_exec, wait = TRUE, remove = TRUE, on_remot
       }
     } else {
       # Execution on remote server
-      ## TODO: Not use transfer machine
-      files_in_remote_dir <- system(paste0("ssh ", hpc_user, "@transfer1.bsc.es 'ls ",
+      files_in_remote_dir <- system(paste0("ssh ", hpc_user, "@", hostname, " 'ls ",
                                            run_dir, "'"),
                                     intern = TRUE)
       sum_received_chunks <- sum(grepl('.*\\.Rds$', files_in_remote_dir))
@@ -447,8 +447,11 @@ Collect_autosubmit <- function(startr_exec, wait = TRUE, remove = TRUE, on_remot
         message("Computation finished on cluster, retrieving files...")
         files_to_retrieve <- paste0(run_dir, files_in_remote_dir[grepl('.*\\.Rds$', files_in_remote_dir)])
         ## TODO: Not use transfer machine
-        system(paste0("ssh ", hpc_user, "@transfer1.bsc.es 'mv ",
-                      run_dir, "/* /gpfs/archive/bsc32/", remote_autosubmit_suite_dir_suite, "'"))
+        ## Alternative without rsync: 'for file in bar*; do scp "$file" user@server:/destination && rm "$file" ; done'
+        system(paste0("rsync -avz --remove-source-files -e ssh ", hpc_user, "@", hostname, ":" run_dir, "/* ",
+                      remote_autosubmit_suite_dir_suite))
+        ## system(paste0("ssh ", hpc_user, "@transfer1.bsc.es 'mv ",
+        ##               run_dir, "/* /gpfs/archive/bsc32/", remote_autosubmit_suite_dir_suite, "'"))
       } else if (!wait) {
         stop("Computation in progress...")
       } else {
diff --git a/R/Utils.R b/R/Utils.R
index 84a6be49..5640e855 100644
--- a/R/Utils.R
+++ b/R/Utils.R
@@ -1030,6 +1030,7 @@ write_autosubmit_confs <- function(chunks, cluster, autosubmit_suite_dir) {
       if (tolower(cluster$queue_host) != "local") {
         conf$Platforms[[cluster$queue_host]]$USER <- cluster$hpc_user
         conf$Platforms[[cluster$queue_host]]$PROCESSORS_PER_NODE <- as.integer(cluster$cores_per_job)
+        conf$Platforms[[cluster$queue_host]]$HOSTNAME <- cluster$hostname
         if (!is.null(cluster$extra_queue_params)) {
           tmp <- unlist(cluster$extra_queue_params)
           for (ii in 1:length(tmp)) {
-- 
GitLab


From 24fae7b2d815419fdd57d944a794cd6708299407 Mon Sep 17 00:00:00 2001
From: vagudets <victoria.agudetse@bsc.es>
Date: Thu, 7 Aug 2025 16:20:56 +0200
Subject: [PATCH 3/9] Fix typos and 'run_dir' definition

---
 R/ByChunks_autosubmit.R | 13 +++++++------
 R/Collect.R             |  2 +-
 2 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/R/ByChunks_autosubmit.R b/R/ByChunks_autosubmit.R
index 4f6767f1..617febc7 100644
--- a/R/ByChunks_autosubmit.R
+++ b/R/ByChunks_autosubmit.R
@@ -248,8 +248,8 @@ ByChunks_autosubmit <- function(step_fun, cube_headers, ..., chunks = 'auto',
          paste(support_hpcs, collapse = ','), '.')
   }
   ### hostname
-  if (is.null(cluster$hostname) {
-    hostname <- hostnames[[cluster$queue_host]]
+  if (is.null(cluster$hostname)) {
+    cluster$hostname <- hostnames[[cluster$queue_host]]
   } else {
     warning("Taking user-defined hostname for HPC platform.")
   }
@@ -403,7 +403,7 @@ ByChunks_autosubmit <- function(step_fun, cube_headers, ..., chunks = 'auto',
   is_autosubmit_suite_dir_shared <- TRUE
   if (!is.null(cluster$run_dir)) {
     if (!dir.exists(cluster$run_dir)) {
-      warning("Cluster component 'run_dir' ", cluster$run_dir" not found.",
+      warning("Cluster component 'run_dir' ", cluster$run_dir, " not found.",
               " It will be created in the remote cluster.")
     is_autosubmit_suite_dir_shared <- FALSE
     }
@@ -427,6 +427,7 @@ ByChunks_autosubmit <- function(step_fun, cube_headers, ..., chunks = 'auto',
     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, '/')
+  cluster[['run_dir']] <- remote_autosubmit_suite_dir_suite
   
