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Libraries update
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- removed nesmio, sfcio, sigio
- update hdf5 to 1.14.4.2
- fix mapl v2.46.0.tar.gz checksum
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@DusanJovic-NOAA
DusanJovic-NOAA committed May 10, 2024
1 parent ff6c36b commit a0ecc3b
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Showing 4 changed files with 295 additions and 153 deletions.
10 changes: 3 additions & 7 deletions build.sh
View file
Original file line number Diff line number Diff line change
Expand Up @@ -120,7 +120,7 @@ printf '%-.30s ' "Building ufslibs .........................."
mkdir build
cd build

cmake .. -DCMAKE_INSTALL_PREFIX=../install -DUSE_ZSTD_AND_DYNAMIC_HDF5=ON
cmake .. -DCMAKE_INSTALL_PREFIX=../install

make -j 8

Expand Down Expand Up @@ -165,16 +165,12 @@ export crtm_ROOT=${ufslibs_install_prefix}/crtm
export g2_ROOT=${ufslibs_install_prefix}/g2
export g2tmpl_ROOT=${ufslibs_install_prefix}/g2tmpl
export ip_ROOT=${ufslibs_install_prefix}/ip
export nemsio_ROOT=${ufslibs_install_prefix}/nemsio
export sfcio_ROOT=${ufslibs_install_prefix}/sfcio
export sigio_ROOT=${ufslibs_install_prefix}/sigio
export sp_ROOT=${ufslibs_install_prefix}/sp
export upp_ROOT=${ufslibs_install_prefix}/UPP
export w3emc_ROOT=${ufslibs_install_prefix}/w3emc

export GFTL_ROOT=${ufslibs_install_prefix}/gftl_shared
export GFTL_SHARED_ROOT=${ufslibs_install_prefix}/gftl_shared
export YAFYAML_ROOT=${ufslibs_install_prefix}/yafyaml
export MAPL_ROOT=${ufslibs_install_prefix}/mapl

export SCOTCH_ROOT=${ufslibs_install_prefix}/scotch
Expand All @@ -192,7 +188,7 @@ printf '%-.30s ' "Building preproc ..........................."
mkdir build
cd build

cmake .. -DCMAKE_INSTALL_PREFIX="${MYDIR}" -DBUILD_TESTING=OFF
cmake .. -DCMAKE_INSTALL_PREFIX="${MYDIR}" -DBUILD_TESTING=OFF -DGBLEVENTS=OFF

make -j 8
make install
Expand Down Expand Up @@ -271,7 +267,7 @@ printf '%-.30s ' "Building post ..........................."
mkdir build
cd build

cmake ..
cmake .. -DBUILD_WITH_NEMSIO=OFF

make -j 8

Expand Down
210 changes: 65 additions & 145 deletions libs/ufslibs/CMakeLists.txt
View file
Original file line number Diff line number Diff line change
Expand Up @@ -14,41 +14,33 @@ find_package(MPI REQUIRED C CXX Fortran)

set(install_prefix ${CMAKE_INSTALL_PREFIX})

if(${CMAKE_Fortran_COMPILER_ID} MATCHES "^(GNU)$")
if(${CMAKE_Fortran_COMPILER_VERSION} VERSION_GREATER_EQUAL 10)
set(FCFLAGS_pio "${FCFLAGS_pio} -fallow-argument-mismatch -fallow-invalid-boz")
set(FCFLAGS_fms "${FCFLAGS_fms} -fallow-argument-mismatch -fallow-invalid-boz")
set(FCFLAGS_esmf "${FCFLAGS_esmf} -fallow-argument-mismatch -fallow-invalid-boz")
endif()
endif()

option(USE_ZSTD_AND_DYNAMIC_HDF5 "Use zstd and dynamic HDF5" OFF)
if(USE_ZSTD_AND_DYNAMIC_HDF5)
message(STATUS "Use zstd and dynamic HDF5")
endif()

