Merge branch 'develop'

quinoacomputing · May 12, 2019 · 10445a3 · 10445a3
2 parents a8282f8 + bae9430
commit 10445a3
Show file tree

Hide file tree

Showing 1,541 changed files with 117,990 additions and 111,739 deletions.
diff --git a/README.md b/README.md
@@ -20,21 +20,15 @@ unknown, heterogeneous, and dynamic load distribution.
 
 ## Directory layout
 
- - `cmake/` - CMake code shared between [external
-   packages](https://github.com/quinoacomputing/quinoa-tpl) (third-party
-   libraries) and `src/`.
- - `doc/` - Documentation, rendered at https://quinoacomputing.github.io.
- - `external/` - External packages (third-party libraries) pulled in as git
-   submodules.
- - `src/` - Compilable sources. For a more detailed description of the contents
-   of the `src/` directory and its subdirectories, see
-   `docs/pages/directories.dox`, rendered at
-   https://quinoacomputing.github.io/files.html.
- - `tests/` - Unit-, and regression tests.
- - `tools/` - Development utilities and docker files.
-
- - `LICENSE` - Copyright and license.
- - `README.md` - This file, rendered at https://github.com/quinoacomputing/quinoa.
+    quinoa
+      ├── cmake/ - CMake code, shared between github.com/quinoacomputing/quinoa-tpl and src/
+      ├── doc/ - Documentation, rendered at quinoacomputing.org
+      ├── external/ - External packages, pulled in as submodules 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
 
 ## More info
 

diff --git a/cmake/.gitignore b/cmake/.gitignore
@@ -1 +1,2 @@
 *~
+*.sw?
diff --git a/cmake/BuildShared.cmake b/cmake/BuildShared.cmake
@@ -1,7 +1,10 @@
 ################################################################################
 #
-# \file      cmake/BuildShared.cmake
-# \copyright 2012-2015, J. Bakosi, 2016-2018, Los Alamos National Security, LLC.
+# \file      BuildShared.cmake
+# \copyright 2012-2015 J. Bakosi,
+#            2016-2018 Los Alamos National Security, LLC.,
+#            2019 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
@@ -1,7 +1,10 @@
 ################################################################################
 #
-# \file      cmake/BuildType.cmake
-# \copyright 2012-2015, J. Bakosi, 2016-2018, Los Alamos National Security, LLC.
+# \file      BuildType.cmake
+# \copyright 2012-2015 J. Bakosi,
+#            2016-2018 Los Alamos National Security, LLC.,
+#            2019 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
@@ -1,7 +1,10 @@
 ################################################################################
 #
-# \file      cmake/CodeCoverage.cmake
-# \copyright 2012-2015, J. Bakosi, 2016-2018, Los Alamos National Security, LLC.
+# \file      CodeCoverage.cmake
+# \copyright 2012-2015 J. Bakosi,
+#            2016-2018 Los Alamos National Security, LLC.,
+#            2019 Triad National Security, LLC.
+#            All rights reserved. See the LICENSE file for details.
 # \brief     Setup target for code coverage analysis
 #
 ################################################################################
@@ -37,8 +40,6 @@
 # the test suite the coverage is being setup for, as well as those that are
 # required for successfully building the tests and the test runner.
 #
-# Author: J. Bakosi
-#
 # ##############################################################################
 FUNCTION(SETUP_TARGET_FOR_COVERAGE suite path targetname testrunner)
 