   # Work out chunked dimensions and target dimensions
   all_dims <- lapply(cube_headers, attr, 'Dimensions')
@@ -591,9 +592,9 @@ ByChunks_autosubmit <- function(step_fun, cube_headers, ..., chunks = 'auto',
   ## TODO: Avoid using transfer machine
   if (!is_autosubmit_suite_dir_shared) {
     system(paste0("ssh ", cluster[['hpc_user']], "@", cluster[['hostname']], 
-                  " 'mkdir -p remote_autosubmit_suite_dir'; rsync -r",
-                  autosubmit_suite_dir, "/.", " " cluster[['hostname']], ":", remote_autosubmit_suite_dir,
-                  " ; sleep 10"))
+                  " 'mkdir -p remote_autosubmit_suite_dir'; rsync -r ",
+                  autosubmit_suite_dir, "/. ", cluster[['hpc_user']], "@", cluster[['hostname']],
+                  ":", remote_autosubmit_suite_dir, " ; sleep 10"))
     # system(paste0("ssh ", cluster[['hpc_user']], "@transfer1.bsc.es 'mkdir -p ",
     #               remote_autosubmit_suite_dir,
     #               ' ; cp -r ', '/gpfs/archive/bsc32/', autosubmit_suite_dir, '/. ', remote_autosubmit_suite_dir,
diff --git a/R/Collect.R b/R/Collect.R
index 61216c96..be9f6d38 100644
--- a/R/Collect.R
+++ b/R/Collect.R
@@ -448,7 +448,7 @@ Collect_autosubmit <- function(startr_exec, wait = TRUE, remove = TRUE, on_remot
         files_to_retrieve <- paste0(run_dir, files_in_remote_dir[grepl('.*\\.Rds$', files_in_remote_dir)])
         ## TODO: Not use transfer machine
         ## Alternative without rsync: 'for file in bar*; do scp "$file" user@server:/destination && rm "$file" ; done'
-        system(paste0("rsync -avz --remove-source-files -e ssh ", hpc_user, "@", hostname, ":" run_dir, "/* ",
+        system(paste0("rsync -avz --remove-source-files -e ssh ", hpc_user, "@", hostname, ":", run_dir, "/* ",
                       remote_autosubmit_suite_dir_suite))
         ## system(paste0("ssh ", hpc_user, "@transfer1.bsc.es 'mv ",
         ##               run_dir, "/* /gpfs/archive/bsc32/", remote_autosubmit_suite_dir_suite, "'"))
-- 
GitLab


From 72b17815e75d3c205e187be6cc3adf0555ba0dd5 Mon Sep 17 00:00:00 2001
From: vagudets <victoria.agudetse@bsc.es>
Date: Thu, 7 Aug 2025 16:27:19 +0200
Subject: [PATCH 4/9] Add example

---
 inst/doc/usecase/ex2_15_margin_run_on_gpfs.R | 70 ++++++++++++++++++++
 1 file changed, 70 insertions(+)
 create mode 100644 inst/doc/usecase/ex2_15_margin_run_on_gpfs.R

