Merge branch 'master' into lmn-stretching-support

.github/workflows/Build.yml

@@ -20,15 +20,15 @@ jobs:
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
     # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     # We don't want to build openmpi each time this workflow is
     # run. Setup caching of OpenMPI after it is built and installed.
     # See "Caching dependencies to speed up workflows" on the GH
     # actions docs.
     - name: Cache OpenMPI
       id: cache-openmpi
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: openmpi-4.1.4/installed
         key: openmpi-4.1.4
@@ -42,20 +42,12 @@ jobs:
         ./configure --prefix=$(pwd)/installed
         make all install
 
-    - name: Build Incompact3d
+    - name: Build Xcompact3d
       run: |
         export PATH=$(pwd)/openmpi-4.1.4/installed/bin/:$PATH
-        make BUILD=debug
-
-    - name: Run TGV case
-      run: |
-        cp test/data/Taylor-Green-Vortex/reference_input.i3d input.i3d
-        export PATH=$(pwd)/openmpi-4.1.4/installed/bin/:$PATH
-        mpirun -np 2 xcompact3d
-
-    - name: Compare output time evolution to reference output
-      run: |
         pip install numpy
-        python test/compare_TGV_time_evolution.py \
-            --input time_evol.dat \
-            --reference test/data/Taylor-Green-Vortex/reference_time_evol.dat
+        export FC=mpif90
+        cmake -S . -B build 
+        cmake --build build -j 2
+        cmake --install build
+        ctest --test-dir build

.readthedocs.yaml

@@ -0,0 +1,35 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+    # You can also specify other tool versions:
+    # nodejs: "20"
+    # rust: "1.70"
+    # golang: "1.20"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
+  # builder: "dirhtml"
+  # Fail on all warnings to avoid broken references
+  # fail_on_warning: true
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#   - pdf
+#   - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+    - requirements: docs/requirements.txt

CMakeLists.txt

@@ -1,11 +1,14 @@
-cmake_minimum_required(VERSION 3.0.2)                        
-cmake_policy(SET CMP0048 NEW)
+cmake_minimum_required(VERSION 3.20)                        
+cmake_policy(SET CMP0074 NEW)
 
-project(xcompact3d LANGUAGES Fortran)
+project(Xcompact3d LANGUAGES Fortran)
+set(version 5.0)
+if (IO_BACKEND MATCHES "adios2")
+  # Can be useful to also activate CXX, sometimes is needed by packages
+  enable_language(C CXX)
+endif (IO_BACKEND MATCHES "adios2")
 
-set(AUTHOR "Stefano Rolfo;Charles Moulinec")
-set(AUTHOR_DETAILS "[email protected];[email protected]")
-set(DESCRIPTION "Building xcompact3d using cmake")
+set(DESCRIPTION "Building Xcompact3d using cmake")
 
 message(STATUS "building ${PROJECT_NAME}")
 
@@ -20,163 +23,50 @@ endif()
 INCLUDE(CMakeDependentOption)
 INCLUDE(CMakeParseArguments)
 