if(USE_ZSTD_AND_DYNAMIC_HDF5)
##
## zstd
##
ExternalProject_Add(zstd
URL https://github.com/facebook/zstd/releases/download/v1.5.5/zstd-1.5.5.tar.gz
URL_HASH MD5=63251602329a106220e0a5ad26ba656f
SOURCE_SUBDIR build/cmake
CMAKE_ARGS -LH
-DCMAKE_INSTALL_PREFIX=${install_prefix}/zstd
-DCMAKE_INSTALL_LIBDIR=lib
-DZSTD_MULTITHREAD_SUPPORT=OFF
-DZSTD_LEGACY_SUPPORT=OFF
-DZSTD_BUILD_STATIC=ON
-DZSTD_BUILD_SHARED=OFF
-DZSTD_BUILD_PROGRAMS=OFF
LOG_DOWNLOAD ON
LOG_CONFIGURE ON
LOG_BUILD ON
LOG_INSTALL ON
)
endif()
# if(${CMAKE_Fortran_COMPILER_ID} MATCHES "^(GNU)$")
# if(${CMAKE_Fortran_COMPILER_VERSION} VERSION_GREATER_EQUAL 10)
# set(FCFLAGS_fms "${FCFLAGS_fms} -fallow-argument-mismatch -fallow-invalid-boz")
# set(FCFLAGS_esmf "${FCFLAGS_esmf} -fallow-argument-mismatch -fallow-invalid-boz")
# endif()
# endif()

##
## zstd
##
ExternalProject_Add(zstd
URL https://github.com/facebook/zstd/releases/download/v1.5.5/zstd-1.5.5.tar.gz
URL_HASH MD5=63251602329a106220e0a5ad26ba656f
SOURCE_SUBDIR build/cmake
CMAKE_ARGS -LH
-DCMAKE_INSTALL_PREFIX=${install_prefix}/zstd
-DCMAKE_INSTALL_LIBDIR=lib
-DZSTD_MULTITHREAD_SUPPORT=OFF
-DZSTD_LEGACY_SUPPORT=OFF
-DZSTD_BUILD_STATIC=ON
-DZSTD_BUILD_SHARED=OFF
-DZSTD_BUILD_PROGRAMS=OFF
LOG_DOWNLOAD ON
LOG_CONFIGURE ON
LOG_BUILD ON
LOG_INSTALL ON
)

##
## zlib
Expand All @@ -57,8 +49,7 @@ ExternalProject_Add(zlib
URL https://github.com/madler/zlib/archive/refs/tags/v1.2.13.tar.gz
URL_HASH MD5=9c7d356c5acaa563555490676ca14d23
BUILD_IN_SOURCE ON
CONFIGURE_COMMAND env "CFLAGS=-fPIC"
./configure --prefix=${install_prefix}/zlib
CONFIGURE_COMMAND ./configure --prefix=${install_prefix}/zlib
--libdir=${install_prefix}/zlib/lib
--static
LOG_DOWNLOAD ON
Expand Down Expand Up @@ -112,88 +103,46 @@ ExternalProject_Add_StepDependencies(libpng build zlib)
##
## hdf5
##
if(USE_ZSTD_AND_DYNAMIC_HDF5)
set(hdf5_enable_shared_libs --enable-shared --disable-static)
else()
set(hdf5_enable_shared_libs --disable-shared --enable-static)
endif()
ExternalProject_Add(hdf5
URL https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5-1_14_0.tar.gz
URL_HASH MD5=7b2d91956be4be8d57e62c1ec4d1a241
BUILD_IN_SOURCE ON
CONFIGURE_COMMAND env "CC=${MPI_C_COMPILER}"
env "CFLAGS=-pthread -fPIC"
./configure --prefix=${install_prefix}/hdf5
--libdir=${install_prefix}/hdf5/lib
${hdf5_enable_shared_libs}
--enable-parallel
--enable-unsupported
--enable-tests=no
--with-zlib=${install_prefix}/zlib
--with-default-plugindir=${install_prefix}/hdf5/lib/plugin
PREFIX ${contrib_prefix}
URL https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5_1.14.4.2.tar.gz
URL_HASH MD5=f1eaf87cc338475deb4aa48fb17cb8f8
PATCH_COMMAND patch -p1 -i ${CMAKE_CURRENT_SOURCE_DIR}/hdf5-1.14.4.2_add_zstd.patch
BUILD_IN_SOURCE OFF
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${install_prefix}/hdf5
-DCMAKE_PREFIX_PATH=${install_prefix}
-DCMAKE_BUILD_TYPE=Release
-DBUILD_SHARED_LIBS=OFF
-DBUILD_TESTING=OFF
-DHDF5_BUILD_TOOLS=OFF
-DHDF5_BUILD_UTILS=OFF
-DHDF5_BUILD_CPP_LIB=OFF
-DHDF5_BUILD_EXAMPLES=OFF
-DHDF5_ENABLE_PARALLEL=ON
-DHDF5_ENABLE_Z_LIB_SUPPORT=ON
-DHDF5_ENABLE_ZSTD_SUPPORT=ON
-Dzstd_ROOT=${install_prefix}/zstd/lib/cmake
-DHDF5_INSTALL_CMAKE_DIR=lib/cmake
LOG_DOWNLOAD ON
LOG_PATCH ON
LOG_CONFIGURE ON
LOG_BUILD ON
LOG_INSTALL ON
)
ExternalProject_Add_StepDependencies(hdf5 build zlib)