diff --git a/inst/doc/usecase/ex2_15_margin_run_on_gpfs.R b/inst/doc/usecase/ex2_15_margin_run_on_gpfs.R
new file mode 100644
index 00000000..51bf1f31
--- /dev/null
+++ b/inst/doc/usecase/ex2_15_margin_run_on_gpfs.R
@@ -0,0 +1,70 @@
+# Author: Victòria Agudetse Roures, Sara Moreno, Núria Pérez Zanón
+# Date: 7th August 2025
+# ------------------------------------------------------------------
+
+# -----------------------------------------------------------------
+# Function working on time dimension e.g.: Season
+# ------------------------------------------------------------------
+library(startR)
+path <- "/esarchive/scratch/vagudets/repos/startR/R/"
+ff <- lapply(list.files(path), function(x) paste0(path, x))
+invisible(lapply(ff, source))
+
+repos <- '/esarchive/exp/ecmwf/system51c3s/monthly_mean/$var$_f6h/$var$_$sdate$.nc'
+data <- Start(dat = repos,
+              var = 'tas',
+              sdate = c('20170101', '20180101'),
+              ensemble = indices(1:20),
+              time = 'all',
+              lat = 'all',
+              lon = indices(1:40),
+              return_vars = list(lat = 'dat', lon = 'dat', time = 'sdate'),
+              retrieve = FALSE)
+
+fun_spring <- function(x) {
+    y <- s2dv::Season(x,  time_dim = 'time', monini = 1, moninf = 3, monsup = 5)
+    return(y)
+}
+
+step1 <- Step(fun = fun_spring,
+             target_dims = c('var', 'time'),
+             output_dims = c('var', 'time'))
+
+
+file_dims <- dim(attr(data, "ExpectedFiles"))
+new_files <- sapply(attr(data, "ExpectedFiles"),
+        function(x) {
+              gsub("/esarchive/", "/gpfs/projects/bsc32/esarchive_cache/", x)
+              })
+dim(new_files) <- file_dims
+attr(data, "ExpectedFiles") <- new_files
+data[2] <- gsub("/esarchive/", "/gpfs/projects/bsc32/esarchive_cache/", data[2])
+
+wf1 <- AddStep(data, step1)
+
+#-----------modify according to your personal info---------
+  queue_host <- 'cte-amd'
+  temp_dir <-  '/gpfs/scratch/bsc32/bsc032762/startR_hpc/'
+  ecflow_suite_dir <- '/gpfs/home/bsc/bsc032762/startR_local/'  #your own local directory
+#------------------------------------------------------------
+  res <- Compute(workflow = wf1,
+                 chunks = list(ensemble = 2,
+             sdate = 2),
+                 threads_load = 2,
+                 threads_compute = 4,
+                 cluster = list(
+                   queue_host = 'amd',
+                   expid = 'a9p5',
+                   hpc_user = "bsc032762",
+                   autosubmit_module = 'autosubmit/4.1.14-foss-2023b-Python-3.11.5',
+                   cores_per_job = 4,
+                   job_wallclock = '01:00',
+                   max_jobs = 100,
+       run_dir = '/gpfs/scratch/bsc32/bsc032762/startR_hpc/'
+                 ),
+                 workflow_manager = 'autosubmit',
+                 autosubmit_suite_dir = "/esarchive/scratch/vagudets/startR_local/",
+                 autosubmit_server = 'bscesautosubmit03',
+                 wait = TRUE
+  )
+
-- 
GitLab


From 225a46d0563496906dc2044ac0ce15373d5b2def Mon Sep 17 00:00:00 2001
From: vagudets <victoria.agudetse@bsc.es>
Date: Thu, 7 Aug 2025 16:27:52 +0200
Subject: [PATCH 5/9] Run unit tests

---
 .Rbuildignore | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.Rbuildignore b/.Rbuildignore
index d79d3e82..698f5e2c 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -9,7 +9,7 @@
 ^inst/doc$
 ^\.gitlab-ci\.yml$
 ## unit tests should be ignored when building the package for CRAN
-^tests$
+#^tests$
 ^inst/PlotProfiling\.R$
 ^.gitlab$
 # Suggested by http://r-pkgs.had.co.nz/package.html
-- 
GitLab


