Updated submit functions in HPC

code/submit-A98-array.sh

@@ -23,12 +23,12 @@ module load R/3.6.2
 filename="$1"
 shift 
 
-output=/data/splot/_data_splot3/output_pred/$(basename $filename .shp)-$SGE_TASK_ID.csv
+output=/data/splot/_data_splot3/output_pred/$(basename $filename .tif)-$SGE_TASK_ID.csv
 
 Rscript \
     cli_A98.r \
     --cores ${NSLOTS:-1} \
-    --typp "shp" \
+    --typp "raster" \
     --chunk.i "$SGE_TASK_ID" \
     --chunkn 99 \
     /data/splot/_data_splot3/header.shp.shp \

code/submit-A98.sh

@@ -3,7 +3,7 @@
 #$ -S /bin/bash
 #$ -N PredictorExtract
 
-#$ -o /work/$USER/$JOB_NAME-$JOB_ID_sd.log
+#$ -o /work/$USER/$JOB_NAME-$JOB_ID.log
 #$ -j y
 
 #$ -l h_rt=00:30:00:00
@@ -12,21 +12,22 @@
 #$ -pe smp 12-32
 
 #$ -cwd
-
-module load R
+module load GCC/8.3.0
+module load OpenMPI/3.1.4
+module load R/3.6.2
 
 filename="$1"
 shift 
 
-output=/data/splot/_data_splot3/output_pred/$(basename $filename .tif)_sd.csv
+output=/data/splot/_data_splot3/output_pred/$(basename "$filename" .tif).csv
 
 Rscript \
     cli_A98.r \
-    --cores ${NSLOTS:-1} \
-    --typp "shp" \
+    --cores "${NSLOTS:-1}" \
+    --typp "raster" \
     --chunk.i 1 \
     --chunkn 1 \
     /data/splot/_data_splot3/header.shp.shp \
-    "NA" \
+    "robust.mean" \
     "$output" \
     "$filename"