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Upgrade pyPDAF to be compatible with PDAF V2.2.1 #4

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merged 6 commits into from
Jul 24, 2024
Merged

Upgrade pyPDAF to be compatible with PDAF V2.2.1 #4

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f6e7867
adding new interface functions; improved documentation; improved file…
yumengch Jul 19, 2024
4958ec4
fixes bugs in C interface code; fixes issues with installation; add C…
yumengch Jul 19, 2024
5af3f1b
update the pointer to submodule
yumengch Jul 19, 2024
ba439f9
add missed subroutine interface c__pdafomi_localize_covar_noniso
yumengch Jul 19, 2024
ef11b9d
separate model ensemble and model integrator
yumengch Jul 22, 2024
2cf2e22
improved robustness of conda installation; allowing conda packaging f…
yumengch Jul 23, 2024
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add missed subroutine interface c__pdafomi_localize_covar_noniso 
work out build process and CI for Linux and Mac; cleaned compile pyPDAF on windows; hopefully improved stability using intel-fortran-rt and mpi when new conda version is published; cannot workout a windows build CI as it seems very difficult to set up Intel Fortran with Visual studio in github runner but it is useful to keep the compiler environment variable options.
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@yumengch
yumengch committed Jul 22, 2024
commit ba439f9da6d447bfa471715196ba1705c71d704e
52 changes: 0 additions & 52 deletions .github/workflows/test_build.yaml
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28 changes: 28 additions & 0 deletions .github/workflows/test_linux_build.yaml
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name: test_linux_build
on: [workflow_dispatch]

jobs:
test_ubuntu_build:
runs-on: ubuntu-latest
steps:
- name: check out code
uses: actions/checkout@v4
with:
submodules: 'true'
ref: upgrade2.2.1

- name: installing dependent libraries
run: sudo apt install -y liblapack-dev libblas-dev libopenmpi-dev

- name: Set up Python 3.x
uses: actions/setup-python@v5

- name: install pyPDAF
run: pip install -v .

- name: run example
run: mpiexec --oversubscribe -n 4 python -u example/main.py

- name: Setup tmate session
if: ${{ failure() }}
uses: mxschmitt/action-tmate@v3
40 changes: 40 additions & 0 deletions .github/workflows/test_mac_build.yaml
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name: test_mac_build
on: [workflow_dispatch]

jobs:
test_mac_build:
runs-on: macos-latest
steps:
- name: check out code
uses: actions/checkout@v4
with:
submodules: 'true'
ref: upgrade2.2.1

- name: Setup Fortran compiler
uses: fortran-lang/[email protected]
id: setup-fortran
with:
compiler: gcc
version: 13

- name: install dependent Libaries
run: brew install openblas lapack open-mpi

- name: Set up Python 3.x
uses: actions/setup-python@v5

- name: install pyPDAF
run: |
mv setup_mac.cfg setup.cfg
pip install -v .

- name: run example
run: |
mv example/config_mac.py example/config.py
mv example/config_obsA_mac.py example/config_obsA.py
mpiexec --oversubscribe -n 4 python -u example/main.py

- name: Setup tmate session
if: ${{ failure() }}
uses: mxschmitt/action-tmate@v3
81 changes: 81 additions & 0 deletions .github/workflows/test_win_build.yaml
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name: test_win_build
on: [workflow_dispatch]

env:
WINDOWS_BASEKIT_URL: https://registrationcenter-download.intel.com/akdlm/IRC_NAS/e83a8e64-04fc-45df-85c6-c2208d03bdb5/w_BaseKit_p_2024.2.0.635_offline.exe
WINDOWS_HPCKIT_URL: https://registrationcenter-download.intel.com/akdlm/IRC_NAS/0d500705-397e-41b3-8b2b-2a3da1753fc2/w_HPCKit_p_2024.2.0.633_offline.exe
WINDOWS_FORTRAN_COMPONENTS: intel.oneapi.win.ifort-compiler
WINDOWS_DPCPP_COMPONENTS: intel.oneapi.win.mkl.devel:intel.oneapi.win.tbb.devel
CACHE_NUMBER: 5
COMPILER_VERSION: 2024.2.0
TBB_VERSION: 2021.13.0
VS_VER: vs2022

jobs:
test_windows_build:
runs-on: windows-latest
steps:
- name: check out oneAPI code
uses: actions/checkout@v4
with:
repository: oneapi-src/oneapi-ci