@@ -78,7 +79,7 @@ FUNCTION(SETUP_TARGET_FOR_COVERAGE suite path targetname testrunner)
     # Combine trace files
     COMMAND ${LCOV} --gcov-tool ${GCOV} --rc lcov_branch_coverage=1 --add-tracefile ${OUTPUT}.base.info --add-tracefile ${OUTPUT}.test.info --output-file ${OUTPUT}.total.info
     # Filter out unwanted files
-    COMMAND ${LCOV} --gcov-tool ${GCOV} --rc lcov_branch_coverage=1 --remove ${OUTPUT}.total.info "UnitTest/tests/*" "*/c++/*" "*/include/*" "*/boost/*" "*/charm/*" "*.decl.h" "*.def.h" "*/STDIN" "*/openmpi/*" "*/pstreams/*" "*/Random123/*" "*/pegtl/*" "*/tut/*" "*/highwayhash/*" "*/moduleinit*" --output-file ${OUTPUT}.filtered.info
+    COMMAND ${LCOV} --gcov-tool ${GCOV} --rc lcov_branch_coverage=1 --remove ${OUTPUT}.total.info "*/tests/*" "*/c++/*" "*/include/*" "*/boost/*" "*/charm/*" "*.decl.h" "*.def.h" "*/STDIN" "*/openmpi/*" "*/pstreams/*" "*/Random123/*" "*/pegtl/*" "*/tut/*" "*/highwayhash/*" "*/moduleinit*" --output-file ${OUTPUT}.filtered.info
     # Copy over report customization files for genhtml
     COMMAND ${CMAKE_COMMAND} -E copy
             ${CMAKE_SOURCE_DIR}/../doc/quinoa.gcov.css
@@ -144,8 +145,6 @@ ENDFUNCTION()
 # the test suite the coverage is being setup for, as well as those that are
 # required for successfully building the tests and the test runner.
 #
-# Author: J. Bakosi
-#
 # ##############################################################################
 FUNCTION(SETUP_TARGET_FOR_ALL_COVERAGE suite path targetname unittestrunner
                                        unittestrunner_ncpus_arg)
@@ -184,7 +183,7 @@ FUNCTION(SETUP_TARGET_FOR_ALL_COVERAGE suite path targetname unittestrunner
     # Combine trace files
     COMMAND ${LCOV} --gcov-tool ${GCOV} --rc lcov_branch_coverage=1 --add-tracefile ${OUTPUT}.base.info --add-tracefile ${OUTPUT}.test.info --output-file ${OUTPUT}.total.info
     # Filter out unwanted files
-    COMMAND ${LCOV} --gcov-tool ${GCOV} --rc lcov_branch_coverage=1 --remove ${OUTPUT}.total.info "UnitTest/tests/*" "*/c++/*" "*/include/*" "*/boost/*" "*/charm/*" "*.decl.h" "*.def.h" "*/STDIN" "*/openmpi/*" "*/pstreams/*" "*/Random123/*" "*/pegtl/*" "*/tut/*" "*/highwayhash/*" "*/moduleinit*" --output-file ${OUTPUT}.filtered.info
+    COMMAND ${LCOV} --gcov-tool ${GCOV} --rc lcov_branch_coverage=1 --remove ${OUTPUT}.total.info "*/tests/*" "*/c++/*" "*/include/*" "*/boost/*" "*/charm/*" "*.decl.h" "*.def.h" "*/STDIN" "*/openmpi/*" "*/pstreams/*" "*/Random123/*" "*/pegtl/*" "*/tut/*" "*/highwayhash/*" "*/moduleinit*" --output-file ${OUTPUT}.filtered.info
     # Copy over report customization files for genhtml
     COMMAND ${CMAKE_COMMAND} -E copy
             ${CMAKE_SOURCE_DIR}/../doc/quinoa.gcov.css

diff --git a/cmake/ConfigExecutable.cmake b/cmake/ConfigExecutable.cmake
@@ -1,12 +1,14 @@
 ################################################################################
 #
-# \file      cmake/ConfigExecutable.cmake
-# \copyright 2016, Los Alamos National Security, LLC.
+# \file      ConfigExecutable.cmake
+# \copyright 2012-2015 J. Bakosi,
+#            2016-2018 Los Alamos National Security, LLC.,
+#            2019 Triad National Security, LLC.
+#            All rights reserved. See the LICENSE file for details.
 # \brief     Configure Charm++ executable targets
 #
 ################################################################################
 
-
 # ##############################################################################
 # Function to configure executable targets
 #
@@ -17,8 +19,6 @@
 #
 # target - Target on which to set properties
 #
-# Author: J. Bakosi
-#
 # ##############################################################################
 function(config_executable target)
 