if(USE_ZSTD_AND_DYNAMIC_HDF5)
##
## hdf5_plugins
##
ExternalProject_Add(hdf5_plugins
URL https://github.com/HDFGroup/hdf5_plugins/archive/refs/tags/1.14.0.tar.gz
URL_HASH MD5=4a23f03245e72c64079b876218fed2b9
BUILD_IN_SOURCE OFF
CMAKE_ARGS -C <SOURCE_DIR>/config/cmake/cacheinit.cmake
-DCMAKE_C_COMPILER=${MPI_C_COMPILER}
-DCMAKE_BUILD_TYPE=Release
-DCMAKE_INSTALL_PREFIX=${install_prefix}/hdf5
-DHDF5_INCLUDE_DIR=${install_prefix}/hdf5/include/
-DHDF5_LINK_LIBS=${install_prefix}/hdf5/lib/
-DUSE_SHARED_LIBS=ON
-DBUILD_SHARED_LIBS=ON
-DENABLE_BSHUF=OFF
-DENABLE_BLOSC=OFF
-DENABLE_BZIP2=OFF
-DENABLE_JPEG=OFF
-DENABLE_LZ4=OFF
-DENABLE_LZF=OFF
-DTGZPATH=<SOURCE_DIR>/libs
-DH5PL_ALLOW_EXTERNAL_SUPPORT=TGZ
-DBUILD_EXAMPLES=OFF
LOG_DOWNLOAD ON
LOG_CONFIGURE ON
LOG_BUILD ON
LOG_INSTALL ON
)
ExternalProject_Add_StepDependencies(hdf5_plugins build hdf5)
endif()
ExternalProject_Add_StepDependencies(hdf5 build zlib zstd)


##
## netcdf
##
if(USE_ZSTD_AND_DYNAMIC_HDF5)
set(netcdf_cppflags_env "CPPFLAGS=-I${install_prefix}/hdf5/include -I${install_prefix}/zstd/include")
set(netcdf_ldflags_env "LDFLAGS=-L${install_prefix}/hdf5/lib -L${install_prefix}/zstd/lib -L${install_prefix}/zlib/lib -Wl,-rpath -Wl,${install_prefix}/hdf5/lib")
set(netcdf_libs_env "LIBS=-lhdf5_hl -lhdf5 -lz -lzstd -lm")
set(netcdf_ld_library_path_env "LD_LIBRARY_PATH=${install_prefix}/hdf5/lib:$ENV{LD_LIBRARY_PATH}")
else()
set(netcdf_cppflags_env "CPPFLAGS=-I${install_prefix}/hdf5/include")
set(netcdf_ldflags_env "LDFLAGS=-L${install_prefix}/hdf5/lib -L${install_prefix}/zlib/lib")
set(netcdf_libs_env "LIBS=-lhdf5_hl -lhdf5 -lz -lm")
set(netcdf_ld_library_path_env "")
endif()
ExternalProject_Add(netcdf
URL https://github.com/Unidata/netcdf-c/archive/v4.9.2.tar.gz
URL_HASH MD5=84acd096ab4f3300c20db862eecdf7c7
BUILD_IN_SOURCE ON
CONFIGURE_COMMAND env "CC=${MPI_C_COMPILER}"
env ${netcdf_cppflags_env}
env ${netcdf_ldflags_env}
env ${netcdf_libs_env}
env ${netcdf_ld_library_path_env}
env "CPPFLAGS=-I${install_prefix}/hdf5/include"
env "LDFLAGS=-L${install_prefix}/hdf5/lib -L${install_prefix}/zstd/lib -L${install_prefix}/zlib/lib"
env "LIBS=-lhdf5_hl -lhdf5 -lzstd -lz -lm"
./configure --prefix=${install_prefix}/netcdf
--libdir=${install_prefix}/netcdf/lib
--enable-cdf5
Expand All @@ -213,40 +162,25 @@ ExternalProject_Add(netcdf
LOG_INSTALL ON
)
ExternalProject_Add_StepDependencies(netcdf build hdf5)
if(USE_ZSTD_AND_DYNAMIC_HDF5)
ExternalProject_Add_StepDependencies(netcdf build zstd)
endif()