- name: cache install fortran
id: cache-install-fortran
uses: actions/cache@v2
with:
path: |
C:\Program Files (x86)\Intel\oneAPI\setvars-vcvarsall.bat
C:\Program Files (x86)\Intel\oneAPI\compiler
key: install-${{ env.CACHE_NUMBER }}-${{ env.WINDOWS_HPCKIT_URL }}-${{ env.WINDOWS_FORTRAN_COMPONENTS }}-compiler-${{ hashFiles('**/scripts/cache_exclude_windows.sh') }}

- name: install fortran
if: steps.cache-install.outputs.cache-hit != 'true'
shell: bash
run: scripts/install_windows.bat $WINDOWS_HPCKIT_URL $WINDOWS_FORTRAN_COMPONENTS

- name: cache install mkl
id: cache-install-mkl
uses: actions/cache@v2
with:
path: |
C:\Program Files (x86)\Intel\oneAPI\setvars-vcvarsall.bat
C:\Program Files (x86)\Intel\oneAPI\compiler
C:\Program Files (x86)\Intel\oneAPI\tbb
C:\Windows\System32\OpenCL.dll
key: install-${{ env.CACHE_NUMBER }}-${{ env.WINDOWS_BASEKIT_URL }}-${{ env.WINDOWS_DPCPP_COMPONENTS }}-compiler-tbb-opencl-${{ hashFiles('**/scripts/cache_exclude_windows.sh') }}

- name: install mkl
if: steps.cache-install.outputs.cache-hit != 'true'
shell: bash
run: scripts/install_windows.bat $WINDOWS_BASEKIT_URL $WINDOWS_DPCPP_COMPONENTS

- name: restore registry on cache hit
if: steps.cache-install.outputs.cache-hit == 'true'
shell: bash
run: scripts/restore_registry.bat $COMPILER_VERSION $TBB_VERSION

- name: check out pyPDAF code
uses: actions/checkout@v4
with:
submodules: 'true'
ref: upgrade2.2.1

- name: install pyPDAF
run: |
cmd.exe /k "C:\Program Files\Microsoft Visual Studio\2022\Community\VC\Auxiliary\Build\vcvars64.bat"
cmd.exe /k "C:\Program Files (x86)\Intel\oneAPI\compiler\latest\env\vars.bat"
cmd.exe /k '"C:\Program Files (x86)\Intel\oneAPI\mkl\latest\env\vars.bat" && powershell'
cd D:\a\pyPDAF\pyPDAF
Move-Item -Path setup_win.cfg -Destination setup.cfg -Force
pip install -v .

- name: run example
run: |
Move-Item -Path example/config_win.py -Destination example/config.py -Force
Move-Item -Path example/config_obsA_win.py -Destination example/config_obsA.py -Force
mpiexec --oversubscribe -n 4 python -u example/main.py

- name: Setup tmate session
if: ${{ failure() }}
uses: mxschmitt/action-tmate@v3
29 changes: 15 additions & 14 deletions PDAFBuild/CMakeLists.txt
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Expand Up @@ -399,27 +399,28 @@ if (${PDAF_NAME} STREQUAL "pdaf-var")
set(SRC_FILES ${SRC_FILES} ${OBJ_3DVAR} ${OBJ_OPTIM})
endif()

# Check if the build type is not explicitly set and default to Release
if(NOT CMAKE_BUILD_TYPE)
set(CMAKE_BUILD_TYPE Release)
if (WIN32)
# This will just compile the MPI library modules
# This is necessary for MS-MPI on windows and cannot be included in the os-dependent config file
add_library(mpimod OBJECT ${MPI_Fortran_MODULE_SRC_FILE})
target_include_directories(mpimod PUBLIC ${MPI_Fortran_MODULE_INCLUDE_PATH})
set_target_properties(mpimod PROPERTIES
Fortran_MODULE_DIRECTORY ${MPI_Fortran_MODULE_DIR})
endif()