diff --git a/cmake/ConfigureDataLayout.cmake b/cmake/ConfigureDataLayout.cmake
@@ -1,7 +1,10 @@
 ################################################################################
 #
-# \file      cmake/ConfigureDataLayout.cmake
-# \copyright 2012-2015, J. Bakosi, 2016-2018, Los Alamos National Security, LLC.
+# \file      ConfigureDataLayout.cmake
+# \copyright 2012-2015 J. Bakosi,
+#            2016-2018 Los Alamos National Security, LLC.,
+#            2019 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
@@ -1,7 +1,10 @@
 ################################################################################
 #
-# \file      cmake/CppCheck.cmake
-# \copyright 2012-2015, J. Bakosi, 2016-2018, Los Alamos National Security, LLC.
+# \file      CppCheck.cmake
+# \copyright 2012-2015 J. Bakosi,
+#            2016-2018 Los Alamos National Security, LLC.,
+#            2019 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
@@ -1,7 +1,10 @@
 ################################################################################
 #
-# \file      cmake/DetectCodeCoverage.cmake
-# \copyright 2012-2015, J. Bakosi, 2016-2018, Los Alamos National Security, LLC.
+# \file      DetectCodeCoverage.cmake
+# \copyright 2012-2015 J. Bakosi,
+#            2016-2018 Los Alamos National Security, LLC.,
+#            2019 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
@@ -1,7 +1,10 @@
 ################################################################################
 #
-# \file      cmake/DetectCompilerVersion.cmake
-# \copyright 2012-2015, J. Bakosi, 2016-2018, Los Alamos National Security, LLC.
+# \file      DetectCompilerVersion.cmake
+# \copyright 2012-2015 J. Bakosi,
+#            2016-2018 Los Alamos National Security, LLC.,
+#            2019 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
@@ -1,7 +1,10 @@
 ################################################################################
 #
-# \file      cmake/DetectOS.cmake
-# \copyright 2012-2015, J. Bakosi, 2016-2018, Los Alamos National Security, LLC.
+# \file      DetectOS.cmake
+# \copyright 2012-2015 J. Bakosi,
+#            2016-2018 Los Alamos National Security, LLC.,
+#            2019 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
@@ -1,7 +1,10 @@
 ################################################################################
 #
-# \file      cmake/DisallowInSourceBuilds.cmake
-# \copyright 2012-2015, J. Bakosi, 2016-2018, Los Alamos National Security, LLC.
+# \file      DisallowInSourceBuilds.cmake
+# \copyright 2012-2015 J. Bakosi,
+#            2016-2018 Los Alamos National Security, LLC.,
+#            2019 Triad National Security, LLC.
+#            All rights reserved. See the LICENSE file for details.
 # \brief     Cmake code to disallow in-source builds
 #
 ################################################################################
@@ -11,7 +14,6 @@ if(__disallow_in_source_builds)
 endif()
 set(disallow_in_source_builds YES)
 
-
 function(disallow_in_source_builds)
 
   # Disallow in-source builds

diff --git a/cmake/FindAEC.cmake b/cmake/FindAEC.cmake
@@ -1,7 +1,10 @@
 ################################################################################
 #
-# \file      cmake/FindAEC.cmake
-# \copyright 2012-2015, J. Bakosi, 2016-2018, Los Alamos National Security, LLC.
+# \file      FindAEC.cmake
+# \copyright 2012-2015 J. Bakosi,
+#            2016-2018 Los Alamos National Security, LLC.,
+#            2019 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
@@ -1,7 +1,10 @@
 ################################################################################
 #
-# \file      cmake/FindBackwardCpp.cmake
-# \copyright 2016-2018, Los Alamos National Security, LLC.
+# \file      FindBackwardCpp.cmake
+# \copyright 2012-2015 J. Bakosi,
+#            2016-2018 Los Alamos National Security, LLC.,
+#            2019 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,
 # those libraries also require other libraries, e.g., elf, ebl, bz2, and lzma.

diff --git a/cmake/FindBrigand.cmake b/cmake/FindBrigand.cmake
@@ -1,12 +1,15 @@
 ################################################################################
 #
-# \file      cmake/FindBrigand.cmake
-# \copyright 2016-2018, Los Alamos National Security, LLC.
-# \brief     Find Brigand
+# \file      FindBrigand.cmake
+# \copyright 2012-2015 J. Bakosi,
+#            2016-2018 Los Alamos National Security, LLC.,
+#            2019 Triad National Security, LLC.
+#            All rights reserved. See the LICENSE file for details.
+# \brief     Find the Brigand template metaprogramming library
 #
 ################################################################################
 
-# See Brigand: https://github.com/edouarda/brigand
+# Brigand: https://github.com/edouarda/brigand
 #
 #  BRIGAND_FOUND - System has Brigand
 #  BRIGAND_INCLUDE_DIRS - The Brigand include directory

diff --git a/cmake/FindCharm.cmake b/cmake/FindCharm.cmake
@@ -1,12 +1,15 @@
 ################################################################################
 #
-# \file      cmake/FindCharm.cmake
-# \copyright 2016, Los Alamos National Security, LLC.
-# \brief     Find the Charm++
+# \file      FindCharm.cmake
+# \copyright 2012-2015 J. Bakosi,
+#            2016-2018 Los Alamos National Security, LLC.,
+#            2019 Triad National Security, LLC.
+#            All rights reserved. See the LICENSE file for details.
+# \brief     Find Charm++
 #
 ################################################################################
 
