Quinoa
Adaptive computational fluid dynamics
Quinoa is a set of computational tools that enables research and numerical analysis in fluid dynamics. Using the Charm++ runtime system, we employ asynchronous (or non-blocking) parallel programming and decompose computational problems into a large number of work units (that may be more than the available number of processors) enabling arbitrary overlap of parallel computation, communication, input, and output. Then the runtime system dynamically and automatically homogenizes computational load across the simulation distributed across many computers.
Our ultimate goal is to simulate large and complex engineering multiphysics problems with a production-quality code that is extensible and maintainable, using hardware resources efficiently, even for problems with a priori unknown, heterogeneous, and dynamic load distribution. Read more at our Philosophy page.
Tools
Quinoa consists of the following tools:
Walker — Time-integrator for stochastic differential equations
Walker is a mathematical tool to analyze and design the behavior of stochastic differential equations. Solving a multivariate Fokker-Planck equation, it allows the estimation of arbitrary coupled statistics and probability distributions as they evolve in time and is used for the design of statistical moment approximations for turbulent flows.
Inciter — Navier-Stokes solver for complex domains
Inciter is a fully asynchronous distributed-memory-parallel fluid solver for complex engineering geometries. We are working on multiple compressible-flow solvers for single-, and multi-material flows, using continuous and discontinuous Galerkin finite element and finite volume methods, and solution-adaptive mesh-, and polynomial-degree refinement, enabling dynamically concentrating compute resources to regions with interesting physics.
RNGTest — Random number generators test suite
RNGTest is a test harness to subject random number generators to stringent statistical tests, enabling quantitative ranking with respect to their quality and computational cost. Multiple generators can be tested from Intel's Math Kernel Library, RNGSSE, and Random123.
UnitTest — Test suite for synchronous and asynchronous functions
UnitTest is an asynchronous distributed-memory-parallel test harness, capable of testing serial, synchronous (e.g., MPI) parallel, and asynchronous parallel (e.g., Charm++) functions.
MeshConv — Tetrahedron-mesh converter
MeshConv is a mesh file converter that can be used to convert tetrahedron meshes from and to either of the following formats: Gmsh, Netgen, ExodusII, HyperMesh, and ASC used in Jacob Waltz's Chicoma code.
Try
The quickest is to try the pre-built executables inside a docker container. See also
For larger problems and computers, however, you should build from source.
Build
The simplest way to build from source is to perform the following steps. For other ways to build, see the page on building Quinoa.
Install prerequisites: Debian/Ubuntu linux (line 1: required, line 2: recommended)
apt-get install cmake gfortran gcc g++ openmpi-bin libopenmpi-dev liblua5.3-dev apt-get install gmsh libpugixml-dev libpstreams-dev libboost-all-dev libblas-dev liblapack-dev liblapacke-dev libhdf5-dev libhdf5-openmpi-dev libnetcdf-mpi-dev libbackward-cpp-dev tao-pegtl-dev intel-mkl binutils-dev flex bison python3-pygments python3-jinja2 texlive-latex-base libdw-dev
Install prerequisites: Mac OS X
spack install cmake libtool autoconf automake spack install environment-modules cmake gcc openmpi%gcc hdf5%gcc+hl module load gcc-9.2.0-clang-10.0.0-apple-vcpkolh openmpi-3.1.4-gcc-9.2.0-my2rkcv hdf5-1.10.5-gcc-9.2.0-prdkirn
Clone, build third-party libraries, build & test
git clone --recurse-submodules https://github.com/quinoacomputing/quinoa.git; cd quinoa mkdir external/build; cd external/build; cmake -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_C_COMPILER=mpicc -DCMAKE_Fortran_COMPILER=mpif90 .. && make; cd - mkdir build; cd build; cmake -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_C_COMPILER=mpicc ../src && make -sj8 && ./charmrun +p8 Main/unittest -v -q && ctest -j8 --output-on-failure -LE extreme
All executables will be under
build/Main/.
We roughly follow the development model described here. As a consequence, our master (stable) branch can lag behind our develop (bleeding edge) branch. If you want the latest, clone with
git clone --recurse-submodules --branch=develop https://github.com/quinoacomputing/quinoa.git
Directory layout
quinoa
├── cmake/ - CMake code, shared between github.com/quinoacomputing/quinoa-tpl and src/
├── doc/ - Documentation, rendered at quinoacomputing.org
├── external/ - External packages from github.com/quinoacomputing/quinoa-tpl
├── src/ - Compilable sources, see quinoacomputing.org/files.html
├── tests/ - Unit-, and regression tests
├── tools/ - Development utilities and docker files
├── LICENSE - Copyright and license
└── README.md - This file, rendered at github.com/quinoacomputing/quinoa
Roadmap
The rough directions in which each of Quinoa's tools are developed are described by the Roadmap.
Contributing
Contributors and collaborators are welcome. Please read the Roadmap and the Contributing guide and contact us.
License
Quinoa is certified Open Source software. It may be used for any purpose, including commercial purposes, at absolutely no cost. It is distributed under the terms of the 3-clause BSD license listed below. See also Legal.
Copyright (c) 2012-2015, J. Bakosi Copyright (c) 2016-2018, Los Alamos National Security, LLC Copyright (c) 2019-2021, Triad National Security, LLC All rights reserved. This program was produced under U.S. Government contract 89233218CNA000001 for Los Alamos National Laboratory (LANL), which is operated by Triad National Security, LLC for the U.S. Department of Energy/National Nuclear Security Administration. All rights in the program are reserved by Triad National Security, LLC, and the U.S. Department of Energy/National Nuclear Security Administration. The Government is granted for itself and others acting on its behalf a nonexclusive, paid-up, irrevocable worldwide license in this material to reproduce, prepare derivative works, distribute copies to the public, perform publicly and display publicly, and to permit others to do so. Additionally, redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of Triad National Security, LLC, Los Alamos National Laboratory, LANL, the U.S. Government, nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY TRIAD NATIONAL SECURITY, LLC AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL TRIAD NATIONAL SECURITY, LLC OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.