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 instructions at https://hub.docker.com/r/quinoacomputing/quinoa/. See also

For larger problems and computers, however, you should build from source.

Build

  • 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 libhypre-dev libhdf5-dev libhdf5-openmpi-dev libhypre-dev 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 cmake openmpi-gcc8 && port select gcc mp-gcc8 && port select mpi openmpi-gcc8-fortran
     port install gmsh pugixml lapack hdf5
    
  • Clone, build third-party libraries, build & test

     git clone --recurse-submodules https://github.com/quinoacomputing/quinoa.git; cd quinoa
     mkdir tpl/build; cd tpl/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; ../script/run_tests.sh
    

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

Read more about other ways of cloning and working with quinoa's repositories on the page detailing Third-party libraries and external tools using git submodules and subtrees.

Contribute

Contributions and collaborators are welcome. Contact us via GitHub, Email or Gitter.

Authors

(in chronological order of contribution)

  1. Jozsef Bakosi
  2. Francisco Gonzalez
  3. Brandon Rogers
  4. Christoph Junghans
  5. Robert Pavel
  6. Aditya Pakki
  7. Bob Bird
  8. Aditya Pandare
  9. Weizhao Li

Resources

License

Copyright (c) 2016-2018, Los Alamos National Security, LLC All rights reserved.

Copyright 2016-2018. Los Alamos National Security, LLC. This software was produced under U.S. Government contract DE-AC52-06NA25396 for Los Alamos National Laboratory (LANL), which is operated by Los Alamos National Security, LLC for the U.S. Department of Energy. The U.S. Government has rights to use, reproduce, and distribute this software. NEITHER THE GOVERNMENT NOR LOS ALAMOS NATIONAL SECURITY, LLC MAKES ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LIABILITY FOR THE USE OF THIS SOFTWARE. If software is modified to produce derivative works, such modified software should be clearly marked, so as not to confuse it with the version available from LANL.

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 Los Alamos 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 LOS ALAMOS 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 LOS ALAMOS 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.