Merge pull request #730 in ATK/axom from v0.3.0-rc to master

* commit '520c6e857670b988d97931d77826ea59cba4dcf5': (507 commits)
  Fix capitalization
  Update host-config, clarify message
  Automatically create list of enabled and full components, More AXOM_ options
  Address comments
  Prefix missing options
  Remove broken Sidre Python Shroud interface
  Remove LUA, Restrict Python in build system, Remove old files, Add AXOM_ to more options, Add CHANGELOG
  Adjust test so test points are not on grid line
  Fix logic error in UniformGrid ctor.  ATK-1214
  BUGFIX: check for convergence on return
  File naming error in mesh_tester; resolved variance of promised behavior from actual behavior of axom::utilities::filesystem::getDirName().
  ENH: apply uncrustify style changes to axom_utils
  ENH: use random_real() variant w/seed value
  ENH: add random_real() variant that takes a seed
  DOC: corrections & improvements to doxygen docs
  ENH: Added AXOM_ prefix to ENABLE_SPARSEHASH, PYTHON and ALL_COMPONENTS.
  ENH: Added AXOM_ prefix to ENABLE_TESTS, DOCS and EXAMPLES.
  BUGFIX: fix loop in eigen_sort()
  DOC: log changes to numerics in release notes
  ENH: apply uncrustify style changes to numerics
  ...

.mailmap

@@ -7,6 +7,7 @@ Austin Stromme <stromme1@llnl.gov>              Austin James Stromme <stromme1@c
 Austin Stromme <stromme1@llnl.gov>              Austin James Stromme <stromme1@cab669.llnl.gov>
 Benjamin Curtice Corbett <corbett5@llnl.gov>    Benjamin Curtice Corbett <corbett5@cab668.llnl.gov>
 Benjamin Curtice Corbett <corbett5@llnl.gov>    Ben Corbett <corbett5@llnl.gov>
+Benjamin Curtice Corbett <corbett5@llnl.gov>    Benjamin Corbett <corbett5@llnl.gov>
 Brian Ryujin <ryujin1@llnl.gov>                 Brian R <bryujin@gmail.com>
 Chris White <white238@llnl.gov>                 Christopher A. White <white238@llnl.gov>
 Cyrus D. Harrison <harrison37@llnl.gov>         Cyrus Harrison <cyrush@llnl.gov>
@@ -19,10 +20,12 @@ Lee A. Taylor <taylor16@llnl.gov>               Lee A. Taylor <taylor@cab688.lln
 Lee A. Taylor <taylor16@llnl.gov>               Lee A. Taylor <taylor@cab688.llnl.gov>
 Lee A. Taylor <taylor16@llnl.gov>               Lee Taylor <ltaylor@llnl.gov>
 Lee A. Taylor <taylor16@llnl.gov>               Lee Taylor <taylor16@llnl.gov>
+Noah S. Elliott <elliott22@llnl.gov>            Noah Elliott <elliott22@llnl.gov>
 Punita P. Sinha <sinha2@llnl.gov>               Punita P. Sinha <sinha2@cab687.llnl.gov>
 Punita P. Sinha <sinha2@llnl.gov>               Punita P. Sinha <sinha2@cab669.llnl.gov>
 Punita P. Sinha <sinha2@llnl.gov>               Punita P. Sinha <sinha2@cab670.llnl.gov>
 Punita P. Sinha <sinha2@llnl.gov>               Punita Sinha <sinha2@llnl.gov>
+Raine Yeh <yeh14@llnl.gov>                      Yo-Sing Yeh <yeh14@llnl.gov>
 Randolph Settgast <settgast1@llnl.gov>          Randolph R. Settgast <rrsettgast@gmail.com>
 Randolph Settgast <settgast1@llnl.gov>          Randolph R. Settgast <settgast1@llnl.gov>
 Randolph Settgast <settgast1@llnl.gov>          Randy Settgast <settgast1@llnl.gov>

LICENSE

@@ -26,4 +26,24 @@ 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.
 
