building.rst

Building

REMORA can be built using either GNU Make or CMake. The following instructions apply to building on any system. We also provide instructions for building on :ref:`Perlmutter<Perlmutter (NERSC)>`.

Minimum Requirements

REMORA requires a C++ compiler that supports the C++17 standard and a C compiler that supports the C99 standard. Building with GPU support may be done with CUDA, HIP, or SYCL. For CUDA, REMORA requires versions >= 11.0. For HIP and SYCL, only the latest compilers are supported. Prerequisites for building with GNU Make include Python (>= 2.7, including 3) and standard tools available in any Unix-like environments (e.g., Perl and sed). For building with CMake, the minimal requirement is version 3.18.

Note

While REMORA is designed to work with SYCL, we do not make any guarantees that it will build and run on your Intel platform.

Paradigm

REMORA uses the paradigm that different executables are built in different subdirectories within the Exec directory. When using gmake (see below), the user/developer should build in the directory of the selected problem. When using cmake (see below), separate executables are built for all of the problem directories listed in Exec/CMakeLists.txt. The problem directories within Exec include Upwelling a test case demonstrating a periodic channel with shelves on each side. #1) science-relevant setups, such as ABL for modeling the atmospheric #boundary layer or DensityCurrent for running the standard density current test case, etc, 2) regression tests in #``Exec/RegTests`` that are used for testing specific known aspects of the code functionality, such as boundary conditions or #Rayleigh damping, and 3) tests for features under development in Exec/DevTests, such as moving terrain. There is a #README in each problem directory that describes the purpose/role of that problem.

NetCDF (Optional)

REMORA uses PnetCDF for optional NetCDF support. To build REMORA with PnetCDF, first install PnetCDF as per the instructions. Make a note of the directory where the library is installed, which we will call PNETCDF_DIR. When compiling, add the PnetCDF pkgconfig directory to the environment variable PKG_CONFIG_PATH, e.g.:

PKG_CONFIG_PATH=$PKG_CONFIG_PATH:$PNETCDF_DIR/lib/pkgconfig

At run-time, you may need to add PnetCDF to the link path, e.g.:

LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$PNETCDF_DIR/lib

See sections below for compiler-specific instructions for how to enable NetCDF support.

GNU Make

The GNU Make system is best for use on large computing facility machines and production runs. With the GNU Make implementation, the build system will inspect the machine and use known compiler optimizations explicit to that machine if possible. These explicit settings are kept up-to-date by the AMReX project.

Using the GNU Make build system involves first setting environment variables for the directories of the dependencies of REMORA which is the repository of AMReX. AMReX is provided as a git submodule in REMORA and can be populated by using git submodule init; git submodule update in the REMORA repo, or before cloning by using git clone --recursive <remora_repo>. Although submodules of these projects are provided, they can be placed externally as long as the <REPO_HOME> environment variables for each dependency is set correctly. An example of setting the <REPO_HOME> environment variables in the user's .bashrc is shown below:

export REMORA_HOME=${HOME}/REMORA
export AMREX_HOME=${REMORA_HOME}/Submodules/AMReX

The GNU Make system is set up to use the path to AMReX submodule by default, so it is not necessary to set these paths explicitly, unless it is desired to do so. It is also possible to use an external version of AMReX, downloaded by running

git clone https://github.com/amrex-codes/amrex.git

in which case the AMREX_HOME environment variable must point to the location where AMReX has been downloaded, which will take precedence over the default path to the submodule. If using bash shell,

export AMREX_HOME=/path/to/external/amrex

or if using tcsh,

setenv AMREX_HOME /path/to/external/amrex

1. cd to the desired build directory, e.g. REMORA/Exec/Upwelling/

2. Edit the GNUmakefile; options include

   Option name	Description	Possible values	Default value
   COMP	Compiler (gnu or intel)	gnu / intel	None
   USE_MPI	Whether to enable MPI	TRUE / FALSE	FALSE
   USE_OMP	Whether to enable OpenMP	TRUE / FALSE	FALSE
   USE_CUDA	Whether to enable CUDA	TRUE / FALSE	FALSE
   USE_HIP	Whether to enable HIP	TRUE / FALSE	FALSE
   USE_SYCL	Whether to enable SYCL	TRUE / FALSE	FALSE
   DEBUG	Whether to use DEBUG mode	TRUE / FALSE	FALSE
   USE_PNETCDF	Whether to compile with PnetCDF	TRUE / FALSE	FALSE
   USE_PARTICLES	Whether to compile with particle functionality enabled	TRUE / FALSE	FALSE
   PROFILE	Include profiling info	TRUE / FALSE	FALSE
   TINY_PROFILE	Include tiny profiling info	TRUE / FALSE	FALSE
   COMM_PROFILE	Include comm profiling info	TRUE / FALSE	FALSE
   TRACE_PROFILE	Include trace profiling info	TRUE / FALSE	FALSE

   Note

   Do not set both USE_OMP and USE_CUDA to true.

   Information on using other compilers can be found in the AMReX documentation at https://amrex-codes.github.io/amrex/docs_html/BuildingAMReX.html .

3. Make the executable by typing

   make

   The name of the resulting executable (generated by the GNUmake system) encodes several of the build characteristics, including dimensionality of the problem, compiler name, and whether MPI and/or OpenMP were linked with the executable. Thus, several different build configurations may coexist simultaneously in a problem folder. For example, the default build in REMORA/Exec/Upwelling will look like REMORA3d.gnu.MPI.ex, indicating that this is a 3-d version of the code, made with COMP=gnu, and USE_MPI=TRUE.

Job info

The build information can be accessed by typing

./REMORA*ex --describe

in the directory where the executable has been built.

CMake

CMake is often preferred by developers of REMORA; CMake allows for building as well as easy testing and verification of REMORA through the use of CTest which is included in CMake. CTest functionality requires additional options, described in :ref:`Testing`.

Using CMake involves an additional configure step before using the make command. It is also expected that the user has cloned the REMORA repo with the --recursive option or performed git submodule init; git submodule update in the REMORA repo to populate its submodules.

To build with CMake, a user typically creates a build directory in the project directory and in that directory the cmake <options> .. command is used to configure the project before building it. REMORA provides an example build directory called Build with example scripts for performing the CMake configure. Once the CMake configure step is done, then the make command will build the executable.

An example CMake configure command to build REMORA with MPI is listed below:

cmake -DCMAKE_BUILD_TYPE:STRING=Release \
      -DREMORA_ENABLE_MPI:BOOL=ON \
      -DCMAKE_CXX_COMPILER:STRING=mpicxx \
      -DCMAKE_C_COMPILER:STRING=mpicc \
      -DCMAKE_Fortran_COMPILER:STRING=mpifort \
      .. && make

An example CMake configure command to build REMORA with MPI, PnetCDF, and particles is listed below:

cmake -DCMAKE_BUILD_TYPE:STRING=Release \
      -DREMORA_ENABLE_MPI:BOOL=ON \
      -DCMAKE_CXX_COMPILER:STRING=mpicxx \
      -DCMAKE_C_COMPILER:STRING=mpicc \
      -DCMAKE_Fortran_COMPILER:STRING=mpifort \
      -DREMORA_ENABLE_PARTICLES:BOOL=ON \
      -DREMORA_ENABLE_PNETCDF:BOOL=ON \
      .. && make

Note that CMake is able to generate makefiles for the Ninja build system as well which will allow for faster building of the executable(s).