Merge pull request #98 from SENSEI-insitu/develop

4.1.0 release
SENSEI-insitu · Jan 10, 2023 · 294f5c8 · 294f5c8
2 parents e0ae9a9 + 6b9a003
commit 294f5c8
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Showing 87 changed files with 1,229 additions and 82 deletions.
diff --git a/.github/ci/configure_python3.cmake b/.github/ci/configure_python3.cmake
@@ -1,13 +1,13 @@
 execute_process(
-  COMMAND "which" "python3"
-  OUTPUT_VARIABLE pyexec
+  COMMAND "python3-config" "--prefix"
+  OUTPUT_VARIABLE PY_ROOT
   OUTPUT_STRIP_TRAILING_WHITESPACE)
-set(Python3_EXECUTABLE "${pyexec}" CACHE PATH "")
-set(Python3_EXECUTABLE "${pyexec}" CACHE PATH "")
 
-get_filename_component(pypath "${pyexec}" DIRECTORY)
-get_filename_component(pypath "${pypath}" DIRECTORY)
-set(Python3_ROOT_DIR "${pypath}" CACHE PATH "")
+set(Python3_ROOT_DIR "${PY_ROOT}" CACHE PATH "")
+set(Python3_EXECUTABLE "${PY_ROOT}/bin/python3" CACHE PATH "")
+
+set(Python3_FIND_STRATEGY "LOCATION" CACHE STRING "")
+set(Python3_FIND_FRAMEWORK "FIRST" CACHE STRING "")
 
 set(ENABLE_PYTHON ON CACHE BOOL "")
 set(SENSEI_PYTHON_VERSION 3 CACHE STRING "")

diff --git a/.github/workflows/base-library.yml b/.github/workflows/base-library.yml
@@ -3,7 +3,7 @@ name: base-library
 on:
   pull_request:
     branches:
-      - main
+      - master
       - develop
 
 jobs:
@@ -19,7 +19,7 @@ jobs:
           export DEBIAN_FRONTEND="noninteractive"
           export TZ="America/Los_Angeles"
           sudo apt-get update -qq
-          sudo apt-get install -qq -y git-core gcc g++ gfortran cmake ninja-build subversion automake m4 wget swig python3-dev mpich python3-numpy python3-mpi4py
+          sudo apt-get install -qq -y git-core gcc g++ gfortran cmake ninja-build subversion automake m4 wget swig python3-dev openmpi-bin libopenmpi-dev python3-numpy python3-mpi4py
       - name: Setup CCache
         uses: hendrikmuhs/ccache-action@v1.2
         with:

diff --git a/.github/workflows/ecp-data-vis-sdk.yml b/.github/workflows/ecp-data-vis-sdk.yml
@@ -3,7 +3,7 @@ name: ecp-sdk-integration
 on:
   pull_request:
     branches:
-      - main
+      - master
       - develop
 
 jobs:

diff --git a/CMake/SENSEIConfig.cmake.in b/CMake/SENSEIConfig.cmake.in
@@ -13,7 +13,7 @@ endif ()
 
 list(APPEND CMAKE_MODULE_PATH "${SENSEI_DIR}")
 
-list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/svtk-9.0")
+list(APPEND CMAKE_PREFIX_PATH "${CMAKE_CURRENT_LIST_DIR}/svtk-9.0")
 find_package(svtk REQUIRED)
 
 set(SENSEI_LIB_TYPE STATIC)
@@ -60,35 +60,45 @@ elseif (ENABLE_VTK_CORE)
   if (NOT VTK_DIR)
     set(VTK_DIR "@VTK_DIR@")
   endif()
-  find_dependency(vtk)
+  find_dependency(VTK)
 endif()
 
+if (ENABLE_VTK_CORE)
+  include(sVTK)
+endif ()
+
 if (ENABLE_VTKM)
   include(sVTKm)
 endif()
+
 if (ENABLE_LIBSIM)
   include(sLibsim)
 endif()
+
 if (ENABLE_ADIOS1)
   include(sADIOS1)
 endif()
+
 if (ENABLE_ADIOS2)
   if(NOT ADIOS2_DIR)
     set(ADIOS2_DIR "@ADIOS2_DIR@")
   endif()
   find_dependency(ADIOS2)
   include(sADIOS2)
 endif()
+
 if (ENABLE_HDF5)
   include(sHDF5)
 endif()
+
 if (ENABLE_CONDUIT)
   if(NOT CONDUIT_DIR)
     set(CONDUIT_DIR "@CONDUIT_DIR@")
   endif()
   find_dependency(Conduit NO_DEFAULT_PATH PATHS ${CONDUIT_DIR})
   include(sConduit)
 endif()
+
 if(ENABLE_ASCENT)
   if(NOT ASCENT_DIR)
     set(ASCENT_DIR "@ASCENT_DIR@")
@@ -100,7 +110,7 @@ endif()
 include(senseiCore)
 
