Added scripts to download grid data and sample input. Revised namelis…

…t read and updated sample namelist files accordingly. Updated README file.

README

@@ -1,121 +1,57 @@
-NORESM2CMOR
------------
+NORESM2CMOR (v20151113)
+-----------------------
 
-1. How does it work? 
+1. General
+----------
 
-noresm2cmor is a command line tool for post-processing NorESM output using 
-the Climate Model Output Rewriter (cmor) libraries. 
+noresm2cmor is a command line tool for post-processing NorESM output using
+the Climate Model Output Rewriter (cmor) libraries.
 
-Path and experiment information are set in a namelist file which the tool
-reads during execution. For each experiment, it is recommended to create 
-a new namelist file and place it in the folder noresm2cmor/namelist. 
+System, model, experiment and variable information are set in namelist files 
+which noresm2cmor reads during its execution. 
 
 2. Installation
-
-Download and unpack:
-  cd ~
-  wget http://ns2345k.norstore.no/cmor/noresm2cmor_v20151109.tbz
-  tar xvf noresm2cmor_v20151109.tbz
-
-Build (modify Makefile before building): 
-  cd  noresm2cmor/build
-  make Makefile
-
-Install sample output on local scratch (modify scratch path if neccessary):
-  cd /scratch/$USER
-  wget http://noresg.norstore.no/thredds/fileServer/esg_dataroot/ns2345k/outputsample.tar
-  tar xf outputsample.tar
-
-3. Testing 
-
-cd ~/noresm2cmor/run 
-../
-
-NOTE: Before running the simple test-script, change ibasedir and obasedir in 
-      all namelist files in ~/noresm2cmor/run_simple/test_simple
-
-Advanced testing using wrapper scripts: 
-  cd ~/noresm2cmor/run_wrapper
-  ./test_wrapper.sh 
-
-NOTE: Before running, change IBASEDIR and OBASEDIR in test_wrapper.sh
-
-3. Processing a new experiment 
-
-Processing a new experiment involves following steps: 1) creation of an
-experiment namelist that contains necessary meta-information like experiment id,
-parent experiment id, transient forcings, branch time and reference year. 2)
-modification of some variable-namelists in case other than the default CMIP5
-variables are to be written. 3) creation of a run script that processes the data
-of the particular experiment. 
-
-3.1. Experiment namelist 
-
-Each experiment needs its own experiment namelist in the "noresm2cmor/namelist"
-folder. 
-
-The file name of the namelist must be "exp_.nml" (e.g. "exp_control.nml"). Valid
-CMIP5 experiment names (long and short versions) are listed at the beginning of
-each CMIP5 table, e.g. in "noresm2cmor/table/CMIP5_aero". 
-
-Only a few of the namelist fields need to be customized. Therefore, the easiest
-way is to copy a namelist from an existing experiment and then modify it. The
-namelist fields that need to be customized will are discussed here: 
-
-The namelist field "experiment_id" must be set to either the long or the short
-version of the CMIP5 experiment name (e.g. " experiment_id = 'piControl', "). 
-
-The namelist field "parent_experiment_id" must be set to the CMIP5 experiment
-name of the parent experiment exists then 'N/A' must be assigned. 
-
-The namelist field "parent_experiment_rip" should be set to 'r1i1p1' if a parent
-experiment exists and to 'N/A' if no parent experiment exists. 
-
-The namelist field "forcings" consists of a comma seperated list of all
-transient forcings (e.g. " forcings='GHG, SA, Oz, Sl, BC, OC', "). The forcing
-acronyms are found at
-http://cmip-pcmdi.llnl.gov/cmip5/docs/cmip5_data_reference_syntax.pdf (appendix
