Merge branch 'oblate_coord_rot' into debug

MintonGroup · Mar 1, 2024 · 80bf131 · 80bf131
2 parents d9d646f + cc8d4fe
commit 80bf131
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Showing 91 changed files with 6,359 additions and 3,154 deletions.
diff --git a/.gitignore b/.gitignore
@@ -37,19 +37,20 @@ swiftest-*
 __pycache__*
 _cmake*
 _dependencies
+!SHTOOLS
+!SHTOOLS/**
 
 
 #Documentation
 !.readthedocs.yaml
 !docs/
 !docs/**/*
-docs/_build/
+!docs/_build/
 docs/_build/**/*
 docs/generated/
 docs/generated/**/*
 docs/**/*.DS_Store
 docs/**/*.swp
-docs/
 !docs/_static/**/*.png
 !docs/_static/**/*.svg
 **/*.ai
@@ -65,14 +66,14 @@ docs/_static/fortran_docs/*/**
 !environment.yml
 !.dockerignore
 
+swiftest/_bindings.cpython*
 bin/
 build/*
-hdf5-*
-netcdf-c-*
-netcdf-fortran-*
-zlib-*
+lib*
 
 actions-runner*
 
 env/**
 venv/**
+
+sandbox/**
diff --git a/.gitmodules b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "SHTOOLS"]
+	path = SHTOOLS
+	url = https://github.com/profminton/SHTOOLS
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -11,7 +11,7 @@
 ##################################################
 # Define the project and the depencies that it has
 ##################################################
-CMAKE_MINIMUM_REQUIRED(VERSION 3.6.0...3.27.1)
+CMAKE_MINIMUM_REQUIRED(VERSION 3.23.1...3.28.3)
 SET(SKBUILD_PROJECT_NAME "swiftest" CACHE STRING "Name of project set by scikit-build")
 
 # Get version stored in text file
@@ -28,27 +28,44 @@ ELSE()
         CMAKE_POLICY(SET CMP0148 OLD)
     ENDIF ()
 
+    # The following section is modified from Numpy f2py documentation
+    IF(PROJECT_SOURCE_DIR STREQUAL PROJECT_BINARY_DIR)
+        MESSAGE(FATAL_ERROR "In-source builds not allowed. Please make a new directory (called a build directory) and run CMake from there.\n")
+    ENDIF()
+
     # Set some options the user may choose
     OPTION(USE_COARRAY "Use Coarray Fortran for parallelization of test particles" OFF)
     OPTION(USE_OPENMP "Use OpenMP for parallelization" ON)
     OPTION(USE_SIMD "Use SIMD vectorization" ON)
     OPTION(BUILD_SHARED_LIBS "Build using shared libraries" ON)
 
+    # Define the paths to the source code and python files
+    SET(SRC "${CMAKE_SOURCE_DIR}/src")
+    SET(PY "${CMAKE_SOURCE_DIR}/swiftest")
+
+    # Make sure paths are correct for Unix or Windows style
+    FILE(TO_CMAKE_PATH ${SRC} SRC)
+    FILE(TO_CMAKE_PATH ${PY} PY)
+
     INCLUDE(GNUInstallDirs)
     IF (SKBUILD)
-        SET(INSTALL_BINDIR ${SKBUILD_PLATLIB_DIR}/${SKBUILD_PROJECT_NAME}) 
-        SET(INSTALL_LIBDIR ${SKBUILD_PLATLIB_DIR}/${SKBUILD_PROJECT_NAME}) 
-        SET(INSTALL_INCLUDEDIR ${INSTALL_LIBDIR}) 
+        SET(INSTALL_BINDIR ${SKBUILD_SCRIPTS_DIR})
+        SET(INSTALL_LIBDIR ${SKBUILD_DATA_DIR}/lib) 
+        SET(INSTALL_INCLUDEDIR ${SKBUILD_HEADERS_DIR}) 
+        SET(INSTALL_PYPROJ ${SKBUILD_PLATLIB_DIR}/${SKBUILD_PROJECT_NAME}) 
         IF (APPLE)
-            SET(CMAKE_INSTALL_RPATH "@loader_path")
+            SET(CMAKE_INSTALL_RPATH "@loader_path;${CMAKE_BINARY_DIR}/bin")
         ELSEIF (LINUX)
-            SET(CMAKE_INSTALL_RPATH $ORIGIN)
+            SET(CMAKE_INSTALL_RPATH "@ORIGIN;${CMAKE_BINARY_DIR}/bin")
         ENDIF ()
     ELSE ()
+        SET(INSTALL_PYPROJ ${PY})
         SET(INSTALL_BINDIR ${CMAKE_INSTALL_BINDIR})
         SET(INSTALL_LIBDIR ${CMAKE_INSTALL_LIBDIR})
         SET(INSTALL_INCLUDEDIR ${CMAKE_INSTALL_INCLUDEDIR})
     ENDIF ()
+
+    SET(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
 