From ea6066123ba3beb7dc862ee043601b89fbf8b3e4 Mon Sep 17 00:00:00 2001
From: vagudets <victoria.agudetse@bsc.es>
Date: Fri, 8 Aug 2025 12:16:39 +0200
Subject: [PATCH 6/9] Use installed autosubmit config files; add/remove TODOs

---
 R/ByChunks_autosubmit.R | 23 +++++++++--------------
 R/Collect.R             |  4 ----
 2 files changed, 9 insertions(+), 18 deletions(-)

diff --git a/R/ByChunks_autosubmit.R b/R/ByChunks_autosubmit.R
index 617febc7..0dd2bcd4 100644
--- a/R/ByChunks_autosubmit.R
+++ b/R/ByChunks_autosubmit.R
@@ -523,10 +523,8 @@ ByChunks_autosubmit <- function(step_fun, cube_headers, ..., chunks = 'auto',
   }
 
   # Copy load_process_save_chunk_autosubmit.R into local folder
-  ## TODO: Change for testing
-  chunk_script <- file("/esarchive/scratch/vagudets/repos/startR/inst/chunking/Autosubmit/load_process_save_chunk_autosubmit.R")
-  ##  chunk_script <- file(system.file('chunking/Autosubmit/load_process_save_chunk_autosubmit.R', 
-  ##                                  package = 'startR'))
+  chunk_script <- file(system.file('chunking/Autosubmit/load_process_save_chunk_autosubmit.R', 
+                                   package = 'startR'))
   chunk_script_lines <- readLines(chunk_script)
   close(chunk_script)
   chunk_script_lines <- gsub('^lib_dir <- *', paste0('lib_dir <- ', 
@@ -589,16 +587,11 @@ ByChunks_autosubmit <- function(step_fun, cube_headers, ..., chunks = 'auto',
   # Modify conf files from template and rewrite to /esarchive/autosubmit/expid/conf/
   write_autosubmit_confs(chunks, cluster, autosubmit_suite_dir)
 
-  ## TODO: Avoid using transfer machine
   if (!is_autosubmit_suite_dir_shared) {
     system(paste0("ssh ", cluster[['hpc_user']], "@", cluster[['hostname']], 
                   " 'mkdir -p remote_autosubmit_suite_dir'; rsync -r ",
                   autosubmit_suite_dir, "/. ", cluster[['hpc_user']], "@", cluster[['hostname']],
                   ":", remote_autosubmit_suite_dir, " ; sleep 10"))
-    # system(paste0("ssh ", cluster[['hpc_user']], "@transfer1.bsc.es 'mkdir -p ",
-    #               remote_autosubmit_suite_dir,
-    #               ' ; cp -r ', '/gpfs/archive/bsc32/', autosubmit_suite_dir, '/. ', remote_autosubmit_suite_dir,
-    #               " ; sleep 10 '"))
   }
   
   # Iterate through chunks
@@ -702,12 +695,14 @@ ByChunks_autosubmit <- function(step_fun, cube_headers, ..., chunks = 'auto',
   if (substr(failed_file_size, 1, 1) != 0) {
     # Remove bigmemory objects (e.g., a68h_1_1 and a68h_1_1.desc) if they exist
     # If run_dir is specified, the files are under run_dir; if not, files are under proj/STARTR_CHUNKING_xxxx/
-    ## TODO: If run_dir is not in esarchive this will not work
     if (!is.null(cluster[['run_dir']])) {
-      file.remove(
-        file.path(cluster[['run_dir']],
-          list.files(cluster[['run_dir']])[grepl(paste0("^", suite_id, "_.*"), list.files(cluster[['run_dir']]))])
-      )
+      if (is_autosubmit_suite_dir_shared) {
+        file.remove(
+          file.path(cluster[['run_dir']],
+            list.files(cluster[['run_dir']])[grepl(paste0("^", suite_id, "_.*"), list.files(cluster[['run_dir']]))])
+        )
+      }
+      ## TODO: Remove files if run_dir is not in esarchive
     } else {
       file.remove(
         file.path(remote_autosubmit_suite_dir_suite,
diff --git a/R/Collect.R b/R/Collect.R
index be9f6d38..49b38917 100644
--- a/R/Collect.R
+++ b/R/Collect.R
@@ -446,12 +446,8 @@ Collect_autosubmit <- function(startr_exec, wait = TRUE, remove = TRUE, on_remot
         # Transfer files back
         message("Computation finished on cluster, retrieving files...")
         files_to_retrieve <- paste0(run_dir, files_in_remote_dir[grepl('.*\\.Rds$', files_in_remote_dir)])
-        ## TODO: Not use transfer machine
-        ## Alternative without rsync: 'for file in bar*; do scp "$file" user@server:/destination && rm "$file" ; done'
         system(paste0("rsync -avz --remove-source-files -e ssh ", hpc_user, "@", hostname, ":", run_dir, "/* ",
                       remote_autosubmit_suite_dir_suite))
-        ## system(paste0("ssh ", hpc_user, "@transfer1.bsc.es 'mv ",
-        ##               run_dir, "/* /gpfs/archive/bsc32/", remote_autosubmit_suite_dir_suite, "'"))
       } else if (!wait) {
         stop("Computation in progress...")
       } else {
-- 
GitLab