# extra option for specific files
# set_source_files_properties (${SRC_FILES} PROPERTIES COMPILE_OPTIONS "${RELEASE_COMPILE_OPTIONS}")

# Define a target for pdaf library
add_library(${PDAF_NAME} STATIC ${SRC_FILES})

# Set properties for pdaf library
target_include_directories(${PDAF_NAME} PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
target_include_directories(${PDAF_NAME} PUBLIC ${CMAKE_CURRENT_BINARY_DIR})

# Set include directory for MPI
target_include_directories(${PDAF_NAME} PUBLIC ${MPI_Fortran_INCLUDE_PATH})
target_include_directories(${PDAF_NAME} PUBLIC ${MPI_Fortran_MODULE_INCLUDE_PATH})
target_include_directories(${PDAF_NAME} PUBLIC ${MPI_Fortran_MODULE_DIR})
set_target_properties(${PDAF_NAME} PROPERTIES
Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/../include)

# Move the static library and include files to given directories.
set_target_properties(${PDAF_NAME} PROPERTIES
ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/../lib
)
set_target_properties(${PDAF_NAME} PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/../include)
install(TARGETS ${PDAF_NAME}
LIBRARY DESTINATION ${CMAKE_CURRENT_SOURCE_DIR}/../lib
ARCHIVE DESTINATION ${CMAKE_CURRENT_SOURCE_DIR}/../lib
RUNTIME DESTINATION ${CMAKE_CURRENT_SOURCE_DIR}/../bin # For Windows DLLs
)
18 changes: 10 additions & 8 deletions PDAFBuild/linux_gfortran_openmpi.cmake
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Expand Up @@ -20,21 +20,23 @@ set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -Wall -Wextra -g -pedantic -fcheck=all -fback

# set MPI library information
set(MPI_Fortran_INCLUDE_PATH
"/home/username/software/spack-0.22.1/opt/spack/linux-ubuntu22.04-skylake/gcc-13.2.0/openmpi-5.0.3-ummuvvrxsncu6txyqbvehgqkpijndmql/include/"
""
CACHE STRING "path to the include directory of MPI_Fortran")
set(MPI_Fortran_MODULE_DIR
"/home/username/software/spack-0.22.1/opt/spack/linux-ubuntu22.04-skylake/gcc-13.2.0/openmpi-5.0.3-ummuvvrxsncu6txyqbvehgqkpijndmql/lib/"
""
CACHE STRING "path to the module directory of MPI_Fortran")

# set BLAS information
set(BLAS_NAME "openblas")
set(BLAS_INCLUDE_PATH "/home/username/software/spack-0.22.1/opt/spack/linux-ubuntu22.04-skylake/gcc-13.2.0/openblas-0.3.26-fhoiyp4jbfxtxry3d6skn5he4hqh7ur7/include")
set(BLAS_LIB_PATH "/homeusernamesoftware/spack-0.22.1/opt/spack/linux-ubuntu22.04-skylake/gcc-13.2.0/openblas-0.3.26-fhoiyp4jbfxtxry3d6skn5he4hqh7ur7/lib")
set(BLAS_INCLUDE_PATH "")
set(BLAS_LIB_PATH "")

# set LAPACK information
set(LAPACK_NAME "scalapack")
set(LAPACK_INCLUDE_PATH "/home/username/software/spack-0.22.1/opt/spack/linux-ubuntu22.04-skylake/gcc-13.2.0/netlib-scalapack-2.2.0-izrouv2qyqsuchli4s3jybeksc6m7zdo/include")
set(LAPACK_LIB_PATH "/home/username/software/spack-0.22.1/opt/spack/linux-ubuntu22.04-skylake/gcc-13.2.0/netlib-scalapack-2.2.0-izrouv2qyqsuchli4s3jybeksc6m7zdo/lib")
set(LAPACK_INCLUDE_PATH "")
set(LAPACK_LIB_PATH "")

