Regional Climatic Model RegCM User's Guide

The Abdus Salam
International Centre for Theoretical Physics
Strada Costiera, 11 I - 34151 Trieste, Italy
Earth System Physics Section - ESP
Regional Climatic
Model RegCM User’s Guide
Version 4.3
Trieste, Italy - May 2011
Filippo Giorgi, Nellie Elguindi,
Stefano Cozzini and Graziano Giuliani
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Contents
1 Release Notes
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2 Obtain the model
2.1 Simple Model User . . . . . . . . . . . . . . . . . . . . . . . . . .
2.2 Model Developer . . . . . . . . . . . . . . . . . . . . . . . . . . .
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3 Installing procedure
3.1 Software requirements . . . .
3.2 Configuring build . . . . . . .
3.2.1 Model configuration at
3.3 Build the model executables .
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build stage
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4 Access global datasets
4.1 Global dataset directory Layout . .
4.2 Static Surface Dataset . . . . . . .
4.3 Aerosol Database . . . . . . . . . .
4.4 CLM Dataset . . . . . . . . . . . .
4.5 Sea Surface Temperature . . . . .
4.6 Atmosphere and Land temperature
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5 Run a test simulation using the model
5.1 Setting up the run environment . . . . . . . .
5.2 Create the DOMAIN file using terrain . . . .
5.3 Create the SST using the sst program . . . .
5.4 Create the ICBC files using the icbc program
5.5 First RegCM model simulation . . . . . . . .
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6 Localize the model and run your simulation
6.1 The commented namelist . . . . . . . . . . .
6.1.1 dimparam stanza . . . . . . . . . . . .
6.1.2 geoparam stanza . . . . . . . . . . . .
6.1.3 aerosolparam stanza . . . . . . . . . .
6.1.4 terrainparam stanza . . . . . . . . . .
6.1.5 globdatparam stanza . . . . . . . . . .
6.1.6 ioparam stanza . . . . . . . . . . . . .
6.1.7 debugparam stanza . . . . . . . . . . .
6.1.8 boundaryparam stanza . . . . . . . . .
6.1.9 restartparam stanza . . . . . . . . . .
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6.2
6.3
6.1.10 timeparam stanza . . . . .
6.1.11 outparam stanza . . . . . .
6.1.12 physicsparam stanza . . . .
6.1.13 subexparam stanza . . . . .
6.1.14 grellparam, emanparam and
6.1.15 uwparam stanza . . . . . .
6.1.16 chemparam stanza . . . . .
The CLM options . . . . . . . . . .
Sensitivity experiments hint . . . .
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tiedtkeparam
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7 Postprocessing tools
7.1 Command line tools . . . . . . . . . . . .
7.1.1 netCDF library tools . . . . . . . .
7.1.2 NetCDF operators NCO . . . . . .
7.1.3 Climate data Operators CDO . . .
7.2 GrADS program . . . . . . . . . . . . . .
7.2.1 GrADS limits . . . . . . . . . . . .
7.3 CISL’s NCL : NCAR Command Language
7.4 R Statistical Computing Language . . . .
7.5 Non free tools . . . . . . . . . . . . . . . .
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8 Getting help and reporting bugs
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8.1 The Gforge site . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
9 Appendices
9.1 Identify Processor . . . . . . . .
9.2 Chose compiler . . . . . . . . . .
9.3 Environment setup . . . . . . . .
9.4 Compression Library Installation
9.5 HDF5 Library installation . . . .
9.6 netCDF Library installation . . .
9.7 OpenMPI library installation . .
9.8 Final step . . . . . . . . . . . . .
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Chapter 1
Release Notes
RegCM-4.2 is a new step in recoding the RegCM3 model after the effort put into
the RegCM4.0 version. The code base now is actively developed by a community
of developers internal and external to ICTP, and this work is merged on the
Gforge site on e-science-lab.org site.
The main new technical features of the code are summarized in the following
points
• New UW PBL option
• Tiedtke cumuluis scheme in early stage of development
• Autotools enabled configure and build
• Multiple calendar support (gregorian, noleap, 360days)
• New daily output file with statistical variables
• Input layer for some of the CMIP5 models
• netCDF I/O format from model components following the CF-1.4 standard
The model code is in Fortran 90 ANSI standard with some language extensions of Fortran 2003 implemented in all the supported compilers. The development is done on Linux boxes, and the model is known to run on Oracle
SolarisTM platforms, IBM AIXTM platforms, MacOSTM platforms. No porting effort has been done towards non Unix-like Operating Systems. We will for this
User Guide assume that the reference platform is a recent Linux distributon
with a bash shell. Typographical convention is the following:
Table 1.1: Conventions
$>
normal shell prompt
#>
root shell prompt
$SHELL_VARIABLE
a shell variable
Any shell variable is supposed to be set by the User with the following
example syntax:
5
$> export REGCM_ROOT="/home/user/RegCM4.2"
Hope you will find this document useful. Any error found belongs to me and
can be reported to be corrected in future revisions. Enjoy.
6
Chapter 2
Obtain the model
2.1
Simple Model User
A packed archive file with the model code can be downloaded from:
http://gforge.ictp.it/gf/project/regcm/frs
and it can be later on decompressed and unpacked using:
$> tar -zxvf RegCM-4.3.tar.gz
2.2
Model Developer
If you plan to become a model developer, source code can be obtained via svn.
The RegCM team strongly encouragethe contributing developers to enroll on
the gforge site to always be up to date and to check on-line all the news of the
package.
https://gforge.ictp.it/gf/project/regcm
The correct procedure is first to register on the e-forge site, then ask the
ICTP scientific team head Filippo Giorgi to be enrolled as a model developer.
After being officially granted the status, you will gain access to the model subversion repository.
Check that Subversion software is installed on your machine typing the
following command:
$> svn --version
If your system answers command not found, refer to your System Administrator or software installation manual of your OS to install the subversion
software. As an example, on Scientific Linux the command to install it as root
is:
#> yum install subversion
If Subversion is installed, just type the following command:
$> svn checkout https://gforge.ictp.it/svn/regcm/tags/RegCM-4.3
7
Chapter 3
Installing procedure
Whatever method is chosen to download the code, we assume that you have now
on your working directory a new directory, named RegCM-4.3. That directory
will be for the rest of this guide referred as $REGCM_ROOT .
All the operations to build the model binaries will be performed in this
directory.
3.1
Software requirements
In order to configure and install the RegCM code, the following software are
needed:
1. Python 2 language interpreter
2. GNU Make program
3. Fortran 90 compiler
4. netCDF Rew and Davis (1990) Format I/O library compiled with the
above compiler. Source code can be found from
ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf.tar.gz
Note that current netCDF version 4.2 is dependent on HDF5 1.8.8.
Optional requirements strongly suggested are :
1. GNU patch program if CLM option is activated.
2. MPI2 Message Passing Library compiled with the above fortran compiler
for parallel runs using multiple core single machines or cluster of machines.
Source code for the implementation code was tested with can be obtained
at:
http://www.open-mpi.org/software/ompi/v1.4/downloads
3. HDF5 Format I/O Library compiled with the above fortran compiler to
enable netCDF V4 features. Source code can be obtained at:
http://www.hdfgroup.org/ftp/HDF5/current/src
8
4. NCO netCDF Operators for manging netCDF file. Most Linux distribution have this already packed, and you should refer to your System
Administrator or OS Software Installation manual to obtain it. Source
code is at:
http://nco.sourceforge.net/src
5. CDO Climatic data Operators for managing netCDF file. Most Linux
distribution have this already packed, and you should refer to your System
Administrator or OS Software Installation manual to obtain it. Source
code is at:
https://code.zmaw.de/projects/cdo/files
6. A Scientific Plotting and Data Analysis Software such as:
• IGES GrADS 2.0 Graphical Analysis and Display System. Convenient helpers are packed in RegCM to use GrADS with RegCM
netCDF output files. Binaries and source code can be obtained from
http://www.iges.org/grads/downloads.html
• NCL, NCAR CISL Command Language. The NCL can read netCDF
output files, and sample scripts can be found in the Tools/Scripts/NCL
directory. Binaries and source code can be obtained from
http://www.ncl.ucar.edu
7. A quick viewer for netCDF files like NcView:
http://meteora.ucsd.edu/ pierce/ncview home page.html
An example session of installation of basic software needed to compile the
RegCM model is detailed in chapter 9.
3.2
Configuring build
The RegCM Version 4.3 is configured by a python2 script, which will select and
edit for you sample configuration files for the supported architectures. These
files are kept in the Arch directory under $REGCM_ROOT.
Currently tested and supported configurations (OS/Compiler) are:
1. Linux with GNU gfortran compiler version ≥ 4.6
2. Linux with IntelTM ifort compiler version ≥ 12.0
3. Linux with PortlandTM pgf90 compiler version ≥ 11.0
4. Mac OsXTM with g95 compiler
5. IBM AIXTM with xlf compiler
6. Oracle SolarisTM with Oracle Solaris StudioTM compiler ≥ 8.3
The 4.3 version of the RegCM model relies on the standard GNU autotools
to configure and build the model code.
The first step is to change working directory to $REGCM_ROOT and run the
configure script giving as arguments the chosen compilers:
9
$> cd $REGCM_ROOT
$> ./configure CC=icc FC=ifort
To know the list of arguments that can be given to the configure script, the
script can be launched with the --help command line argument.
$> ./configure --help
The useful arguments to successfully build the model are:
--with-netcdf
Path to NetCDF installation (default: NETCDF
environment)
--with-hdf5
Path to HDF5 installation (default: HDF5
environment)
--with-szip
Path to SZIP installation (default: SZIP
environment)
CC=
C compiler command
CFLAGS=
C compiler flags
LDFLAGS=
linker flags, e.g. -L<lib dir> if you have libraries in a
nonstandard directory <lib dir>
LIBS=
libraries to pass to the linker, e.g. -l<library>
CPPFLAGS=
(Objective) C/C++ preprocessor flags, e.g. -I<include dir> if
you have headers in a nonstandard directory <include dir>
CPP=
C preprocessor
FC=
Fortran compiler command
FCFLAGS=
Fortran compiler flags
MPIFC=
MPI Fortran compiler command
3.2.1
Model configuration at build stage
1. Enable debug
--enable-debug
Enable debugging flags and per processor log file
If enabled, the model will be compiled using debug flags for the compiler,
which will allow the use of a debugger such as gdb. More diagnostics will
also be generated during model run. The default is to build production
binaries with all optimization flags turned on.
2. Serial code using stub MPI library
--enable-mpiserial
Use the included MPI replacement library for single
processor
The model is coded to use an MPI2 library to run in parallel mode using
multiple cores/processors or run on a cluster. To enable instead a serial
compilation option, a stub MPI library with empty callbacks needs to be
compiled and linked to the executable. The RegCM team strongly suggest
to build MPI enabled model also on standalone systems, to take advantage
of the multicore capabilities of any modern processor.
3. CLM option
10
--enable-clm
Supply this option if you plan on using CLM option.
This option switches off the default Land model of RegCM (derived from
BATS1e), and enables the use of the Community Land Model V3.5 inside
RegCM. The default is to use the RegCM BATS Land Model. 1 For the
scope of the tutorial test run in chapter 5, use the default option.
3.3
Build the model executables
Now that everything is hopefully configured, you may use the make program to
build executables.
$> make
This target will builds all model parts. The compilation is started in the
whole model tree (PreProc, Main and PostProc). Lot of messages will appear
on screen, abd at the end all executables are built int the source directories. To
copy them to the Bin directory, esplicitly issue the command:
$> make install
Congratulations! You can now go to next step and run a test simulation.
