Merge pull request #280 from LLNL/rc-v2024.06.0

v2024.06.0 Release

.gitlab/os.yml

@@ -4,7 +4,7 @@
 .sys_config:
   variables:
     LLNL_SERVICE_USER: sphapp
-    UPSTREAM_DIR: /usr/WS2/wciuser/Spheral/spheral-spack-tpls
+    UPSTREAM_DIR: /usr/WS2/sduser/Spheral/spack_upstream/0.22
     DISPLAY: ':0.0'
 
 .on_toss_3_x86:

.gitlab/scripts.yml

@@ -12,7 +12,6 @@
     - cd $CI_BUILD_DIR
     - echo $SPEC
 
-    - ml load python/3
     - $BUILD_ALLOC ./$SCRIPT_DIR/gitlab/build_and_install.py --spec="$SPEC" --extra-cmake-args="$EXTRA_CMAKE_ARGS"
 
 .build_and_test:

.uberenv_config.json

@@ -3,7 +3,7 @@
   "package_version" : "develop",
   "package_source_dir" : "../../..",
   "spack_url" : "https://github.com/spack/spack",
-  "spack_commit" : "5e0d2107348eed6cbe6deca43a30f5b06c5e40af",
+  "spack_commit" : "5fe93fee1eec46a0750bd340198bffcb92ff9eec",
   "spack_configs_path" : "scripts/spack/configs",
   "spack_packages_path" : "scripts/spack/packages"
 }

Dockerfile

@@ -31,7 +31,7 @@ ARG HOST_CONFIG=docker-$SPEC
 ENV DEBIAN_FRONTEND=noninteractive
 RUN apt-get update -y
 RUN apt-get upgrade -y
-RUN apt-get install -y build-essential git gfortran mpich autotools-dev autoconf sqlite pkg-config uuid gettext cmake libncurses-dev libgdbm-dev libffi-dev libssl-dev libexpat-dev libreadline-dev liblapack-dev libbz2-dev locales python python3 unzip libtool wget curl tk-dev
+RUN apt-get install -y build-essential git gfortran mpich autotools-dev autoconf sqlite pkg-config uuid gettext cmake libncurses-dev libgdbm-dev libffi-dev libssl-dev libexpat-dev libreadline-dev libbz2-dev locales python python3 unzip libtool wget curl tk-dev
 
 # Setup system locale for pip package encoding/decoding 
 RUN locale-gen en_US.UTF-8

RELEASE_NOTES.md

@@ -1,3 +1,34 @@
+Version v2024.06.0 -- Release date 2024-06-27
+==============================================
+  * Important Notes:
+    * External users of the code will need to supply config files for tpl-manager to find system libraries correctly. Steps to do this are detailed in the external user build guide. 
+
+Notable changes include:
+
+  * New features / API changes:
+    * Added MFV hydro from Hopkins 2015 with extension for ALE options.
+    * Adding optional user specified smoothing scale method for SPH, FSISPH, and CRKSPH.
+
+  * Build changes / improvements:
+    * PYBind11 libraries no longer depend on the structure of the PYB11 source directory.
+      * CMake interface for adding PYBind11 target libraries is modified to more closely match how C++ libraries are created.
+      * Multiple Spheral Python modules / CMake targets can be specified for a single directory.
+      * KernelIntegrator and FieldList directories are divided into 2 modules / targets.
+    * tpl-manager.py will no longer use generic x86_64 configs for non LC systems. Users will be required to supply their own configs for pointing spack at external packages.
+    * Spack version is increased from 0.19 to 0.22.
+    * Spack upstream is updated.
+    * Removed the python 3 module load for the Gitlab CI to fix an issue with pkg-config changing.
+    * Zlib target and TPL cmake file is removed.
+    * PYB11Generator repo is updated.
+    * Spack config and package files inside Spheral are updated to accommodate Spack 0.22.
+      * Package recipes for py-numpy-stl, py-pillow, py-pipreqs, td, and tk are removed.
+      * Versions for python dependencies in the Spheral spack recipe are fixed and updated (in some cases).
+
+  * Bug Fixes / improvements:
+    * Corrected an erroneous VERIFY in the P-alpha porosity constructor (with Fields of porosity and sound speed) that forced runs to stop even with correct input parameters
+    * Fixed a bug in the standard ASPH hydros (ASPH, SolidASPH, and RZ varieties) that gave incorrect results.  FSI ad CRK models with ASPH smoothing scales were OK, but standard
+      SPH using ASPH smoothing scales were simply incorrect for non-unit aspect ratio H's.  Also added ATS tests to help catch such errors going forward.
+
 Version v2024.01.1 -- Release date 2024-02-17
 ==============================================
   * Important Notes:
@@ -9,15 +40,22 @@ Notable changes include:
     * Adding an optional second-stage problem start-up hook to the Physics package interface: Physics::initializeProblemStartupDependencies.  The idea is to keep basic sizing
       of arrays and such in the first stage (Physics::initializeProblemStartup), while this new hook is used for updating any initial Physics state (and therefore provides a
       State and StateDerivatives object).
-
+    * DEM
+      * new field list to track max particle overlap
+      * user can optional turn off fast time stepping
+
   * Build changes / improvements:
-    * 
+    * Improved the target export functionality.
 
