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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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fixes bugs in C interface code; fixes issues with installation; add C… 
…Make configurations; uses single precision integer in examples for compatibility with Fortran and Cython declaration.
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@yumengch
yumengch committed Jul 19, 2024
commit 4958ec4571908307e09474933e3fe4868dd23141
86 changes: 45 additions & 41 deletions PDAFBuild/CMakeLists.txt
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Original file line number Diff line number Diff line change
@@ -1,14 +1,10 @@
cmake_minimum_required(VERSION 3.12)
project(PDAF VERSION 2.1.0 LANGUAGES Fortran)
project(PDAF VERSION 2.2.1 LANGUAGES Fortran)

set(CMAKE_INSTALL_PREFIX ${CMAKE_CURRENT_SOURCE_DIR}/..)
# Set the PDAF library version
set(PDAF_VERSION "2.2.1")

# In windows, MPI.mod must be compiled by ourselves
if(WIN32)
add_library(mpimod STATIC ${MPI_Fortran_MODULE_DIR}/mpi.f90)
set_source_files_properties(${MPI_Fortran_MODULE_DIR}/mpi.f90 PROPERTIES COMPILE_OPTIONS "/Qdiag-disable:10448")
target_include_directories(mpimod PUBLIC ${MPI_Fortran_INCLUDE_PATH})
endif()
set(CMAKE_INSTALL_PREFIX ${CMAKE_CURRENT_SOURCE_DIR}/..)

set(MOD_PDAF
PDAF_timer.F90
Expand Down Expand Up @@ -74,6 +70,9 @@ set(OBJ_PDAF_GEN
PDAF_reset_forget.F90
PDAF_get_ensstats.F90
PDAF_set_debug_flag.F90
PDAF_analysis_utils.F90
PDAF_reset_dim_p.F90
PDAF_set_offline_mode.F90
)

# Specific PDAF-routines for SEIK
Expand Down Expand Up @@ -238,6 +237,7 @@ set(OBJ_LNETF
PDAF_lnetf_update.F90
PDAF_lnetf_analysis.F90
PDAF_lnetf_smootherT.F90
PDAF_mod_lnetf.F90
PDAF_smoother_lnetf.F90
)

Expand Down Expand Up @@ -291,11 +291,11 @@ set(OBJ_3DVAR_INI
PDAF_3dvar_init.F90
PDAF_3dvar_alloc.F90
PDAF_3dvar_options.F90
PDAF_3dvar_memtime.F90
)

# Specific PDAF-routines for 3DVAR
set(OBJ_3DVAR
PDAF_3dvar_memtime.F90
set(OBJ_3DVAR
PDAF_put_state_3dvar.F90
PDAF_assimilate_3dvar.F90
PDAF_3dvar_update.F90
Expand Down Expand Up @@ -361,6 +361,9 @@ set(OBJ_OPTIM
../external/LBFGS/timer.f
)

set (OBJ_INTERFACE
PDAF_interfaces_module.F90
)
# List all source files
set(SRC_FILES
${MOD_PDAF}
Expand All @@ -379,43 +382,44 @@ set(SRC_FILES
${OBJ_PF}
${OBJ_LKNETF}
${OBJ_OBSGEN}
${OBJ_3DVAR_INI}
${OBJ_3DVAR}
${OBJ_PDAFOMI}
${OBJ_OPTIM}
${OBJ_OPTIM}
${OBJ_INTERFACE}
${OBJ_3DVAR_INI}
)

# Customize compiler flags
if(${CMAKE_Fortran_COMPILER_ID} STREQUAL "GNU")
set_source_files_properties (${SRC_FILES} PROPERTIES COMPILE_OPTIONS "-O3;-ffree-line-length-none -fdefault-real-8")
elseif(${CMAKE_Fortran_COMPILER_ID} STREQUAL "Cray")
set_source_files_properties (${SRC_FILES} PROPERTIES COMPILE_OPTIONS "-O3;-N;1023")
elseif(${CMAKE_Fortran_COMPILER_ID} STREQUAL "Intel")
if(WIN32)
set_source_files_properties (${SRC_FILES} PROPERTIES COMPILE_OPTIONS "/O3;/4R8;/Qdiag-disable:10448")
set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} /Od")
else()
# set (CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -r8")
set_source_files_properties (${SRC_FILES} PROPERTIES COMPILE_OPTIONS "-O3;-r8")
set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS} -mkl")
#KB For newer versions of CMake - this is the way to go
enable_language(C)
set(BLA_VENDOR Intel10_64lp_seq)
#KB https://cmake.org/cmake/help/latest/module/FindBLAS.html
endif()
# check if Config Path is provided
if(NOT Config_PATH)
message(FATAL_ERROR "Config_PATH is not given. Providing a Config_PATH in commandline by specify -DConfig_PATH=PATH_TO_CONFIG_FILE")
endif()

# Define a target for pdaf-var
add_library(pdaf-var STATIC ${SRC_FILES})
# import configuration file
include(${Config_PATH})