1 The
CLM option needs the GNU patch program to be installed.
11
Chapter 4
Access global datasets
The first step to run a test simulation is to obtain static data to localize model
DOMAIN and Atmosphere and Ocean global model dataset to build initial and
boundary conditions ICBC to run a local area simulation.
ICTP maintains a public accessible web repository of datasets on:
http://users.ictp.it/ pubregcm/RegCM4/globedat.htm
As of now you are requested to download required global data on your local
disk storage before any run attempt. In the future, the ICTP ESP team has
planned to make available an OpenDAP THREDDS Server to give remote access
to global dataset for creating DOMAIN and ICBC without the need to download
the global dataset, but just the required subset in space and time, using the
ICTP web server capabilities to create that subset.
4.1
Global dataset directory Layout
You are suggested to establish a convenient location for global datasets on your
local storage. Keep in mind that required space for a year of global data can be
as large as 8 GBytes.
Having this in mind, we will now consider that you the user have identified
on your system or have network access to such a storage resource to store say 100
GB of data, and have it reachable on your system under the $REGCM_GLOBEDAT
location. On this directory, you are required to make the following directories:
$> cd $REGCM_GLOBEDAT
$> mkdir SURFACE CLM SST AERGLOB EIN15
This does not fill all possible global data sources paths, but will be enough
for the scope of running the model for testing its capabilities.
4.2
Static Surface Dataset
The model needs to be localized on a particular DOMAIN. The needed information are topography, land type classification and optionally lake depth (to run
the Hostetler lake model) and soil texture classification (to run the chemistry
option with DUST enabled).
12
This means downloading four files, which are global archives at 30second
horizontal resolution on a global latitude-longitude grid of the above data.
$> cd $REGCM_GLOBEDAT
$> cd SURFACE
$> curl -o GTOPO_DEM_30s.nc.gz \
> http://clima-dods.ictp.it/data/d4/SURFACE/GTOPO_DEM_30s.nc.gz
$> gunzip GTOPO_DEM_30s.nc.gz
$> curl -o GLCC_BATS_30s.nc.gz \
> http://clima-dods.ictp.it/data/d4/SURFACE/GLCC_BATS_30s.nc.gz
$> gunzip GLCC_BATS_30s.nc.gz
Optional Lake and Texture datasets:
$> cd $REGCM_GLOBEDAT
$> cd SURFACE
$> curl -o ETOPO_BTM_30s.nc.gz \
> http://clima-dods.ictp.it/data/d4/SURFACE/ETOPO_BTM_30s.nc.gz
$> gunzip ETOPO_BTM_30s.nc.gz
$> curl -o GLZB_SOIL_30s.nc.gz \
> http://clima-dods.ictp.it/data/d4/SURFACE/GLZB_SOIL_30s.nc.gz
$> gunzip GLZB_SOIL_30s.nc.gz
4.3
Aerosol Database
If you are planning to enable aerosol in the model, you will need a single file,
which contains sources of optical active species used in the model regridded from
global model run.
$> cd $REGCM_GLOBEDAT
$> cd AERGLOB
$> curl -o AEROSOL.dat \
> http://clima-dods.ictp.it/data/d4/AEROSOL/AEROSOL.dat
This is the input file for the aerosol icbc program.
4.4
CLM Dataset
If you are planning to enable the CLM option in the model, you will need a series
of files with global land surface characteristics datasets.
$> cd $REGCM_GLOBEDAT
$> cd CLM
$> CLMURL="clima-dods.ictp.it/data/d4/CLM"
$> curl -o mksrf_fmax.nc.gz \
> http://$CLMURL/mksrf_fmax.nc.gz
$> curl -o mksrf_glacier.nc.gz \
> http://$CLMURL/mksrf_glacier.nc.gz
$> curl -o mksrf_lai.nc.gz \
> http://$CLMURL/mksrf_lai.nc.gz
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$> curl -o mksrf_lanwat.nc.gz \
> http://$CLMURL/mksrf_lanwat.nc.gz
$> curl -o mksrf_navyoro_20min.nc.gz \
> http://$CLMURL/mksrf_navyoro_20min.nc.gz
$> curl -o mksrf_pft.nc.gz \
> http://$CLMURL/mksrf_pft.nc.gz
$> curl -o mksrf_soicol_clm2.nc.gz \
> http://$CLMURL/mksrf_soicol_clm2.nc.gz
$> curl -o mksrf_soitex.10level.nc.gz \
> http://$CLMURL/mksrf_soitex.10level.nc.gz
$> curl -o mksrf_urban.nc.gz \
> http://$CLMURL/mksrf_urban.nc.gz
$> curl -o pft-physiology.c070207.gz \
> http://$CLMURL/pft-physiology.c070207.gz
$> curl -o pft-physiology.c070207.readme.gz \
> http://$CLMURL/pft-physiology.c070207.readme.gz
$> curl -o rdirc.05.061026.gz \
> http://$CLMURL/rdirc.05.061026.gz
$> gunzip *.gz
This is the input file for the clm2rcm program (see at 6.2).
4.5
Sea Surface Temperature
The model needs a global SST dataset to feed the model with ocean temperature.
You have multiple choices for SST data:
1. GISST - UKMO SST (Rayner et al 1996), 1 degree from
http://www.badc.rl.ac.uk
UKMO DATA archive reformed as direct access binary format from the
original ASCII format.
2. OISST - CAC Monthly Optimal Interpolation dataset in the original
netCDF format.
3. OI2ST - Same as above, but both SST and Sea Ice dataset (used if seaice
option is enabled in the model).
4. OI WK - OISST CAC Weekly Optimal Interpolation dataset in the original netCDF format
5. OI2WK - Same as above, but both SST and Sea Ice dataset
6. EH5RF - EC-MPI 6 hourly 1.875x1.875, reference from 1941 to 2000
7. EH5A2 - Same as above, from 2001 to 2100 IPCC A2 scenario
8. EH5B1 - Same as above, from 2001 to 2100 IPCC B1 scenario
9. EHA1B - Same as above, from 2001 to 2100 IPCC A1B scenario
10. ERSST - ERA interim Project 6 hourly 1.5x1.5 degree SST
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11. ERSKT - ERA interim as above but Skin temperature
12. FV RF - HadAMH SST in the original netCDF format, from 1959 to 1991
13. FV A2 - Same as above, IPCC A2 scenario
14. FV B2 - Same as above, IPCC B2 scenario
15. CCSST - CCSM3 POP gx1v3 regridded 1x1 data
16. HA XX - HadGEM CMPI5 dataset with XX in RF,26,45,85
17. CA XX - CanESM CMPI5 dataset with XX in RF,26,45,85
We will for now for our test run download just CAC OISST weekly for the
period 1981 - present.
$> cd $REGCM_GLOBEDAT
$> cd SST
$> CDCSITE="ftp.cdc.noaa.gov/pub/Datasets/noaa.oisst.v2"
$> curl -o sst.wkmean.1981-1989.nc \
> ftp://$CDCSITE/sst.wkmean.1981-1989.nc
$> curl -o sst.wkmean.1990-present.nc \
> ftp://$CDCSITE/sst.wkmean.1990-present.nc
4.6
Atmosphere and Land temperature Global
Dataset
The model needs to build initial and boundary conditions for the regional scale,
interpolating on the RegCM grid the data from a Global Climatic Model output.
The GCM dataset can come from any of the supported models:
1. EINXX - ECMWF INTERIM 10 year reanalysis datasets, XX can have
values 25, 15 or 75 for resolution 2.5x2.5L37, 1.5x1.5L37, 0.75x0.75L37.
Time resolution is 4 times daily.
2. ECMWF - ECMWF TOGA/WCRP Uninitialized Data - (ECWCRP).
Reformatted by PWC/ICTP to direct-access binary, T42L15, Gaussian
Grid. 1
3. ERA40 - ECMWF 40 year reanalysis datasets, available from
http://data.ecmwf.int/data/d/era40 daily,
Pressure levels, 2.5x2.5L23, 4 times daily.
4. ERAHI - ECMWF 40 year reanalysis datasets, origigal model level fields:
T, U, V and log(Ps) are in spectral coefficients, Oro and Q are at the
reduced Gaussian grids. T159L60 (N80L60).
1 As
of RegCM 4.2 this input source is not tested
15
5. NNRPY - NCEP/NCAR Reanalysis datasets, Y can have values 1 and
2 for the two reanalysis experimens. Data are available in the original
netCDF format at
ftp://ftp.cdc.noaa.gov/Datasets/ncep.reanalysis
(1948 − present, 2.5x2.5L13) and
ftp://ftp.cdc.noaa.gov/Datasets/ncep.reanalysis2
(1979 − 2009, 2.5x2.5L13).
6. NRP2W - Small Window (instead of global) of NNRP1/2 to save disk
space. This window can be created from original files with NCO tools. 2
7. GFS11 - NCEP Global Forecast System (GFS) product FNL, from
http://dss.ucar.edu/datasets/ds083.2/data/fnl-yyyymm,
Pressure levels, 1.0x1.0L27, 4 times daily.
8. FVGCM - FVGCM run by the PWC group of Abdus Salam ICTP.
3
9. EH5XX - Echam run by the MPI at Hamburg, T63, Gaussian grid. For
present day run: 1941 − 2000, for A1B scenario run: 2001 − 2100. 17
pressure levels, 4 times daily, direct-access binary.
10. ECEXY - ECMWF Ensemble forecast member, where X is the model
version number, and Y is the ensemble member number, i.e. for example
ECE24 stands for ECMWF model version 2, ensemble number 4. Dataset
contains 6 hourly global data on model levels with surface geopotential
and natural logarithm of surface pressure.
11. CCSMN - unpacked CCSM3 NETCDF L26 (six hourly) data, either global
or window, can be obtained from
http://www.earthsystemgrid.org
12. HA XX - HadGEM CMPI5 dataset with XX in RF,26,45,85
13. CA XX - CanESM CMPI5 dataset with XX in RF,26,45,85
14. FNEST - Further oneway NESTing from previous RegCM run.
We will for now for our test run download just the EIN15 dataset for the
year 1990 (Jan 01 00:00:00 UTC to Dec 31 18:00:00 UTC)
$>
$>
$>
$>
$>
$>
>
>
>
>
>
>
>
cd $REGCM_GLOBEDAT
cd EIN15
mkdir 1990
cd 1990
ICTPSITE="clima-dods.ictp.it/data/d9/ERAIN150/1990/"
for type in "air hgt rhum uwnd vwnd"
do
for hh in "00 06 12 18"
do
curl -o ${type}.1990.${hh}.nc \
http://$ICTPSITE}/${type}.1990.${hh}.nc
done
done
2 As
3 As
of RegCM 4.2 this input source is not tested
of RegCM 4.2 this input source is not tested
16
With this dataset we are now ready to go through the RegCM Little Tutorial
in the next chapter of this User Guide.
17
Chapter 5
Run a test simulation using
the model
We will in this chapter go through a sample session in using the model with a
sample configuration file prepared for this task.
5.1
Setting up the run environment
The model executables prepared in chapter 3 are waiting for us to use them. So
let’s give them a chance.
The model test run proposed here requires around 100Mb of disk space to
store the DOMAIN and ICBC in input and the output files. We will assume
here that you, the user, have already established a convenient directory on
a disk partition with enough space identified in the following discussion with
$REGCM_RUN
We will setup in this directory a standard environment where the model can
be executed for the purpose of learning how to use it.