-Please see the NOTICE file for additional restrictions.
+Additional BSD Notice
+
+1. This notice is required to be provided under our contract with the U.S. 
+Department of Energy (DOE). This work was produced at Lawrence Livermore 
+National Laboratory under Contract No. DE-AC52-07NA27344 with the DOE.
+
+2. Neither the United States Government nor Lawrence Livermore National 
+Security, LLC nor any of their employees, makes any warranty, express or 
+implied, or assumes any liability or responsibility for the accuracy, 
+completeness, or usefulness of any information, apparatus, product, or 
+process disclosed, or represents that its use would not infringe 
+privately-owned rights.
+
+3. Also, reference herein to any specific commercial products, process, 
+or services by trade name, trademark, manufacturer or otherwise does not 
+necessarily constitute or imply its endorsement, recommendation, or favoring 
+by the United States Government or Lawrence Livermore National Security, LLC. 
+The views and opinions of authors expressed herein do not necessarily state 
+or reflect those of the United States Government or Lawrence Livermore 
+National Security, LLC, and shall not be used for advertising or product 
+endorsement purposes.

README.md

@@ -1,7 +1,10 @@
 
-axom
+Axom
 ====
 
-https://lc.llnl.gov/axom/
+Axom provides a robust, flexible software infrastructure for the development of multi-physics applications and computational tools.
+
+See https://lc.llnl.gov/axom/ for more information.
+
 
 

RELEASE

@@ -1,11 +1,10 @@
 *******************************************************************************
 
-Axom: ................................, version 0.2.9
+Axom: ................................, version 0.3.0
 
 Copyright (c) 2017-2018, Lawrence Livermore National Security, LLC. 
 Produced at the Lawrence Livermore National Laboratory.
-All rights reserved. See details in axom/LICENSE and 
-axom/NOTICE files.
+All rights reserved. See details in the file axom/LICENSE.
 