 if (ENABLE_PYTHON)
-  set(SENSEI_PYTHON_DIR "${CMAKE_CURRENT_LIST_DIR}/../../@SENSEI_PYTHON_DIR@")
+  set(SENSEI_PYTHON_DIR "${CMAKE_CURRENT_LIST_DIR}/../../../@SENSEI_PYTHON_DIR@")
 
   include(sPython)
 

diff --git a/CMake/adios.cmake b/CMake/adios.cmake
@@ -8,6 +8,6 @@ if(ENABLE_ADIOS1)
     target_compile_definitions(sADIOS1 INTERFACE ${ADIOS1_DEFINITIONS})
   endif()
   install(TARGETS sADIOS1 EXPORT sADIOS1)
-  install(EXPORT sADIOS1 DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake
+  install(EXPORT sADIOS1 DESTINATION ${sensei_CMAKE_INSTALL_CMAKEDIR}
     EXPORT_LINK_INTERFACE_LIBRARIES)
 endif()
diff --git a/CMake/adios2.cmake b/CMake/adios2.cmake
@@ -5,6 +5,6 @@ if(ENABLE_ADIOS2)
   add_library(sADIOS2 INTERFACE)
   target_link_libraries(sADIOS2 INTERFACE adios2::adios2)
   install(TARGETS sADIOS2 EXPORT sADIOS2)
-  install(EXPORT sADIOS2 DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake
+  install(EXPORT sADIOS2 DESTINATION ${sensei_CMAKE_INSTALL_CMAKEDIR}
     EXPORT_LINK_INTERFACE_LIBRARIES)
 endif()
diff --git a/CMake/ascent.cmake b/CMake/ascent.cmake
@@ -15,6 +15,6 @@ if(ENABLE_ASCENT)
   target_include_directories(sAscent SYSTEM INTERFACE ${ASCENT_INCLUDE_DIRS})
 
   install(TARGETS sAscent EXPORT sAscent)
-  install(EXPORT sAscent DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake
+  install(EXPORT sAscent DESTINATION ${sensei_CMAKE_INSTALL_CMAKEDIR}
     EXPORT_LINK_INTERFACE_LIBRARIES)
 endif()
diff --git a/CMake/build.cmake b/CMake/build.cmake
@@ -41,6 +41,7 @@ include(GNUInstallDirs)
 set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/${CMAKE_INSTALL_LIBDIR}")
 set(CMAKE_LIBRARY_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/${CMAKE_INSTALL_LIBDIR}")
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/${CMAKE_INSTALL_BINDIR}")
+set(sensei_CMAKE_INSTALL_CMAKEDIR ${CMAKE_INSTALL_LIBDIR}/cmake/sensei)
 
 message(STATUS "CMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}")
 message(STATUS "CMAKE_CXX_FLAGS=${CMAKE_CXX_FLAGS}")

diff --git a/CMake/catalyst.cmake b/CMake/catalyst.cmake
@@ -29,7 +29,7 @@ if (ENABLE_CATALYST)
   add_library(sVTK INTERFACE)
   target_link_libraries(sVTK INTERFACE ${ParaView_LIBRARIES} ${VTK_LIBRARIES})
   install(TARGETS sVTK EXPORT sVTK)
-  install(EXPORT sVTK DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake
+  install(EXPORT sVTK DESTINATION ${sensei_CMAKE_INSTALL_CMAKEDIR}
     EXPORT_LINK_INTERFACE_LIBRARIES)
 
 endif()
diff --git a/CMake/conduit.cmake b/CMake/conduit.cmake
@@ -7,6 +7,6 @@ if(ENABLE_CONDUIT)
   target_include_directories(sConduit SYSTEM INTERFACE ${CONDUIT_INCLUDE_DIRS})
 
   install(TARGETS sConduit EXPORT sConduit)
-  install(EXPORT sConduit DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake
+  install(EXPORT sConduit DESTINATION ${sensei_CMAKE_INSTALL_CMAKEDIR}
     EXPORT_LINK_INTERFACE_LIBRARIES)
 endif()
diff --git a/CMake/config.cmake b/CMake/config.cmake
@@ -5,11 +5,11 @@ install(FILES ${CMAKE_BINARY_DIR}/senseiConfig.h DESTINATION include)
 set(SENSEI_BUILD OFF)
 
 configure_file(CMake/SENSEIConfig.cmake.in
-  ${CMAKE_INSTALL_LIBDIR}/cmake/SENSEIConfig.cmake @ONLY)
+  ${sensei_CMAKE_INSTALL_CMAKEDIR}/SENSEIConfig.cmake @ONLY)
 
 configure_file(CMake/SENSEIConfigVersion.cmake.in
-  ${CMAKE_INSTALL_LIBDIR}/cmake/SENSEIConfigVersion.cmake @ONLY)
+  ${sensei_CMAKE_INSTALL_CMAKEDIR}/SENSEIConfigVersion.cmake @ONLY)
 