From 5e0aa4a8cbf16016de57d7522502f867055c4ff6 Mon Sep 17 00:00:00 2001
From: vagudets <victoria.agudetse@bsc.es>
Date: Mon, 25 Aug 2025 15:42:13 +0200
Subject: [PATCH 7/9] Replace PCICt dependency with ClimProjDiags

---
 DESCRIPTION                          |  3 +--
 NAMESPACE                            |  2 +-
 R/NcDataReader.R                     | 11 ++++++-----
 tests/testthat/test-Start-calendar.R |  5 ++++-
 4 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 35bb1b9f..e3809c00 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: startR
 Title: Automatically Retrieve Multidimensional Distributed Data Sets
-Version: 2.4.0
+Version: 2.4.1
 Authors@R: c(
     person("Nicolau", "Manubens", , "nicolau.manubens@bsc.es", role = c("aut")),
     person("An-Chi", "Ho", , "an.ho@bsc.es", role = c("aut"), comment = c(ORCID = "0000-0002-4182-5258")), 
@@ -32,7 +32,6 @@ Imports:
     easyNCDF,
     s2dv,
     ClimProjDiags,
-    PCICt,
     methods
 Suggests:
     stats,
diff --git a/NAMESPACE b/NAMESPACE
index c6bca724..c3232eda 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -16,7 +16,7 @@ export(Start)
 export(Step)
 export(indices)
 export(values)
-import(PCICt)
+import(ClimProjDiags)
 import(abind)
 import(bigmemory)
 import(easyNCDF)
diff --git a/R/NcDataReader.R b/R/NcDataReader.R
index 47817c65..66d58fd7 100644
--- a/R/NcDataReader.R
+++ b/R/NcDataReader.R
@@ -43,8 +43,9 @@
 #'                            first_round_indices, synonims)
 #'@seealso \code{\link{NcOpener}} \code{\link{NcDimReader}} 
 #'  \code{\link{NcCloser}} \code{\link{NcVarReader}}
-#'@import easyNCDF PCICt
+#'@import easyNCDF ClimProjDiags
 #'@export
+
 NcDataReader <- function(file_path = NULL, file_object = NULL, 
                          file_selectors = NULL, inner_indices = NULL,
                          synonims) {
@@ -303,8 +304,8 @@ NcDataReader <- function(file_path = NULL, file_object = NULL,
                 result_vec[result_i] <- tmp
               }
               # Transfer the strings to time class
-              new_array <- PCICt::as.PCICt(result_vec, cal = 'gregorian')
-              new_array <- suppressWarnings(PCICt::as.POSIXct.PCICt(new_array, tz = "UTC"))
+              new_array <- ClimProjDiags::as.PCICt(result_vec, cal = 'gregorian')
+              new_array <- suppressWarnings(ClimProjDiags::as.POSIXct.PCICt(new_array, tz = "UTC"))
 
