Getting started with RegCM for ISC24 SCC
Overview
The ICTP Regional Climate Model (RegCM), originally developed at the National Center for Atmospheric Research (NCAR), is maintained in the Earth System Physics (ESP) section of the ICTP. The latest version includes major upgrades in the structure of the code and its pre- and post- processors, along with the inclusion of some new physics parameterizations.
The model is flexible, portable and easy to use. It can be applied to any region of the World, with grid spacing of up to about 3 km, and for a wide range of studies, from process studies to paleo climate and future climate simulation.
The RegCM application is a state of the art limited are Regional Climate Model implementing the physical solution to the atmosphere part of an Earth System Model by solving the primitive Navier-Stokes partial differential equation by using finite difference methods for the dynamics. Multiple physics packages are added to compute the terms parametrized in the used equations, providing to the user a configurable set of options giving her the opportunity to best represent in the model the area of interest.
For more details about RegCM see the model reference descriptive paper.
The model source code is available under the GPLv3 license at:
Note: The page may be changed until the competition stats, maybe sure to follow up until the opening ceremony.
RegCM Presentation to the teams:
Presentation file:
Building and Running example
The model code is written in Fortran programming language using features up to the 2008 revision of the standard, and thus to compile the model a working Fortran compiler is required, along with the GNU make and the autotools (autoconf/automake/libtool) to create the configure script.
The required libraries are:
MPI - Any MPI will do. Most users would pick the OpenMPI at https://www.open-mpi.org/
The procedure to obtain the code is straightforward using the git tool:
git clone https://github.com/ICTP/RegCM.git
For the ISC24, the participants are requested to switch to the target branch:
cd RegCM
git checkout ISC24
Once the model is on disk, the user should create the configure script:
autoreconf -f -i
The above command is also contained in a bootstrap.sh script, which has in comment other possible options to use if the autotools are in a non standard path.
The created configure script contains various options to conditionally activate some part of the code, provide different I/O options or optimize for some HPC platforms the ICTP has had access to in the past years.
Not all the legacy platforms/compilers combination are anymore relevant, supported or even tested if the ICTP has not access to them.
Set the path to point your NetCDF installation to avoid from using another NetCDF version.
To configure the build system using the GNU make program should be enough on most systems to just type in:
The configure script will (hopefully) find a working combination of Fortran compiler and libraries compiled with it for the above required requisites. If the required libraries are not installed on the system, but the user has access to the working compiler toolchain, an example script to download and install in the USER accessible directories the netCDF and OpenMPI is provided in:
The user can modify it to mirror what is available on the target system.
To compile model executables and copy them in the bin directory, if the GNU make program is in the path, it is enough to
Sample build script on PSC:
For the ISC24 competition, the build system is configured to make the RCEMIP model. This setting will initialize a prescribed initial vertical profile simulation with periodic boundary conditions, that will be used to evaluate the model in the ensemble Radiative-Convective Equilbrium Model Intercomparison Project. In this framework, the model is run in an idealized setting using a prescribed convection permitting configuration over an ocean box domain. The selected configuration it is very much stressing the dynamical core, the radiation package, the model micro-physics and the turbulence parameterization of the boundary layer over the ocean.
Once the compilation is complete, the model executable files can by default be found under the bin directory. Only the regcmMPIRCEMIP executable will be required for the competition.
The user needs two input text files, which can be found in the Testing directory.
In the following, we will identify the model source code root directory (where the configure is) with the shell variable REGCM_ROOT.
To run the model, the standard procedure is to create a running directory:
possibly on a convenient I/O system partition with high throughput. The user must then link/copy some files in the run directory:
To run the model, the user needs to invoke the executable using mpirun providing as argument the name of the namelist file used for the competition:
While running, the model will produce diagnostic text on the standard output. The below is an example relative to a model test run on an ICTP Intel Core i7-8700 CPU @ 3.20GHz desktop computer with 6 cores:
The above diagnostic printout of the surface pressure readings from the model internal status in hPa should show a constant pressure increase throughout the model run of about 10 hPa (mb) per month due to the radiative cooling of the atmosphere.
Tasks and Submissions
To practice with the model, a standard Linux desktop with almost any distribution is enough, but you should use a reduced domain setting by running the model using a different input file, nominally:
The above input file will run a much smaller simulation, which concludes in some minutes on my 6 core desktop. For convenience, on a clean Ubuntu installation, the required packages to compile the model using GNU gcc compilers are:
build-essential gfortran libopenmpi-dev libnetcdff-dev
The expected tasks for the competition are:
Build and Run the application with the given input isc24.in using 4 CPU nodes, submit the best performance to the team’s folder.
Run IPM or another MPI profiler and show the most 3 MPI calls being used, show your work in the teams presentation.
Visualize the output netCDF files (in the output directory) and create video or set of photos based on that using any tool. show your work in the teams presentation. The netCDF output data should contain all the metadata required to use most of the visualization packages.
4. Bonus task: Try to optimize the code of the micro physics package in Main/microlib/mod_micro_nogtom.F90 and show your work in the teams presentation.