$>
$>
$>
$>
$>
cd $REGCM_RUN
mkdir input output
ln -sf $REGCM_ROOT/Bin .
cp $REGCM_ROOT/Testing/test_001.in .
cd $REGCM_RUN
Now we are ready to modify the input namelist file to reflect this directory
layout. A namelist file in Fortran90 is a convenient way to give input to a program in a formatted file, read at runtime by the program to setup its execution
behaviour. So the next step is somewhat tricky, as you need to edit the namelist
file respecting its well defined syntax. Open your preferred text file editor and
load the test_001.in file. You will need to modify for the scope of the present
tutorial the following lines:
FROM:
dirter = ’/set/this/to/where/your/domain/file/is’,
TO:
dirter = ’input/’,
18
FROM:
inpter = ’/set/this/to/where/your/surface/dataset/is’,
TO:
inpter = ’$REGCM_GLOBEDAT’,
where $REGCM_GLOBEDAT is the directory where input data have been downloaded in chapter 4.
FROM:
dirglob = ’/set/this/to/where/your/icbc/for/model/is’,
TO:
dirglog = ’input/’,
FROM:
inpglob = ’/set/this/to/where/your/input/global/data/is’,
TO:
inpglob = ’$REGCM_GLOBEDAT’,
and last bits:
FROM:
dirout=’/set/this/to/where/your/output/files/will/be/written’
TO:
dirout=’output/’
These modifications just reflect the above directory layout proposed for this
tutorial, and any of these paths can point anywhere on your system disks. The
path is limited to 256 characters. We are now ready to execute the first program
of the RegCM model.
5.2
Create the DOMAIN file using terrain
The first step is to create the DOMAIN file to localize the model on a world
region. The program which does this for you reading the global databases is
terrain .
To launch the terrain program, enter the following commands:
$> cd $REGCM_RUN
$> ./Bin/terrain test_001.in
If everything is correctly configured up to this point, the model should print
something on stdout, and the last lines will be:
Grid data written to output file
Successfully completed terrain fields generation
In the input directory the program will write the following two files:
$> ls input
test_001_DOMAIN000.nc test_001_LANDUSE
19
The DOMAIN file contains the localized topography and landuse databases,
as well as projection information and land sea mask. The second file is an ASCII
encoded version of the landuse, used for modifying it on request. We will cover
it’s usage later on. To have a quick look at the DOMAIN file content, you may
want to use the GrADSNcPlot program:
$> ./Bin/GrADSNcPlot input/test_001_DOMAIN000.nc
If not familiar with GrADS program, enter in sequence the following commands at the ga-> prompt:
ga->
ga->
ga->
ga->
ga->
ga->
ga->
ga->
ga->
q file
set gxout shaded
set mpdset hires
set cint 50
d topo
c
set cint 1
d landuse
quit
this will plot the topography and the landuse on the X11 window.
5.3
Create the SST using the sst program
We are now ready to create the Sea Surface Temperature for the model, reading
a global dataset. The program which does this for you is the sst program,
which is executed with the following commands:
$> cd $REGCM_RUN
$> ./Bin/sst test_001.in
If everything is correctly configured up to this point, the model should print
something on stdout, and the last line will be:
Successfully generated SST
The input directory now contains a new file:
$> ls input
test_001_DOMAIN000.nc test_001_LANDUSE test_001_SST.nc
The SST file contains the Sea Surface temperature to be used in generating
the Initial and Boundary Conditions for the model for the period specified in
the namelist file. Again you may want to use the GrADSNcPlot program to
look at file content:
$> ./Bin/GrADSNcPlot input/test_001_SST.nc
If not familiar with GrADS program, enter in sequence the following commands at the ga-> prompt:
20
ga->
ga->
ga->
ga->
ga->
ga->
q file
set gxout shaded
set mpdset hires
set cint 2
d sst
quit
this will plot the interpolated sst field on the X11 window.
5.4
Create the ICBC files using the icbc program
Next step is to create the ICBC (Initial Condition, Boundary Conditions) for
the model itself. The program which does this for you is the icbc program,
executed with the following commands:
$> cd $REGCM_RUN
$> ./Bin/icbc test_001.in
If everything is correctly configured up to this point, the model should print
something on stdout, and the last line will be:
Successfully completed ICBC
The input directory now contains two more files:
$> ls -1 input
test_001_DOMAIN000.nc
test_001_ICBC.1990060100.nc
test_001_ICBC.1990070100.nc
test_001_LANDUSE
test_001_SST.nc
The ICBC files contain the surface pressure, surface temperature, horizontal
3D wind components, 3D temperature and mixing ratio for the RegCM domain
for the period and time resolution specified in the input file. Again you may
want to use the GrADSNcPlot program to look at file content:
$> ./Bin/GrADSNcPlot input/test_001_ICBC.1990060100.nc
If not familiar with GrADS program, enter in sequence the following commands at the ga-> prompt:
ga->
ga->
ga->
ga->
ga->
ga->
ga->
ga->
q file
set gxout shaded
set mpdset hires
set cint 2
d ts
c
set lon 10
set lat 43
21
ga-> set t 1 last
ga-> d ts
ga-> quit
this will plot the interpolated surface temperature field on the X11 window,
first at first time step and then a time section in one of the domain points for a
whole month.
We are now ready to run the model!
5.5
First RegCM model simulation
The model has now all needed data to allow you to launch a test simulation,
the final goal of our little tutorial.
The model command line now will differ if you have prepared the Serial or the
MPI version. For the MPI enabled version we will assume that your machine is
a dual core processor (baseline for current machines, even for laptops). Change
the -np 2 argument to the number of processors you have on Your platform (on
my laptop QuadCore I use -np 4).
• MPI version
$> cd $REGCM_RUN
$> mpirun -np 2 ./Bin/regcmMPI test_001.in
• Serial version
1
$> cd $REGCM_RUN
$> ./Bin/regcmSerial test_001.in
Now the model will start running, and a series of diagnostic messages will
be printed on screen. As this is a simulation known to behave well, no stoppers
will appear, so you may want now to have a coffee break and come back in 10
minutes from now.
At the end of the run, the model will print the following message:
RegCM V4 simulation successfully reached end
The output directory now contains four files:
$> ls output
test_001_ATM.1990060100.nc test_001_SRF.1990060100.nc
test_001_RAD.1990060100.nc test_001_SAV.1990070100
the ATM file contains the atmosphere status from the model, the SRF file
contains the surface diagnostic variables, and the RAD file contains radiation
fluxes information. The SAV file stores the status of the model at the end of the
simulation period to enable a restart, thus allowing a long simulation period to
be splitted in shorter simulations.
To have a look for example at surface fields, you may want to use the following command:
1 Deprecated.
Support will be dropped in future releases.
22
$> ./Bin/GrADSNcPlot output/test_001_SRF.1990060100.nc
Assuming the previous crash course in using GraDS was received, you should
be able to plot the variables in the file.
This is the end of this little tutorial, and in the next chapter we will examine
how to configure the model for your research needs.
23
Chapter 6
Localize the model and run
your simulation
We will examine in this chapter in more detail the namelist configuration file,
to give you the User a deeper knowledge of model capabilities.
6.1
The commented namelist
In this section we will show you the commented namelist input file you will find
under $REGCM_ROOT/Doc with the name README.namelist . All model programs
seen so far, with the exception of the GrADS helper program, use as input this
namelist file, which is unique to a particular simulation. The model input
namelist file is divided in stanzas, each one devoted to configuring the model
capabilities. A stanza in the namelist is identified with a starting & character
followed by stanza name, and ends on a single line with the \ character.
6.1.1
dimparam stanza
This stanza contains the base X,Y,Z domain dimension information, used by the
model dynamic memory allocator to request the Operating System the memory
space to store the model internal variables.
&dimparam
iy
= 34,
jx
= 48,
kz
= 18,
dsmin = 0.01,
dsmax = 0.05,
nsg
= 1,
!
!
!
!
!
!
!
!
This is number of points in the N/S direction
This is number of points in the E/W direction
Number of vertical levels
Minimum sigma spacing (only used if kz is not 14, 18, or 23)
Maximum sigma spacing (only used if kz is not 14, 18, or 23)
For subgridding, number of points to decompose. If nsg=1,
no subgridding is performed. CLM does NOT work as of now with
subgridding enabled.
/
The things you need to know here:
1. In the current version 4.3 the model parallelizes execution dividing the
work between the processors along the jx (longitude) dimension. The
minimum work per processor is 3 points along the jx dimension, so the
maximum number of processors which can be used in a parallel run for the
24
above configuration is just 16. In future revision ICTP plans to introduce
2D decomposition.
2. If a custom number of sigma level is chosen (not 14, 18 or 23), the actual sigma values are calculated mimimizing the a, b coefficients for the
equation:
dsig(i) = dsmax ∗ ai−1 ∗ b0.5∗(i−2)∗(i−1)
(6.1)
derived from the recursive relation:
dsig(i) = a(i) ∗ dsig(i − 1)
(6.2)
where a(i) = b ∗ a(i − 1). We at ICTP normally use 18 levels.
3. Specifying an nsg number greater than one triggers the subgrid BATS
model on. There is no plan to extend this feature to CLM model. This
affects only surface variable calculations. All dynamical variables are calculated still on the coarser grid. Rain in the current implementation is
also calculated on the coarser grid.
6.1.2
geoparam stanza
This stanza is used by the terrain program to geolocate the model grid on the
earth surface. The RegCM model uses a limited number of projection engines.
The value here are used by the other model programs to assert consistency with
the geolocation information written by the terrain program in the DOMAIN file.
The first step in any application is the selection of model domain and resolution. There are no strict rules for this selection, which in fact is mostly
determined by the nature of the problem and the availability of computing resources. The domain should be large enough to allow the model to develop
its own circulations and to include all relevant forcings and processes, and the
resolution should be high enough to capture local processes of interest (e.g. due
to complex topography or land surface).
On the other hand the model computational cost increases rapidly with
resolution and domain size, so a compromise needs to be usually reached between
all these factors.
This is usually achieved by experience, understanding of the problem or trial
and error, however one tip to remember is to avoid that the boundaries of the
domain cross major topographical systems.
This is because the mismatch in the resolution of the coarse scale lateral
driving fields and the model fields in the presence of steep topography may
generate spurious local effects (e.g. localized precipitation areas) which can
affect the model behavior, at least in adjacent areas.
&geoparam
iproj = ’LAMCON’, !
!
!
!
!
ds = 60.0,
!
Domain cartographic projection. Supported values are:
’LAMCON’, Lambert conformal.
’POLSTR’, Polar stereographic. (Doesn’t work)
’NORMER’, Normal Mercator.
’ROTMER’, Rotated Mercator.
Grid point horizontal resolution in km
25
ptop = 5.0,
clat = 45.39,
clon = 13.48,
plat = 45.39,
plon = 13.48,
truelatl = 30.0,
truelath = 60,
i_band = 0,
!
!
!
!
!
!
!
!
!
!
!
Pressure of model top in cbar
Central latitude of model domain in degrees
North hemisphere is positive
Central longitude of model domain in degrees
West is negative.
Pole latitude (only for rotated Mercator Proj)
Pole longitude (only for rotated Mercator Proj)
Lambert true latitude (low latitude side)
Lambert true latitude (high latitude side)
Use this to enable a tropical band. In this case the ds,
iproj, clat, clon parameters are not considered.
/
The things you need to know here:
1. The different projection engines produce better results depending on the
position and extent of the domain. In particular, regardless of hemisphere:
•
•
•
•
Middle latitudes (around 45 degrees) - Lambert Conformal
Polar latitudes (more than 75 degrees) - Polar Stereographic
Low latitudes (up to 30 degrees and crossing the equator) - Mercator
Crossing more than 45 degrees extent in latitude - Rotated Mercator
2. The model hydrostatic engine does not allow a resolution lower than 20km.
If you want a higher resolution consider using the subgridding scheme.