     # Have the .mod files placed in the include folder
     SET(CMAKE_Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod)
@@ -57,6 +74,7 @@ ELSE()
     FILE(TO_CMAKE_PATH "${CMAKE_SOURCE_DIR}/cmake/Modules" LOCAL_MODULE_PATH)
     LIST(APPEND CMAKE_MODULE_PATH ${LOCAL_MODULE_PATH})
 
+    # Add in the external dependency libraries 
     IF (CMAKE_Fortran_COMPILER_ID MATCHES "^Intel")
         SET(COMPILER_OPTIONS "Intel" CACHE STRING "Compiler identified as Intel")
     ELSEIF (CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
@@ -65,10 +83,22 @@ ELSE()
         MESSAGE(FATAL_ERROR "Compiler ${CMAKE_Fortran_COMPILER_ID} not recognized!") 
     ENDIF ()
 
-    # The following section is modified from Numpy f2py documentation
-    IF(PROJECT_SOURCE_DIR STREQUAL PROJECT_BINARY_DIR)
-    MESSAGE(FATAL_ERROR "In-source builds not allowed. Please make a new directory (called a build directory) and run CMake from there.\n")
+    IF (COMPILER_OPTIONS STREQUAL "GNU")
+        IF (APPLE)
+            SET(BLA_VENDOR "Apple" CACHE STRING "BLAS vendor")
+        ELSE ()
+            SET(BLA_VENDOR "OpenBLAS" CACHE STRING "BLAS vendor")
+        ENDIF ()
+    ELSEIF (COMPILER_OPTIONS STREQUAL "INTEL")
+        SET(BLA_VENDOR "Intel10_64lp" CACHE STRING "BLAS vendor")
     ENDIF()
+    SET(BLA_STATIC ON)
+    FIND_PACKAGE(BLAS REQUIRED)
+    FIND_PACKAGE(LAPACK REQUIRED)
+    FIND_PACKAGE(FFTW3 REQUIRED)
+    FIND_PACKAGE(SHTOOLS REQUIRED)
+
+
 
     FIND_PACKAGE(NETCDF_Fortran REQUIRED)
     IF (MSVC)
@@ -85,9 +115,6 @@ ELSE()
     FIND_PACKAGE(Python COMPONENTS Interpreter Development.Module REQUIRED)
 
 
-    SET(SRC "${CMAKE_SOURCE_DIR}/src")
-    SET(PY "${CMAKE_SOURCE_DIR}/swiftest")
-
     #####################################
     # Tell how to install this executable
     #####################################
@@ -99,11 +126,6 @@ ELSE()
         SET(CMAKE_INSTALL_PREFIX /usr/local CACHE PATH "Path for install")
     ENDIF()
 
-
-    # Make sure paths are correct for Unix or Windows style
-    FILE(TO_CMAKE_PATH ${SRC} SRC)
-    FILE(TO_CMAKE_PATH ${PY} PY)
-
     # Set the name of the swiftest library
     SET(SWIFTEST_LIBRARY ${SKBUILD_PROJECT_NAME})
 
@@ -113,13 +135,11 @@ ELSE()
     ENDIF(NOT CMAKE_Fortran_COMPILER_SUPPORTS_F90)
     INCLUDE(SetParallelizationLibrary)
 
-    IF (COMPILER_OPTIONS STREQUAL "Intel" AND NOT CMAKE_SYSTEM_NAME STREQUAL "Windows")
-        INCLUDE(SetMKL)
-    ENDIF ()
     INCLUDE(SetSwiftestFlags) 
 
-
-
+    IF (NOT BUILD_SHARED_LIBS)
+        SET(CMAKE_POSITION_INDEPENDENT_CODE ON)
+    ENDIF()
     # The source for the SWIFTEST binary and have it placed in the bin folder
     ADD_SUBDIRECTORY(${SRC} ${CMAKE_INSTALL_BINDIR})
     ADD_SUBDIRECTORY(${PY})

diff --git a/Dockerfile.GNU-Linux b/Dockerfile.GNU-Linux
@@ -13,9 +13,8 @@
 # dynamically. 
 
