rev5.0 minor improvements

SCRIPTS/5_doNetcdfCombine.R

@@ -31,6 +31,8 @@ if (submitscript) {
 
 variables<-names(variableInfo)
 
+FillValue <- 1e20
+
 dir.create(outPath, recursive = TRUE, showWarnings = FALSE)
 for (iMember in members) {
   for (initYear in initYears) {
@@ -57,13 +59,14 @@ for (iMember in members) {
         NCtimeAtt<-ncatt_get( ncid_in, "time", "units" )$value
         nc_close(ncid_in)
         
+        NCdata[is.na(NCdata)] <- FillValue
+        
         ## CREATE NETCDF
         if (firstVar == TRUE) {
           dimT <- ncdim_def("time", NCtimeAtt, NCtime, unlim = FALSE)
           dimY <- ncdim_def("lat", "degrees_north",round(NClat,2))
           dimX <- ncdim_def("lon", "degrees_east", round(NClon,2))
           
-          FillValue <- 1e20
           
           ## SAVE AS NC-DATA
           nameFileNCout <- sprintf("%s/forcing_seas15_%s_%s_E%02d_INIT%4d_%02d.nc4", 
@@ -73,7 +76,7 @@ for (iMember in members) {
                                    iMember,
                                    initYear,
                                    initMonth)
-          data <- ncvar_def( variableName, variableInfo[[variableName]]$units, list(dimX,dimY,dimT), FillValue, prec="float")#, compression=4)
+          data <- ncvar_def( variableName, variableInfo[[variableName]]$units, list(dimX,dimY,dimT), FillValue, prec="float", compression=4)
           print(paste0("Creating: ", nameFileNCout, " for: ", variableName))
           ncid_out <- nc_create( nameFileNCout,data)
           
@@ -107,9 +110,10 @@ for (iMember in members) {
         
         ncatt_put( ncid_out, variableName, "standard_name", variableInfo[[variableName]]$standardName)
         ncatt_put( ncid_out, variableName, "long_name", variableInfo[[variableName]]$longName)
-        ncatt_put( ncid_out, variableName, "_FillValue", FillValue)
+        #ncatt_put( ncid_out, variableName, "_FillValue", FillValue)
         
         firstVar<-FALSE
+        rm(data, NCdata)
       }
       nc_close(ncid_out)
     } ## end initMonth

SCRIPTS/5_jobScriptNetcdfCombine

 #!/bin/bash
 #SBATCH --account=5120867-01
 #SBATCH --time=5000
-#SBATCH --mem=4024
+#SBATCH --mem=16024
 #SBATCH --ntasks=1
 #SBATCH --output=./log/log_5_doNetcdfCombine_<location>_<bcInfo>_<resolution>deg_initMonth<initMonth>_%j.txt
 #SBATCH --job-name=Combine