##
## netcdf_fortran
##
if(USE_ZSTD_AND_DYNAMIC_HDF5)
set(netcdf_fortran_cppflags_env "CPPFLAGS=-I${install_prefix}/netcdf/include")
set(netcdf_fortran_ldflags_env "LDFLAGS=-L${install_prefix}/hdf5/lib -L${install_prefix}/zstd/lib -L${install_prefix}/netcdf/lib -L${install_prefix}/zlib/lib -Wl,-rpath -Wl,${install_prefix}/hdf5/lib")
set(netcdf_fortran_libs_env "LIBS=-lnetcdf -lhdf5_hl -lhdf5 -lz -lzstd -lm")
set(netcdf_fortran_ld_library_path_env "LD_LIBRARY_PATH=${install_prefix}/hdf5/lib:$ENV{LD_LIBRARY_PATH}")
else()
set(netcdf_fortran_cppflags_env "CPPFLAGS=-I${install_prefix}/netcdf/include")
set(netcdf_fortran_ldflags_env "LDFLAGS=-L${install_prefix}/hdf5/lib -L${install_prefix}/netcdf/lib -L${install_prefix}/zlib/lib")
set(netcdf_fortran_libs_env "LIBS=-lnetcdf -lhdf5_hl -lhdf5 -lz -lm")
set(netcdf_fortran_ld_library_path_env "")
endif()

ExternalProject_Add(netcdf_fortran
URL https://github.com/Unidata/netcdf-fortran/archive/v4.6.1.tar.gz
URL_HASH MD5=8c200fcf7d9d2761037dfd2dabe2216b
BUILD_IN_SOURCE ON
CONFIGURE_COMMAND env "CC=${MPI_C_COMPILER}"
env "FC=${MPI_Fortran_COMPILER}"
env ${netcdf_fortran_cppflags_env}
env ${netcdf_fortran_ldflags_env}
env ${netcdf_fortran_libs_env}
env ${netcdf_fortran_ld_library_path_env}
env "CPPFLAGS=-I${install_prefix}/netcdf/include"
env "LDFLAGS=-L${install_prefix}/hdf5/lib -L${install_prefix}/netcdf/lib -L${install_prefix}/zstd/lib -L${install_prefix}/zlib/lib"
env "LIBS=-lnetcdf -lhdf5_hl -lhdf5 -lzstd -lz -lm"
env "HDF5_PLUGIN_PATH=${install_prefix}/hdf5/lib/plugin"
./configure --prefix=${install_prefix}/netcdf
--libdir=${install_prefix}/netcdf/lib
--enable-static
--disable-shared
--enable-logging
--enable-zstandard_plugin
LOG_DOWNLOAD ON
LOG_CONFIGURE ON
LOG_BUILD ON
Expand All @@ -265,6 +199,8 @@ ExternalProject_Add(pio
-DCMAKE_C_COMPILER=${MPI_C_COMPILER}
-DCMAKE_Fortran_COMPILER=${MPI_Fortran_COMPILER}
-DPIO_ENABLE_TIMING=OFF
-DPIO_ENABLE_DOC=OFF
-DPIO_ENABLE_EXAMPLES=OFF
-DNetCDF_PATH=${install_prefix}/netcdf
-DHDF5_PATH=${install_prefix}/hdf5
-DLIBZ_PATH=${install_prefix}/zlib
Expand Down Expand Up @@ -317,7 +253,7 @@ if(NOT MPITYPE)
if(MPI_C_LIBRARY_VERSION_STRING MATCHES ".*CRAY MPICH.*" AND MPI_C_VERSION_MAJOR MATCHES "3")
set(MPITYPE "mpi")
elseif(MPI_C_LIBRARY_VERSION_STRING MATCHES ".*MPICH.*" AND MPI_C_VERSION_MAJOR MATCHES "3")
set(MPITYPE "mpich3")
set(MPITYPE "mpich")
elseif(MPI_C_LIBRARY_VERSION_STRING MATCHES ".*MPICH.*" AND MPI_C_VERSION_MAJOR MATCHES "4")
set(MPITYPE "mpich")
elseif(MPI_C_LIBRARY_VERSION_STRING MATCHES ".*Open MPI.*" AND MPI_C_VERSION_MAJOR MATCHES "3")
Expand Down Expand Up @@ -345,7 +281,7 @@ list(APPEND esmf_env ESMF_MPIRUN=mpiexec)
list(APPEND esmf_env ESMF_NETCDF_INCLUDE=${install_prefix}/netcdf/include)
list(APPEND esmf_env ESMF_NETCDF_LIBPATH=${install_prefix}/netcdf/lib)
list(APPEND esmf_env ESMF_NETCDF=split)
list(APPEND esmf_env "ESMF_NETCDF_LIBS=-lnetcdff -lnetcdf -L${install_prefix}/hdf5/lib -lhdf5_hl -lhdf5 -L${install_prefix}/zlib/lib -lz -ldl -lm")
list(APPEND esmf_env "ESMF_NETCDF_LIBS=-lnetcdff -lnetcdf -L${install_prefix}/hdf5/lib -lhdf5_hl -lhdf5 -L${install_prefix}/zstd/lib -lzstd -L${install_prefix}/zlib/lib -lz -ldl -lm")
list(APPEND esmf_env ESMF_PIO=external)
list(APPEND esmf_env ESMF_PIO_INCLUDE=${install_prefix}/pio/include)
list(APPEND esmf_env ESMF_PIO_LIBPATH=${install_prefix}/pio/lib)
Expand Down Expand Up @@ -377,22 +313,10 @@ set(bacio_tag 2.4.1)
set(g2_tag 3.4.5)
set(g2tmpl_tag 1.10.2)
set(ip_tag 4.3.0)
set(nemsio_tag 2.5.4)
set(sfcio_tag 1.4.1)
set(sigio_tag 2.3.2)
set(sp_tag 2.5.0)
set(w3emc_tag 2.10.0)

