Quinoa

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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:

  • WalkerTime-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.

  • InciterNavier-Stokes solver for complex domains

    Inciter is a fully asynchronous distributed-memory-parallel fluid solver for complex engineering geometries. We are working on a compressible-flow solver using continuous and discontinuous Galerkin finite element methods, and solution-adaptive mesh-, and polynomial-degree refinement, enabling dynamically concentrating compute resources to regions with interesting physics.

  • RNGTestRandom 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.

  • UnitTestTest 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.

  • MeshConvTetrahedron-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
     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-dcpp-dev tao-pegtl-dev intel-mkl binutils-dev flex bison python3-pygments python3-jinja2 texlive-latex-base libdw-dev
    
  • Install prerequisites: Mac OS X (line 1: required, line 2: recommended)

     port install openmpi-clang60 & port select clang mp-clang-6.0 && port select mpi openmpi-clang60-fortran
     port install pugixml hdf5 +openmpi+clang60+hl
    
  • 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, 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
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