 #            if (calendar == 'gregorian') {
 #              # Find how many years + months 
@@ -373,8 +374,8 @@ NcDataReader <- function(file_path = NULL, file_object = NULL,
           }
 
           if (!(units %in% c('month', 'months') & calendar == 'gregorian')) {
-            new_array <- PCICt::as.PCICt(result, cal = calendar, origin = parts[2])[]
-            new_array <- suppressWarnings(PCICt::as.POSIXct.PCICt(new_array, tz = "UTC"))
+            new_array <- ClimProjDiags::as.PCICt(result, cal = calendar, origin = parts[2])[]
+            new_array <- suppressWarnings(ClimProjDiags::as.POSIXct.PCICt(new_array, tz = "UTC"))
           }
           #new_array <- seq(as.POSIXct(parts[2]), 
           #                  length = max(result, na.rm = TRUE) + 1, 
diff --git a/tests/testthat/test-Start-calendar.R b/tests/testthat/test-Start-calendar.R
index 43651ab4..0ba03c84 100644
--- a/tests/testthat/test-Start-calendar.R
+++ b/tests/testthat/test-Start-calendar.R
@@ -243,8 +243,11 @@ expect_equal(
 dim(attr(data_obs, 'Variables')$common$time),
 c(date = 4, time = 1)
 )
+
+## NOTE: as.character() behavior changes in R/4.?.?, midnight dates become YYYYmmdd without
+##   the hour information. This is why the unit test fails in the hub.
 expect_equal(
-as.character(attr(data_obs, 'Variables')$common$time),
+format(attr(data_obs, 'Variables')$common$time),
 c("1960-11-16 00:00:00", "1960-12-16 12:00:00", "1961-01-16 12:00:00", "1961-02-15 00:00:00")
 )
 
-- 
GitLab


From fc28d09a0982b67b7924eb04a3e52d202ac7ad2d Mon Sep 17 00:00:00 2001
From: vagudets <victoria.agudetse@bsc.es>
Date: Tue, 26 Aug 2025 15:16:39 +0200
Subject: [PATCH 8/9] Changes from master!

---
 R/ByChunks_autosubmit.R | 2 +-
 R/Utils.R               | 7 +++----
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/R/ByChunks_autosubmit.R b/R/ByChunks_autosubmit.R
index 0dd2bcd4..796c0112 100644
--- a/R/ByChunks_autosubmit.R
+++ b/R/ByChunks_autosubmit.R
@@ -365,7 +365,7 @@ ByChunks_autosubmit <- function(step_fun, cube_headers, ..., chunks = 'auto',
   if (is.null(cluster[['special_setup']])) {
     cluster[['special_setup']] <- 'none'
   }
-  if (!(cluster[['special_setup']] %in% c('none', 'gpfs', 'nord4'))) {
+  if (!(cluster[['special_setup']] %in% c('none', 'marenostrum4', 'nord4'))) {
     stop("The value provided for the component 'special_setup' of the parameter ",
          "'cluster' is not recognized.")
   }
diff --git a/R/Utils.R b/R/Utils.R
index 5640e855..56a5e54e 100644
--- a/R/Utils.R
+++ b/R/Utils.R
@@ -885,10 +885,9 @@ write_autosubmit_bash <- function(chunks, cluster, autosubmit_suite_dir) {
     chunk_args[2, ] <- paste0('%JOBS.CHUNK_', n_chunk, '.', chunk_names, '_N%')
     chunk_args <- paste0('(', paste(c(chunk_args), collapse = ' '), ')')
 
-    ## TODO: Change back
-    bash_script_template <- file("/esarchive/scratch/vagudets/repos/startR/inst/chunking/Autosubmit/startR_autosubmit.sh")
-    ## bash_script_template <- file(system.file('chunking/Autosubmit/startR_autosubmit.sh',
-    ##                              package = 'startR'))
+
+    bash_script_template <- file(system.file('chunking/Autosubmit/startR_autosubmit.sh',
+                                 package = 'startR'))
     bash_script_lines <- readLines(bash_script_template)
     close(bash_script_template)
 