-# Find the modules included with Xcompact
-#SET(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/cmake ${CMAKE_MODULE_PATH})
-
 # make sure that the default is a RELEASE
 if (NOT CMAKE_BUILD_TYPE)
   set (CMAKE_BUILD_TYPE RELEASE CACHE STRING
-      "Choose the type of build, options are: None Debug Release."
-      FORCE)
+       "Choose the type of build, options are: NONE DEV DEBUG RELEASE."
+       FORCE)
 endif (NOT CMAKE_BUILD_TYPE)
-
-set(Fortran_COMPILER_NAME ${CMAKE_Fortran_COMPILER_ID} )
-message(STATUS "COMP ID ${Fortran_COMPILER_NAME}")
-message(STATUS "Fortran compiler name ${Fortran_COMPILER_NAME}")
-message(STATUS "Fortran compiler version ${CMAKE_Fortran_COMPILER_VERSION}")
-if (Fortran_COMPILER_NAME MATCHES "GNU")
-  # gfortran
-  message(STATUS "Setting gfortran flags")
-  set(CMAKE_Fortran_FLAGS "-cpp -funroll-loops -floop-optimize -g -Warray-bounds -fcray-pointer -fbacktrace -ffree-line-length-none")
-  if (CMAKE_Fortran_COMPILER_VERSION GREATER_EQUAL "10")
-    message(STATUS "Set New Fortran basic flags")
-    set(CMAKE_Fortran_FLAGS "-cpp -funroll-loops -floop-optimize -g -Warray-bounds -fcray-pointer -fbacktrace -ffree-line-length-none -fallow-argument-mismatch")
-  endif (CMAKE_Fortran_COMPILER_VERSION GREATER_EQUAL "10")
-  set(CMAKE_Fortran_FLAGS_RELEASE "-funroll-all-loops -fno-f2c -O3")
-  set(CMAKE_Fortran_FLAGS_DEBUG   "-DDEBG -O0 -g")
-elseif (Fortran_COMPILER_NAME MATCHES "Intel")
-  message(STATUS "Setting ifort flags")
-  set(CMAKE_Fortran_FLAGS "-fpp -xHost -heaparrays -safe-cray-ptr -g -traceback")
-  set (CMAKE_Fortran_FLAGS_RELEASE "-O3 -ipo")
-  set (CMAKE_Fortran_FLAGS_DEBUG   "-O0 -g -DDEBG")
-  #set(CMAKE_Fortran_FLAGS "-cpp xSSE4.2 -axAVX,CORE-AVX-I,CORE-AVX2 -ipo -fp-model fast=2 -mcmodel=large -safe-cray-ptr")
-elseif (Fortran_COMPILER_NAME MATCHES "NAG")
-  message(STATUS "Setting nagfor flags")
-  set(CMAKE_Fortran_FLAGS "-fpp")
-  set (CMAKE_Fortran_FLAGS_RELEASE "-O3")
-  set (CMAKE_Fortran_FLAGS_DEBUG   "-O0 -g")
-elseif (Fortran_COMPILER_NAME MATCHES "Cray")
-  message(STATUS "Setting cray fortran flags")
-  set(CMAKE_Fortran_FLAGS "-eF -g -N 1023")
-  set (CMAKE_Fortran_FLAGS_RELEASE "-O3")
-  set (CMAKE_Fortran_FLAGS_DEBUG   "-O0 -g")
-elseif (Fortran_COMPILER_NAME MATCHES "NVHPC")
-  message(STATUS "Setting NVHPC fortran flags")
-  set(CMAKE_Fortran_FLAGS "-cpp -Mfree -Kieee -g")
-  set (CMAKE_Fortran_FLAGS_RELEASE "-O3 -fast")
-  set (CMAKE_Fortran_FLAGS_DEBUG   "-O0 -DDEBG")
-elseif (Fortran_COMPILER_NAME MATCHES "Fujitsu")
-  message(STATUS "Setting Fujitsu fortran flags")
-  set (CMAKE_Fortran_FLAGS "-Cpp")
-  set (CMAKE_Fortran_FLAGS_RELEASE "-O3")
-  set (CMAKE_Fortran_FLAGS_DEBUG "-O0")
-else (Fortran_COMPILER_NAME MATCHES "GNU")
-  message ("CMAKE_Fortran_COMPILER full path: " ${CMAKE_Fortran_COMPILER})
-  message ("Fortran compiler: " ${Fortran_COMPILER_NAME})
-  message ("No optimized Fortran compiler flags are known, we just try -O2...")
-  set (CMAKE_Fortran_FLAGS_RELEASE "-O2")
-  set (CMAKE_Fortran_FLAGS_DEBUG   "-O0 -g")
-endif (Fortran_COMPILER_NAME MATCHES "GNU")
-
-if (CMAKE_BUILD_TYPE MATCHES "DEBUG")
-  add_definitions("-DDEBG")
-endif (CMAKE_BUILD_TYPE MATCHES "DEBUG")
-
-
-find_package(MPI REQUIRED)