-install(FILES ${CMAKE_BINARY_DIR}/${CMAKE_INSTALL_LIBDIR}/cmake/SENSEIConfig.cmake
-  ${CMAKE_BINARY_DIR}/${CMAKE_INSTALL_LIBDIR}/cmake/SENSEIConfigVersion.cmake
-  DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake)
+install(FILES ${CMAKE_BINARY_DIR}/${sensei_CMAKE_INSTALL_CMAKEDIR}/SENSEIConfig.cmake
+  ${CMAKE_BINARY_DIR}/${sensei_CMAKE_INSTALL_CMAKEDIR}/SENSEIConfigVersion.cmake
+  DESTINATION ${sensei_CMAKE_INSTALL_CMAKEDIR})
diff --git a/CMake/hdf5.cmake b/CMake/hdf5.cmake
@@ -10,6 +10,6 @@ if (ENABLE_HDF5)
   target_include_directories(sHDF5 SYSTEM INTERFACE ${HDF5_INCLUDE_DIRS})
 
   install(TARGETS sHDF5 EXPORT sHDF5)
-  install(EXPORT sHDF5 DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake
+  install(EXPORT sHDF5 DESTINATION ${sensei_CMAKE_INSTALL_CMAKEDIR}
     EXPORT_LINK_INTERFACE_LIBRARIES)
 endif()
diff --git a/CMake/libsim.cmake b/CMake/libsim.cmake
@@ -4,6 +4,6 @@ if(ENABLE_LIBSIM)
   target_link_libraries(sLibsim INTERFACE ${LIBSIM_LIBRARIES})
   target_include_directories(sLibsim SYSTEM INTERFACE ${LIBSIM_INCLUDE_DIRS})
   install(TARGETS sLibsim EXPORT sLibsim)
-  install(EXPORT sLibsim DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake
+  install(EXPORT sLibsim DESTINATION ${sensei_CMAKE_INSTALL_CMAKEDIR}
     EXPORT_LINK_INTERFACE_LIBRARIES)
 endif()
diff --git a/CMake/mpi.cmake b/CMake/mpi.cmake
@@ -16,7 +16,7 @@ elseif (ENABLE_CORI_GPU OR (NOT DEFINED ENABLE_CORI_GPU AND NOT ("$ENV{OPENMPI_D
     set(MPIEXEC srun CACHE STRING "Platform MPI run equivalent")
     set(MPI_C_FOUND CACHE BOOL ON "status of MPI config")
 else()
-    find_package(MPI COMPONENTS C)
+    find_package(MPI COMPONENTS C CXX)
 endif()
 
 if (NOT MPI_C_FOUND)
@@ -35,5 +35,5 @@ target_include_directories(sMPI SYSTEM INTERFACE
 target_link_libraries(sMPI INTERFACE ${MPI_C_LIBRARIES})
 
 install(TARGETS sMPI EXPORT sMPI)
-install(EXPORT sMPI DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake
+install(EXPORT sMPI DESTINATION ${sensei_CMAKE_INSTALL_CMAKEDIR}
   EXPORT_LINK_INTERFACE_LIBRARIES)
diff --git a/CMake/opts.cmake b/CMake/opts.cmake
@@ -6,7 +6,7 @@ if(ENABLE_OPTS)
     $<INSTALL_INTERFACE:include>)
 
   install(TARGETS sOPTS EXPORT sOPTS)
-  install(EXPORT sOPTS DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake)
+  install(EXPORT sOPTS DESTINATION ${sensei_CMAKE_INSTALL_CMAKEDIR})
   install(DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/utils/opts/include" DESTINATION include)
 endif()
 
diff --git a/CMake/python.cmake b/CMake/python.cmake
@@ -21,10 +21,6 @@ if (ENABLE_PYTHON)
   find_package(PythonInterp ${SENSEI_PYTHON_VERSION} REQUIRED)
   find_package(PythonLibs ${SENSEI_PYTHON_VERSION} REQUIRED)
   find_package(NUMPY REQUIRED)
-  find_program(swig_cmd NAMES swig swig3.0 swig4.0)
-  if (swig_cmd-NOTFOUND)
-  	message(SEND_ERROR "Failed to locate swig")
-  endif()
 
