Merge pull request #256 from LLNL/rc-v2024.01.0

Release Candidate v2024.01.0 (APPROVAL PR)

.gitignore

@@ -41,8 +41,8 @@ spack-build*
 *.logs
 rz*
 rz*
-toss_3*.cmake
-blueos_3*.cmake
+toss_*.cmake
+blueos_*.cmake
 
 
 # These are files automatically generated in our configure process.

.gitlab/machines.yml

@@ -20,6 +20,7 @@
     HOSTNAME: 'lassen'
     BUILD_ALLOC: lalloc 1 -W 60
     TEST_ALLOC: $BUILD_ALLOC
+    LC_MODULES: "cuda/11.1.0"
   extends: [.on_blueos_3_ppc64]
 
 # ------------------------------------------------------------------------------

.gitlab/scripts.yml

@@ -5,7 +5,7 @@
 .build:
   stage: build_and_install
   script:
-    - CI_BUILD_DIR=$SPHERAL_BUILDS_DIR/$CI_JOB_ID
+    - CI_BUILD_DIR=$SPHERAL_BUILDS_DIR/$CI_JOB_ID/project
     - echo $CI_BUILD_DIR &> ci-dir.txt && echo $CI_JOB_NAME &> job-name.txt
     - echo $CI_BUILD_DIR && echo $CI_PROJECT_DIR
     - mkdir -p $CI_BUILD_DIR && cp -a $CI_PROJECT_DIR/. $CI_BUILD_DIR

.readthedocs.yml

@@ -5,20 +5,17 @@
 # Required
 version: 2
 
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py
 
-# Build documentation with MkDocs
-#mkdocs:
-#  configuration: mkdocs.yml
-
-# # Optionally build your docs in additional formats such as PDF
-# formats:
-#   - pdf
-
-# # Optionally set the version of Python and requirements required to build your docs
-# python:
-#   version: 3.7
-#   install:
-#     - requirements: docs/requirements.txt
+# Explicitly set the version of Python and its requirements
+python:
+  install:
+    - requirements: docs/requirements.txt

CMakeLists.txt

@@ -1,9 +1,10 @@
 # CMakeLists to build the Spheral library.
 
-cmake_minimum_required(VERSION 3.10)
-project(spheral LANGUAGES C CXX Fortran)
+cmake_minimum_required(VERSION 3.18)
+include(cmake/SpheralVersion.cmake)
+project(spheral LANGUAGES C CXX Fortran VERSION ${SPHERAL_VERSION})
 
-set(SPHERAL_ROOT_DIR ${CMAKE_CURRENT_SOURCE_DIR})
+set(SPHERAL_ROOT_DIR ${CMAKE_CURRENT_SOURCE_DIR} CACHE PATH "Path to Spheral source directory")
 set(SPHERAL_TEST_INSTALL_PREFIX ${CMAKE_INSTALL_PREFIX})
 
 include(cmake/SetupSpheral.cmake)

License.txt

@@ -1,7 +1,7 @@
 Copyright (c) 2012, Lawrence Livermore National Security, LLC. 
 Produced at the Lawrence Livermore National Laboratory
 Written by J. Michael Owen <[email protected]>
-CODE-OCEC-12-049
+LLNL-CODE-561852
 All rights reserved.
 
 The files in this directory and below are part of Spheral++. For details, see

README.md

@@ -17,7 +17,7 @@ Release and license:
 Copyright (c) 2012, Lawrence Livermore National Security, LLC.  
 Produced at the Lawrence Livermore National Laboratory  
 Written by J. Michael Owen <[email protected]>  
-CODE-OCEC-12-049  
+LLNL-CODE-561852  
 All rights reserved.
 
 Please see full license at https://github.com/jmikeowen/spheral/blob/master/License.txt

