Working version of gener_perturb_restart.bash on zenobe

util/gener_perturb_restart.bash

@@ -4,27 +4,46 @@
 # -- Date   : 30 Jan 2015
 # -- At     : IC3, Barcelona
 # -- Modified : 19 Jan 2016, omar.bellprat@bsc.es 
-#
+#               November 2017, francois.massonnet@uclouvain.be
 # -- Purpose: Generation of an arbitrary number of NEMO oceanic restarts that are copies of a reference, plus a perturbation
 #
 # -- Method : The reference file is duplicated in this script, then read by a R script. The perturbation is introduced and finally written to this latter file.
-#             The script must be placed into the restart directory (e.g. NEMO_Restart_23). The generated restarts have to be renamed after generation. This 
-#             script has been tested on MareNostrum3.
-#
-# -- Input  : NEMO ocean restart from an EC-Earth 3.1 run
-# -- Output : N restarts with the same name,but with an index fc0, fc1, ... fcN-1 appended
-#
-# -- Limitations: Only the surface conditions are perturbed (level index: 1) but this can be changed in the R script
 
 module load R
 
 set -o errexit
 set -o nounset
-set -x
+#set -x
 
 
 if [ $# == 0 ] ; then
-  echo "gener_perturbation.bash ocean_restart_file Nmembers"
+  echo ""
+  echo "  Usage: gener_perturb_restart.bash NETCDF-file NUMBER-members"
+  echo "      PURPOSE : "
+  echo "        Creates NUMBER-members copies of the input NETCDF-file file"
+  echo "        and adds for each copy a white noise to sea surface"
+  echo "        temperature (standard deviation: 10^(-4) K)"
+  echo "        This script can be used to generate ensemble members"
+  echo "        for coupled simulations"
+  echo "      ARGUMENTS : "
+  echo "        NETCDF-file : Restart file of NEMO (NetCDF format). The file"
+  echo "                      must contain a variable named tn"
+  echo "        NUMBER-members : number of perturbed restarts to generate"
+  echo "      OUTPUT : "
+  echo "        NUMBER-members copies of the original files with perturbed"
+  echo "        variable tn. The file names are the same as the input files"
+  echo "        but with suffix pertXX where XX = 01, 02, 03, ..."
+  echo "      EXAMPLE : "
+  echo "        ./gener_perturb_restart.bash EC04_00046752_restart_oce_0005.nc 5"
+  echo "        --> will create:"
+  echo "              EC04_00046752_restart_oce_0005_pert01.nc"
+  echo "              EC04_00046752_restart_oce_0005_pert02.nc"
+  echo "              EC04_00046752_restart_oce_0005_pert03.nc"
+  echo "              EC04_00046752_restart_oce_0005_pert04.nc"
+  echo "              EC04_00046752_restart_oce_0005_pert05.nc"
+  echo "      HELPDESK : "
+  echo "        francois.massonnet@uclouvain.be"
+  echo ""
   exit
 fi
 
@@ -39,17 +58,18 @@ per=0.0001      # Standard deviation of gaussian perturbation to be applied,
 
 cp $filein ${filein}.backup # Do a backup
 
-for jmemb in `seq 0 $(( $nmemb -1 ))`
+for jmemb in `seq 1 $nmemb`
 do
-  echo $jmemb
+  echo "Doing copy $jmemb out of $nmemb"
+  jmemb=$(printf "%02d" $jmemb)
   # 1. Make a copy of the original file, with the new name
-  filenew="${filein%.nc}_fc${jmemb}.nc"
+  filenew="${filein%.nc}_pert${jmemb}.nc"
   cp $filein $filenew
 
   # 2. Prepare the R script
 
   echo "#!/usr/bin/env Rscript
-  library(ncdf)
+  library(ncdf4)
 
   # François Massonnet, 30 Jan 2015
   # Adds a gaussian perturbation at the first level of a 3D field
@@ -59,10 +79,10 @@ do
 
   varname='$var'
   filein <- '$filenew'
-  ex.nc           <- open.ncdf(filein,write=TRUE)
+  ex.nc           <- nc_open(filein,write=TRUE)
   spert <- $per
 
-  myvar     <- get.var.ncdf(ex.nc, varname)
+  myvar     <- ncvar_get(ex.nc, varname)
   myvarpert <- myvar
   for (i in seq(1,dim(myvar)[1])){
     for (j in seq(1,dim(myvar)[2])){
@@ -72,8 +92,8 @@ do
     }
   }
 
-  put.var.ncdf(ex.nc,varname,myvarpert)
-  close.ncdf(ex.nc)" > Rtmpfile.R
+  ncvar_put(ex.nc,varname,myvarpert)
+  nc_close(ex.nc)" > Rtmpfile.R
 
   chmod 744 Rtmpfile.R