   * Bug Fixes / improvements:
     * Fixed bug with ConstantBoundary in the presence of porosity with the new porosity models introduced in v2024.01.00.
     * Updating header lists for including Spheral modules in external projects.
     * Adding effective viscous pressure back to FSISPH.
     * Initial volumes for damage models were incorrectly not taking into account pore space when computing failure statistics for seeding flaws.  Fixed.
+    * DEM
+      * fixed bug in solid boundary unique indices that causes particle sticking
+      * fixed bug in solid boundary update policies 
+      * fixed solid boundary restartability for moving bcs
 
 Version v2024.01.00 -- Release date 2024-01-19
 ==============================================

cmake/CMakeDefinitions.cmake

@@ -73,5 +73,5 @@ if (ENABLE_TIMER)
 endif()
 
 if (ENABLE_MPI)
-    add_definitions(-DUSE_MPI=1)
+  add_definitions(-DUSE_MPI=1)
 endif()

cmake/InstallTPLs.cmake

@@ -19,6 +19,7 @@ if (NOT ENABLE_CXXONLY)
   # Find the appropriate Python
   find_package(Python3 COMPONENTS Interpreter Development)
   set(PYTHON_EXE ${Python3_EXECUTABLE})
+  set(SPHERAL_SITE_PACKAGES_PATH "lib/python${Python3_VERSION_MAJOR}.${Python3_VERSION_MINOR}/site-packages" )
   list(APPEND SPHERAL_BLT_DEPENDS Python3::Python)
 
   # Set the PYB11Generator path
@@ -88,7 +89,7 @@ foreach(_comp ${AXOM_COMPONENTS_ENABLED})
 endforeach()
 
 # TPLs that must be imported
-list(APPEND SPHERAL_EXTERN_LIBS zlib boost eigen qhull silo hdf5 polytope)
+list(APPEND SPHERAL_EXTERN_LIBS 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)
@@ -107,6 +108,7 @@ endforeach()
 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" )

cmake/SetupSpheral.cmake

@@ -5,7 +5,6 @@ include(ExternalProject)
 #-------------------------------------------------------------------------------
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_EXPORT_COMPILE_COMMANDS On)
-set(CMAKE_EXPORT_COMPILE_COMMANDS On)
 
 if (NOT SPHERAL_CMAKE_MODULE_PATH)
   set(SPHERAL_CMAKE_MODULE_PATH "${SPHERAL_ROOT_DIR}/cmake")
@@ -27,6 +26,7 @@ set(Python3_EXECUTABLE ${python_DIR}/bin/python3)
 
 set(ENABLE_MPI ON CACHE BOOL "")
 set(ENABLE_OPENMP ON CACHE BOOL "")
+set(BLT_DOCS_TARGET_NAME "blt_docs" CACHE STRING "")
 
 if(NOT SPHERAL_BLT_DIR) 
   set (SPHERAL_BLT_REL_DIR "${SPHERAL_ROOT_DIR}/cmake/blt" CACHE PATH "")
@@ -83,8 +83,6 @@ if(ENABLE_CUDA)
   list(APPEND SPHERAL_CXX_DEPENDS cuda)
 endif()
 
