From f9ffacf58adbd6df850868f6c94a6bf8d1775422 Mon Sep 17 00:00:00 2001
From: Francesco Sabatini <francesco.sabatini@idiv.de>
Date: Fri, 14 Feb 2020 13:03:11 +0100
Subject: [PATCH] Fixed minor bugs for submitting array jobs
---
code/A98_PredictorsExtract.R | 7 ++++++-
code/cli_A98.r | 2 +-
code/submit-A98.sh | 10 +++++-----
3 files changed, 12 insertions(+), 7 deletions(-)
diff --git a/code/A98_PredictorsExtract.R b/code/A98_PredictorsExtract.R
index fd9e1b3..7b8aad7 100644
--- a/code/A98_PredictorsExtract.R
+++ b/code/A98_PredictorsExtract.R
@@ -7,11 +7,14 @@ PredExtr <- function(x.shp, myfunction=NA, output,
require(doParallel)
require(raster)
require(rgeos)
-
+ require(rgdal)
+
print(paste("Loading", typp, "data :", toextract))
if(typp=="raster"){ mypredictor <- raster(toextract)} else
mypredictor <- readOGR(toextract)
header.shp <-readOGR(x.shp)
+ crs(mypredictor) <- crs(header.shp) #should be verified beforehand!
+
## Divide in chunks if requested
if(chunkn>1 & !is.na(chunk.i)){
print(paste("divide in chunks and run on chunk n.", chunk.i))
@@ -41,6 +44,8 @@ PredExtr <- function(x.shp, myfunction=NA, output,
} else {
out <- sp::over(x=header.shp, y=mypredictor)
toassign <- header.shp[which(is.na(out[,1])),]
+ print(paste(length(toassign), "plots not matched directely - seek for NN"))
+
nearest <- foreach(i=1:length(toassign), .packages=c('raster'), .combine=rbind) %dopar% {
nearest.tmp <- geosphere::dist2Line(toassign[i,], mypredictor)
diff --git a/code/cli_A98.r b/code/cli_A98.r
index 5e0e49e..178e1c1 100644
--- a/code/cli_A98.r
+++ b/code/cli_A98.r
@@ -30,7 +30,7 @@ options <- list (
metavar = "4"
),
make_option(
- opt_str = c("-c", "--chunkn"),
+ opt_str = c("-n", "--chunkn"),
dest = "chunkn",
type = "integer",
default = 1,
diff --git a/code/submit-A98.sh b/code/submit-A98.sh
index 0a54ff1..28b7664 100644
--- a/code/submit-A98.sh
+++ b/code/submit-A98.sh
@@ -7,9 +7,9 @@
#$ -j y
#$ -l h_rt=00:30:00:00
-#$ -l h_vmem=3G
+#$ -l h_vmem=1G
-#$ -pe smp 4-32
+#$ -pe smp 8-32
#$ -cwd
@@ -26,10 +26,10 @@ output=/work/$USER/output_pred/$(basename $filename .shp).csv
Rscript \
cli_A98.r \
--cores ${NSLOTS:-1} \
- --typp \
+ --typp "shp" \
--chunk.i $SGE_TASK_ID \
--chunkn 99 \
- /data/splot/_data/header.shp.RData \
+ /data/splot/_data_splot3/header.shp.shp \
robust.mean \
"$output" \
- "$filename"
\ No newline at end of file
+ "$filename"
--
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