 Unlimited Open Source - BSD Distribution
 LLNL-CODE-741217

RELEASE-NOTES.md

@@ -0,0 +1,128 @@
+# Axom Software Release Notes
+
+Notes describing significant changes in each Axom release are documented
+in this file.
+
+The format of this file is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
+
+The Axom project release numbers follow [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
+
+
+## [Version 0.3.0] - Release date 2018-07-25
+
+### Added
+- Added AXOM_ENABLE_TESTS which is a CMake dependent option of ENABLE_TESTS
+- Added AXOM_ENABLE_DOCS which is a CMake dependent option of ENABLE_DOCS
+- Added AXOM_ENABLE_EXAMPLES which is a CMake dependent option of ENABLE_EXAMPLES
+- Added jacobi_eigensolve() method for computing the eigenvalues and eigenvectors
+  of real, symmetric matrices.
+- Added matrix_norm() operator for computing matrix norms. The implementations
+  supports the p1-norm, infinity-norm and frobenious matrix norm.
+- Added eigen_sort() routine for sorting the supplied eigenvalues and corresponding
+  eigenvectors in ascending order.
+- Initial integration of Mint and Sidre. Mint can now operate on meshes 
+  stored in Sidre and conform to the [computational mesh blueprint conventions](http://llnl-conduit.readthedocs.io/en/latest/blueprint.html).
+- Added a sphere-sphere intersection test to Primal.
+- Added a utility function to Quest to *weld* vertices in a triangle mesh that 
+  are within a given tolerance. After welding, all triangles incident in a 
+  vertex have the same index for that vertex. This function has been integrated
+  into the ``mesh_tester`` utility.
+- Added a bounded All-Nearest-Neighbor query to Quest. This query takes a list
+  of point locations and associated regions, and for each point reports the 
+  nearest point in a different region that is no farther than a max search 
+  radius.
+- Axom now exports [sparsehash version 2.0.3](https://github.com/sparsehash/sparsehash). Previously, it was only used internally.
+- Added a BitSet class to Slam.
+- Added a Tetrahedron primitive to Primal.
+- Added an in_sphere operator to Primal, which is a predicate that
+  is used extensively for Delaunay triangulations.
+
+### Removed
+- Axom no longer depends on the Boost library.
+- Removed ENABLE_PYTHON CMake option. Python was only used by Shroud so restricted Python
+  checks to when Shroud generation is enabled
+- Removed Lua as a dependency of Axom.
+
+### Deprecated
+- 
+
+### Changed
+- The root CMake file for Axom is now located in ``<axom>/src``'s root directory,
+  rather than in ``<axom>``
+- Prefixed all Axom CMake options with AXOM_ to avoid conflicts
+- ENABLE_SPARSEHASE -> AXOM_ENABLE_SPARSEHASH
+- ENABLE_ALL_COMPONENTS -> AXOM_ENABLE_COMPONENTS
+- ENABLE_<component name> -> AXOM_ENABLE_<component name>
+- MINT_USE_64BIT_INDEXTYPE -> AXOM_MINT_USE_64BIT_INDEXTYPE
+- MINT_USE_SIDRE -> AXOM_MINT_USE_SIDRE
+- CMake minimum is now 3.8 for non-CUDA builds and 3.9 for CUDA builds
+- Axom now requires a C++11 compiler.
+- Refactored Axom's Matrix/Vector operators and consolidated them in one file.
+- Removed overloaded arithmetic operators from the Matrix class to avoid 
+  potential negative performance impacts. Applications should use the new 
+``matvecops`` methods for such operations.
+- Quest STL reader now returns a status code, indicating whether reading
+  the STL file was successful. Also, the reader now leverages the improved
+  Mint API to reserve storage for mesh and avoid re-allocations when reading
+  the STL mesh data into the Mint mesh.
+- Refactored and cleaned up Primal's Sphere class.
+- Refactored Mint and removed all STL usage in preparation for GPUs.
+
+### Fixed
+-
+
+### Known Bugs
+-
+
+
+## [Version 0.2.9] - Release date 2018-03-08
+
+### Added
+- Updated to [conduit version 0.3.1](https://github.com/LLNL/conduit/tree/v0.3.1)
+- Updated to [shroud version 0.8.8](https://github.com/LLNL/shroud/tree/v0.8.0)
+- Improved platform support for LLNL's ``blue_os`` and ``bg/q`` systems.
+  Axom now builds with Fortran enabled using the xlc and clang compilers.
+- Improved support for Axom on Windows, including new host-configs for
+  Microsoft's Visual Studio compiler and for the intel compiler on Windows.
+  All Axom components can now be built on Windows, but we do not yet support
+  hdf5 or Fortran on Windows.
+- Added geometric Plane primitive to Primal. The Plane defines an oriented
+  plane in 2D and 3D and provides support for operations such as projection of
+  a point to a plane, signed distance and orientation.
+- Added ability to configure Axom (in particular Sidre and Spio) without hdf5.
+- Improved testing of [Scalable Checkpoint Restart (SCR)] library in Sidre.
+- Added a Point-In-Cell query to Quest. The Point In Cell query finds the cell
+  in a computational mesh that contains an arbitrary point in space.
+  If such a cell exists, it also finds the isoparametric coordinates of the
+  point with respect to the cell. The query supports higher order
+  [mfem](http://mfem.org) meshes.
+- Added cross-product and linspace operators to the vector utilities in 
+``numerics``
+
+### Removed
+- 
+
+### Deprecated
+- 
+
+### Changed
+- The root cmake file for Axom is now located in ``<axom>``'s root directory,
+  rather than in ``<axom>/src``
+- ``primal`` is no longer a header-only library.
+- Modified ``quest`` API to allow using a ``mint`` mesh that is already
+  resident in memory.
+
+### Fixed
+- Fixed a divide-by-zero problem in ``primal::intersect()``
+- Fixed the calculation of the Jacobian in ``mint::FiniteElement`` to support
+  elements that are in higher-dimensional ambient space, e.g., surface elements,
+  a Triangle or Quad in 3D.
+
+### Known Bugs
+-
+
+
+[Unreleased]: https://lc.llnl.gov/bitbucket/projects/ATK/repos/axom/compare/commits?targetBranch=refs%2Ftags%2Fv0.2.9&sourceBranch=refs%2Fheads%2Fdevelop&targetRepoId=1066
+[Version 0.2.9]: https://lc.llnl.gov/bitbucket/projects/ATK/repos/axom/compare/commits?targetBranch=refs%2Ftags%2Fv0.2.8&sourceBranch=refs%2Ftags%2Fv0.2.9&targetRepoId=1066
+
+[Scalable Checkpoint Restart (SCR)]: https://computation.llnl.gov/projects/scalable-checkpoint-restart-for-mpi

config-build.py

@@ -165,6 +165,8 @@ def setup_install_dir(args, platform_info):
 # Check if executable exists 
 ############################
 def executable_exists(path):
+    if path == "cmake":
+        return True
     return os.path.isfile(path) and os.access(path, os.X_OK)
 