-option(BOOST_HEADER_ONLY "only use the header only components of Boost" OFF)
-
 #-------------------------------------------------------------------------------#
 # Set a default build type if none was specified
 #-------------------------------------------------------------------------------#

cmake/SpheralVersion.cmake

@@ -1 +1 @@
-set(SPHERAL_VERSION 2024.01.1)
+set(SPHERAL_VERSION 2024.06.0)

cmake/spheral/InstantiateCXX.cmake

@@ -40,7 +40,7 @@ function(instantiate _inst_var _source_var)
         # Uses BLT's python for instantiations to work when building CXX_ONLY as well as with python
         add_custom_command(OUTPUT  ${CMAKE_CURRENT_BINARY_DIR}/${_inst_file}
                            DEPENDS ${_inst_py}
-                           COMMAND ${PYTHON_EXECUTABLE} ${SPHERAL_ROOT_DIR}/src/helpers/InstantiationGenerator.py ${_inst_py} ${_inst_file} ${_dim}
+                           COMMAND ${Python3_EXECUTABLE} ${SPHERAL_ROOT_DIR}/src/helpers/InstantiationGenerator.py ${_inst_py} ${_inst_file} ${_dim}
                            BYPRODUCTS ${_inst_file}
                            COMMENT "Generating instantiation ${_inst_file}..."
                            )

cmake/spheral/SpheralAddLibs.cmake

@@ -123,26 +123,35 @@ function(spheral_add_cxx_library package_name _cxx_obj_list)
   set_target_properties(Spheral_${package_name} PROPERTIES INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
 endfunction()
 
+#----------------------------------------------------------------------------------------
+#                                   spheral_add_pybin11_library_package
+#----------------------------------------------------------------------------------------
+# -------------------------------------------
+# VARIABLES THAT NEED TO BE PREVIOUSLY DEFINED
+# -------------------------------------------
+# SPHERAL_BLT_DEPENDS    : REQUIRED : List of external dependencies
+# EXTRA_PYB11_SPHERAL_ENV_VARS : OPTIONAL : Additional directories containing python filed, used by LLNLSpheral
+# <package_name>_headers : OPTIONAL : List of necessary headers to include
+# <package_name>_sources : OPTIONAL : List of necessary source files to include
+# SPHERAL_SUBMOD_DEPENDS : REQUIRED : List of submodule dependencies
+# ----------------------
+# INPUT-OUTPUT VARIABLES
+# ----------------------
+# package_name     : REQUIRED : Desired package name
+# module_list_name : REQUIRED : The NAME of the global variable that is the list of
+#                               Spheral python modules (not the list itself)
+# INCLUDES : OPTIONAL : Target specific includes
+# DEPENDS : OPTIONAL : Target specific dependencies
+# SOURCE : OPTIONAL : Target specific sources
+# -----------------------
+# OUTPUT VARIABLES TO USE - Made available implicitly after function call
+# -----------------------
+# Spheral<package_name> : Target for a given Spheral python module
+# Spheral<package_name>_src : Target for the PYB11Generated source code for a given Spheral module
+# <module_list_name> : List of Spheral python modules, appended with current module name
+#----------------------------------------------------------------------------------------
 
-#-----------------------------------------------------------------------------------
-# spheral_add_pybind11_library
-#     - Generate the python friendly Spheral package lib
-#
-# Args:
-#   package_name : *name* of spheral package to make into a library
-#   INCLUDES     : optional, any additional include paths
-#   SOURCES      : optional, any additional source files to compile into the library
-#   DEPENDS      : optional, extra dependencies
-# 
-# Variables that must be set before calling spheral_add_obj_library:
-#     spheral_depends
-#         - List of targets the library depends on
-#     SPHERAL_BLT_DEPENDS
-#         - List of blt/libs the library depends on
-#
-#-----------------------------------------------------------------------------------
-
-function(spheral_add_pybind11_library package_name)
+function(spheral_add_pybind11_library package_name module_list_name)
 