ICTP plans to introduce in the future a non-hydrostatic compressible core
to the RegCM model.
3. Lowering the top pressure of the model can give you problems in regions
with complex topography. Touch the default after thinking twice on that.
4. Always specify clat and clon, the central domain point, and do fine
adjustment of the position moving it around a little bit. A little shift in
position and some tests can help you obtain a better representation of
coastlines and topography at the coarse resolutions.
5. If using LAMCON projection, take care to place the two true latitudes at
around one fourth and three fourth of the domain latitude space to better
correct the projection distortion of the domain.
6. The pole position for the rotated mercator position should be as near as
possible to the center domain position.
7. For the i_band parameter, selecting this will enable the tropical band experiment, and the horizontal resolution will be calculated from the number
of jx points. The projection is set to Normal Mercator, the center of the
projection is set to clat = 0.0, clon = 180.0, and the grid point resolution is calculated as:
2 ∗ π ∗ 6370.0
(6.3)
jx
Just remember:
(a) The model for a tropical band simulation is heavy, as the number of
points is usually huge to obtain a good horizontal resolution. Check
any memory limit is disabled on your platform before attempting a
run.
26
(b) The model scales well on a cluster with a large number of processors.
6.1.3
aerosolparam stanza
This stanza allows the user to specify aerosol usage in the model. It does
enable building of soil texture database in the terrain program and controls
the dimension of the number of optical active tracers used in the active chemistry
tracers part of the model.
&aerosolparam
aertyp = ’AER00D0’ !
!
!
!
!
!
!
!
!
!
ntr = 4,
!
/
Aerosol dataset used
One in :
AER00D0 -> Neither aerosol, nor dust used
AER01D0 -> Biomass, SO2 + BC + OC, no dust
AER10D0 -> Anthropogenic, SO2 + BC + OC, no dust
AER11D0 -> Anthropogenic+Biomass, SO2 + BC + OC, no dust
AER00D1 -> No aerosol, with dust
AER01D1 -> Biomass, SO2 + BC + OC, with dust
AER10D1 -> Anthropogenic, SO2 + BC + OC, with dust
AER11D1 -> Anthropogenic+Biomass, SO2 + BC + OC, with dust
Tracer parameters: number of tracers
The things you need to know here:
1. If aertyp is left to AER00D0, it is nonsense to activate chemistry in the
model.
2. If Anthropogenic and/or Biomass is activated, the model will also need
the user to run the aerosol program. It can be run at the same level as the
sst program, with the same calling syntax. Just replace sst with aerosol.
$> cd $REGCM_RUN
$> ./Bin/aerosol myregcm.in
The aerosol program prepares an emission dataset used by the model
to consider optical active chemistry species effects in the radiation calculation. The surface dust emission are calculated using the soil texture
dataset prepared by the terrain program if the last 0 is set to 1 in aertyp.
6.1.4
terrainparam stanza
This stanza is used by the terrain program to know how you want to generate
the DOMAIN file. You can control its work using a number of parameters to obtain what you consider the best representation of the physical reality. Do not
underestimate what you can do at this early stage, having a good representation of the surface can lead to valuable results later when the model calculates
climatic parameters.
&terrainparam
domname = ’AQWA’,
smthbdy = .false.,
lakedpth
= .false.,
fudge_lnd
= .false.,
fudge_lnd_s = .false.,
fudge_tex
= .false.,
!
!
!
!
!
!
!
!
Name of the domain. Controls naming of input files
Smoothing Control flag
true -> Perform extra smoothing in boundaries
If using lakemod (see below), produce from
terrain program the domain bathymetry
Fudging Control flag, for landuse of grid
Fudging Control flag, for landuse of subgrid
Fudging Control flag, for texture of grid
27
fudge_tex_s = .false.,
fudge_lak
= .false.,
fudge_lak_s = .false.,
h2opct = 50.,
h2ohgt = .false.,
dirter = ’input/’,
inpter = ’globdata/’,
/
!
!
!
!
!
!
!
Fudging Control flag, for texture of subgrid
Fudging Control flag, for lake of grid
Fudging Control flag, for lake of subgrid
Surface minimum H2O percent to be considered water
Allow water points to have elevation greater than 0
Output directory for terrain files
Input directory for SURFACE dataset
The things you need to know here:
1. The domname will control the output file naming convention, all generated
files will add this prefix to the old V3 naming convention, giving you the
capability to recognize different runs. Try to use always meaningful names.
2. You can control the final land-water mask using the h2opct parameter.
This parameter can be used to have more land points than calculated by
the simple interpolation engine. Try it with different values to find best
land shapes. A zero value means use just the interpolation engine, higher
values will extend into ocean points the land at land-water interface. The
h2ohgt parameter allows also water points to have elevation greater than
zero to avoid wall effects on the coasts.
3. A number of flags control the capability of the terrain program to modify
on request the class type variables in the DOMAIN file. You can modify on
request the landuse, the texture and the lake/land interface. Running
once the terrain program, it will generate for you aside from the DOMAIN
file a series of ASCII files you can modify with any text editor. Running
the terrain program the second time and setting a fudge flag, will tell
the program to overwrite the selected variable with the modified value in
the ASCII file. This can be useful for sensitivity experiments in the BATS
surface model or to design a scenario experiment.
4. Some of the land surface types in BATS have been little tested and used or
are extremely simplified and thus should be used cautiously. Specifically
the types are: sea ice, bog/marsh, irrigated crop, glacier. If such types
are present in a domain, the user is advised to carefully check the model
behavior at such points and eventually substitute these types with others.
5. The inpter directory is expected to contain a SURFACE directory where
the actual netCDF global dataset are stored. The overall path is limited
to 256 characters.
6. If the netCDF library is compiled with OpenDAP support, an URL can
be used as a path in the dirter and inpter variables. Note that the
256 character limit for paths holds in the whole program. For terrain
program you may want to try the following URL:
http://clima-dods.ictp.it/thredds/dodsC
7. The texture dataset is built if the aerosol model is activated. This is
controlled by the AERTYP flag. See above in 6.1.3.
28
6.1.5
globdatparam stanza
This stanza is used by the sst and icbc ICBC programs. You can tell them
how to build initial and bondary conditions.
&globdatparam
ibdyfrq =
6,
ssttyp = ’OI_WK’,
! boundary condition interval (hours)
! Type of Sea Surface Temperature used
! One in: GISST, OISST, OI2ST, OI_WK, OI2WK,
!
FV_RF, FV_A2, FV_B2,
!
EH5RF, EH5A2, EH5B1, EHA1B,
!
ERSST, ERSKT, CCSST, CA_XX, HA_XX
dattyp = ’EIN15’,
! Type of global analysis datasets used
! One in: ECMWF, ERA40, EIN75, EIN15, EIN25,
!
ERAHI, NNRP1, NNRP2, NRP2W, GFS11,
!
FVGCM, FNEST, EH5RF, EH5A2, EH5B1,
!
EHA1B, CCSMN, ECEXY, CA_XX, HA_XX
gdate1 = 1990060100,
! Start date for ICBC data generation
gdate2 = 1990070100,
! End data for ICBC data generation
calendar = ’gregorian’,
! Calendar to use (gregorian, noleap or 360_day)
dirglob = ’input/’,
! Path for ICBC produced input files
inpglob = ’globdata/’,
! Path for ICBC global input datasets.
! Look http://users.ictp.it/~pubregcm/RegCM4/globedat.htm
! on how to download them.
/
Things you need to know here:
1. The gdate time window to build ICBC must be always greater or equal
to the time window you plan to run the model in. Different GCMs and
reanalysis products have different length of the year. For example, the
reanalysis products employ the real year length (365 days + real leap
years, i.e. and average length of 365.2422), the CCSM has a length of 365
days (no leap year), the HadCM has a length of 360 days (30 day months).
The RegCM4 length of the year has to be the same as in the forcing fields,
and this can be set in the variable dayspy. Please remember to always
check the consistency of the length of the year.
2. Even if listed, not all the input engines are fully tested. Some of them need
data which have been reformatted by ICTP (they are not in the original
format with which they are distributed by the institution producing them).
Some input data are not freely distibutable by ICTP, and you need a
special agreement with the owner to use them. Hopefully the situation
is changing, and data exchange is becoming more and more the basis for
good science in the climatic field.
3. For notes on path, you can see the above in terrainparam stanza description at 5.
6.1.6
ioparam stanza
&ioparam
ibyte = 4,
/
! Number of bytes in reclen. Usually 4
Leave this untouched. The model expects input record syze to be 4 bytes.
You will need to change some compilation parameters if you change this value.
29
1
6.1.7
debugparam stanza
This stanza is used by all RegCM programs to enable/disable some debug printout. In the current release this flag is honored only by the model itself. If you
are not a developer you may find this flags useless.
&debugparam
debug_level = 0, ! Currently value of 2 and 3 control previous DIAG flag
dbgfrq = 3,
! Interval for printout if debug_level >= 3
/
Just note that with current implementation, the output file syncing is left
to the netCDF library. If You want to examine step by step the output while
the model is running, set the debug_level at value 3.
6.1.8
boundaryparam stanza
Being a limited area model, in order to be run RegCM4 requires the provision of
meteorological initial and time dependent lateral boundary conditions, typically
for wind components, temperature, water vapor and surface pressure. These are
obtained by interpolation from output from reanalysis of observations or global
climate model simulations, which thus drive the regional climate model.
The lateral boundary conditions (LBC) are provided through the so called
relaxation/diffusion technique which consists of:
1. selecting a lateral buffer zone of n grid point width (nspgx)
2. interpolating the driving large scale fields onto the model grid
3. applying the relaxation + diffusion term
∂α
= F (n)F1 ∗ (αLBC − αmod ) − F (n)F 2 ∗ ∆2 (αLBC − αmod )
∂t
(6.4)
where α is a prognostic variable (wind components, temperature, water
vapor, surface pressure). The first term on the rhs is a Newtonian relaxation term which brings the model solution (mod) towards the LBC
field (LBC) and the second term diffuses the differences between model
solution and LBC. F (n) is an exponential function given by:
−(n − 1)
(6.5)
F (n) = exp
anudge(k)
Where n is the grid point distance from the boundary (varying from 1 to
nspgx): n − 1 is the outermost grid point, n = 2 the adjacent one etc. The
anudge array determines the strength of the LBC forcing and depends on
the model level k. In practice F (n) is equal to 1 at the outermost grid
point row and decreases exponentially to 0 at the internal edge of the
buffer zone (nspgd) at a rate determined by anudge. Larger buffer zones
and larger values of anudge will yield a greater forcing by the LBC.
1 This
namelist stanza will be removed in future versions
30
Typically for domain sizes of 100 grid points we use a buffer zone width of
10 − 12 grid points, for large domains this buffer zone can increase to values of
15 or even 20.
In the model anudge has three increasing values from the lower, to the mid
and higher troposphere. For example for nspgx = 10 we use anudge equals to
1, 2, 3 for the lower, mid and upper troposphere, respectively.
This allows a stronger forcing in the upper troposphere to insure a greater
consistency of large scale circulations with the forcing LBC while allowing more
freedom to the model in the lower troposphere where local high resolution forcings (e.g. complex topography) are more important.
For nspgx of 15−20, for example, anudge values could be increased to 2, 3, 4.
As a rule of thumb, the choice of the maximum anudge value should follow the
conditions:
(nspgx − 1)
≥3
anudge(k)
&boundaryparam
nspgx = 12, !
!
nspgd = 12, !