-1.2).  
-
-The namelist field "branch_time" should be identical to the time value in the
-atmospheric restart file that is used to initialize the experiment (e.g. "
-branch_time=255135, " is used when branching from year 700 of a spinup/control
-experiment). Use ncdump to obtain the time value of the restart file, e.g.
-"ncdump -v time NAER1850CNOC_f19_g16_05.cam2.r.0700-01-01-00000.nc". The value
-for branch_time must be set to 0 in case "parent_experiment=N/A". 
-
-The namelist field "expstartyear" must be set to the reference year used in the
-atmospheric output of the current experiment (e.g. " expstartyear=700, "). Use
-ncdump to obtain the reference date, e.g. "ncdump -h
-NRCP45AERCN_f19_g16_01.cam2.h0.2006-01.nc | grep time:units". 
-
-3.2. Adding new variables 
-
-For each model compont exists one namelist in the namelist folder that specifies
-the variables to be processed, namely: var_cam2cmor.nml, var_cice2cmor.nml,
-var_clm2cmor.nml and var_micom2cmor.nml. 
-
-Each variable namelist is devided into several sections which correspond to the
-data collections defined in the tables in "noresm2cmor/table". The tables define
-all possible/valid variables that can be delivered to the project. 
-
-Each variable that should be processed is presented by one line in the variable
-namelist. The first argument specifies the variable name as written in the model
-output (alternatively, a linear combination of several variables can be
-specified). The second argument specifies the variable name as declared in the
-corresponding table. The third argument specifies special actions that should be
-applied before writing the data. Further information on the syntax etc is found
-in the namelists.   
-
-3.3 Run script 
-
-An example for a run script is stored in "noresm2cmor/run_wrapper/test_wrapper.sh". 
-
-The run script calls the wrappers for the corresponding model components. The
-syntax of the wrapper call is:  
-"cam2cmor.sh <noresm case name> <cmip5 exp. id> <first year> <last year>
-<output group> <output variable> <in dir> <out dir> "
-If all years are to be processed then one can optionally set <first year> and
-<last year> to 0 and 9999, respectively. If all variables are to be processed
-then both <output group> and <output variable> should be set to "All". 
-
+---------------
+
+2.1 Download
+
+Download noresm2cmor with
+ git clone https://github.com/NorwegianClimateCentre/noresm2cmor
+
+2.2 Build 
+
+Change directory to noresm2cmor/build/  
+
+Make a copy of Makefile.norstore_default - e.g., Makefile.xxx - and customize 
+your make file. IMPORTANT: The build of noresm2cmor requires the fortran version 
+of the cmor-library (see https://pcmdi.github.io/cmor-site/download.htm for 
+download instructions).  
+
+Build with
+ make –f Makefile.xxx 
+
+2.3 Installation of grid data and sample input
+
+Change directory to noresm2cmor/
+
+Run installation script for grid data 
+ ./install_griddata.sh <absolute path to folder where grid data should be stored> 
+
+Run installation script for input data sample 
+ ./install_griddata.sh <absolute path to folder where sample input should be stored> 
+
+3. Testing
+----------
+
+Change directory to noresm2cmor/run 
+
+Run test with 
+ ./noresm2cmor ../namelist/all_CMIP5_NorESM1-M_historical_r1i1p1.nml
+
+To get general usage instructions for noresm2cmor, run
+ ./noresm2cmor 
+
+4. Customization of namelists 
+-----------------------------
+
+coming soon...

