Polish README and scripts

.gitignore

@@ -3,3 +3,4 @@ dynamico
 XIOS
 Grib/*
 *~
+*.log

README.md

 # Multiscale Transport
 
-Transport experiments with DYNAMICO meshes : quasi_uniform and variable-resolution
\ No newline at end of file
+Transport experiments with DYNAMICO meshes : quasi_uniform and variable-resolution
+
+## Install on camelot ##
+
+```
+cd /homedata/$USER
+git clone git@gitlab.in2p3.fr:ipsl/projets/dynamico/multiscale_transport.git
+cd multiscale_transport
+./scripts/dynamico.sh install camelot
+module load git python/3.6-anaconda50
+```
+
+## Pre-process ##
+
+```
+./scripts/netcdf.sh unpack
+./scripts/netcdf.sh extract
+./scripts/netcdf.sh create
+./scripts/netcdf.sh merge
+./scripts/netcdf.sh pressure
+```
+
+## Uniform-resolution run on camelot ##
+
+```
+cd RUN
+qsub camelot.sh
+```

scripts/camelot.sh

+#!/bin/bash
+#PBS -N multiscale-pp
+#PBS -q std
+#PBS -n
+#PBS -l nodes=1:ppn=1
+#PBS -l walltime=06:00:00
+#PBS -l mem=4gb
+#PBS -l vmem=4gb
+
+# Jobs start in the HOME directory, cd to submitted directory
+cd "$PBS_O_WORKDIR"
+
+module load git python/3.6-anaconda50
+
+./scripts/netcdf.sh unpack
+./scripts/netcdf.sh extract
+./scripts/netcdf.sh create
+./scripts/netcdf.sh merge
+./scripts/netcdf.sh pressure

scripts/netcdf.py

@@ -15,10 +15,6 @@ def invert_lev(time, name, var):
     for it in range(len(time)):
         print("Inverting %s at time %d."%(name, time[it]) )
         buf1 = var[it,:,:,:]
-#        for l in range((llm-1)//2):
-#            buf = buf3[l,:,:]
-#            buf3[l,:,:] = buf3[llm-l-1,:,:]
-#            buf3[llm-l-1,:,:] = buf
         buf2 = buf1[::-1,:,:]
         var[it,:,:,:] = buf2
 
@@ -30,12 +26,12 @@ def pressure(time,A,B,ps, p):
             p[it,iz,:,:] = A[iz]+B[iz]*ps_it[:,:]
 
 with cdf.Dataset('merged.nc', 'a') as data:
-    time, lev, A, B, ps = getvars(data, 'time', 'lev', 'hyam', 'hybm', 'var134')
-    p, u, v, t = getvars(data, 'q', 'u', 'v', 't')
+    time, lev, A, B = getvars(data, 'time', 'lev', 'hyam', 'hybm')
+    ps, p, u, v, t  = getvars(data, 'var134', 'q', 'u', 'v', 't')
 
     time, A, B = time[:], A[:], B[:]
 
     pressure(time, A[::-1], B[::-1], ps, p)
-    invert_lev(time, 'u', u)
-    invert_lev(time, 'v', v)
-    invert_lev(time, 't', t)
+    invert_lev(time, 'Zonal wind', u)
+    invert_lev(time, 'Meridional wind', v)
+    invert_lev(time, 'Temperature', t)

scripts/netcdf.sh

@@ -3,10 +3,11 @@
 function cmd_unpack()
 {
     cd $ROOT
-    rmdir Grib
+    rm -rf Grib
     mkdir Grib
     echo Extracting $(ls ECMWF*.tar)
     cd Grib
+    date
     tar --strip-components=5 -x -v -f ../ECMWF*.tar
     cmd_unzip
 }
@@ -15,6 +16,7 @@ function cmd_unzip()
 {
     cd $ROOT/Grib
     for ZIPFILE in *.zip ; do
+	date
 	echo "Extracting $PWD/$ZIPFILE"
 	unzip $ZIPFILE && rm -f $ZIPFILE
     done
@@ -30,6 +32,7 @@ function cmd_extract()
 	tar xf "${DATE}"/surf.$DATE.tar
 	tar xf "${DATE}"/uvtqz.$DATE.tar
 	rm -f *.*_12
+	date
 	ls -lh *.${DATE}*_*
     done
 }
@@ -53,6 +56,7 @@ function cmd_create()
     mkdir NetCDF
     for FILE in surf uvtqz ; do
 	LIST=$(cmd_list $FILE)
+	date
 	echo $LIST
 	cdo -f nc4 copy $LIST NetCDF/$FILE.nc
     done
@@ -61,9 +65,17 @@ function cmd_create()
 function cmd_merge()
 {
     cd $ROOT/NetCDF
+    date
     cdo merge surf.nc uvtqz.nc merged.nc
 }
 
+function cmd_pressure()
+{
+    cd $ROOT/NetCDF
+    date
+    python3 ../scripts/netcdf.py
+}
+
 function cmd_()
 {
 cat <<EOF
@@ -72,18 +84,22 @@ $0 unpack        Unpack master archive ECMWF*.tar then unzip the *.zip files it
 $0 extract       Unpack *.tar files unpacked with above command
 $0 create        From files obtained at previous step, create surf.nc and uvtqz.nc for the whole period
 $0 merge         Merge surf.nc and uvtqz.nc into merged.nc, and invert vertical axis to match DYNAMICO order
+$0 pressure      In merged.nc, compute 3D pressure field and flip vertical axis of 3D fields 
 
 Debug commands :
 $0 unzip              Unzip and delete *.zip files contained in master archive
 $0 list surf|uvtqz    List Grib files to be concatenated by $0 create
+
+On camelot you must :
+  module load git python/3.6-anaconda50
 EOF
 }
 
-# DAYS="01 02 03 04 05 06 07 08 09 10"
-DAYS="01 02"
+DAYS="01 02 03 04 05 06 07 08 09 10"
+# DAYS="01 02"
 TIMES="00_00 00_03 00_06 00_09 12_00 12_03 12_06 12_09"
 
 ROOT=$(cd -P $(dirname $0)/.. ; pwd)
 
 CMD=$1 ; shift
-cmd_$CMD $*
+cmd_$CMD $* | tee $CMD.log