foreach(lib_name
bacio
g2
g2tmpl
ip
nemsio
sfcio
sigio
sp
w3emc)
foreach(lib_name bacio g2 g2tmpl ip sp w3emc)

ExternalProject_Add(${lib_name}
GIT_REPOSITORY https://github.com/NOAA-EMC/NCEPLIBS-${lib_name}
Expand All @@ -408,9 +332,6 @@ foreach(lib_name
-Dg2_ROOT=${install_prefix}/g2
-Dg2tmpl_ROOT=${install_prefix}/g2tmpl
-Dip_ROOT=${install_prefix}/ip
-Dnemsio_ROOT=${install_prefix}/nemsio
-Dsfcio_ROOT=${install_prefix}/sfcio
-Dsigio_ROOT=${install_prefix}/sigio
-Dsp_ROOT=${install_prefix}/sp
-Dw3emc_ROOT=${install_prefix}/w3emc
-DBUILD_WITH_BUFR=OFF
Expand All @@ -424,7 +345,6 @@ endforeach()

ExternalProject_Add_StepDependencies(g2 build jasper libpng)
ExternalProject_Add_StepDependencies(ip build sp)
ExternalProject_Add_StepDependencies(nemsio build bacio w3emc)
ExternalProject_Add_StepDependencies(w3emc build bacio)

##
Expand Down Expand Up @@ -505,7 +425,7 @@ message(STATUS "Set MAPL's MPI_STACK to ${MPITYPE}")

ExternalProject_Add(mapl
URL https://github.com/GEOS-ESM/MAPL/archive/refs/tags/v2.46.0.tar.gz
URL_HASH MD5=031bf295ba831f7bf308ace66fd23af1
URL_HASH MD5=7be5f4dc91597db772086691d80bfbfc
BUILD_IN_SOURCE OFF
LIST_SEPARATOR ,
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${install_prefix}/mapl
Expand All @@ -514,7 +434,7 @@ ExternalProject_Add(mapl
-DCMAKE_PREFIX_PATH=${install_prefix}/ecbuild
-DCMAKE_MODULE_PATH=${install_prefix}/esma_cmake,${install_prefix}/ecbuild
-DNetCDF_ROOT=${install_prefix}/netcdf
-DNetCDF_Fortran_EXTRA_LIBRARIES=-L${install_prefix}/netcdf/lib,-lnetcdf,-L${install_prefix}/hdf5/lib,-lhdf5_hl,-lhdf5,-L${install_prefix}/zlib/lib,-lz,-ldl,-lm
-DNetCDF_Fortran_EXTRA_LIBRARIES=-L${install_prefix}/netcdf/lib,-lnetcdf,-L${install_prefix}/hdf5/lib,-lhdf5_hl,-lhdf5,-L${install_prefix}/zstd/lib,-lzstd,-L${install_prefix}/zlib/lib,-lz,-ldl,-lm
-DHDF5_ROOT=${install_prefix}/hdf5
-DGFTL_ROOT=${install_prefix}/gftl_shared
-DGFTL_SHARED_ROOT=${install_prefix}/gftl_shared
Expand Down
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