!
high_nudge
=
medium_nudge =
low_nudge
=
/
6.1.9
(6.6)
nspgx-1 represent the number of cross point slices on
the boundary sponge or relaxation boundary conditions.
nspgd-1 represent the number of dot point slices on
the boundary sponge or relaxation boundary conditions.
3.0, ! Nudge value high range
2.0, ! Nudge value medium range
1.0 ! Nudge value low range
restartparam stanza
This stanza lets you control the time period the model is currently simulating
in this particular run. You may want to split longer runs for which you have
prepared the ICBC’s into shorter runs, to schedule HPC resource usage in a
more collaborative way with other researcher sharing it: the regcm model allows
restart, so be friendly with other research projects which may not have this
fortune (unless you are late for publication).
&restartparam
ifrest = .false. ,
mdate0 = 1990060100,
mdate1 = 1990060100,
mdate2 = 1990060200,
/
!
!
!
!
If a restart
Global start (is gdate1, most probably)
Start date of this run
End date for this run
Things you need to know here:
1. After the simulation starts, on restart NEVER change the mdate0 value.
The correct scheme for restart is:
• Set ifrest to .true.
• Set mdate1 to the value in mdate2
• Define the new value for mdate2
2. Consider that current RegCM convention is to place midnight of first day
of month as the last timestep in previous month, except on first model
output file (ifrest = .false.). It is for this reason better to use as start
31
and end time a month boundary. We usually consider a month data file
the basic unit of output, each time you cross a month a new output file
will be created for you.
6.1.10
timeparam stanza
This stanza contains model internal timesteps, used by the model as basic integration timestep and triggers for calling internal parametric schemes.
&timeparam
dt
=
150., ! time step in seconds
dtrad =
30., ! time interval solar radiation calculated (minutes)
dtabem =
18., ! time interval absorption-emission calculated (hours)
dtsrf =
600., ! time interval at which land model is called (seconds)
/
Things you need to know here:
1. The dynamical hydrostatical core of RegCM requires a fixed timestep, and
you need to manually find the correct value which permits not to break
the CourantFriedrichsLewy condition considering R. Courant and Lewy
(1928). A good rule of thumb is to have a dt not greater than three times
the ds value in km specified in the geoparam stanza at 6.1.2. A greater
value may lower computing time, but in case of strong advection may lead
to non accurate computation or even the violation of CFL condition and
the divergence of the solution.
2. All the other internal timesteps need to be multiples of the base timestep.
Note that the units are different, so you need to convert the other timesteps
in seconds before the check.
3. In case of strong surface gradients, a low value for the surface timesteps
may help the model better describe the interaction with the atmosphere
and obtain a stable solution.
4. If you hit a non stable condition, the restart capability of the model may
help find the correct timestep just for a particular period, using a different
timestep at different times.
6.1.11
outparam stanza
This stanza controls the model output engine, allowing you to enable/disable
any of the output file writeout, or to modify the frequency the fields are written
in the files.
&outparam
ifsave =
savfrq =
ifatm
=
atmfrq =
ifrad
=
radfrq =
ifsrf
=
ifsts
=
ifsub
=
srffrq =
iflak
=
.true. ,
48.,
.true. ,
6.,
.true. ,
6.,
.true. ,
.true. ,
.true. ,
3.,
.true.,
!
!
!
!
!
!
!
!
!
!
!
Create SAV files for restart
Frequency in hours to create them
Output ATM ?
Frequency in hours to write to ATM
Output RAD ?
Frequency in hours to write to RAD
Output SRF ?
Output STS ?
Output SUB ?
Frequency in hours to write SRF and SUB (and CLM)
Output LAK ?
32
lakfrq
=
6.,
ifchem = .true.,
chemfrq =
6.,
atm_enablevar = 14*.true.,
srf_enablevar = 24*.true.,
sts_enablevar = 9*.true.,
lak_enablevar = 16*.true.,
sub_enablevar = 16*.true.,
rad_enablevar = 15*.true.,
che_enablevar = 17*.true.,
dirout = ’./output’,
/
!
!
!
!
!
!
!
!
!
!
!
!
Frequency in hours to write to LAK if lakemod is 1
It must be an integer multiple of batfrq
Output CHE ?
Frequency in hours to write to CHE
Mask to eventually disable variables ATM
Mask to eventually disable variables SRF
Mask to eventually disable variables STS
Mask to eventually disable variables LAK
Mask to eventually disable variables SUB
Mask to eventually disable variables RAD
Mask to eventually disable variables CHE
Path where all output will be placed
Things you need to know here:
1. The surface fields are the mean values in the interval specified by the
frequency values. The dynamical fields are instead the point value at the
output time. Refer to the Reference Manual Giorgi (2011) for a detailed
description of the model output fields.
2. If the chemistry or lake model are not enabled, the values specified in
the control flags are not considered. If nsg is not greater than one in
dimparam at 6.1.1, the ifsub flag is not considered.
3. For the output directory, the path variable has a limit of 256 characters.
This path must be a local path on disk where the user running the model
has write permissions granted.
4. The enablevar logical arrays can be used to avoid saving one of the time
dependent variables in the output file, in the order they are saved in the
output file itself. Note that the variables time, tbnds and ps cannot be
disabled.
6.1.12
physicsparam stanza
This stanza controls the model physics. You have a number of option here,
and the best way to select the right set is to carefully read the the Reference
Manual Giorgi (2011). We are for the purposes of this User Guide not going
in detail in here, except in saying that probably you will need to run some
experiments especially with different cumulus convection schemes before finding
out the best model setting. Although the mixed convection scheme (Grell over
land and Emanuel over ocean) seems to provide an overall better performance,
our experience is that there is no scheme that works best everywhere, therefore
we advice to always do some sensitivity experiments to select the best scheme
for your application.
&physicsparam
iboudy =
5,
ibltyp
1,
=
! Lateral Boundary conditions scheme
!
0 => Fixed
!
1 => Relaxation, linear technique.
!
2 => Time-dependent
!
3 => Time and inflow/outflow dependent.
!
4 => Sponge (Perkey & Kreitzberg, MWR 1976)
!
5 => Relaxation, exponential technique.
! Boundary layer scheme
!
0 => Frictionless
33
icup
=
4,
igcc
=
1,
ipptls
=
1,
iocnflx =
2,
iocnrough =
ipgf
=
0,
iemiss =
lakemod =
ichem
=
scenario =
idcsst
iseaice
idesseas
iconvlwp
1,
0,
0,
1,
’A1B’,
=
=
=
=
0,
0,
1,
1,
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
1 => Holtslag PBL (Holtslag, 1990)
2 => UW PBL (Bretherton and McCaa, 2004)
99 => Holtslag PBL, with UW in diag. mode
Cumulus convection scheme
1 => Kuo
2 => Grell
3 => Betts-Miller (1986) DOES NOT WORK !!!
4 => Emanuel (1991)
5 => Tiedtke (1986) UNTESTED !!!
99 => Use Grell over land and Emanuel over ocean
98 => Use Emanuel over land and Grell over ocean
Grell Scheme Cumulus closure scheme
1 => Arakawa & Schubert (1974)
2 => Fritsch & Chappell (1980)
Moisture scheme
1 => Explicit moisture (SUBEX; Pal et al 2000)
Ocean Flux scheme
1 => Use BATS1e Monin-Obukhov
2 => Zeng et al (1998)
Zeng Ocean model roughness formula to use.
1 => (0.0065*ustar*ustar)/egrav
2 => (0.013*ustar*ustar)/egrav + 0.11*visa/ustar
Pressure gradient force scheme
0 => Use full fields
1 => Hydrostatic deduction with pert. temperature
Calculate emission
Use lake model
Use active aerosol chemical model
IPCC Scenario to use in A1B,RF,A2,B1,B2
RCP Scenarios in RCP3PD,RCP4.5,RCP6,RCP8.5
Use diurnal cycle sst scheme
Model seaice effects
Model desert seasonal albedo variability
Use convective liquid water path as the large-scale
liquid water path
\
6.1.13
subexparam stanza
This stanza controls the moisture scheme. Please consider carefully reporting
in your work the tuning you perform on this parameters. The parameters below
are the ones currently used at ICTP.
&subexparam
ncld
=
fcmax
=
qck1land =
qck1oce
=
gulland
=
guloce
=
rhmax
=
rh0oce
=
rh0land
=
tc0
=
cevap
=
caccr
=
cllwcv
=
clfrcvmax =
cftotmax =
/
1,
0.80,
.250E-03,
.250E-03,
0.4,
0.4,
1.01,
0.90,
0.80,
238.0,
.100E-02,
3.000,
0.3E-3,
0.25,
0.75,
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
# of bottom model levels with no clouds
Maximum cloud fraction cover
Autoconversion Rate for Land
Autoconversion Rate for Ocean
Fract of Gultepe eqn (qcth) when precip occurs
Fract of Gultepe eqn (qcth) for ocean
RH at whicn FCC = 1.0
Relative humidity threshold for ocean
Relative humidity threshold for land
Below this temperature, rh0 begins to approach unity
Raindrop evap rate coef [[(kg m-2 s-1)-1/2]/s]
Raindrop accretion rate [m3/kg/s]
Cloud liquid water content for convective precip.
Max cloud fractional cover for convective precip.
Max total cover cloud fraction for radiation
We found that RegCM4 is especially sensitive to:
34
1. cevap : increasing cevap will generally decrease precipitation
2. gulland, guloce : increase of guland/guloce will generally lead to reduce
precipitation
6.1.14
grellparam, emanparam and tiedtkeparam stanzas
You are allowed here to tune the convection scheme selected above in 6.1.12
with the icup number if selected number is 2, 4, 98, 99.
&grellparam
shrmin = 0.25,
shrmax = 0.50,
edtmin = 0.25,
edtmax = 0.50,
edtmino = 0.25,
edtmaxo = 0.50,
edtminx = 0.25,
edtmaxx = 0.50,
shrmin_ocn = 0.25,
shrmax_ocn = 0.50,
edtmin_ocn = 0.25,
edtmax_ocn = 0.50,
edtmino_ocn = 0.25,
edtmaxo_ocn = 0.50,
edtminx_ocn = 0.25,
edtmaxx_ocn = 0.50,
pbcmax = 150.0,
mincld = 150.0,
htmin = -250.0,
htmax = 500.0,
skbmax = 0.4,
dtauc = 30.0,
/
&emanparam
minsig = 0.95,
elcrit = 0.0011,
tlcrit = -55.0,
entp = 1.5,
sigd = 0.05,
sigs = 0.12,
omtrain = 50.0,
omtsnow = 5.5,
coeffr = 1.0,
coeffs = 0.8,
cu = 0.7,
betae = 10.0,
dtmax = 0.9,
alphae = 0.2,
damp = 0.1,
/
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
&tiedtkeparam
iconv = 1,
entrpen = 1.0D-4,
entrscv = 3.0D-4,
entrmid = 1.0D-4,
entrdd = 2.0D-4,
cmfcmax = 1.0D0,
cmfcmin = 1.0D-10,
cmfdeps = 0.3D0,
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
Minimum Shear effect on precip eff.
Maximum Shear effect on precip eff.
Minimum Precipitation Efficiency
Maximum Precipitation Efficiency
Minimum Precipitation Efficiency (o var)
Maximum Precipitation Efficiency (o var)
Minimum Precipitation Efficiency (x var)
Maximum Precipitation Efficiency (x var)
Minimum Shear effect on precip eff. OCEAN points
Maximum Shear effect on precip eff.
Minimum Precipitation Efficiency
Maximum Precipitation Efficiency
Minimum Precipitation Efficiency (o var)
Maximum Precipitation Efficiency (o var)
Minimum Precipitation Efficiency (x var)
Maximum Precipitation Efficiency (x var)
Max depth (mb) of stable layer b/twn LCL & LFC
Min cloud depth (mb).