build/Makefile.norstore_default

@@ -0,0 +1,63 @@
+# Targets 
+TARGET=noresm2cmor
+
+# Objects
+OBJ=m_namelists.o m_utilities.o m_modelsatm.o m_modelsice.o m_modelslnd.o m_modelsocn.o noresm2cmor.o
+
+# Paths 
+SRCDIR=../source
+BINDIR=../run
+
+# Fortran compiler
+FC=gfortran 
+
+# Linker
+LD=$(FC)
+
+# Libraries
+CMOR=/diverse/software/cmor-2.7.1
+UUID=/diverse/software/uuid-1.5.1
+NETCDF=/diverse/software/old_software/netcdf.gnu-4.2.1.1
+
+# Directory list to search for library files
+LIBS=-L$(CMOR)/lib -Wl,-rpath=$(CMOR)/lib -L$(UUID)/lib -Wl,-rpath=$(UUID)/lib -lcmor -lnetcdff -lnetcdf -lhdf5 -lhdf5_hl -luuid -l:libudunits2.so.0 -l:libexpat.so.1
+
+# Compiler flags
+#FFLAGS=-g -fbounds-check -fdefault-real-8 -I$(CMOR)/include -I$(NETCDF)/include
+FFLAGS=-O3 -fdefault-real-8 -I$(CMOR)/include -I$(NETCDF)/include
+
+# Linker flags
+#LDFLAGS=$(LIBS) -g -fbounds-check
+LDFLAGS=$(LIBS) 
+
+.PHONY: all clean
+
+all: $(TARGET)
+
+clean:
+	rm -f *.o *.f *.h *.inc *.mod *2cmor* 
+
+$(TARGET): $(OBJ) 
+	$(LD) -o $(TARGET) $(OBJ) $(LDFLAGS)
+	cp -f $(TARGET) $(BINDIR)
+
+noresm2cmor.o: $(SRCDIR)/noresm2cmor.F
+	$(FC) $(FFLAGS) -c $(SRCDIR)/noresm2cmor.F
+
+m_modelsatm.o: $(SRCDIR)/m_modelsatm.F
+	$(FC) $(FFLAGS) -c $(SRCDIR)/m_modelsatm.F
+
+m_modelsice.o: $(SRCDIR)/m_modelsice.F
+	$(FC) $(FFLAGS) -c $(SRCDIR)/m_modelsice.F
+
+m_modelslnd.o: $(SRCDIR)/m_modelslnd.F
+	$(FC) $(FFLAGS) -c $(SRCDIR)/m_modelslnd.F
+
+m_modelsocn.o: $(SRCDIR)/m_modelsocn.F
+	$(FC) $(FFLAGS) -c $(SRCDIR)/m_modelsocn.F
+
+m_namelists.o: $(SRCDIR)/m_namelists.F
+	$(FC) $(FFLAGS) -c $(SRCDIR)/m_namelists.F
+
+m_utilities.o: $(SRCDIR)/m_utilities.F
+	$(FC) $(FFLAGS) -c $(SRCDIR)/m_utilities.F

install_griddata.sh

@@ -0,0 +1,33 @@
+#!/bin/sh -e 
+
+# print help information if input arguments are incorrect 
+if [[ ! $1 || `echo $1 | head -1c` == '-' ]] 
+then 
+  echo "Usage: $0 <absolute path to folder where the grid data can be stored"
+  echo 
+  echo "Example: $0 /work/${USER}/cmor/griddata"
+  echo 
+  exit
+fi 
+
+# create folder and cd 
+PWDDIR=`pwd`
+echo "Create $1 if it does not exist"
+mkdir -p $1
+echo "Change to $1" 
+cd $1 
+
+# fetch data
+echo "Download grid data" 
+wget -N http://ns2345k.norstore.uio.no/cmor/griddata/wget_all.sh 
+chmod +x wget_all.sh
+./wget_all.sh
+
+# remove wget script
+rm wget_all.sh
+
+# create symbolic link 
+echo "Place symbolic link to grid data directory in run directory"
+cd $PWDDIR/run
+ln -sf $1 griddata 
+echo completed

install_inputdata.sh

@@ -0,0 +1,33 @@
+#!/bin/sh -e 
+
+# print help information if input arguments are incorrect 
+if [[ ! $1 || `echo $1 | head -1c` == '-' ]] 
+then 
+  echo "Usage: $0 <absolute path to folder where sample input data can be stored"
+  echo 
+  echo "Example: $0 /work/${USER}/cmor/inputdata"
+  echo 
+  exit
+fi 
+
+# create folder and cd 
+PWDDIR=`pwd`
+echo "Create $1 if it does not exist"
+mkdir -p $1
+echo "Change to $1" 
+cd $1 
+
+# fetch data
+echo "Download input data sample" 
+wget -N http://ns2345k.norstore.uio.no/cmor/inputdata/N20TRAERCN_f19_g16_01.tar
+
+# unpack tar file
+echo "Unpack tar file"
+tar xf N20TRAERCN_f19_g16_01.tar
+rm N20TRAERCN_f19_g16_01.tar
+
+# create symbolic link 
+echo "Place symbolic link to input data directory in run directory"
+cd $PWDDIR/run
+ln -sf $1 inputdata 
+echo completed