   # Define our arguments
   set(options )
@@ -205,8 +214,6 @@ function(spheral_add_pybind11_library package_name)
 
   # Get the TPL dependencies
   get_property(SPHERAL_BLT_DEPENDS GLOBAL PROPERTY SPHERAL_BLT_DEPENDS)
-  get_property(spheral_tpl_includes GLOBAL PROPERTY spheral_tpl_includes)
-  get_property(spheral_tpl_libraries GLOBAL PROPERTY spheral_tpl_libraries)
   # If building shared libraries, use the SPHERAL_OBJ_LIBS global list
   # Note, LLNLSpheral has appended any local targets to this list as well
   if(ENABLE_DEV_BUILD)
@@ -222,8 +229,7 @@ function(spheral_add_pybind11_library package_name)
                             SOURCE          ${package_name}_PYB11.py
                             DEPENDS         ${SPHERAL_BLT_DEPENDS} ${SPHERAL_CXX_DEPENDS} ${EXTRA_CXX_DEPENDS} ${SPHERAL_DEPENDS}
                             PYTHONPATH      ${PYTHON_ENV_STR}
-                            INCLUDES        ${CMAKE_CURRENT_SOURCE_DIR} ${SPHERAL_INCLUDES} ${${package_name}_INCLUDES} ${spheral_tpl_includes} ${PYBIND11_ROOT_DIR}/include 
-                            LINKS           ${spheral_tpl_libraries}
+                            INCLUDES        ${CMAKE_CURRENT_SOURCE_DIR} ${${package_name}_INCLUDES} ${PYBIND11_ROOT_DIR}/include
                             COMPILE_OPTIONS ${SPHERAL_PYB11_TARGET_FLAGS}
                             USE_BLT         ON
                             EXTRA_SOURCE    ${${package_name}_SOURCES}
@@ -233,9 +239,9 @@ function(spheral_add_pybind11_library package_name)
   target_compile_options(${MODULE_NAME} PRIVATE ${SPHERAL_PYB11_TARGET_FLAGS})
 
   install(TARGETS     ${MODULE_NAME}
-          DESTINATION Spheral
+          DESTINATION ${SPHERAL_SITE_PACKAGES_PATH}/Spheral
           )
-
+  set_property(GLOBAL APPEND PROPERTY ${module_list_name} ${package_name})
   # Set the r-path of the C++ lib such that it is independent of the build dir when installed
   set_target_properties(${MODULE_NAME} PROPERTIES INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
 

cmake/spheral/SpheralInstallPythonFiles.cmake

@@ -7,13 +7,14 @@
 # Note, if ENABLE_CXXONLY is set, this function does nothing
 #-----------------------------------------------------------------------------------
 
+
 function(spheral_install_python_files)
 
   if (NOT ENABLE_CXXONLY)
     install(FILES ${ARGV}
-            DESTINATION Spheral)
+      DESTINATION ${SPHERAL_SITE_PACKAGES_PATH}/Spheral)
     install(CODE "execute_process( \
-            COMMAND ${PYTHON_EXE} -m compileall Spheral \
+    COMMAND ${PYTHON_EXE} -m compileall DESTINATION ${SPHERAL_SITE_PACKAGES_PATH}/Spheral \
             WORKING_DIRECTORY ${CMAKE_INSTALL_PREFIX})")
   endif()
 

cmake/spheral_cxx-config.cmake.in

@@ -1,17 +1,47 @@
 
 @PACKAGE_INIT@
 
-if(NOT axom_DIR)
-  set(axom_DIR "@axom_DIR@" CACHE PATH "")
-endif()
-set(SPHERAL_BLT_DIR "@SPHERAL_BLT_DIR@")
-set(SPHERAL_CXX_INSTALL_PREFIX "@CMAKE_INSTALL_PREFIX@")
-set(SPHERAL_CXX_INCLUDE_DIRS "${SPHERAL_CXX_INSTALL_PREFIX}/include")
-if(NOT TARGET axom)
-  find_package(axom REQUIRED QUIET NO_DEFAULT_PATH PATHS ${axom_DIR} ${axom_DIR}/lib ${axom_DIR}/lib/cmake)
-endif()
-include("${SPHERAL_CXX_INSTALL_PREFIX}/lib/cmake/spheral_cxx-targets.cmake")
+if(NOT SPHERAL_FOUND)
+  #----------------------------------------------------------------------------
+  # Set user configuration options and features
+  #----------------------------------------------------------------------------
+
+  # Language features
+  set(SPHERAL_ENABLE_MPI "@ENABLE_MPI@")
+  set(SPHERAL_ENABLE_OPENMP "@ENABLE_OPENMP@")
+  set(SPHERAL_ENABLE_CUDA "@ENABLE_CUDA@")
+  if(NOT axom_DIR)
+    set(axom_DIR "@axom_DIR@" CACHE PATH "")
+  endif()
 