 ############################
@@ -219,7 +221,7 @@ def create_cmake_command_line(args, unknown_args, buildpath, hostconfigpath, ins
         cmakeline += " " + " ".join( unknown_args )
 
     rootdir = os.path.dirname( os.path.abspath(sys.argv[0]) )
-    cmakeline += " %s " % rootdir
+    cmakeline += " %s " % os.path.join(rootdir,"src")
 
     # Dump the cmake command to file for convenience
     with open("%s/cmake_cmd" % buildpath, "w") as cmdfile:

host-configs/blueos_3_ppc64le_ib-clang@coral_xlf.manual.edits.txt

@@ -25,22 +25,22 @@ set(ENABLE_GTEST_DEATH_TESTS ON CACHE BOOL "")
 set(BLT_FORTRAN_FLAGS "-WF,-C!" CACHE STRING "")
 
 # Adds a missing rpath for libraries associated with the fortran compiler
-set(BLT_EXE_LINKER_FLAGS "-Wl,-rpath,/usr/tce/packages/xl/xl-beta-2017.10.13/lib" CACHE STRING "")
+set(BLT_EXE_LINKER_FLAGS "-Wl,-rpath,/usr/tce/packages/xl/xl-2018.05.18/lib/" CACHE STRING "")
 
 ##############################################################################
 # MPI - manually added for now
 ##############################################################################
 
 set(ENABLE_MPI ON CACHE BOOL "")
 
-set(MPI_HOME                 "/usr/tce/packages/spectrum-mpi/spectrum-mpi-2017.08.24-clang-coral-2017.10.13/" CACHE PATH "")
+set(MPI_HOME                 "/usr/tce/packages/spectrum-mpi/spectrum-mpi-2018.04.27-clang-coral-2018.05.23/" CACHE PATH "")
 set(MPI_C_COMPILER           "${MPI_HOME}/bin/mpicc"   CACHE PATH "")
 set(MPI_CXX_COMPILER         "${MPI_HOME}/bin/mpicxx"  CACHE PATH "")
 set(MPI_Fortran_COMPILER     "${MPI_HOME}/bin/mpifort" CACHE PATH "")
 
-set(MPIEXEC              "mpirun" CACHE PATH "")
-set(MPIEXEC_NUMPROC_FLAG "-np" CACHE PATH "")
-
+set(MPIEXEC                "${MPI_HOME}/bin/mpirun" CACHE PATH "")
+set(MPIEXEC_NUMPROC_FLAG   "-np" CACHE PATH "")
+set(BLT_MPI_COMMAND_APPEND "mpibind" CACHE PATH "")
 
 ##############################################################################
 # !---------------------------------------------------------------------------

host-configs/blueos_3_ppc64le_ib-gcc@4.9.3.manual.edits.txt

@@ -27,14 +27,14 @@ set(ENABLE_GTEST_DEATH_TESTS ON CACHE BOOL "")
 
 set(ENABLE_MPI ON CACHE BOOL "")
 
-set(MPI_HOME                 "/usr/tcetmp/packages/spectrum-mpi/spectrum-mpi-2017.04.03-gcc-4.9.3" CACHE PATH "")
+set(MPI_HOME                 "/usr/tce/packages/spectrum-mpi/spectrum-mpi-2018.04.27-gcc-4.9.3" CACHE PATH "")
 set(MPI_C_COMPILER           "${MPI_HOME}/bin/mpicc"   CACHE PATH "")
 set(MPI_CXX_COMPILER         "${MPI_HOME}/bin/mpicxx"  CACHE PATH "")
-set(MPI_Fortran_COMPILER     "${MPI_HOME}/bin/mpif90" CACHE PATH "")
-
-set(MPIEXEC              "mpirun" CACHE PATH "")
-set(MPIEXEC_NUMPROC_FLAG "-np" CACHE PATH "")
+set(MPI_Fortran_COMPILER     "${MPI_HOME}/bin/mpif90"  CACHE PATH "")
 
+set(MPIEXEC                "${MPI_HOME}/bin/mpirun" CACHE PATH "")
+set(MPIEXEC_NUMPROC_FLAG   "-np" CACHE PATH "")
+set(BLT_MPI_COMMAND_APPEND "mpibind" CACHE PATH "")
 ##############################################################################
 # !---------------------------------------------------------------------------
 ##############################################################################