Quinoa v0.3, 2020 summer

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. Quinoa consists of the following tools: (1) Walker, 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 in engineering. (2) Inciter, is a distributed-memory-parallel fluid solver for complex 3D engineering geometries. Inciter can solve the Euler equations, modeling ideal single-material compressible flow, using continuous and discontinuous Galerkin finite element methods, with solution-adaptive mesh-, and polynomial-degree refinement, enabling dynamically concentrating compute resources to regions with interesting physics. Compared to the previous release (LA-CC-17-087) current development continues in the following directions: (A) a new solver for multi-material flows (single velocity, multiple densities, multiple mass fractions, and multiple internal energies) solving the Euler equations for simple ideal gases, (B) polynomial adaptation for both single-, and multi-material flows, (C) productize the solvers (i.e., increase robustness, user-friendliness, and add practicality features), and (D) prototype implementation of 3D parallel mesh-to-mesh solution transfer to enable fluid-structure interaction problems, coupling compressible flow with the kinematics of rigid body motion of objects embedded in a fluid flow, allowing the computation of body motion in response to aerodynamic forces. (3) RNGTest, a test harness to subject random number generators to stringent statistical tests enabling quantitative ranking with respect to their quality and computational cost. (4) UnitTest, a unit test harness, running hundreds of tests per second, capable of testing serial, synchronous, and asynchronous functions. (5) MeshConv, a mesh file converter that can be used to convert 3D tetrahedron meshes to and from the following formats: * Gmsh, http://www.geuz.org/gmsh, * Netgen, http://sourceforge.net/apps/mediawiki/netgen-mesher, * ExodusII/SEACAS, https://github.com/gsjaardema/seacas, * HyperMesh, https://www.altair.com/hypermesh, * ASC, https://www.researchgate.net/scientific-contributions/2014382994_Jacob_Waltz, * Omega_h, https://github.com/SNLComputation/omega_h, * UGRID, http://www.simcenter.msstate.edu/software/downloads/doc/ug_io, * RDGFLO, https://www.mae.ncsu.edu/people/hluo2.
quinoacomputing · Sep 12, 2020 · 2dd7ead · 2dd7ead
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diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 Copyright (c) 2012-2015, J. Bakosi
 Copyright (c) 2016-2018, Los Alamos National Security, LLC
-Copyright (c) 2019, Triad National Security, LLC
+Copyright (c) 2019-2020, Triad National Security, LLC
 All rights reserved.
 
 This program was produced under U.S. Government contract 89233218CNA000001 for

diff --git a/README.md b/README.md
@@ -18,6 +18,8 @@ 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.
 
+This software has been acknowledged by the U.S. Department of Energy / National
+Nuclear Security Administration for open source release, C20072.
+
 For more details on philosophy, documentation, software design, journal papers,
 license, and contributing see the [documentation](https://quinoacomputing.org).
-
diff --git a/cmake/BuildShared.cmake b/cmake/BuildShared.cmake
@@ -3,7 +3,7 @@
 # \file      BuildShared.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Set default value for building shared libs if none was specified
 #

diff --git a/cmake/BuildType.cmake b/cmake/BuildType.cmake
@@ -3,7 +3,7 @@
 # \file      BuildType.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Set a default build type if none was specified
 #

diff --git a/cmake/CodeCoverage.cmake b/cmake/CodeCoverage.cmake
@@ -3,7 +3,7 @@
 # \file      CodeCoverage.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Setup target for code coverage analysis
 #
@@ -169,7 +169,7 @@ FUNCTION(SETUP_TARGET_FOR_ALL_COVERAGE suite path targetname unittestrunner
     COMMAND ${FASTCOV} --zerocounters
     # Run all test suites
     COMMAND ${unittestrunner} ${unittestrunner_ncpus_arg} ${PROCESSOR_COUNT} Main/${UNITTEST_EXECUTABLE} -v
-    COMMAND ${CMAKE_CTEST_COMMAND} -j${PROCESSOR_COUNT} -LE insane
+    COMMAND ${CMAKE_CTEST_COMMAND} -j${PROCESSOR_COUNT} #-LE insane
     # Process gcov output for genhtml
     COMMAND ${FASTCOV} --branch-coverage --exceptional-branch-coverage --lcov -o ${OUTPUT}.info --exclude tests/ c++/ include/ boost/ charm/ decl.h def.h openmpi pstreams Random123 pegtl tut/ highwayhash/ moduleinit
     # Copy over report customization files for genhtml

diff --git a/cmake/ConfigExecutable.cmake b/cmake/ConfigExecutable.cmake
@@ -3,7 +3,7 @@
 # \file      ConfigExecutable.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Configure Charm++ executable targets
 #