# set PDAF information
set(PDAF_INCLUDE_PATH "/home/username/Documents/pyPDAF/PDAF_V2.2.1/include")
# Check if the build type is not explicitly set and default to Release
if(NOT CMAKE_BUILD_TYPE)
set(CMAKE_BUILD_TYPE Release)
endif()
24 changes: 8 additions & 16 deletions PDAFBuild/linux_gfortran_openmpi_pypdaf.cmake
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Expand Up @@ -7,34 +7,26 @@ set(CMAKE_AR "ar" CACHE FILEPATH "Archiver")
# RANKLIB is used to deal with static libraries
set(CMAKE_RANLIB "ranlib" CACHE FILEPATH "Ranlib")
# Here a linker is specified it can be the compiler used
set(CMAKE_LINKER "/home/username/software/spack-0.22.1/opt/spack/linux-ubuntu22.04-skylake/gcc-13.2.0/openmpi-5.0.3-ummuvvrxsncu6txyqbvehgqkpijndmql/bin/mpif90" CACHE FILEPATH "Linker")
set(CMAKE_LINKER "mpif90" CACHE FILEPATH "Linker")
# CPP is the C preprocessor
set(CMAKE_CPP "cpp" CACHE FILEPATH "C Preprocessor")

# set compiler executable
set(CMAKE_Fortran_COMPILER "/home/username/software/spack-0.22.1/opt/spack/linux-ubuntu22.04-skylake/gcc-13.2.0/openmpi-5.0.3-ummuvvrxsncu6txyqbvehgqkpijndmql/bin/mpif90")
set(CMAKE_Fortran_COMPILER "mpif90")
# Set compiler flags for Release/Production configurations
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -ffree-line-length-none -fdefault-real-8 -fPIC")
# Set compiler flags for Debug configurations
set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -Wall -Wextra -g -pedantic -fcheck=all -fbacktrace -ffree-line-length-none -fdefault-real-8 -fPIC")

# set MPI library information
set(MPI_Fortran_INCLUDE_PATH
"/home/username/software/spack-0.22.1/opt/spack/linux-ubuntu22.04-skylake/gcc-13.2.0/openmpi-5.0.3-ummuvvrxsncu6txyqbvehgqkpijndmql/include/"
""
CACHE STRING "path to the include directory of MPI_Fortran")
set(MPI_Fortran_MODULE_DIR
"/home/username/software/spack-0.22.1/opt/spack/linux-ubuntu22.04-skylake/gcc-13.2.0/openmpi-5.0.3-ummuvvrxsncu6txyqbvehgqkpijndmql/lib/"
""
CACHE STRING "path to the module directory of MPI_Fortran")

# set BLAS information
set(BLAS_NAME "openblas")
set(BLAS_INCLUDE_PATH "/home/username/software/spack-0.22.1/opt/spack/linux-ubuntu22.04-skylake/gcc-13.2.0/openblas-0.3.26-fhoiyp4jbfxtxry3d6skn5he4hqh7ur7/include")
set(BLAS_LIB_PATH "/home/username/software/spack-0.22.1/opt/spack/linux-ubuntu22.04-skylake/gcc-13.2.0/openblas-0.3.26-fhoiyp4jbfxtxry3d6skn5he4hqh7ur7/lib")

# set LAPACK information
set(LAPACK_NAME "scalapack")
set(LAPACK_INCLUDE_PATH "/home/username/software/spack-0.22.1/opt/spack/linux-ubuntu22.04-skylake/gcc-13.2.0/netlib-scalapack-2.2.0-izrouv2qyqsuchli4s3jybeksc6m7zdo/include")
set(LAPACK_LIB_PATH "/home/username/software/spack-0.22.1/opt/spack/linux-ubuntu22.04-skylake/gcc-13.2.0/netlib-scalapack-2.2.0-izrouv2qyqsuchli4s3jybeksc6m7zdo/lib")

# set PDAF information
set(PDAF_INCLUDE_PATH "/home/username/Documents/pyPDAF/PDAF_V2.2.1/include")
# Check if the build type is not explicitly set and default to Release
if(NOT CMAKE_BUILD_TYPE)
set(CMAKE_BUILD_TYPE Release)
endif()
32 changes: 32 additions & 0 deletions PDAFBuild/osx_gfortran_openmpi_pypdaf.cmake
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# Set the PDAF library name, it can be pdaf-var or pdaf-d
set(PDAF_NAME "pdaf-var")