-- 
GitLab


From 976084053c1543320f4887566b1b76a9701e8950 Mon Sep 17 00:00:00 2001
From: vagudets <victoria.agudetse@bsc.es>
Date: Tue, 26 Aug 2025 15:17:38 +0200
Subject: [PATCH 9/9] Remove file

---
 inst/doc/usecase/ex2_15_margin_run_on_gpfs.R | 70 --------------------
 1 file changed, 70 deletions(-)
 delete mode 100644 inst/doc/usecase/ex2_15_margin_run_on_gpfs.R

diff --git a/inst/doc/usecase/ex2_15_margin_run_on_gpfs.R b/inst/doc/usecase/ex2_15_margin_run_on_gpfs.R
deleted file mode 100644
index 51bf1f31..00000000
--- a/inst/doc/usecase/ex2_15_margin_run_on_gpfs.R
+++ /dev/null
@@ -1,70 +0,0 @@
-# Author: Victòria Agudetse Roures, Sara Moreno, Núria Pérez Zanón
-# Date: 7th August 2025
-# ------------------------------------------------------------------
-
-# -----------------------------------------------------------------
-# Function working on time dimension e.g.: Season
-# ------------------------------------------------------------------
-library(startR)
-path <- "/esarchive/scratch/vagudets/repos/startR/R/"
-ff <- lapply(list.files(path), function(x) paste0(path, x))
-invisible(lapply(ff, source))
-
-repos <- '/esarchive/exp/ecmwf/system51c3s/monthly_mean/$var$_f6h/$var$_$sdate$.nc'
-data <- Start(dat = repos,
-              var = 'tas',
-              sdate = c('20170101', '20180101'),
-              ensemble = indices(1:20),
-              time = 'all',
-              lat = 'all',
-              lon = indices(1:40),
-              return_vars = list(lat = 'dat', lon = 'dat', time = 'sdate'),
-              retrieve = FALSE)
-
-fun_spring <- function(x) {
-    y <- s2dv::Season(x,  time_dim = 'time', monini = 1, moninf = 3, monsup = 5)
-    return(y)
-}
-
-step1 <- Step(fun = fun_spring,
-             target_dims = c('var', 'time'),
-             output_dims = c('var', 'time'))
-
-
-file_dims <- dim(attr(data, "ExpectedFiles"))
-new_files <- sapply(attr(data, "ExpectedFiles"),
-        function(x) {
-              gsub("/esarchive/", "/gpfs/projects/bsc32/esarchive_cache/", x)
-              })
-dim(new_files) <- file_dims
-attr(data, "ExpectedFiles") <- new_files
-data[2] <- gsub("/esarchive/", "/gpfs/projects/bsc32/esarchive_cache/", data[2])
-
-wf1 <- AddStep(data, step1)
-
-#-----------modify according to your personal info---------
-  queue_host <- 'cte-amd'
-  temp_dir <-  '/gpfs/scratch/bsc32/bsc032762/startR_hpc/'
-  ecflow_suite_dir <- '/gpfs/home/bsc/bsc032762/startR_local/'  #your own local directory
-#------------------------------------------------------------
-  res <- Compute(workflow = wf1,
-                 chunks = list(ensemble = 2,
-             sdate = 2),
-                 threads_load = 2,
-                 threads_compute = 4,
-                 cluster = list(
-                   queue_host = 'amd',
-                   expid = 'a9p5',
-                   hpc_user = "bsc032762",
-                   autosubmit_module = 'autosubmit/4.1.14-foss-2023b-Python-3.11.5',
-                   cores_per_job = 4,
-                   job_wallclock = '01:00',
-                   max_jobs = 100,
-       run_dir = '/gpfs/scratch/bsc32/bsc032762/startR_hpc/'
-                 ),
-                 workflow_manager = 'autosubmit',
-                 autosubmit_suite_dir = "/esarchive/scratch/vagudets/startR_local/",
-                 autosubmit_server = 'bscesautosubmit03',
-                 wait = TRUE
-  )
-
-- 
GitLab