diff --git a/cmake/ConfigureDataLayout.cmake b/cmake/ConfigureDataLayout.cmake
@@ -3,7 +3,7 @@
 # \file      ConfigureDataLayout.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Configure data layouts
 #

diff --git a/cmake/CppCheck.cmake b/cmake/CppCheck.cmake
@@ -3,7 +3,7 @@
 # \file      CppCheck.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Setup target for code coverage analysis
 #

diff --git a/cmake/DetectCodeCoverage.cmake b/cmake/DetectCodeCoverage.cmake
@@ -3,7 +3,7 @@
 # \file      DetectCodeCoverage.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Detect prerequesites for code coverage analysis
 #

diff --git a/cmake/DetectCompilerVersion.cmake b/cmake/DetectCompilerVersion.cmake
@@ -3,7 +3,7 @@
 # \file      DetectCompilerVersion.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Detect C, C++, Fortran compiler major, minor, and patch version
 #

diff --git a/cmake/DetectOS.cmake b/cmake/DetectOS.cmake
@@ -3,7 +3,7 @@
 # \file      DetectOS.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Detect operating system
 #

diff --git a/cmake/DisallowInSourceBuilds.cmake b/cmake/DisallowInSourceBuilds.cmake
@@ -3,7 +3,7 @@
 # \file      DisallowInSourceBuilds.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Cmake code to disallow in-source builds
 #

diff --git a/cmake/FindAEC.cmake b/cmake/FindAEC.cmake
@@ -3,7 +3,7 @@
 # \file      FindAEC.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Find the Adaptive Entropy Coding library
 #

diff --git a/cmake/FindBackwardCpp.cmake b/cmake/FindBackwardCpp.cmake
@@ -3,7 +3,7 @@
 # \file      FindBackwardCpp.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Find the Backward-cpp header-only library
 # \note      BackwardCPP requires other libraries, and for a static build,

diff --git a/cmake/FindBrigand.cmake b/cmake/FindBrigand.cmake
@@ -3,7 +3,7 @@
 # \file      FindBrigand.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Find the Brigand template metaprogramming library
 #

diff --git a/cmake/FindCharm.cmake b/cmake/FindCharm.cmake
@@ -3,7 +3,7 @@
 # \file      FindCharm.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Find Charm++
 #

diff --git a/cmake/FindExodiff.cmake b/cmake/FindExodiff.cmake
@@ -3,7 +3,7 @@
 # \file      FindExodiff.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Find Exodiff
 #

diff --git a/cmake/FindGmsh.cmake b/cmake/FindGmsh.cmake
@@ -3,7 +3,7 @@
 # \file      FindGmsh.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Find Gmsh
 #

diff --git a/cmake/FindH5Part.cmake b/cmake/FindH5Part.cmake
@@ -3,7 +3,7 @@
 # \file      FindH5Part.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Find the H5Part library
 #

diff --git a/cmake/FindHighwayHash.cmake b/cmake/FindHighwayHash.cmake
@@ -3,7 +3,7 @@
 # \file      FindHighwayHash.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Find HighwayHash
 #

diff --git a/cmake/FindHypre.cmake b/cmake/FindHypre.cmake
@@ -3,7 +3,7 @@
 # \file      FindHypre.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Find the Hypre library from LLNL
 #

diff --git a/cmake/FindLAPACKE.cmake b/cmake/FindLAPACKE.cmake
@@ -3,7 +3,7 @@
 # \file      FindLAPACKE.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Find the C-interface to LAPACK as well as LAPACK/BLAS
 #

diff --git a/cmake/FindLibCXX.cmake b/cmake/FindLibCXX.cmake
@@ -3,7 +3,7 @@
 # \file      FindLibCXX.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Find libc++
 #

diff --git a/cmake/FindMCSS.cmake b/cmake/FindMCSS.cmake
@@ -3,7 +3,7 @@
 # \file      FindMCSS.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Find m.css
 #

diff --git a/cmake/FindMKL.cmake b/cmake/FindMKL.cmake
@@ -3,7 +3,7 @@
 # \file      FindLMKL.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Find the Math Kernel Library from Intel
 #

diff --git a/cmake/FindNetCDF.cmake b/cmake/FindNetCDF.cmake
@@ -3,7 +3,7 @@
 # \file      cmake/FindLNetCDF.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Find NetCDF
 #

diff --git a/cmake/FindNumDiff.cmake b/cmake/FindNumDiff.cmake
@@ -3,7 +3,7 @@
 # \file      FindNumDiff.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Find NumDiff
 #

diff --git a/cmake/FindOmega_h.cmake b/cmake/FindOmega_h.cmake
@@ -3,7 +3,7 @@
 # \file      FindOmega_h.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Find the Omega_h library
 #