RELEASE_NOTES.md

@@ -1,3 +1,44 @@
+Version v2024.01.00 -- Release date 2024-01-19
+==============================================
+  * Important Notes:
+    * The PolyClipper, BLT, and PYB11Generator submodules have been modified. Be sure to recursively update the submodules.  
+
+Notable changes include:
+
+  * New features/ API changes:
+    * Adding P-alpha porosity model.
+    * Updating treatment of various state variables in the presence of porosity.
+    * Introduced a new common base class for porosity physics (PorosityModel), which PalphaPorosity and StrainPorosity share.
+    * Revamped interaction UpdatePolicies with FieldLists:
+      - UpdatePolicies have a new virtual method: clonePerField: True means when registering a FieldList copy the Policy for each Field in the FieldList; False means register the FieldList for update itself with the single instance of the Policy.
+      - This change removes most of our redundant Field/FieldList update policies, and allows us to be more granular in applying different policies to single Field values in a FieldList.
+    * Adding more Shadow Python interfaces wrapping our C++ classes, in particular PalphaPorosity and StrainPorosity.
+    * EquationOfState now requires instances to provide \partial P/\partial \rho and \partial P/\partial \epsilon.  All current equations of state have been updated accordingly.
+    * Tillotson and Gruneisen EOSs implementations updated a bit in the revamping.
+    * Added more material options to MaterialPropertiesLib.py (mostly from Melosh's 89 book).
+
+  * Build changes / improvements:
+    * Spheral now provides First Class CMake support (using the BLT nomenclature). Spheral and its dependencies are now exported to simplify importing the project. To import Spheral into another project using CMake, use:
+      ```
+      find_package(Spheral_CXX <path_to_spheral_installation>)
+      ```
+    * CMake variables have a more consistent naming convention. Unused variables are removed.
+    * Added ENABLE_DEV_BUILD option to improve build times during code development.
+    * Upped our required C++ standard to 17.
+
+  * Bug Fixes / improvements:
+    * Fixed melt behavior in Steinberg-Guinan strength model, which was ignoring melt for damaged material.
+    * Fixed range of dimensionless melt temperature for Johnson-Cook strength.
+    * FSISPH new features and modifications to method. 
+      * NOTE constructor inputs have changed.
+      * strength implementation modified.
+      * new features added including plane strain option and settable minP for interfaces.
+      * new, more rigorous, interface and free surface tracking.
+    * Fixed initialization of longitudinal sound speed and Youngs modulus for damage models.
+    * Corrected some minor bugs/inconsistencies in the Tillotson EOS.
+    * lcats updated to work with current TOSS4 machine configurations.
+    * Updated various tests to make out automated testing more robust.
+
 Version v2023-06-0 -- Release date 2023-06-20
 ==============================================
 
@@ -125,3 +166,15 @@ Notable changes include:
     * CullenDehnen segfault fix.
 
 **Full Changelog**: https://github.com/LLNL/spheral/compare/2022.2.0-pre-spack...v2022.6.0
+
+Version vYYYY.MM.p -- Release date YYYY-MM-DD
+==============================================
+  * Important Notes:
+
+Notable changes include:
+
+  * New features/ API changes:
+
+  * Build changes / improvements:
+
+  * Bug Fixes / improvements:

cmake/Compilers.cmake

@@ -64,12 +64,15 @@ message("-- Fortran flags: ${CMAKE_Fortran_FLAGS}")
 # PYB11 Target Flags
 #-------------------------------------------------------------------------------
 set(SPHERAL_PYB11_TARGET_FLAGS
+  -O1
   -Wno-unused-local-typedefs 
   -Wno-overloaded-virtual)
 if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
   list(APPEND SPHERAL_PYB11_TARGET_FLAGS
     -Wno-self-assign-overloaded 
-    -Wno-delete-non-abstract-non-virtual-dtor)
+    -Wno-inconsistent-missing-override
+    -Wno-delete-non-abstract-non-virtual-dtor
+    -Wno-delete-abstract-non-virtual-dtor)
 elseif ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
   list(APPEND SPHERAL_PYB11_TARGET_FLAGS
     -Wno-pedantic)

cmake/InstallTPLs.cmake

@@ -5,88 +5,126 @@
 # Do NOT add any TPLs to the clean target
 set_directory_properties(PROPERTIES CLEAN_NO_CUSTOM 1)
 
+# Set the location of the <tpl>.cmake files
+set(TPL_SPHERAL_CMAKE_DIR ${SPHERAL_ROOT_DIR}/cmake/tpl)
+
+# Initialize TPL options
+include(${SPHERAL_ROOT_DIR}/cmake/spheral/SpheralHandleTPL.cmake)
+
 #-----------------------------------------------------------------------------------
 # Submodules
 #-----------------------------------------------------------------------------------
 
