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Installation

RDycore builds and runs on the following platforms:

  • Linux and Mac laptops and workstations
  • Frontier (Oak Ridge National Laboratory)
  • Perlmutter (NERSC)

Required Software

To build RDycore, you need:

  • CMake v3.14+
  • GNU Make
  • reliable C, C++, and Fortran compilers
  • a working MPI installation (like OpenMPI or MPICH)
  • PETSc (Git revision b3128c15e0e), built with the following third-party libraries:
    • cgns
    • exodusii
    • fblaslapack
    • hdf5
    • libceed
    • metis
    • netcdf
    • parmetis
    • pnetcdf
    • zlib

You can obtain all of these freely on the Linux and Mac platforms. On Linux, just use your favorite package manager. On a Mac, you can get the Clang C/C++ compiler by installing XCode, and then use a package manager like Homebrew or MacPorts to get the rest.

Clone the Repository

First, go get the source code at GitHub:

git clone git@github.com:RDycore/RDycore.git

git clone https://github.com/RDycore/RDycore.git

This places an RDycore folder into your current path.

Configure RDycore

RDycore uses CMake, and can be easily configured as long as PETSc is installed and the PETSC_DIR and PETSC_ARCH environment variables are set properly. Usually all you need to do is change to your RDycore source directory and type

cmake -S . -B build

where build is the name of your build directory relative to the source directory. If you want to install RDycore somewhere afterward, e.g. to be able to configure E3SM to use it, you can set the prefix for the installation path using the CMAKE_INSTALL_PREFIX parameter:

cmake -S . -B build -DCMAKE_INSTALL_PREFIX=/path/to/install

Build, Test, and Install RDycore

After you've configured RDycore, you can build it:

  1. From the build directory, type make -j to build the library.
  2. To run tests for the library (and the included drivers), type make test.
  3. To install the model to the location (indicated by your CMAKE_INSTALL_PREFIX, if you specified it), type make install. By default, products are installed in the include, lib, bin, and share subdirectories of this prefix.

Making code changes and rebuilding

Notice that you must build RDycore in a build tree, separate from its source trees. This is standard practice in CMake-based build systems, and it allows you to build several different configurations without leaving generated and compiled files all over your source directory. However, you might have to change the way you work in order to be productive in this kind of environment.

When you make a code change, make sure you build from the build directory that you created in step 1 above:

cd /path/to/RDycore/build
make -j

You can also run tests from this build directory with make test.

This is very different from how some people like to work. One method of making this easier is to use an editor in a dedicated window, and have another window open with a terminal, sitting in your build directory. If you're using a fancy modern editor, it might have a CMake-based workflow that handles all of this for you.

The build directory has a structure that mirrors the source directory, and you can type make in any one of its subdirectories to do partial builds. In practice, though, it's safest to always build from the top of the build tree.

Preinstalled PETSc for RDycore on certain DOE machines

The RDycore team supports installation of the model at following DOE machines:

  1. Perlmutter at NERSC
  2. Frontier at OLCF
  3. Aurora at ALCF

First, run the shell script, config/set_petsc_settings.sh, to set PETSc-related environmental variables for the pre-installed PETSc on these supported machines and load appropriate modules. PETSc has been pre-installed with support for 32-bit and 64-bit integers on these supported machines, and the 32-bit PETSc installation is the default setting. The 64-bit PETSc installation can be used by passing the optional command line argument --64bit to config/set_petsc_settings.sh.

The Perlmutter system has two types of compute nodes: CPU-only and CPU-GPU nodes. The PETSc settings for CPU or GPU nodes can be selected via --pm cpu or --pm gpu, respectively.

source config/set_petsc_settings.sh --pm <cpu|gpu> <--64bit>

On all other systems, the script can be run as

source config/set_petsc_settings.sh <--64bit>

After setting PETSc variables and loading the appropriate modules, follow the steps outlined in the previous section to build the code.