 # This build target compiles all dependencies and the swiftest driver itself
-FROM continuumio/miniconda3:23.5.2-0 as build-deps
+FROM ubuntu:focal-20240123 as build-deps
 SHELL ["/bin/bash", "--login", "-c"]
-ENV PATH="/opt/conda/bin:${PATH}"
 WORKDIR /swiftest
 
 ENV INSTALL_DIR=/usr/local
@@ -29,69 +28,29 @@ ENV LD_LIBRARY_PATH="${INSTALL_DIR}/lib"
 ENV LDFLAGS="-L${INSTALL_DIR}/lib"
 ENV CPPFLAGS="-I${INSTALL_DIR}/include"
 
-COPY ./buildscripts/swiftest-build-env.yml ./
-COPY ./buildscripts/fetch_dependencies.sh ./
-RUN ./fetch_dependencies.sh -d ./
+COPY ./buildscripts/ ./buildscripts/
+RUN apt-get update && \
+  DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
+  m4 && \
+  rm -rf /var/lib/apt/lists/*  && \
+  buildscripts/build_dependencies.sh -p ${INSTALL_DIR} 
 
-# Get the HDF5, NetCDF-C, and NetCDF-Fortran libraries
-RUN conda update --all -y && \
-    conda install conda-libmamba-solver -y && \
-    conda config --set solver libmamba && \
-    conda env create --file swiftest-build-env.yml --name swiftest-build-env && \
-    conda init bash && \
-    echo "conda activate swiftest-build-env" >> ~/.bashrc 
-
-RUN cd zlib-* && \
-    ./configure \
-        --prefix=${INSTALL_DIR} \
-        --static && \
-    make && make install && \
-    cd ../hdf5-* && \
-    ./configure \
-        --prefix=${INSTALL_DIR} \
-        --disable-shared \
-        --enable-build-mode=production \
-        --disable-fortran \
-        --disable-java \
-        --disable-cxx \
-        --with-zlib=${INSTALL_DIR} && \
-    make && make install && \
-    cd ../netcdf-c-* && \
-    ./configure \
-        --prefix=${INSTALL_DIR} \
-        --disable-shared \
-        --disable-dap \
-        --disable-libxml2 \
-        --disable-byterange && \
-    make && make install && \
-    cd ../netcdf-fortran-* && \
-    export CFLAGS="-fPIC" && \
-    export FCFLAGS="${CFLAGS}" && \
-    export FFLAGS=${CFLAGS} && \
-    export LIBS=$(${INSTALL_DIR}/bin/nc-config --libs --static) && \
-    ./configure --disable-shared --prefix=${NFDIR} && \
-    make && make install
-
-FROM continuumio/miniconda3:23.5.2-0 as build-swiftest
+FROM ubuntu:focal-20240123 as build-swiftest
 SHELL ["/bin/bash", "--login", "-c"]
 ENV SHELL="/bin/bash"
 WORKDIR /swiftest
 
 # Copy build artifacts over to the swiftest package builder stage
 ENV INSTALL_DIR=/usr/local
 COPY --from=build-deps ${INSTALL_DIR}/ ${INSTALL_DIR}/
-COPY --from=build-deps /opt/conda/envs/ /opt/conda/envs/
-COPY --from=build-deps /root/.bashrc /root/
 
 # Compile the Swiftest project
 COPY ./cmake/ ./cmake/
+COPY ./pyproject.toml ./
 COPY ./src/ ./src/
 COPY ./swiftest/ ./swiftest/
+COPY ./tests/  ./tests/
 COPY ./CMakeLists.txt ./
-COPY ./setup.py ./
-COPY ./environment.yml ./
-COPY ./pyproject.toml ./
-COPY ./requirements.txt ./
 COPY ./version.txt ./
 