Min convective heating
Max convective heating
Max cloud base height in sigma
Fritsch & Chappell (1980) ABE Removal Timescale (min)
Lowest sigma level from which convection can originate
Autoconversion threshold water content (g/g)
Below tlcrit auto-conversion threshold is zero
Coefficient of mixing in the entrainment formulation
Fractional area covered by unsaturated dndraft
Fraction of precipitation falling outside of cloud
Fall speed of rain (Pa/s)
Fall speed of snow (Pa/s)
Coefficient governing the rate of rain evaporation
Coefficient governing the rate of snow evaporation
Coefficient governing convective momentum transport
Controls downdraft velocity scale
Max negative parcel temperature perturbation below LFC
Controls the approach rate to quasi-equilibrium
Controls the approach rate to quasi-equilibrium
!
!
!
!
!
!
!
!
Actual used scheme.
Entrainment rate for penetrative convection
Entrainment rate for shallow convection
Entrainment rate for midlevel convection
Entrainment rate for cumulus downdrafts
Maximum massflux value
Minimum massflux value (for safety)
Fractional massflux for downdrafts at lfs
35
rhcdd = 1.0D0,
cmtcape = 40.0D0,
zdlev = 1.5D4,
cprcon = 1.0D-4,
nmctop = 4,
cmfctop = 0.35D0,
lmfpen = .true.,
lmfscv = .true.,
lmfmid = .true.,
lmfdd = .true.,
lmfdudv = .true.,
/
!
!
!
!
!
!
!
!
!
!
!
Relative saturation in downdrafts
CAPE adjustment timescale parameter
Restrict rainfall up to this elevation
Coefficients for determining conversion
max. level for cloud base of mid level conv.
Relat. cloud massflux at level above nonbuoyancy
true if penetrative convection is switched on
true if shallow convection is switched on
true if midlevel convection is switched on
true if cumulus downdraft is switched on
true if cumulus friction is switched on
Things you need to know here:
1. In case of the mixed schemes 98, 99, both the Grell and Emanuel stanzas
are read in. Note in this case for Grell scheme only the relevant (Ocean
or Land) control values are used.
2. Minimum and maximum values of the fraction of reevaporated water in
the downdraft for the Grell scheme is essentially a measure of the precipitation efficiency: increasing their value generally decrease convective
precipitation.
3. Again, read carefully the Reference Manual before attempting any tuning,
and report in any work modification of this parameters.
6.1.15
uwparam stanza
You are allowed here to tune the UW PBL scheme selected above in 6.1.12 with
the ibltyp number if selected number is 2, 99.
&uwparam
iuwvadv = 0,
ilenparam = 0,
atwo = 15.0D0,
rstbl = 1.5D0,
/
!
!
!
!
?????????????
?????????????
?????????????
?????????????
Travis need to add something here.
6.1.16
chemparam stanza
This stanza controls the optical active aerosols scheme in the RegCM model.
&chemparam
chemsimtype = ’CBMZ
’, ! Which chemical tracers to be activated.
! One in :
!
DUST : Activate 4 dust bins scheme
!
SSLT : Activate 2 bins Sea salt scheme
!
CARB : Activate 4 species black/anthropic
!
carbon simulations
!
SULF : Activate SO2 and SO4 tracers
!
SUCA : Activate both SUKF and CARB
!
AERO : Activate all DUST, SSLT, CARB and SULF
!
CBMZ : Activate gas phase and sulfate
ichsolver = 1, ! Activate the chemical solver
idirect
= 1, ! enable or not aerosol feedbacks on radiation and
2 In
the future model version a more complete chemical scheme will be introduced
36
2
! dynamics (aerosol direct and semi direct effcts):
! 0 = no coupling. Aerosol are only transported and
!
don’t interact with radiation scheme.
! 1 = no coupling to dynamic and thermodynamic. However
!
the clear sky surface and top of atmosphere
!
aerosol radiative forcings are diagnosed.
! 2 = allows aerosol feedbacks on radiative,
!
thermodynamic and dynamic fields.
ichdrdepo = 0, ! 1 = enable tracer surface dry deposition. For dust,
!
it is calculated by a size settling and dry
!
deposition scheme. For other aerosol,a dry
!
deposition velocity is simply prescribed further.
!
Next release will include an improved aerosol dry
!
deposition scheme for non dust aerosols.
ichcumtra = 1, ! 1 = enable tracer convective transport and mixing.
/
6.2
The CLM options
We will now discuss from the user point of view how to use the model setup
which need to be activated at configure stage.
The CLM option if activated allows the user to run a simulation using the
CLM surface model instead of the default BATS1e model. We will not here go
in deep in the difference between the two models, read the Reference Manual for
this. The executable of the model is different in the case of the CLM, and is named
regcmMPI_clm. Note that in the CLM case only the MPI enabled compilation
is supported (no serial), and no subgridding is possible (nsg is always 1).
Enable
At configure stage (see 3.2.1), the option is to be enabled with the right command line argument to the configure script
--enable-clm
Supply this option if you plan on using CLM option.
This will enable a preprocessing flag, and build a different model executable.
Note that no modifications are needed for any other part of the model, but this
triggers the building of another pre-processing program, clm2rcm.
Prepare and run
The CLM configuration requires a separate stanza in the namelist input file.
&clmparam
dirclm = ’input/’, !
!
!
clmfrq = 12.,
!
imask =
1,
!
!
!
!
!
!
/
CLM path to Input data produced by clm2rcm. If
relative, It should be how to reach the Input dir
from the Run dir.
Frequency for CLM own output write
For CLM, Type of land surface parameterization
1 => using DOMAIN.INFO for landmask (same as BATS)
2 => using mksrf_navyoro file landfraction for
landmask and perform a weighted average over
ocean/land gridcells; for example:
tgb = tgb_ocean*(1-landfraction)+tgb_land*landfraction
Things you need to know here:
37
1. The inpter path defined in terrainparam stanza described in 6.1.4 is used
also by the clm2rcm program. See at 4.4 how to obtain needed datasets.
2. The file pft-physiology.c070207 should be manually copied in the dirclm
directory before running the model.
3. The clmfrq is relative to the output produced by the CLM model itself, and
does not control the RegCM model output. To know the CLM output file
content, refer to CLM 3.5 documentation.
4. The imask = 2 option cannot be used with the icup cumulus convection
schemes 2, 98, 99, which rely on the BATS1e landmask.
In the case of CLM run, the user needs to run, after the terrain program,
the clm2rcm program, and copy the pft-physiology.c070207 in the input
directory:
$>
$>
$>
$>
cd $REGCM_RUN
./Bin/terrain regcm.in
./Bin/clm2rcm regcm.in
cp $REGCM_GLOBEDAT/CLM/pft-physiology.c070207 input/
The clm2rcm program interpolates global land characteristics datasets to
the RegCM projected grid. The content of the pft-physiology.c070207 file
are described in the pft-physiology.c070207.readme file. All the other preprocessing steps are just equal to the one detailed in chapter 5. To run the CLM
option in the RegCM model, just substitute the executable name:
$> mpirun -np 2 ./Bin/regcmMPI_clm regcm.in
Note that the CLM land model is much heavier than the BATS1e model, and
computing time increases.
6.3
Sensitivity experiments hint
Although the LBC forcing does provide a constraint for the model, as any RCM,
RegCM4 is characterized by a certain level of internal variability due to its nonliner processes (e.g. convection).
For example, if small perturbations are introduced in the initial or lateral
boundary conditions, the model will generally produce different patterns of,
e.g. precipitation, that appear as (sometimes seemingly organized) noise when
compared to the control simulation.
This noise depends on domain size and climatic regimes, for example it
is especially pronounced in warm climate regimes (e.g. tropics or during the
summer season) and large doamins.
When doing for example sensitivity experiments to model modifications,
e.g. to land use change, this internal variability noise can be misinterpreted as
a model response to the factor modified.
Users of RegCM4 should be aware of this when they do sensitivity experiments. The best way to filter out this noise is to perform ensembles of simulations and lok at the ensemble averages to extract the real model response from
the noise.
38
Chapter 7
Postprocessing tools
The new netCDF output format allows users to use a number of general purpose
tools to postprocess model output files. We will in this section do a quick review
of some of the Open Source and Free Software ones.
7.1
Command line tools
Three major set of tools may help you do even complex calculation just from
command line prompt.
7.1.1
netCDF library tools
The netCDF library itself offers three basic tools to play with netCDF archived
data.
• ncdump program, generates a text representation of a specified netCDF
file on standard output. The text representation is in a form called CDL
(network Common Data form Language) that can be viewed, edited, or
serve as input to ncgen, thus ncdump and ncgen can be used as inverses
to transform data representation between binary and text representations.
ncdump may also be used as a simple browser for netCDF datasets, to display the dimension names and lengths; variable names, types, and shapes;
attribute names and values; and optionally, the values of data for all variables or selected variables in a netCDF dataset. Sample usage patterns:
1. Look at the structure of the data in the netCDF dataset:
ncdump -c test_001_SRF.1990060100.nc
2. Produce a fully-annotated (one data value per line) listing of the
data for the variables time and t2m, using FORTRAN conventions
for indices, and show the floating-point data with only four significant
digits of precision and the time values with ISO format:
ncdump -v time,t2m -p 4 -t -f \
fortran test_001_SRF.1990060100.nc
39
• ncgen program, the reverse of the ncdump program: generates a netCDF
file or a C or FORTRAN program that creates a netCDF dataset from a
CDL input. Sample usage patterns:
1. From a CDL file, generate a binary netCDF file:
ncgen -o test_001_SRF.1990060100_modif.nc \
test_001_SRF.1990060100.cdl
2. From a CDL file, generate a Fortran 77 program to write the netCDF
file:
ncgen -f test_001_SRF.1990060100.cdl > prog.f
• nccopy utility copies an input netCDF file to an output netCDF file, in
any of the four format variants, if possible, and in function of the selected
output format add compression filter and/or data chunking. Sample usage
patterns:
1. Convert a netCDF dataset to a netCDF 4 classic model compressed
data file using shuffling to enhance compression level:
nccopy -k 4 -d 9 -s test_001_SRF.1990060100.nc \
test_001_SRF.1990060100_compressed.nc
You can also find, in the Tools/Programs/RegCM_read directory under
$REGCM_ROOT a sample program to read an output file using the netCDF library
you can modify to fit your needs. Another sample program to read SAV output
file format can be found under the directory SAV_read in the Tools/Programs
directory.
7.1.2
NetCDF operators NCO
This set of tools can be considered a swiss army knife to manage netCDF
datasets. There are multiple operators, and Each operator takes netCDF files as
input, then operates (e.g., derives new data, averages, hyperslabs, manipulates
metadata) and produces a netCDF output file. The single-command style of
NCO allows users to manipulate and analyze files interactively, or with simple
scripts that avoid some overhead of higher level programming environments.