-# Stop if there is no MPI_Fortran_Compiler
-if (MPI_Fortran_COMPILER)
-    message(STATUS "MPI_Fortran_COMPILER found: ${MPI_Fortran_COMPILER}")
-else (MPI_Fortran_COMPILER)
-    message(SEND_ERROR "This application cannot compile without MPI")
-endif(MPI_Fortran_COMPILER)
-# Warning if Include are not found => can be fixed with more recent cmake version
-if (MPI_FOUND)
-    message(STATUS "MPI FOUND: ${MPI_FOUND}")
-    include_directories(SYSTEM ${MPI_INCLUDE_PATH})
-    message(STATUS "MPI INCL ALSO FOUND: ${MPI_INCLUDE_PATH}")
-else (MPI_FOUND)
-    message(STATUS "NO MPI include have been found. The executable won't be targeted with MPI include")
-    message(STATUS "Code will compile but performaces can be compromised")
-    message(STATUS "Using a CMake vers > 3.10 should solve the problem")
-    message(STATUS "Alternatively use ccmake to manually set the include if available")
-endif (MPI_FOUND)
-
-execute_process(
-  COMMAND git describe --tag --long --always
-  WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
-  OUTPUT_VARIABLE GIT_VERSION
-  OUTPUT_STRIP_TRAILING_WHITESPACE
-)
-add_definitions("-DVERSION=\"${GIT_VERSION}\"")
-option(DOUBLE_PRECISION "Build Xcompact with double precision" ON)
-if (DOUBLE_PRECISION)
-  add_definitions("-DDOUBLE_PREC")
-endif()
-
-option(SINGLE_PRECISION_OUTPUT "Build XCompact with output in single precision" OFF)
-if (SINGLE_PRECISION_OUTPUT)
-  add_definitions("-DSAVE_SINGLE")
-endif()
-
-# FFT options
-set(FFT_Choice "generic" CACHE STRING "FFT for XCompact3d project (generic is the default)")
-set_property(CACHE FFT_Choice PROPERTY STRINGS generic fftw3 mkl)
-
-# Look for ADIOS2 library
-option(USE_ADIOS2 "Build XCompact with ADIOS2 library" OFF)
-if(USE_ADIOS2)
-  #find_package(ADIOS2 COMPONENTS fortran)
-  find_package(ADIOS2)
-endif()
-if(ADIOS2_FOUND)
-  message(STATUS "ADIOS INCLUDE ${ADIOS2_INCLUDE_DIRS}")
-  include_directories(${ADIOS2_INCLUDE_DIRS})
-  add_definitions("-DADIOS2")
-else(ADIOS_FOUND)
-  message(STATUS "ADIOS2 not found")
-endif()
-
-# Create a static library for the fft
-add_subdirectory(decomp2d)
-
-# Create the Xcompact3d executable
+string(TOUPPER ${CMAKE_BUILD_TYPE} CMAKE_BUILD_TYPE)
+if (CMAKE_BUILD_TYPE MATCHES "NONE")
+  message (STATUS "Selected build type : None")
+elseif (CMAKE_BUILD_TYPE MATCHES "RELEASE")
+  message (STATUS "Selected build type : Release")
+elseif (CMAKE_BUILD_TYPE MATCHES "DEBUG")
+  message (STATUS "Selected build type : Debug")
+elseif (CMAKE_BUILD_TYPE MATCHES "DEV")
+  message (FATAL_ERROR "DEV build is a work in progress and currently not supported by Xcompact3d")
+else (CMAKE_BUILD_TYPE MATCHES "NONE")
+  message (FATAL_ERROR "Invalid build type, options are: NONE DEV DEBUG RELEASE.")
+endif (CMAKE_BUILD_TYPE MATCHES "NONE")
+
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake" "${CMAKE_SOURCE_DIR}/cmake/compilers" "${CMAKE_SOURCE_DIR}/cmake/fft")
+find_package(DECOMP2D REQUIRED)
+
+# Despite IO is handled by 2DECOMP&FFT we need to set it
+set (IO_BACKEND "mpi" CACHE STRING "Default IO backend (mpi (default) or adios2)")
+set_property(CACHE IO_BACKEND PROPERTY STRINGS mpi adios2)
+
+include(X3D_MPI)
+
+include(X3D_Compilers)
+
+# Add the sources
 add_subdirectory(src)
 
