From c34c5f38d16b4244fc1a75988fcacc28eb53b970 Mon Sep 17 00:00:00 2001
From: Francesco Sabatini <francesco.sabatini@idiv.de>
Date: Mon, 24 Feb 2020 22:44:15 +0100
Subject: [PATCH] Optimized A97 for cluster
---
code/A97_ElevationExtract.R | 15 +++++++--------
code/cli_A97.r | 4 ++--
code/submit-A97.sh | 2 +-
3 files changed, 10 insertions(+), 11 deletions(-)
diff --git a/code/A97_ElevationExtract.R b/code/A97_ElevationExtract.R
index 611eb55..ef9e403 100644
--- a/code/A97_ElevationExtract.R
+++ b/code/A97_ElevationExtract.R
@@ -55,12 +55,12 @@ ElevationExtract <- function(header, output, ncores, chunk.i){
print(paste(length(todo), "tiles to do"))
print("divide in chunks")
- #divide in chunks #should take around 40'
- indices <- 1:length(todo)
- todo.chunks <- split(indices, sort(indices%%99))
+ #divide in chunks
+ todo.chunks <- split(todo, sort(todo%%10))
print(paste("start main foreach loop on chunk n=", chunk.i))
- foreach(i = todo.cunks[[chunk.i]]) %dopar% {
+ print(paste(length(todo.chunks[[chunk.i]]), "to do"))
+ foreach(i = todo.chunks[[chunk.i]]) %dopar% {
print(paste("doing", i))
#create sp and project data
if(nrow(header.tiles %>%
@@ -82,11 +82,10 @@ ElevationExtract <- function(header, output, ncores, chunk.i){
)
if(!exists("raster.tile")) {
raster.tile <- NA
+ print(paste("tile", i, "doesn't work!, skip to next"))
save(raster.tile, file = paste(output, "elevation_tile_", i, "failed.RData", sep=""))
- message(paste("tile", i, "doesn't work!, skip to next"))
rm(raster.tile)
- next
- }
+ } else {
# clip dem tile with continent shape
raster.tile <- mask(raster.tile, continent.high.merc)
@@ -111,7 +110,7 @@ ElevationExtract <- function(header, output, ncores, chunk.i){
#save output
save(output.tile, file = paste(output, "elevation_tile_", i, ".RData", sep=""))
print(paste(i, "done"))
- }
+ }}
stopCluster(cl)
}
diff --git a/code/cli_A97.r b/code/cli_A97.r
index 653390d..d376731 100644
--- a/code/cli_A97.r
+++ b/code/cli_A97.r
@@ -21,7 +21,7 @@ options <- list (
),
make_option(
opt_str = c("-i", "--chunk.i"),
- dest = "chunkn",
+ dest = "chunk.i",
type = "integer",
default = 1,
help = "which chunk out of 99",
@@ -45,7 +45,7 @@ cli <- parse_args(parser, positional_arguments = 2)
header <- cli$args[1]
output <- cli$args[2]
ncores <- cli$options$ncores
-chunkn <- cli$options$chunk.i
+chunk.i <- cli$options$chunk.i
# ------------------------------------------------------------------------------
diff --git a/code/submit-A97.sh b/code/submit-A97.sh
index e0b14fe..dd9e18b 100644
--- a/code/submit-A97.sh
+++ b/code/submit-A97.sh
@@ -13,7 +13,7 @@
#$ -cwd
-#$ -t 1-99
+#$ -t 1-10
module load R
--
GitLab