From dc9b16cfee93e08cd339a97166280a6c19fbd820 Mon Sep 17 00:00:00 2001
From: Carlos Delgado <carlos.delgado@bsc.es>
Date: Wed, 22 Feb 2023 12:25:08 +0100
Subject: [PATCH 1/2] included paralelisation but does not reduce the
 computational time

---
 R/CDORemap.R | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/R/CDORemap.R b/R/CDORemap.R
index 927b107..9e16011 100644
--- a/R/CDORemap.R
+++ b/R/CDORemap.R
@@ -77,6 +77,8 @@
 #'  files for CDO to work. By default, the R session temporary directory is 
 #'  used (\code{tempdir()}).
 #'
+#'@param ncores Number of theats used for interpolation.
+#'
 #'@return A list with the following components:
 #'  \item{'data_array'}{The interpolated data array (if an input array 
 #'  is provided at all, NULL otherwise).}
@@ -223,7 +225,8 @@
 #'@export
 CDORemap <- function(data_array = NULL, lons, lats, grid, method, 
                      avoid_writes = TRUE, crop = TRUE,
-                     force_remap = FALSE, write_dir = tempdir()) {  #, mask = NULL) {
+                     force_remap = FALSE, write_dir = tempdir(),
+                     ncores = NULL) {  #, mask = NULL) {
   .isRegularVector <- function(x, tol = 0.1) {
     if (length(x) < 2) {
       #stop("The provided vector must be of length 2 or greater.")
@@ -564,6 +567,12 @@ CDORemap <- function(data_array = NULL, lons, lats, grid, method,
   if (!dir.exists(write_dir)) {
     stop("Parameter 'write_dir' must point to an existing directory.")
   }
+  # Check ncores
+  if (is.null(ncores)) {
+    ncores <- 1
+  } else if (!is.integer(ncores) | ncores < 1)
+    stop("Parameter 'ncores' must be NULL or an integer equal or greater than 1")
+  }
 #  if (!is.null(mask)) {
 #    if (!is.numeric(mask) || !is.array(mask)) {
 #      stop("Parameter 'mask' must be a numeric array.")
@@ -814,7 +823,7 @@ CDORemap <- function(data_array = NULL, lons, lats, grid, method,
                                            ',', format(lat_extremes[2], scientific = FALSE), ' -')
       }
       err <- try({
-        system(paste0("cdo -s ", sellonlatbox, "remap", method, ",", grid, " ", tmp_file, " ", tmp_file2), ignore.stdout = T, ignore.stderr = T)
+        system(paste0("cdo -P ", ncores," -s ", sellonlatbox, "remap", method, ",", grid, " ", tmp_file, " ", tmp_file2), ignore.stdout = T, ignore.stderr = T)
       })
       file.remove(tmp_file)
       if (is(err, 'try-error') || err > 0) {
-- 
GitLab


From fa323427879dcd6d7b7b142f259b237d82d8c0ea Mon Sep 17 00:00:00 2001
From: aho <an.ho@bsc.es>
Date: Mon, 22 May 2023 09:33:21 +0200
Subject: [PATCH 2/2] Refine ncores

---
 R/CDORemap.R    | 28 +++++++++++++++++++---------
 man/CDORemap.Rd |  7 ++++++-
 2 files changed, 25 insertions(+), 10 deletions(-)

diff --git a/R/CDORemap.R b/R/CDORemap.R
index f67c70f..4ea14fd 100644
--- a/R/CDORemap.R
+++ b/R/CDORemap.R
@@ -76,8 +76,9 @@
 #'@param write_dir Path to the directory where to create the intermediate 
 #'  files for CDO to work. By default, the R session temporary directory is 
 #'  used (\code{tempdir()}).
-#'
-#'@param ncores Number of theats used for interpolation.
+#'@param ncores An integer indicating the number of theads used for 
+#'  interpolation (i.e., \code{-P} in cdo command.) The default value is NULL
+#'  and \code{-P} is not used.
 #'
 #'@return A list with the following components:
 #'  \item{'data_array'}{The interpolated data array (if an input array 
@@ -568,10 +569,11 @@ CDORemap <- function(data_array = NULL, lons, lats, grid, method,
     stop("Parameter 'write_dir' must point to an existing directory.")
   }
   # Check ncores
-  if (is.null(ncores)) {
-    ncores <- 1
-  } else if (!is.integer(ncores) | ncores < 1)
-    stop("Parameter 'ncores' must be NULL or an integer equal or greater than 1")
+  if (!is.null(ncores)) {
+    if (!is.numeric(ncores) | any(ncores %% 1 != 0) | any(ncores < 0) |
+        length(ncores) > 1) {
+      stop("Parameter 'ncores' must be a positive integer.")
+    }
   }
 #  if (!is.null(mask)) {
 #    if (!is.numeric(mask) || !is.array(mask)) {
@@ -823,9 +825,17 @@ CDORemap <- function(data_array = NULL, lons, lats, grid, method,
                                            ',', format(lat_extremes[1], scientific = FALSE), 
                                            ',', format(lat_extremes[2], scientific = FALSE), ' -')
       }
-      err <- try({
-        system(paste0("cdo -P ", ncores," -s ", sellonlatbox, "remap", method, ",", grid, " ", tmp_file, " ", tmp_file2), ignore.stdout = T, ignore.stderr = T)
-      })
+      if (is.null(ncores)) {
+        err <- try({
+          system(paste0("cdo -s ", sellonlatbox, "remap", method, ",", grid, " ", 
+                        tmp_file, " ", tmp_file2), ignore.stdout = T, ignore.stderr = T)
+        })
+      } else {
+        err <- try({
+          system(paste0("cdo -P ", ncores," -s ", sellonlatbox, "remap", method, ",", 
+                        grid, " ", tmp_file, " ", tmp_file2), ignore.stdout = T, ignore.stderr = T)
+        })
+      }
       file.remove(tmp_file)
       if (is(err, 'try-error') || err > 0) {
         stop("CDO remap failed. Possible problem: parameter 'grid'.")
diff --git a/man/CDORemap.Rd b/man/CDORemap.Rd
index 61f6101..d7eee21 100644
--- a/man/CDORemap.Rd
+++ b/man/CDORemap.Rd
@@ -13,7 +13,8 @@ CDORemap(
   avoid_writes = TRUE,
   crop = TRUE,
   force_remap = FALSE,
-  write_dir = tempdir()
+  write_dir = tempdir(),
+  ncores = NULL
 )
 }
 \arguments{
@@ -85,6 +86,10 @@ is already on the target grid.}
 \item{write_dir}{Path to the directory where to create the intermediate 
 files for CDO to work. By default, the R session temporary directory is 
 used (\code{tempdir()}).}
+
+\item{ncores}{An integer indicating the number of theads used for 
+interpolation (i.e., \code{-P} in cdo command.) The default value is NULL
+and \code{-P} is not used.}
 }
 \value{
 A list with the following components:
-- 
GitLab