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)
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 properties for pdaf-var
target_include_directories(pdaf-var PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
target_include_directories(pdaf-var PUBLIC ${CMAKE_CURRENT_BINARY_DIR})
target_include_directories(pdaf-var PUBLIC ${MPI_Fortran_INCLUDE_PATH})
target_include_directories(pdaf-var PUBLIC ${MPI_Fortran_MODULE_DIR})
# Set include directory for MPI
target_include_directories(${PDAF_NAME} PUBLIC ${MPI_Fortran_INCLUDE_PATH})
target_include_directories(${PDAF_NAME} PUBLIC ${MPI_Fortran_MODULE_DIR})

set_target_properties(pdaf-var PROPERTIES
# 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-var PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/../include)
set_target_properties(${PDAF_NAME} PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/../include)
40 changes: 40 additions & 0 deletions PDAFBuild/linux_gfortran_openmpi_pypdaf.cmake
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Original file line number Diff line number Diff line change
@@ -0,0 +1,40 @@
# 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 "/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")
# 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 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")
4 changes: 2 additions & 2 deletions example/PDAF_system.py
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Original file line number Diff line number Diff line change
Expand Up @@ -128,7 +128,7 @@ def setEnKFOptions(self, dim_pint:int, dim_preal:int) -> tuple[np.ndarray[int],
dim_preal : int
size of float filter options
"""
filter_param_i:np.ndarray = np.zeros(dim_pint, dtype=int)
filter_param_i:np.ndarray = np.zeros(dim_pint, dtype=np.intc)
filter_param_r:np.ndarray = np.zeros(dim_preal)

filter_param_i[0] = self.sv.dim_state_p
Expand All @@ -151,7 +151,7 @@ def setETKFOptions(self, dim_pint:int, dim_preal:int) -> tuple[np.ndarray[int],
dim_preal : int
size of float filter options
"""
filter_param_i:np.ndarray = np.zeros(dim_pint, dtype=int)
filter_param_i:np.ndarray = np.zeros(dim_pint, dtype=np.intc)
filter_param_r:np.ndarray = np.zeros(dim_preal)

filter_param_i[0] = self.sv.dim_state_p
Expand Down
6 changes: 3 additions & 3 deletions example/obsA.py
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Original file line number Diff line number Diff line change
Expand Up @@ -161,15 +161,15 @@ def init_dim(self, step:int, dim_obs:int) -> int:
ocoord_p = ocoord_p + 1


id_obs_p:np.ndarray = np.zeros((self.nrows, len(obs_p)))
id_obs_p:np.ndarray = np.zeros((self.nrows, len(obs_p)), dtype=np.intc)
if self.nrows == 1:
# The relationship between observation and state vector
# id_obs_p gives the indices of observed field in state vector
# the index starts from 1
# The index is based on the full state vector instead of the index in the local domain
# The following code is used because in our example, observations are masked and
# have the same shape as the model grid
state_vector_index_p:np.ndarray = np.arange(1, self.model.nx_p*self.model.ny_p + 1, dtype=int)
state_vector_index_p:np.ndarray = np.arange(1, self.model.nx_p*self.model.ny_p + 1, dtype=np.intc)
id_obs_p[0] = state_vector_index_p[condition]
else:
# If interpolation is required for a 2D domain
Expand Down Expand Up @@ -252,7 +252,7 @@ def init_dim_obs_l(self, domain_p:int, step:int, dim_obs:int, dim_obs_l:int) ->
coords_l[1] = np.repeat(np.arange(self.model.ny_p), self.model.nx_p)[domain_p - 1]
coords_l = coords_l + 1

return PDAF.omi_init_dim_obs_l(self.i_obs, coords_l,
return PDAF.omi_init_dim_obs_l_iso(self.i_obs, coords_l,
self.local.loc_weight,
self.local.cradius,
self.local.sradius, dim_obs_l)
Expand Down
6 changes: 3 additions & 3 deletions example/obsB.py
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Original file line number Diff line number Diff line change
Expand Up @@ -160,15 +160,15 @@ def init_dim(self, step:int, dim_obs:int) -> int:
ocoord_p = ocoord_p + 1


id_obs_p:np.ndarray = np.zeros((self.nrows, len(obs_p)))
id_obs_p:np.ndarray = np.zeros((self.nrows, len(obs_p)), dtype=np.intc)
if self.nrows == 1:
# The relationship between observation and state vector
# id_obs_p gives the indices of observed field in state vector
# the index starts from 1
# The index is based on the full state vector instead of the index in the local domain
# The following code is used because in our example, observations are masked and
# have the same shape as the model grid
state_vector_index_p:np.ndarray = np.arange(1, self.model.nx_p*self.model.ny_p + 1, dtype=int)
state_vector_index_p:np.ndarray = np.arange(1, self.model.nx_p*self.model.ny_p + 1, dtype=np.intc)
id_obs_p[0] = state_vector_index_p[condition]
else:
# If interpolation is required for a 2D domain
Expand Down Expand Up @@ -251,7 +251,7 @@ def init_dim_obs_l(self, domain_p:int, step:int, dim_obs:int, dim_obs_l:int) ->
coords_l[1] = np.repeat(np.arange(self.model.ny_p), self.model.nx_p)[domain_p - 1]
coords_l = coords_l + 1

return PDAF.omi_init_dim_obs_l(self.i_obs, coords_l,
return PDAF.omi_init_dim_obs_l_iso(self.i_obs, coords_l,
self.local.loc_weight,
self.local.cradius,
self.local.sradius, dim_obs_l)
Expand Down
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