The major tools are:
• ncap2 netCDF Arithmetic Processor
• ncatted netCDF Attribute Editor
• ncbo netCDF Binary Operator
• ncea netCDF Ensemble Averager
• ncecat netCDF Ensemble Concatenator
• ncflint netCDF File Interpolator
• ncks netCDF Kitchen Sink
• ncpdq netCDF Permute Dimensions Quickly, Pack Data Quietly
40
• ncra netCDF Record Averager
• ncrcat netCDF Record Concatenator
• ncrename netCDF Renamer
• ncwa netCDF Weighted Averager
A comprehensive user guide can be found at:
http://nco.sourceforge.net/nco.html
Sample usage patterns:
1. Get value of t2m variable at a particular point for all timesteps with a
prescribed format one per line on stdout:
ncks -C -H -s "%6.2f\n" -v t2m -d iy,16 -d jx,16 \
test_001_SRF.1990060100.nc
2. Extract one timestep of t2m from a file and save into a new netCDF file:
ncks -c -v t2m -d time,6 test_001_SRF.1990060100.nc \
test_001_SRF.1990060212.nc
3. Cat together a year worth of output data for the single t2m variable into
a single file:
ncrcat -c -v t2m test_001_SRF.1990??0100.nc \
test_001_T2M.1990.nc
4. Get the DJF mean value of the tempertaure from a multiyear run:
ncra -c -v t2m test_001_SRF.????120100.nc \
test_001_SRF.????010100.nc \
test_001_SRF.????020100.nc \
test_001_DJF_T2M.nc
We strongly encourage you to read the on-line user guide of the NCO tools.
You will for sure get a boost on your data manipulation and analysis skills.
7.1.3
Climate data Operators CDO
The monolithic cdo program from the Max Planck Institut f´’ur Meteorologie
implements a really comprehensive collection of command line Operators to manipulate and analyse Climate and NWP model Data either in netCDF or GRIB
format. There are more than 400 operators available, covering the following
topics:
• File information and file operations
• Selection and Comparision
• Modification of meta data
• Arithmetic operations
41
• Statistical analysis
• Regression and Interpolation
• Vector and spectral Transformations
• Formatted I/O
• Climate indices
We wont make here a comprehensive analysis of this tool, but you can find
some ideas in the PostProc directory on $REGCM_ROOT reading the two sample
average and regrid scripts, which use a combination of NCO programs and cdo
operators to reach goal. A very simple usage pattern for example to obtain a
monthly mean is:
cdo monmean test_001_T2M.1990.nc
7.2
GrADS program
This tool is the one mostly used at ICTP to analyze and plot model output
results. It can be used either as an interactive tool either as a batch data
analysis tool. We have already written in chapter 5 about the helper program
GrADSNcPlot which can be used to interactively plot model output results. We
will here detail why an helper program is needed and how it does work. For
information regarding the grads program itself, a comprehensive guide may be
found at:
http://www.iges.org/grads/gadoc/users.html
7.2.1
GrADS limits
The grads program is powerful, yet has limits:
1. Only the equirectangular projection or Plate Carr´ee is supported. Some
other projections can be used through a pdef entry in the CTL file using
the internal direct preprojection engines, but not all RegCM supported
projections are supported using direct engine.
2. NetCDF format allows multidimensional variables, while grads supports
just four dimensional (time,level,latitude,longitude) variables.
Luckily, these limits can be exceeded, carefully telling grads the RegCM
data structure using the CTL file and one ancillary proj file:
1. The grads program allows usage of the pdef BILIN option in the CTL file,
which allows the user to specify a supplementary file name. In this file are
stored three lat-lon floating-point grids which have for each point on the
equirectangular grid the indexes i,j on the projected grid, as well as wind
rotation values.
2. The grads program allows identifying four dimentional slices of a multidimensional variable as new variables, providing them a unique name. This
is how we are able to see in grads chemical output variables.
42
While the GrADSNcPlot program allows interactive plotting and after quitting the grads program removes the CTL file and the proj file, the GrADSNcPrepare
program only creates this two files, allowing share of the proj file between multiple CTL files sharing the same RegCM domain (i.e. it creates just only once
the proj file). To use the grads program, you need to have both this ancillary
files together with the data netCDF file.
A collection of sample grads scripts commonly used at ICTP to plot simulation results can be found in the Tools/Scripts/GrADS directory under $REGCM_ROOT.
7.3
CISL’s NCL : NCAR Command Language
This awesome tool from NCAR is an interpreted language designed for scientific
data analysis and visualization. Noah Diffenbaugh and Mark Snyder have created a website dedicated to visualizing RegCM3 output using the NCAR Command Language (NCL). These scripts where built using RegCM3 model output
converted to netCDF using an external converter. They have been adapted
to serve as very basic example scripts to process a native RegCM 4.2 output
data file or do some data analysis using the NCL language and are available
in the Tools/Scripts/NCL/examples directory. Travis O’Brien from the User
Community also contributed sample scripts, which may be found under the
Tools/Scripts/NCL directory.
7.4
R Statistical Computing Language
The R statistical computing language is able with an add on package to load into
interal data structure a meteorological field read from a netCDF RegCM output.
A sample script to load and plot the 2m Temperature at a selected timestep can
be used as a reference to develop a real powerful statistical analysis of model
results: it is under Tools/Scripts/R.
7.5
Non free tools
Note that the netCDF format, using plugins or native capabilities, allows clean
access to model output from a number of non free tools like MatlabTM or IDLTM .
For a more complete list of tools, you are invited to scroll down the very
long list of tools at:
http://www.unidata.ucar.edu/software/netcdf/software.html
43
Chapter 8
Getting help and reporting
bugs
8.1
The Gforge site
A new welcoming home for the RegCM Community has been built with the help
of Italian National Research Council CNR Democritos Group on the e-science
Lab E-Forge web site:
https://gforge.ictp.it/gf/project/regcm
Figure 8.1: The Gforge site
On this site you have access with a simple registration to a friendly bug
tracking system under the tracker link, allowing the users to post problems and
bugs they discover.
It allows posting also of files to give you the opportunity to provide as much
information as possible about the environment the model is running at your
institution, helping us better understand and solve efficiently your problems.
44
Help us grow the model to fit your requirements, giving the broader user
community the benefit of a valuable tool to do better research.
45
46
Chapter 9
Appendices
We will review here a sample installation session of software needed to install
the RegCM model.
The starting point is here a Linux system on a multicore processor box,
and the final goal is to have an optimized system to run the model. I will
use bash as my shell and assume that GNU development tools like make, sed,
awk are installed as part of the default Operating System environment as is
the case in most Linux distro. I will require also for commodity a command
line web downloader such as curl installed on the system, along its development
libraries to be used to enable OpenDAP remote data access protocol capabilities
of netCDF library. Standard file management tools such as tar and gzip are
also required. The symbol $> will stand for a shell prompt. I will assume
that the process is performed as a normal system user, which will own all the
toolchain. I will be now just the regcm user.
9.1
Identify Processor
First step is to identify the processor to know its capabilities:
$> cat /proc/cpuinfo
This command will ask to the operating system to print processor informations. A sample answer on my laptop is:
processor
vendor_id
cpu family
model
model name
stepping
cpu MHz
cache size
physical id
siblings
core id
cpu cores
:
:
:
:
:
:
:
:
:
:
:
:
0
GenuineIntel
6
30
Intel(R) Core(TM) i7 CPU
5
933.000
6144 KB
0
8
0
4
47
Q 740
@ 1.73GHz
apicid
: 0
initial apicid : 0
fpu
: yes
fpu_exception
: yes
cpuid level
: 11
wp
: yes
flags
: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge
mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall
nx rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology
nonstop_tsc aperfmperf pni dtes64 monitor ds_cpl vmx smx est tm2 ssse3
cx16 xtpr pdcm sse4_1 sse4_2 popcnt lahf_lm ida dts tpr_shadow vnmi
flexpriority ept vpid
bogomips
: 3467.81
clflush size
: 64
cache_alignment : 64
address sizes
: 36 bits physical, 48 bits virtual
power management:
repeated eight time with Processor Ids from 0 to 7: I have a Quad Core Intel
with Hyperthreading on (this multiply by 2 the reported processor list). The
processor reports here also to support Intel Streaming SIMD Extensions V4.2,
which can be later used to speed up code execution vectorizing floating point
operation on any single CPU core.
9.2
Chose compiler
Depending on the processor, we can chose which compiler to use. On a Linux
box, we have multiple choices:
• GNU Gfortran
• G95
• Intel ifort compiler
• Portland pgf90 compiler
• Absoft ProFortran
• NAG Fortran Compiler
and for sure other which I may not be aware of. All of these compilers have
pros and cons, so I am just for now selecting one in the pool only to continue
the exposition. I am not selecting the trivial solution of Gfortran as most Linux
distributions have it already packaged, and all the other required software as
well (most complete distribution I am aware of for this is Fedora: all needed
software is packaged and it is a matter of yum install).
So let us assume I have licensed the Intel Composer XE Professional Suite
12.0.2 on my laptop. My system administrator installed it on the default location under /opt/intel, and I have my shell environment update loading vendor
provided script:
48
$> source /opt/intel/bin/compilervars.sh intel64
With some modification (the path, the script, the arguments to the script),
same step is to be performed for all non-GNU compilers in the above list, and
is documented in the installation manual of the compiler itself.
In case of Intel, to check the correct behaviour of the compiler, try to type
the following command:
$> ifort --version
ifort (IFORT) 12.0.2 20110112
Copyright (C) 1985-2011 Intel Corporation.
All rights reserved.
I am skipping here any problem that may arise from license installation for
any of the compilers, so I am assuming that if the compiler is callable, it works.
As this step is usually performed by a system administrator on the machine, I
am assuming a skilled professional will take care of that.
9.3
Environment setup
To efficiently use the compilers, I will setup now some environment variables.
On my system (see the above processor informations) I will use:
$> # Where all the software will be installed ?
$> # I am chosing here a place under my home directory.
$> export INTELROOT=/home/regcm/intelsoft
$> export INTELSRC=/home/regcm/intelsoft/src
$> mkdir -p $INTELROOT/{bin,include,lib,share/man,src}
$> # the C compiler. I am assuming here to have the whole Intel
$> # Composer XE suite, so I will use the intel C compiler.
$> export CC=icc
$> # the C++ compiler, the intel one.
$> export CXX=icpc
$> # the Fortran 9X compiler.
$> export FC=ifort
$> # the Foirtran 77 compiler. For intel, is just the fortran one.
$> export F77=ifort
$> # C Compiler flags
$> export CFLAGS="-O3 -xHost -axSSE4.2 -fPIC"
$> # F9X Compiler flags
$> export FCFLAGS="-O3 -xHost -axSSE4.2 -fPIC"
$> # F77 Compiler flags
$> export FFLAGS="-O3 -xHost -axSSE4.2 -fPIC"
$> # CXX Compiler flags
$> export CXXFLAGS="-O3 -xHost -axSSE4.2 -fPIC"
$> # Linker flags
$> export LDFLAGS="-Wl,-rpath=$INTELROOT/lib \
> -Wl,-rpath=/opt/intel/lib/intel64 -i-dynamic"
$> # Preset PATH to use the installed software during build
$> export PATH=$INTELROOT/bin:$PATH
49
$> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$INTELROOT/lib
$> export MANPATH=$INTELROOT/share/man:$MANPATH
This step will allow me not to specify those variables at every following step.
Depending on the above compiler selected, those flags my differ for you, but the
concept is that I am selecting a performance target build for the machine I am
on. I am now ready to compile software.
9.4
Compression Library Installation
To have a complete optimized stack, I will compile also here the compression
libraries optionally needed by HDF5 library.
I will need the sources:
$> cd $INTELSRC
$> curl -o zlib-1.2.5.tar.gz http://zlib.net/zlib-1.2.5.tar.gz
$> curl -o szip-2.1.tar.gz \
> http://www.hdfgroup.org/ftp/lib-external/szip/2.1/src/szip-2.1.tar.gz
Please note that the szip library license allows to use that software only
together with HDF5 library.