   # find MPI
   find_package(MPI4PY REQUIRED)
@@ -34,18 +30,18 @@ if (ENABLE_PYTHON)
   target_include_directories(sPython INTERFACE ${PYTHON_INCLUDE_PATH} ${MPI4PY_INCLUDE_DIR})
   target_link_libraries(sPython INTERFACE ${PYTHON_LIBRARIES})
   install(TARGETS sPython EXPORT sPython)
-  install(EXPORT sPython DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake
+  install(EXPORT sPython DESTINATION ${sensei_CMAKE_INSTALL_CMAKEDIR}
     EXPORT_LINK_INTERFACE_LIBRARIES)
 
   # find SWIG
   cmake_policy(SET CMP0078 NEW)
   cmake_policy(SET CMP0086 NEW)
-  find_package(SWIG COMPONENTS python)
+  find_package(SWIG REQUIRED COMPONENTS python)
   include(UseSWIG)
 
   # the destination of all SENSEI Python codes
   set(SENSEI_PYTHON_SITE
-    "${CMAKE_INSTALL_LIBDIR}/python-${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}/site-packages/"
+    "${CMAKE_INSTALL_LIBDIR}/python${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}/site-packages/"
     CACHE STRING "Where Python modules are compiled and installed.")
 
   set(SENSEI_PYTHON_DIR "${SENSEI_PYTHON_SITE}/sensei/"

diff --git a/CMake/svtk.cmake b/CMake/svtk.cmake
@@ -5,5 +5,5 @@ add_library(sSVTK INTERFACE)
 target_link_libraries(sSVTK INTERFACE ${SVTK_LIBRARIES})
 
 install(TARGETS sSVTK EXPORT sSVTK)
-install(EXPORT sSVTK DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake
+install(EXPORT sSVTK DESTINATION ${sensei_CMAKE_INSTALL_CMAKEDIR}
   EXPORT_LINK_INTERFACE_LIBRARIES)
diff --git a/CMake/threads.cmake b/CMake/threads.cmake
@@ -4,5 +4,5 @@ set_property(TARGET Threads::Threads PROPERTY IMPORTED_GLOBAL TRUE)
 add_library(thread INTERFACE)
 target_link_libraries(thread INTERFACE ${CMAKE_THREAD_LIBS_INIT})
 install(TARGETS thread EXPORT thread)
-install(EXPORT thread DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake
+install(EXPORT thread DESTINATION ${sensei_CMAKE_INSTALL_CMAKEDIR}
   EXPORT_LINK_INTERFACE_LIBRARIES)
diff --git a/CMake/version.cmake b/CMake/version.cmake
@@ -1,14 +1,27 @@
-set(tmp)
-find_package(Git QUIET)
-if(GIT_FOUND)
-    execute_process(COMMAND ${GIT_EXECUTABLE}
-        --git-dir=${CMAKE_SOURCE_DIR}/.git describe --tags
-        OUTPUT_VARIABLE tmp OUTPUT_STRIP_TRAILING_WHITESPACE)
-endif()
-if(NOT tmp)
-    set(tmp "v0.0.0")
+set(SENSEI_VERSION "<DEFAULT>" CACHE STRING "SENSEI version")
+
+# Default detection of version
+if (SENSEI_VERSION STREQUAL "<DEFAULT>")
+  # The default version is the current major release
+  # This is required for computing version in released
+  # source tarballs.
+  set(tmp "v4.0.0")
+
+  # If inside a git repo, attempt to inspect the tag instead
+  # of using the hardcoded value
+  if (EXISTS ${CMAKE_SOURCE_DIR}/.git)
+    find_package(Git QUIET)
+    if(GIT_FOUND)
+      execute_process(COMMAND ${GIT_EXECUTABLE}
+          --git-dir=${CMAKE_SOURCE_DIR}/.git describe --tags
+          OUTPUT_VARIABLE tmp OUTPUT_STRIP_TRAILING_WHITESPACE)
+    endif()
+  endif ()
+
+  # Override the CACHE variable for configure with the computed
+  # version
+  set(SENSEI_VERSION ${tmp})
 endif()
-set(SENSEI_VERSION ${tmp} CACHE STRING "SENSEI version" FORCE)
 
 string(REGEX REPLACE "^v([0-9]+)\\.([0-9]+)\\.([0-9]+)(.*$)"
   "\\1" SENSEI_VERSION_MAJOR ${SENSEI_VERSION})

diff --git a/CMake/vtk.cmake b/CMake/vtk.cmake
@@ -7,7 +7,7 @@ if (ENABLE_VTK_MPI OR ENABLE_VTK_IO OR ENABLE_VTK_MPI OR
 