-# Create the Xcompact3d executable
-add_subdirectory(post_vtk)
-
-# Create an example dir with all input.i3d example files
-option(BUILD_TESTING "Build with tests" ON)
-set(test_dir "${PROJECT_BINARY_DIR}/Test")
-add_subdirectory(examples)
-message(STATUS "Before test main ${test_dir}")
+# Add tests
+option(BUILD_TESTING "Build with test and use only TGV case" ON)
+option(BUILD_TESTING_FULL "Build all tests" OFF)
 if (${BUILD_TESTING})
   include(CTest)
-  message(STATUS "MPI INCL ALSO FOUND: ${MPI_INCLUDE_PATH}")
-  message(STATUS "MPI EXEC: ${MPIEXEC_EXECUTABLE}")
-  # ABL
-  add_test(NAME ABL-Convective-old COMMAND ${MPIEXEC_EXECUTABLE} -n ${MPIEXEC_MAX_NUMPROCS} ${CMAKE_INSTALL_PREFIX}/bin/xcompact3d input_convective_test.i3d WORKING_DIRECTORY ${test_dir}/ABL-Convective-old)
-  add_test(NAME ABL-Neutral-old COMMAND ${MPIEXEC_EXECUTABLE} -n ${MPIEXEC_MAX_NUMPROCS} ${CMAKE_INSTALL_PREFIX}/bin/xcompact3d input_neutral_test.i3d WORKING_DIRECTORY ${test_dir}/ABL-Neutral-old)
-  add_test(NAME ABL-Stable-old COMMAND ${MPIEXEC_EXECUTABLE} -n ${MPIEXEC_MAX_NUMPROCS} ${CMAKE_INSTALL_PREFIX}/bin/xcompact3d input_stable_test.i3d WORKING_DIRECTORY ${test_dir}/ABL-Stable-old)
-  add_test(NAME ABL-Neutral COMMAND ${MPIEXEC_EXECUTABLE} -n ${MPIEXEC_MAX_NUMPROCS} ${CMAKE_INSTALL_PREFIX}/bin/xcompact3d input_neutral_test.i3d WORKING_DIRECTORY ${test_dir}/ABL-Neutral)
-  # Channel
-  add_test(NAME Channel-Flow-X COMMAND ${MPIEXEC_EXECUTABLE} -n ${MPIEXEC_MAX_NUMPROCS} ${CMAKE_INSTALL_PREFIX}/bin/xcompact3d input_test_x.i3d WORKING_DIRECTORY ${test_dir}/Channel-Flow-X)
-  add_test(NAME Channel-Flow-Z COMMAND ${MPIEXEC_EXECUTABLE} -n ${MPIEXEC_MAX_NUMPROCS} ${CMAKE_INSTALL_PREFIX}/bin/xcompact3d input_test_z.i3d WORKING_DIRECTORY ${test_dir}/Channel-Flow-Z)
-  # Cylinder
-  if(NOT ${USE_ADIOS2})
-    add_test(NAME Cylinder COMMAND ${MPIEXEC_EXECUTABLE} -n ${MPIEXEC_MAX_NUMPROCS} ${CMAKE_INSTALL_PREFIX}/bin/xcompact3d input_test.i3d WORKING_DIRECTORY ${test_dir}/Cylinder)
-    add_test(NAME CylinderMoving COMMAND ${MPIEXEC_EXECUTABLE} -n ${MPIEXEC_MAX_NUMPROCS} ${CMAKE_INSTALL_PREFIX}/bin/xcompact3d input_test_moving.i3d WORKING_DIRECTORY ${test_dir}/CylinderMoving)
-  endif()
-  # Lock excahnge
-  add_test(NAME Lock-exchange COMMAND ${MPIEXEC_EXECUTABLE} -n ${MPIEXEC_MAX_NUMPROCS} ${CMAKE_INSTALL_PREFIX}/bin/xcompact3d input_test.i3d WORKING_DIRECTORY ${test_dir}/Lock-exchange)
-  # Mixing Layer
-  add_test(NAME Mixing-layer COMMAND ${MPIEXEC_EXECUTABLE} -n ${MPIEXEC_MAX_NUMPROCS} ${CMAKE_INSTALL_PREFIX}/bin/xcompact3d input_test.i3d WORKING_DIRECTORY ${test_dir}/Mixing-layer)
-  # TGV
-  add_test(NAME TGvortex COMMAND ${MPIEXEC_EXECUTABLE} -n ${MPIEXEC_MAX_NUMPROCS} ${CMAKE_INSTALL_PREFIX}/bin/xcompact3d input_test.i3d WORKING_DIRECTORY ${test_dir}/TGV)
-  # TBL
-  add_test(NAME TBL COMMAND ${MPIEXEC_EXECUTABLE} -n ${MPIEXEC_MAX_NUMPROCS} ${CMAKE_INSTALL_PREFIX}/bin/xcompact3d input_test.i3d WORKING_DIRECTORY ${test_dir}/TBL)
-  # Wind Turbines
-  add_test(NAME Wind-Turbine COMMAND ${MPIEXEC_EXECUTABLE} -n ${MPIEXEC_MAX_NUMPROCS} ${CMAKE_INSTALL_PREFIX}/bin/xcompact3d input_test.i3d WORKING_DIRECTORY ${test_dir}/Wind-Turbine)
-endif()
+  add_subdirectory(examples)
+  add_subdirectory(tests) 
+endif (${BUILD_TESTING})
+
+# Add a prettify target
+#add_custom_target(format sh ${CMAKE_SOURCE_DIR}/scripts/format.sh
+#  WORKING_DIRECTORY ${CMAKE_SOURCE_DIR})
+
 

CONTRIBUTORS

@@ -3,9 +3,11 @@ Alphabetic order:
 Paul Bartholomew (EPCC, UK)
 Nikos Bempedelis (ICL, UK)
 Georgios (Yorgos) Deskos (NREL, USA)
+Jian Fang (STFC, UK)
 Cedric Flageul (Poitiers, France)
 Ricardo Frantz (Paris, France)
 Athanasios Giannenas (ICL, UK)
+Gaurav Gupta (IIST, India)
 Arash Hamzehloo (ICL, UK)
 Sylvain Laizet (ICL, UK)
 Eric Lamballais (Poitiers, France)