-# Things all Spheral packages have in their include path
-set(SPHERAL_EXTERN_INCLUDES )
-
-# PolyClipper
-if (NOT polyclipper_DIR)
-  set(polyclipper_DIR "${SPHERAL_ROOT_DIR}/extern/PolyClipper" CACHE PATH "")
-endif()
-set(polyclipper_INCLUDES "${polyclipper_DIR}/src")
-
-list(APPEND SPHERAL_EXTERN_INCLUDES ${polyclipper_INCLUDES})
-
-
 if (NOT ENABLE_CXXONLY)
   # Find the appropriate Python
-  set(Python3_ROOT_DIR ${python_DIR})
   find_package(Python3 COMPONENTS Interpreter Development)
+  set(PYTHON_EXE ${Python3_EXECUTABLE})
+  list(APPEND SPHERAL_BLT_DEPENDS Python3::Python)
 
   # Set the PYB11Generator path
   if (NOT PYB11GENERATOR_ROOT_DIR)
     set(PYB11GENERATOR_ROOT_DIR "${SPHERAL_ROOT_DIR}/extern/PYB11Generator" CACHE PATH "")
   endif()
-  include(${PYB11GENERATOR_ROOT_DIR}/cmake/PYB11Generator.cmake)
-
   # Set the pybind11 path
   if (NOT PYBIND11_ROOT_DIR)
     set(PYBIND11_ROOT_DIR "${PYB11GENERATOR_ROOT_DIR}/extern/pybind11" CACHE PATH "")
   endif()
+  include(${PYB11GENERATOR_ROOT_DIR}/cmake/PYB11Generator.cmake)
+  list(APPEND SPHERAL_BLT_DEPENDS pybind11_headers)
+  install(TARGETS pybind11_headers
+    EXPORT spheral_cxx-targets
+    DESTINATION lib/cmake)
+  set_target_properties(pybind11_headers PROPERTIES EXPORT_NAME spheral::pybind11_headers)
+endif()
 
-  list(APPEND SPHERAL_EXTERN_INCLUDES ${PYBIND11_ROOT_DIR}/include)
+# This is currently unfilled in spheral
+set_property(GLOBAL PROPERTY SPHERAL_SUBMOD_INCLUDES "${SPHERAL_SUBMOD_INCLUDES}")
+
+# PolyClipper
+if (NOT polyclipper_DIR)
+  # If no PolyClipper is specified, build it as an internal target
+  set(polyclipper_DIR "${SPHERAL_ROOT_DIR}/extern/PolyClipper")
+  # Must set this so PolyClipper doesn't include unnecessary python scripts
+  set(POLYCLIPPER_MODULE_GEN OFF)
+  set(POLYCLIPPER_ENABLE_DOCS OFF)
+  set(POLYCLIPPER_INSTALL_DIR "PolyClipper/include")
+  add_subdirectory(${polyclipper_DIR} ${CMAKE_CURRENT_BINARY_DIR}/PolyClipper)
+  # Treat includes as system to prevent warnings
+  blt_convert_to_system_includes(TARGET PolyClipperAPI)
+  list(APPEND SPHERAL_BLT_DEPENDS PolyClipperAPI)
+  install(TARGETS PolyClipperAPI
+    EXPORT spheral_cxx-targets
+    DESTINATION lib/cmake)
+  set_target_properties(PolyClipperAPI PROPERTIES EXPORT_NAME spheral::PolyClipperAPI)
+else()
+  Spheral_Handle_TPL(polyclipper ${TPL_SPHERAL_CMAKE_DIR})
+  list(APPEND SPHERAL_BLT_DEPENDS polyclipper)
 endif()
 
 #-----------------------------------------------------------------------------------
 # Find pre-compiled TPLs
 #-----------------------------------------------------------------------------------
 