Then I must decompress the sources:
$> cd $INTELSRC
$> tar -zxvf zlib-1.2.5.tar.gz
$> tar -zxvf szip-2.1.tar.gz
Let us start with zlib:
$> cd $INTELSRC
$> cd zlib-1.2.5
$> LDSHARED="icc -shared -Wl,-soname \
> -Wl,libz.so.1,--version-script,zlib.map" \
> ./configure --prefix=$INTELROOT
$> make
$> make check
$> make install
This will install the zlib software under /home/regcm/intelsoft. Let us
continue with szip.
$>
$>
$>
$>
$>
$>
cd $INTELSRC
cd szip-2.1
./configure --prefix=$INTELROOT
make
make check
make install
This will install the szip software under /home/regcm/intelsoft.
50
9.5
HDF5 Library installation
Download the source pack:
$> cd $INTELSRC
$> curl -o hdf5-1.8.6.tar.bz2 \
> ftp://ftp.hdfgroup.org/HDF5/current/src/hdf5-1.8.6.tar.bz2
Install it:
$> cd $INTELSRC
$> cd hdf5-1.8.6
$> ./configure --prefix=$INTELROOT --enable-hl --enable-linux-lfs \
> --enable-production --with-pic --docdir=$INTELROOT/share/doc/hdf5/ \
> --with-szlib=$INTELROOT --with-zlib=$INTELROOT
$> make
$> make check
$> make install
9.6
netCDF Library installation
Download the source pack:
$> cd $INTELSRC
$> curl -o netcdf-4.1.3.tar.gz \
> http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-4.1.3.tar.gz
Install it:
$> cd $INTELSRC
$> cd netcdf-4.1.3
$> ./configure --prefix=$INTELROOT --enable-shared --enable-netcdf-4 \
> --with-udunits --with-libcf --enable-dap-netcdf --enable-cxx-4 \
> CPPFLAGS="$CPPFLAGS -I$INTELROOT/include" \
> LDFLAGS="$LDFLAGS -L$INTELROOT/lib"
$> make
$> make check
$> make install
9.7
OpenMPI library installation
This optional step will install OpenMPI message passing library to enable parallel run of the RegCM model using all cores of my processor. Download the
souece pack:
$> cd $INTELSRC
$> curl -o openmpi-1.4.3.tar.bz2 \
> http://www.open-mpi.org/software/ompi/v1.5/downloads/openmpi-1.4.3.tar.bz2
Install it:
51
$> cd $INTELSRC
$> cd openmpi-1.4.3
$> ./configure --prefix=$INTELROOT --sysconfdir=$INTELROOT/etc/openmpi \
> --mandir=$INTELROOT/share/man --libdir=$INTELROOT/lib --enable-mpi-f90
$> make
$> make check
$> make install
9.8
Final step
To enable all the ready installed software to be used by the regcm user whenever
it logs in the box, edit the .bashrc file in the home directory and add the
following lines:
export PATH=$INTELROOT/bin:$PATH
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$INTELROOT/lib
export MANPATH=$INTELROOT/share/man:$MANPATH
52
Bibliography
Giorgi, F., Regcm version 4.1 reference manual, Tech. rep., ICTP Trieste, 2011.
R. Courant, K. F., and H. Lewy, u
¨ber die partiellen differenzengleichungen der
mathematischen physik, Mathematische Annalen, 100 (1), 3274, 1928.
Rew, R. K., and G. P. Davis, Netcdf: An interface for scientific data access,
IEEE Computer Graphics and Applications, 10 (4), 76–82, 1990.
53
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K. For any section Entitled "Acknowledgements" or "Dedications",
Preserve the Title of the section, and preserve in the section all
the substance and tone of each of the contributor acknowledgements
and/or dedications given therein.
L. Preserve all the Invariant Sections of the Document,
unaltered in their text and in their titles. Section numbers
or the equivalent are not considered part of the section titles.
M. Delete any section Entitled "Endorsements". Such a section
may not be included in the Modified Version.
N. Do not retitle any existing section to be Entitled "Endorsements"
or to conflict in title with any Invariant Section.
O. Preserve any Warranty Disclaimers.
If the Modified Version includes new front-matter sections or
appendices that qualify as Secondary Sections and contain no material
copied from the Document, you may at your option designate some or all
of these sections as invariant. To do this, add their titles to the
list of Invariant Sections in the Modified Version’s license notice.
These titles must be distinct from any other section titles.
You may add a section Entitled "Endorsements", provided it contains
nothing but endorsements of your Modified Version by various
parties--for example, statements of peer review or that the text has
been approved by an organization as the authoritative definition of a
standard.
58
You may add a passage of up to five words as a Front-Cover Text, and a
passage of up to 25 words as a Back-Cover Text, to the end of the list
of Cover Texts in the Modified Version. Only one passage of
Front-Cover Text and one of Back-Cover Text may be added by (or
through arrangements made by) any one entity. If the Document already
includes a cover text for the same cover, previously added by you or
by arrangement made by the same entity you are acting on behalf of,
you may not add another; but you may replace the old one, on explicit
permission from the previous publisher that added the old one.
The author(s) and publisher(s) of the Document do not by this License
give permission to use their names for publicity for or to assert or
imply endorsement of any Modified Version.
5. COMBINING DOCUMENTS
You may combine the Document with other documents released under this
License, under the terms defined in section 4 above for modified
versions, provided that you include in the combination all of the
Invariant Sections of all of the original documents, unmodified, and
list them all as Invariant Sections of your combined work in its
license notice, and that you preserve all their Warranty Disclaimers.
The combined work need only contain one copy of this License, and
multiple identical Invariant Sections may be replaced with a single
copy. If there are multiple Invariant Sections with the same name but
different contents, make the title of each such section unique by
adding at the end of it, in parentheses, the name of the original
author or publisher of that section if known, or else a unique number.
Make the same adjustment to the section titles in the list of
Invariant Sections in the license notice of the combined work.
In the combination, you must combine any sections Entitled "History"
in the various original documents, forming one section Entitled
"History"; likewise combine any sections Entitled "Acknowledgements",
and any sections Entitled "Dedications". You must delete all sections
Entitled "Endorsements".
6. COLLECTIONS OF DOCUMENTS
You may make a collection consisting of the Document and other
documents released under this License, and replace the individual
copies of this License in the various documents with a single copy
that is included in the collection, provided that you follow the rules
of this License for verbatim copying of each of the documents in all
other respects.
You may extract a single document from such a collection, and
distribute it individually under this License, provided you insert a
copy of this License into the extracted document, and follow this
License in all other respects regarding verbatim copying of that
document.
7. AGGREGATION WITH INDEPENDENT WORKS
A compilation of the Document or its derivatives with other separate
and independent documents or works, in or on a volume of a storage or
distribution medium, is called an "aggregate" if the copyright
resulting from the compilation is not used to limit the legal rights
59
of the compilation’s users beyond what the individual works permit.
When the Document is included in an aggregate, this License does not
apply to the other works in the aggregate which are not themselves
derivative works of the Document.
If the Cover Text requirement of section 3 is applicable to these
copies of the Document, then if the Document is less than one half of
the entire aggregate, the Document’s Cover Texts may be placed on
covers that bracket the Document within the aggregate, or the
electronic equivalent of covers if the Document is in electronic form.
Otherwise they must appear on printed covers that bracket the whole
aggregate.
8. TRANSLATION
Translation is considered a kind of modification, so you may
distribute translations of the Document under the terms of section 4.
Replacing Invariant Sections with translations requires special
permission from their copyright holders, but you may include
translations of some or all Invariant Sections in addition to the
original versions of these Invariant Sections. You may include a
translation of this License, and all the license notices in the
Document, and any Warranty Disclaimers, provided that you also include
the original English version of this License and the original versions
of those notices and disclaimers. In case of a disagreement between
the translation and the original version of this License or a notice
or disclaimer, the original version will prevail.
If a section in the Document is Entitled "Acknowledgements",
"Dedications", or "History", the requirement (section 4) to Preserve
its Title (section 1) will typically require changing the actual
title.
9. TERMINATION
You may not copy, modify, sublicense, or distribute the Document
except as expressly provided under this License. Any attempt
otherwise to copy, modify, sublicense, or distribute it is void, and
will automatically terminate your rights under this License.
However, if you cease all violation of this License, then your license
from a particular copyright holder is reinstated (a) provisionally,
unless and until the copyright holder explicitly and finally
terminates your license, and (b) permanently, if the copyright holder
fails to notify you of the violation by some reasonable means prior to
60 days after the cessation.
Moreover, your license from a particular copyright holder is
reinstated permanently if the copyright holder notifies you of the
violation by some reasonable means, this is the first time you have
received notice of violation of this License (for any work) from that
copyright holder, and you cure the violation prior to 30 days after
your receipt of the notice.
Termination of your rights under this section does not terminate the
licenses of parties who have received copies or rights from you under
this License. If your rights have been terminated and not permanently
reinstated, receipt of a copy of some or all of the same material does
not give you any rights to use it.
60
10. FUTURE REVISIONS OF THIS LICENSE
The Free Software Foundation may publish new, revised versions of the
GNU Free Documentation License from time to time. Such new versions
will be similar in spirit to the present version, but may differ in
detail to address new problems or concerns. See
http://www.gnu.org/copyleft/.
Each version of the License is given a distinguishing version number.
If the Document specifies that a particular numbered version of this
License "or any later version" applies to it, you have the option of
following the terms and conditions either of that specified version or
of any later version that has been published (not as a draft) by the
Free Software Foundation. If the Document does not specify a version
number of this License, you may choose any version ever published (not
as a draft) by the Free Software Foundation. If the Document
specifies that a proxy can decide which future versions of this
License can be used, that proxy’s public statement of acceptance of a
version permanently authorizes you to choose that version for the
Document.
11. RELICENSING
"Massive Multiauthor Collaboration Site" (or "MMC Site") means any
World Wide Web server that publishes copyrightable works and also
provides prominent facilities for anybody to edit those works. A
public wiki that anybody can edit is an example of such a server. A
"Massive Multiauthor Collaboration" (or "MMC") contained in the site
means any set of copyrightable works thus published on the MMC site.
"CC-BY-SA" means the Creative Commons Attribution-Share Alike 3.0
license published by Creative Commons Corporation, a not-for-profit
corporation with a principal place of business in San Francisco,
California, as well as future copyleft versions of that license
published by that same organization.
"Incorporate" means to publish or republish a Document, in whole or in
part, as part of another Document.
An MMC is "eligible for relicensing" if it is licensed under this
License, and if all works that were first published under this License
somewhere other than this MMC, and subsequently incorporated in whole or
in part into the MMC, (1) had no cover texts or invariant sections, and
(2) were thus incorporated prior to November 1, 2008.
The operator of an MMC Site may republish an MMC contained in the site
under CC-BY-SA on the same site at any time before August 1, 2009,
provided the MMC is eligible for relicensing.
ADDENDUM: How to use this License for your documents
To use this License in a document you have written, include a copy of
the License in the document and put the following copyright and
license notices just after the title page:
Copyright (c) YEAR YOUR NAME.
Permission is granted to copy, distribute and/or modify this document
under the terms of the GNU Free Documentation License, Version 1.3
or any later version published by the Free Software Foundation;
with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts.
61
A copy of the license is included in the section entitled "GNU
Free Documentation License".
If you have Invariant Sections, Front-Cover Texts and Back-Cover Texts,
replace the "with...Texts." line with this:
with the Invariant Sections being LIST THEIR TITLES, with the
Front-Cover Texts being LIST, and with the Back-Cover Texts being LIST.
If you have Invariant Sections without Cover Texts, or some other
combination of the three, merge those two alternatives to suit the
situation.
If your document contains nontrivial examples of program code, we
recommend releasing these examples in parallel under your choice of
free software license, such as the GNU General Public License,
to permit their use in free software.
62