-# Find Charm++
+# Charm++: http://charmplusplus.org
 #
 #  CHARM_FOUND        - True if the charmc compiler wrapper was found
 #  CHARM_INCLUDE_DIRS - Charm++ include files paths

diff --git a/cmake/FindExodiff.cmake b/cmake/FindExodiff.cmake
@@ -1,8 +1,11 @@
 ################################################################################
 #
-# \file      cmake/FindExodiff.cmake
-# \copyright 2016, Los Alamos National Security, LLC.
-# \brief     Find the Adaptive Entropy Coding library
+# \file      FindExodiff.cmake
+# \copyright 2012-2015 J. Bakosi,
+#            2016-2018 Los Alamos National Security, LLC.,
+#            2019 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
@@ -1,20 +1,23 @@
 ################################################################################
 #
-# \file      cmake/FindGmsh.cmake
-# \copyright 2012-2015, J. Bakosi, 2016-2018, Los Alamos National Security, LLC.
+# \file      FindGmsh.cmake
+# \copyright 2012-2015 J. Bakosi,
+#            2016-2018 Los Alamos National Security, LLC.,
+#            2019 Triad National Security, LLC.
+#            All rights reserved. See the LICENSE file for details.
 # \brief     Find Gmsh
 #
 ################################################################################
 
-# Find Gmsh
+# Gmsh: http://gmsh.info
 #
-#  GMSH_FOUND - System has gmsh
-#  GMSH_EXECUTABLE - The gmsh executable
+# GMSH_FOUND - System has gmsh
+# GMSH_EXECUTABLE - The gmsh executable
 #
-#  Usage:
+# Usage:
 #
-#  set(GMSH_ROOT "/path/to/custom/gmsh") # prefer over system
-#  find_package(Gmsh)
+# set(GMSH_ROOT "/path/to/custom/gmsh") # prefer over system
+# find_package(Gmsh)
 
 if(GMSH_EXECUTABLE)
   # Already in cache, be silent

diff --git a/cmake/FindH5Part.cmake b/cmake/FindH5Part.cmake
@@ -1,12 +1,15 @@
 ################################################################################
 #
-# \file      cmake/FindH5Part.cmake
-# \copyright 2016, Los Alamos National Security, LLC.
+# \file      FindH5Part.cmake
+# \copyright 2012-2015 J. Bakosi,
+#            2016-2018 Los Alamos National Security, LLC.,
+#            2019 Triad National Security, LLC.
+#            All rights reserved. See the LICENSE file for details.
 # \brief     Find the H5Part library
 #
 ################################################################################
 
-# Find H5Part headers and libraries
+# H5Part: https://dav.lbl.gov/archive/Research/AcceleratorSAPP
 #
 #  H5PART_FOUND        - True if H5Part is found
 #  H5PART_INCLUDE_DIRS - H5Part include files paths

diff --git a/cmake/FindHighwayHash.cmake b/cmake/FindHighwayHash.cmake
@@ -1,12 +1,15 @@
 ################################################################################
 #
-# \file      cmake/FindHighwayHash.cmake
-# \copyright 2016-2018, Los Alamos National Security, LLC.
+# \file      FindHighwayHash.cmake
+# \copyright 2012-2015 J. Bakosi,
+#            2016-2018 Los Alamos National Security, LLC.,
+#            2019 Triad National Security, LLC.
+#            All rights reserved. See the LICENSE file for details.
 # \brief     Find HighwayHash
 #
 ################################################################################
 
-# See HighwayHash: https://github.com/google/highwayhash
+# HighwayHash: https://github.com/google/highwayhash
 #
 #  HighwayHash_FOUND - System has HighwayHash
 #  HIGHWAYHASH_INCLUDE_DIRS - The HighwayHash include directory

diff --git a/cmake/FindHypre.cmake b/cmake/FindHypre.cmake
@@ -1,12 +1,15 @@
 ################################################################################
 #
-# \file      cmake/FindHypre.cmake
-# \copyright 2012-2015, J. Bakosi, 2016-2018, Los Alamos National Security, LLC.
+# \file      FindHypre.cmake
+# \copyright 2012-2015 J. Bakosi,
+#            2016-2018 Los Alamos National Security, LLC.,
+#            2019 Triad National Security, LLC.
+#            All rights reserved. See the LICENSE file for details.
 # \brief     Find the Hypre library from LLNL
 #
 ################################################################################
 
-# Find the Hypre library from LLNL
+# Hypre: https://github.com/LLNL/hypre
 #
 #  HYPRE_FOUND - System has Hypre
 #  HYPRE_INCLUDE_DIRS - The Hypre include directory