   # lets build the list of modules for VTK pre-8.90 and post 8.90
   set(sensei_vtk_components_legacy)
-  set(sensei_vtk_components_modern)
+  set(sensei_vtk_components_modern CommonDataModel)
 
   if (ENABLE_VTK_MPI)
     list(APPEND sensei_vtk_components_legacy vtkParallelMPI)
@@ -75,7 +75,7 @@ if (ENABLE_VTK_MPI OR ENABLE_VTK_IO OR ENABLE_VTK_MPI OR
       endif()
 
       install(TARGETS sVTK EXPORT sVTK)
-      install(EXPORT sVTK DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake
+      install(EXPORT sVTK DESTINATION ${sensei_CMAKE_INSTALL_CMAKEDIR}
         EXPORT_LINK_INTERFACE_LIBRARIES)
     endif()
   endif()

diff --git a/CMake/vtkm.cmake b/CMake/vtkm.cmake
@@ -13,6 +13,6 @@ if (ENABLE_VTKM)
   #target_include_directories(sVTKm SYSTEM INTERFACE ${VTKm_INCLUDE_DIRS})
   #target_compile_definitions(sVTKm INTERFACE ${VTKm_COMPILE_OPTIONS})
   install(TARGETS sVTKm EXPORT sVTKm)
-  install(EXPORT sVTKm DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake
+  install(EXPORT sVTKm DESTINATION ${sensei_CMAKE_INSTALL_CMAKEDIR}
     EXPORT_LINK_INTERFACE_LIBRARIES)
 endif()
diff --git a/rtd-docs/conf.py b/rtd-docs/conf.py
@@ -66,6 +66,7 @@
 # source_suffix = ['.rst', '.md']
 source_suffix = '.rst'
 
+
 # The master toctree document.
 master_doc = 'index'
 
@@ -82,8 +83,9 @@
 # add any included files to this list to silence warnings about 
 # duplicate references
 exclude_patterns = [u'_build', 'Thumbs.db', '.DS_Store', \
-     'reaction_rate_demo', 'adaptor_apisi.rst', 'data_addaptor_apis.rst', \
-     'analysis_adaptor_apis.rst']
+    'data_adaptor_api.rst', 'analysis_adaptor_api.rst', 'ascent_back_end.rst', \
+    'catalyst_back_end.rst', 'histogram_back_end.rst', 'autocorrelation_back_end.rst', \
+    'reaction_rate_demo.rst', 'pipeline_demo.rst']
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'friendly'
@@ -107,6 +109,12 @@
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ['_static']
 
+# These paths are either relative to html_static_path
+# or fully qualified paths (eg. https://...)
+html_css_files = [
+    'theme_overrides.css',
+]
+
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
 #

diff --git a/rtd-docs/data_adaptor_api.rst b/rtd-docs/data_adaptor_api.rst
@@ -15,8 +15,8 @@ Finally the data adaptor is a key piece of SENSEI's in transit system. The
 analysis back end can be run in a different parallel job and be given an in
 transit data adaptor in place of the simulation's data adaptor. In this scenario
 the in transit data adaptor helps move data needed by the analysis back end.
-The data adaptor API enables this scenario to apear the same to the simulation
-and the analysis back end. Neither simulaiton nor analysis need be modified for
+The data adaptor API enables this scenario to appear the same to the simulation
+and the analysis back end. Neither simulation nor analysis need be modified for
 in transit processing.
 
 

diff --git a/rtd-docs/data_model.rst b/rtd-docs/data_model.rst
@@ -1,4 +1,5 @@
 .. _data_model:
+
 Data model
 ==========
 The data model is a key piece of the system. It allows data to be packaged and

diff --git a/rtd-docs/examples.rst b/rtd-docs/examples.rst
@@ -1,9 +1,8 @@
 .. _examples:
+
 *********
 Examples
 *********
 
 .. include:: reaction_rate_demo.rst
 .. include:: pipeline_demo.rst
-
-
-Original file line number
+Diff line change
@@ Expand Up / @@ -3,7 +3,7 @@ name: ecp-sdk-integration @@
     on:
       pull_request:
         branches:
-          - main
+          - master
           - develop
     jobs:
@@ Expand Down @@