# Set preprocessor and linker for current system
# AR is used to generate static libraries
set(CMAKE_AR "ar" CACHE FILEPATH "Archiver")
# RANKLIB is used to deal with static libraries
set(CMAKE_RANLIB "ranlib" CACHE FILEPATH "Ranlib")
# Here a linker is specified it can be the compiler used
set(CMAKE_LINKER "mpif90" CACHE FILEPATH "Linker")
# CPP is the C preprocessor
set(CMAKE_CPP "cpp" CACHE FILEPATH "C Preprocessor")

# set compiler executable
set(CMAKE_Fortran_COMPILER "mpif90")
# Set compiler flags for Release/Production configurations
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -ffree-line-length-none -fdefault-real-8 -fPIC -mmacosx-version-min=11.0")
# Set compiler flags for Debug configurations
set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -Wall -Wextra -g -pedantic -fcheck=all -fbacktrace -ffree-line-length-none -fdefault-real-8 -fPIC")

# set MPI library information
set(MPI_Fortran_INCLUDE_PATH
""
CACHE STRING "path to the include directory of MPI_Fortran")
set(MPI_Fortran_MODULE_DIR
""
CACHE STRING "path to the module directory of MPI_Fortran")

# Check if the build type is not explicitly set and default to Release
if(NOT CMAKE_BUILD_TYPE)
set(CMAKE_BUILD_TYPE Release)
endif()
33 changes: 33 additions & 0 deletions PDAFBuild/win_intel_msmpi.cmake
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# Set the PDAF library name, it can be pdaf-var or pdaf-d
set(PDAF_NAME "pdaf-var")

# set MPI library information
set(MPI_NAME "msmpi;msmpifec")
set(MPI_Fortran_INCLUDE_PATH
"C:/Program Files (x86)/Microsoft SDKs/MPI/Include"
CACHE STRING "path to the MPI Fortran mpi.h include directory")
set(MPI_Fortran_MODULE_INCLUDE_PATH
"C:/Program Files (x86)/Microsoft SDKs/MPI/Include/x64"
CACHE STRING "path to the include directory to compile MPI Fortran module")
set(MPI_Fortran_MODULE_DIR
"C:/Users/cymji/Desktop/pyPDAF/PDAF_V2.2.1/mpi_include"
CACHE STRING "path to the installed module directory of MPI_Fortran")
# We have to compile MPI-MPI mod file ourselves in Windows
set(MPI_Fortran_MODULE_SRC_FILE "C:/Program Files (x86)/Microsoft SDKs/MPI/Include/mpi.f90"
CACHE STRING "path to the MPI Fortran module source file" )
# We have to compile MPI-MPI mod file ourselves in Windows
set(MPI_Fortran_LINK_DIR "C:/Program Files (x86)/Microsoft SDKs/MPI/Lib/x64"
CACHE STRING "path to the MPI Fortran libraries" )
# This overrides any language flags and must be given before add_library
set_source_files_properties(${MPI_Fortran_MODULE_SRC_FILE} PROPERTIES COMPILE_FLAGS "/O2 /Qdiag-disable:10448 /Qdiag-disable:10423")

# ideally, we should provide compiler options based on target or source files,
# but this will force us to use multiple config files or encode it in the CMakelist.txt file
set(CMAKE_Fortran_FLAGS_RELEASE "/O2 /4R8 /Qdiag-disable:10448 /Qdiag-disable:10423" CACHE STRING "RELEASE FLAGS" FORCE)
# Set compiler flags for Debug configurations
set(CMAKE_Fortran_FLAGS_DEBUG "/Od /debug:full /traceback /check:all /Qtrapuv /4R8 /Qdiag-disable:10448 /Qdiag-disable:10423" CACHE STRING "DEBUG FLAGS" FORCE)

# set BLAS information
set(BLAS_NAME "mkl_core;mkl_intel_lp64;mkl_sequential")
set(BLAS_INCLUDE_PATH "")
set(BLAS_LIB_PATH "C:/Program Files (x86)/Intel/oneAPI/mkl/2024.2/lib")
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