-set_property(TARGET Spheral_CXX
-  APPEND PROPERTY
-  INTERFACE_INCLUDE_DIRECTORIES ${SPHERAL_CXX_INCLUDE_DIRS})
+  set(SPHERAL_CXX_INSTALL_PREFIX "@CMAKE_INSTALL_PREFIX@")
+  set(SPHERAL_CXX_INCLUDE_DIRS "${SPHERAL_CXX_INSTALL_PREFIX}/include")
+  if(NOT @ENABLE_CXXONLY@ AND NOT TARGET Python3)
+    set(python_DIR "@python_DIR@")
+    set(Python_EXECUTABLE ${python_DIR}/bin/python3)
+    set(Python3_EXECUTABLE ${python_DIR}/bin/python3)
+    find_package(Python3 COMPONENTS Interpreter Development)
+    set(PYTHON_EXE ${Python3_EXECUTABLE})
+  endif()
+
+  if(NOT TARGET axom)
+    find_package(axom REQUIRED QUIET NO_DEFAULT_PATH PATHS ${axom_DIR} ${axom_DIR}/lib ${axom_DIR}/lib/cmake)
+  endif()
+  if(SPHERALC_STANDALONE)
+    set(CMAKE_C_COMPILER "@CMAKE_C_COMPILER@" CACHE PATH "Spheral C compiler path")
+    set(CMAKE_CXX_COMPILER "@CMAKE_CXX_COMPILER@" CACHE PATH "Spheral C++ compiler path")
+    set(CMAKE_Fortran_COMPILER "@CMAKE_Fortran_COMPILER@" CACHE PATH "Spheral C++ compiler path")
+    set(ENABLE_MPI @ENABLE_MPI@ CACHE BOOL "")
+    if(SPHERAL_ENABLE_MPI)
+      set(MPI_C_COMPILER "@MPI_C_COMPILER@" CACHE PATH "")
+      set(MPI_CXX_COMPILER "@MPI_CXX_COMPILER@" CACHE PATH "")
+      set(MPI_Fortran_COMPILER "@MPI_Fortran_COMPILER@" CACHE PATH "")
+    endif()
+  endif()
+  include("${SPHERAL_CXX_INSTALL_PREFIX}/lib/cmake/spheral_cxx-targets.cmake")
+
+  set_property(TARGET Spheral_CXX
+    APPEND PROPERTY
+    INTERFACE_INCLUDE_DIRECTORIES ${SPHERAL_CXX_INCLUDE_DIRS})
+  set(SPHERAL_FOUND TRUE)
+endif()

docs/CMakeLists.txt

@@ -1,11 +1,4 @@
-#find_package(Sphinx)
-set(SPHINX_FOUND true)
-if (NOT DEFINED SPHINX_EXEC)
-  set(SPHINX_EXEC "${sphinx_DIR}/bin/sphinx-build" CACHE STRING "Path to sphinx documentation generator")
-endif()
-message("-- Sphinx ${SPHINX_EXEC}")
-
-if(ENABLE_DOCS AND NOT SPHINX_EXEC STREQUAL "SPHINX_EXEC-NOTFOUND")
+if(ENABLE_DOCS)
   if(NOT DEFINED SPHINX_THEME)
     set(SPHINX_THEME sphinx_rtd_theme)
   endif()
@@ -28,8 +21,8 @@ if(ENABLE_DOCS AND NOT SPHINX_EXEC STREQUAL "SPHINX_EXEC-NOTFOUND")
     "${BINARY_BUILD_DIR}/conf.py"
     @ONLY)
 
-  add_custom_target(Spheral_docs ALL
-    ${CMAKE_COMMAND} -E env PYTHONPATH=${SPACK_PYTHONPATH} ${PYTHON_EXE} -m sphinx
+  add_custom_target(docs ALL
+    env PYTHONPATH=${SPACK_PYTHONPATH} ${PYTHON_EXE} -m sphinx
     -q -b html
     -c "${BINARY_BUILD_DIR}"
     -d "${SPHINX_CACHE_DIR}"

docs/build_guide/external/index.rst

@@ -9,7 +9,7 @@ This guide is designed to help external users build and install Spheral on non L
    :caption: External Building Guide:
 
    quickstart.rst
-   ubuntu_update.rst
+   system_packages.rst
    cloning.rst
    updating.rst
    tpls.rst