-# Initialize TPL options
-include(${SPHERAL_ROOT_DIR}/cmake/spheral/SpheralHandleTPL.cmake)
-
-# These libs are always needed
-Spheral_Handle_TPL(zlib spheral_depends cxx)
-Spheral_Handle_TPL(boost spheral_depends cxx)
-Spheral_Handle_TPL(eigen spheral_depends cxx)
-Spheral_Handle_TPL(qhull spheral_depends cxx)
-Spheral_Handle_TPL(silo spheral_depends cxx)
-
-# AXOM PUlls in HDF5 and Conduit for us
-#Spheral_Handle_TPL(conduit spheral_depends cxx)
+# Use find_package to get axom (which brings in fmt) and patch fmt
 find_package(axom REQUIRED QUIET NO_DEFAULT_PATH PATHS ${axom_DIR}/lib/cmake)
 if(axom_FOUND)
-  list(APPEND spheral_blt_cxx_depends axom fmt)
-  blt_patch_target(NAME fmt TREAT_INCLUDES_AS_SYSTEM On)
-  message(STATUS "Found axom: ${axom_DIR} (found version ${axom_VERSION})")
-endif()
-
-# Axom imports hdf5 lib but Spheral also requires hdf5_hl
-Spheral_Handle_TPL(hdf5 spheral_depends cxx)
-
-# Some libraries are optional
-if (ENABLE_ANEOS)
-  Spheral_Handle_TPL(aneos spheral_depends cxx)
-endif()
-if (ENABLE_OPENSUBDIV)
-  Spheral_Handle_TPL(opensubdiv spheral_depends cxx)
-endif()
-if(ENABLE_TIMER)
-  Spheral_Handle_TPL(caliper spheral_depends cxx)
-endif()
-
-# Only needed when building the python interface of spheral
-if(NOT ENABLE_CXXONLY)
-  Spheral_Handle_TPL(python spheral_depends cxx)
-  #Spheral_Handle_TPL(pyb11generator spheral_depends py)
-  #Spheral_Handle_TPL(pybind11 spheral_depends py)
+  list(APPEND SPHERAL_BLT_DEPENDS axom)
+  # Add fmt library to external library list
+  set(fmt_name fmt)
+  # Newer Axom versions call fmt target axom::fmt
+  if(NOT TARGET fmt)
+    set(fmt_name axom::fmt)
+  endif()
+  list(APPEND SPHERAL_BLT_DEPENDS ${fmt_name})
+  # BLT Macro for doing this
+  blt_convert_to_system_includes(TARGET ${fmt_name})
 endif()
+# This is a hack to handle transitive issues that come
+# from using object libraries with newer version of axom
+foreach(_comp ${AXOM_COMPONENTS_ENABLED})
+  list(APPEND SPHERAL_BLT_DEPENDS axom::${_comp})
+  get_target_property(axom_deps axom::${_comp} INTERFACE_LINK_LIBRARIES)
+  list(APPEND SPHERAL_BLT_DEPENDS ${axom_deps})
+endforeach()
+
+# TPLs that must be imported
+list(APPEND SPHERAL_EXTERN_LIBS zlib boost eigen qhull silo hdf5 polytope)
+
+blt_list_append( TO SPHERAL_EXTERN_LIBS ELEMENTS aneos IF ENABLE_ANEOS)
+blt_list_append( TO SPHERAL_EXTERN_LIBS ELEMENTS opensubdiv IF ENABLE_OPENSUBDIV)
+blt_list_append( TO SPHERAL_EXTERN_LIBS ELEMENTS caliper IF ENABLE_TIMER)
+
+# Create and install target library for each external library
+foreach(lib ${SPHERAL_EXTERN_LIBS})
+  if(NOT TARGET ${lib})
+    Spheral_Handle_TPL(${lib} ${TPL_SPHERAL_CMAKE_DIR})
+  endif()
+  list(APPEND SPHERAL_BLT_DEPENDS ${lib})
+endforeach()
+# Note: SPHERAL_BLT_DEPENDS is made global after this in SetupSpheral.cmake
 
-Spheral_Handle_TPL(polytope spheral_depends cxx)
-#Spheral_Handle_TPL(polyclipper spheral_depends cxx)
-
+# This calls LLNLSpheralInstallTPLs.cmake
 if (EXISTS ${EXTERNAL_SPHERAL_TPL_CMAKE})
   include(${EXTERNAL_SPHERAL_TPL_CMAKE})
 endif()
+# Copied from serac, needed to bypass generator expression issue during export
+set(_props)
+if( ${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.13.0" )
+  list(APPEND _props INTERFACE_LINK_OPTIONS)
+endif()
+list(APPEND _props INTERFACE_COMPILE_OPTIONS)
+foreach(_target axom axom::openmp)
+  if(TARGET ${_target})
+    message(STATUS "Removing OpenMP Flags from target[${_target}]")
+    foreach(_prop ${_props})
+      get_target_property(_flags ${_target} ${_prop})
+      if ( _flags )
+	string( REPLACE "${OpenMP_CXX_FLAGS}" ""
+	  correct_flags "${_flags}" )
+	string( REPLACE "${OpenMP_Fortran_FLAGS}" ""
+	  correct_flags "${correct_flags}" )
+	set_target_properties( ${_target} PROPERTIES ${_prop} "${correct_flags}" )
+      endif()
+    endforeach()
+  endif()
+endforeach()