 # Generate the build environment in conda
@@ -107,4 +66,8 @@ RUN export NFCFG="${INSTALL_DIR}/bin/nf-config" && \
 
 #Export the generated wheel file to the host machine
 FROM scratch as export-wheel
-COPY --from=build-swiftest /swiftest/dist/ ./
+COPY --from=build-swiftest /swiftest/dist/ ./
+
+FROM scratch as export-driver
+COPY --from=build-swiftest /swiftest/build/bin/swiftest_driver ./
+COPY --from=build-swiftest /swiftest/build/bin/libswiftest.so ./
diff --git a/Dockerfile.Intel b/Dockerfile.Intel
@@ -34,44 +34,12 @@ ENV LD_LIBRARY_PATH="${INSTALL_DIR}/lib"
 ENV LDFLAGS="-L${INSTALL_DIR}/lib"
 ENV CPPFLAGS="-I${INSTALL_DIR}/include"
 
-COPY ./buildscripts/fetch_dependencies.sh ./
+COPY ./buildscripts/ ./buildscripts/
 RUN apt-get update && \
   DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
   m4 && \
   rm -rf /var/lib/apt/lists/*  && \
-  ./fetch_dependencies.sh -d ./
-
-# Get the HDF5, NetCDF-C, and NetCDF-Fortran libraries
-RUN cd zlib-* && \
-    ./configure \
-        --prefix=${INSTALL_DIR} \
-        --static && \
-    make && make install && \
-    cd ../hdf5-* && \
-    ./configure \
-        --prefix=${INSTALL_DIR} \
-        --disable-shared \
-        --enable-build-mode=production \
-        --disable-fortran \
-        --disable-java \
-        --disable-cxx \
-        --with-zlib=${INSTALL_DIR} && \
-    make && make install && \
-    cd ../netcdf-c-* && \
-    ./configure \
-        --prefix=${INSTALL_DIR} \
-        --disable-shared \
-        --disable-dap \
-        --disable-libxml2 \
-        --disable-byterange && \
-    make && make install 
-RUN cd netcdf-fortran-* && \
-    export CFLAGS="-fPIC" && \
-    export FCFLAGS="${CFLAGS}  -standard-semantics" && \
-    export FFLAGS=${CFLAGS} && \
-    export LIBS=$(${INSTALL_DIR}/bin/nc-config --libs --static) && \
-    ./configure --disable-shared --prefix=${NFDIR} && \
-    make && make install
+  buildscripts/build_dependencies.sh -p ${INSTALL_DIR} 
 
 FROM intel/oneapi-hpckit:2023.1.0-devel-ubuntu20.04 as build-swiftest
 ENV SCRIPT_DIR="buildscripts"
@@ -98,18 +66,15 @@ ENV LD_LIBRARY_PATH="${INSTALL_DIR}/lib:${LD_LIBRARY_PATH}"
 COPY --from=build-deps ${INSTALL_DIR}/ ${INSTALL_DIR}/
 
 # Compile the Swiftest project
-COPY ./requirements.txt ./
-COPY ./environment.yml ./
 COPY ./cmake/ ./cmake/
 COPY ./pyproject.toml ./
-COPY ./setup.py ./
 COPY ./src/ ./src/
 COPY ./swiftest/ ./swiftest/
+COPY ./tests/  ./tests/
 COPY ./CMakeLists.txt ./
 COPY ./version.txt ./
 RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install python3-pip python3.8-venv -y
 
-# Generate the build environment in conda
 ENV PIP_ROOT_USER_ACTION=ignore
 ENV LDFLAGS="-L${INSTALL_DIR}/lib"
 ENV CFLAGS="-fPIC"
@@ -123,4 +88,8 @@ RUN export NFCFG="${INSTALL_DIR}/bin/nf-config" && \
 
 #Export the generated wheel file to the host machine
 FROM scratch as export-wheel
-COPY --from=build-swiftest /swiftest/dist/ ./
+COPY --from=build-swiftest /swiftest/dist/ ./
+
+FROM scratch as export-driver
+COPY --from=build-swiftest /swiftest/build/bin/swiftest_driver ./
+COPY --from=build-swiftest /swiftest/build/bin/libswiftest.so ./