diff --git a/cmake/FindPEGTL.cmake b/cmake/FindPEGTL.cmake
@@ -3,7 +3,7 @@
 # \file      FindPEGTL.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Find PEGTL
 #

diff --git a/cmake/FindPStreams.cmake b/cmake/FindPStreams.cmake
@@ -3,7 +3,7 @@
 # \file      FindLPstreams.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Find the Pstreams library
 #

diff --git a/cmake/FindPugixml.cmake b/cmake/FindPugixml.cmake
@@ -3,7 +3,7 @@
 # \file      cmake/FindPugixml.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Find the pugixml library
 #

diff --git a/cmake/FindRNGSSE2.cmake b/cmake/FindRNGSSE2.cmake
@@ -3,7 +3,7 @@
 # \file      FindRNGSSE2.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Find the RNGSSE2 library
 #

diff --git a/cmake/FindRandom123.cmake b/cmake/FindRandom123.cmake
@@ -3,7 +3,7 @@
 # \file      FindRandom123.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Find Random123
 #

diff --git a/cmake/FindRoot.cmake b/cmake/FindRoot.cmake
@@ -3,7 +3,7 @@
 # \file      FindRoot.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Find the Root library from CERN
 #

diff --git a/cmake/FindSol2.cmake b/cmake/FindSol2.cmake
@@ -0,0 +1,47 @@
+################################################################################
+#
+# \file      FindSol2.cmake
+# \copyright 2012-2015 J. Bakosi,
+#            2016-2018 Los Alamos National Security, LLC.,
+#            2019-2020 Triad National Security, LLC.
+#            All rights reserved. See the LICENSE file for details.
+# \brief     Find the Sol2 Lua C++ binding library
+#
+################################################################################
+
+# Sol2: https://github.com/ThePhD/sol2
+#
+#  SOL2_FOUND - System has Sol2
+#  SOL2_INCLUDE_DIRS - The Sol2 include directory
+#
+#  Set the SOL2_ROOT cmake variable or shell environment variable before
+#  calling find_package to a path to add an additional search path, e.g.,
+#
+#  Usage:
+#
+#  set(SOL2_ROOT "/path/to/custom/brigand") # prefer over system
+#  find_package(Sol2)
+#  include_directories(${SOL2_INCLUDE_DIRS})
+
+# If already in cache, be silent
+if(SOL2_INCLUDE_DIRS)
+  set (SOL2_FIND_QUIETLY TRUE)
+endif()
+
+find_path(SOL2_INCLUDE_DIR NAMES sol.hpp
+                           HINTS ${SOL2_ROOT}
+                                 $ENV{SOL2_ROOT}
+                           PATH_SUFFIXES sol include)
+
+# Remove last 'sol' from path found, otherwise some compilers will not find
+# sol.hpp.
+get_filename_component(SOL2_INCLUDE_DIR ${SOL2_INCLUDE_DIR} DIRECTORY)
+
+set(SOL2_INCLUDE_DIRS ${SOL2_INCLUDE_DIR})
+
+# Handle the QUIETLY and REQUIRED arguments and set SOL2_FOUND to TRUE if
+# all listed variables are TRUE.
+INCLUDE(FindPackageHandleStandardArgs)
+FIND_PACKAGE_HANDLE_STANDARD_ARGS(Sol2 REQUIRED_VARS SOL2_INCLUDE_DIRS)
+
+MARK_AS_ADVANCED(SOL2_INCLUDE_DIRS)
diff --git a/cmake/FindTUT.cmake b/cmake/FindTUT.cmake
@@ -3,7 +3,7 @@
 # \file      FindTUT.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Find the Template Unit Test library headers
 #

diff --git a/cmake/FindTestU01.cmake b/cmake/FindTestU01.cmake
@@ -3,7 +3,7 @@
 # \file      FindTestU01.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Find the TestU01 library
 #

diff --git a/cmake/LICENSE b/cmake/LICENSE
@@ -1,6 +1,6 @@
 Copyright (c) 2012-2015, J. Bakosi
 Copyright (c) 2016-2018, Los Alamos National Security, LLC
-Copyright (c) 2019, Triad National Security, LLC
+Copyright (c) 2019-2020, Triad National Security, LLC
 All rights reserved.
 
 This program was produced under U.S. Government contract 89233218CNA000001 for

diff --git a/cmake/MPICompilers.cmake b/cmake/MPICompilers.cmake
@@ -3,7 +3,7 @@
 # \file      MPICompilers.cmake
 # \copyright 2012-2015 J. Bakosi,
 #            2016-2018 Los Alamos National Security, LLC.,
-#            2019 Triad National Security, LLC.
+#            2019-2020 Triad National Security, LLC.
 #            All rights reserved. See the LICENSE file for details.
 # \brief     Find the MPI wrappers
 #