如何安装 Weather Research and Forecasting Model 系统相关组件

发布于: Oct 10, 2022

以下流程图可以看出，WRF 模式系统主要包含的组件有：
• WRF Preprocessing System（WPS）
• OBSGRID
• WRF-DA
• ARW Solver（WRF 计算主程序）
• 后处理和可视化

以下步骤包含了对 WRF 主程序，WPS，WRFDA，OBSGRID 的安装：
首先 WRF 依赖于 gfortan 编译器和 gcc、cpp 的库，在此基础之上依赖于基本库 NetCDF 和用于并行计算的库 MPICH，在运行 WRF 任务之前，还需要通过WPS（WRF Pre-processing System）做数据的预处理。所以在 WRF 的安装过程中，首先要更新依赖的编译器和库，然后安装 NetCDF 和 MPICH，然后安装和编译 WRF，设定好目录后安装和编译 WPS。
在本次实验中，为了获得更好的性能，我们将会使用 GCC 10.2 进行编译。GCC 10 包含了大量的新架构特性，相比 GCC 旧版本，性能更好。下图是 GCC 8/9/10 相对 GCC7 的性能提升  

1. 登录主节点

打开 Amazon Web Service 控制台，选择 EC2 服务，找到集群主节点（默认标签为Master），ssh登录。登录后，可以看到 Amazon FSx for Lustre 高性能文件系统已经挂载在 /fsx。该实验会将软件的源码下载 /fsx/tools，编译后的二进制文件则存放在 /fsx/wrf-arm。创建相关目录

$ mkdir /fsx/wrf-arm
$ mkdir /fsx/tools

为了安装方便，我们将安装过程中的相关变量写在文件

/fsx/wrf-arm/wrf-install.env里
$ view /fsx/wrf-arm/wrf-install.env
export DOWNLOAD=/fsx/tools
export WRF_INSTALL=/fsx/wrf-arm
export WRF_DIR=${WRF_INSTALL}/WRF-4.2.2
export GCC_VERSION=10.2.0
export OPENMPI_VERSION=4.1.0
export PATH=${WRF_INSTALL}/gcc-${GCC_VERSION}/bin:$PATH
export LD_LIBRARY_PATH=${WRF_INSTALL}/gcc-${GCC_VERSION}/lib64:$LD_LIBRARY_PATH
export CC=gcc
export CXX=g++
export FC=gfortran
export PATH=${WRF_INSTALL}/openmpi-${OPENMPI_VERSION}/bin:$PATH
export LD_LIBRARY_PATH=${WRF_INSTALL}/openmpi-${OPENMPI_VERSION}/lib:$LD_LIBRARY_PATH
export CC=mpicc
export CXX=mpic++
export FC=mpifort
export F90=mpifort
export CXX=mpicxx
export FC=mpif90
export F77=mpif90
export F90=mpif90
export CFLAGS="-g -O2 -fPIC"
export CXXFLAGS="-g -O2 -fPIC"
export FFLAGS="-g -fPIC -fallow-argument-mismatch"
export FCFLAGS="-g -fPIC -fallow-argument-mismatch"
export FLDFLAGS="-fPIC"
export F90LDFLAGS="-fPIC"
export LDFLAGS="-fPIC"
export HDF5=${WRF_INSTALL}/hdf5
export PNET=${WRF_INSTALL}/pnetcdf
export ZLIB=${WRF_INSTALL}/zlib
export CPPFLAGS="-I$HDF5/include -I${PNET}/include"
export CFLAGS="-I$HDF5/include -I${PNET}/include"
export CXXFLAGS="-I$HDF5/include -I${PNET}/include"
export FCFLAGS="-I$HDF5/include -I${PNET}/include"
export FFLAGS="-I$HDF5/include -I${PNET}/include"
export LDFLAGS="-I$HDF5/include -I${PNET}/include -L$ZLIB/lib -L$HDF5/lib -L${PNET}/lib"
export NCDIR=${WRF_INSTALL}/netcdf
export LD_LIBRARY_PATH=${NCDIR}/lib:${LD_LIBRARY_PATH}
export CPPFLAGS="-I$HDF5/include -I$NCDIR/include"
export CFLAGS="-I$HDF5/include -I$NCDIR/include"
export CXXFLAGS="-I$HDF5/include -I$NCDIR/include"
export FCFLAGS="-I$HDF5/include -I$NCDIR/include"
export FFLAGS="-I$HDF5/include -I$NCDIR/include"
export LDFLAGS="-L$HDF5/lib -L$NCDIR/lib"
export PHDF5=${WRF_INSTALL}/hdf5
export NETCDF=${WRF_INSTALL}/netcdf
export PNETCDF=${WRF_INSTALL}/pnetcdf
export PATH=${WRF_INSTALL}/netcdf/bin:${PATH}
export PATH=${WRF_INSTALL}/pnetcdf/bin:${PATH}
export PATH=${WRF_INSTALL}/hdf5/bin:${PATH}
export LD_LIBRARY_PATH=${WRF_INSTALL}/netcdf/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=${WRF_INSTALL}/pnetcdf/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=${WRF_INSTALL}/hdf5/lib:$LD_LIBRARY_PATH
export WRFIO_NCD_LARGE_FILE_SUPPORT=1
export NETCDF_classic=1
export F77=mpifort
export FFLAGS="-g -fPIC"
export FCFLAGS="-g -fPIC"
export JASPERLIB=${WRF_INSTALL}/jasper/lib
export JASPERINC=${WRF_INSTALL}/jasper/include

2. 安装 GCC 10.2 

$ source /fsx/wrf-arm/wrf-install.env
$ wget https://ftp.gnu.org/gnu/gcc/gcc-${GCC_VERSION}/gcc-${GCC_VERSION}.tar.gz
$ tar -xzvf gcc-${GCC_VERSION}.tar.gz
$ cd gcc-${GCC_VERSION}
$ ./contrib/download_prerequisites
$ mkdir obj.gcc-${GCC_VERSION}
$ cd obj.gcc-${GCC_VERSION}
$ ../configure --disable-multilib --enable-languages=c,c++,fortran --prefix=${WRF_INSTALL}/gcc-${GCC_VERSION}
$ make -j $(nproc) && make install

编译过程大概需要30分钟。

3. 安装 OpenMPI

浏览器打开 https://www.open-mpi.org/ 查看最新版本的 open-mpi 源码的下载地址，以下命令下载并编译 OpenMPI 4.1.0

$ source /fsx/wrf-arm/wrf-install.env
$ cd $DOWNLOAD
$ wget -N https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.0.tar.gz
$ tar -xzvf openmpi-4.1.0.tar.gz
$ cd openmpi-4.1.0
$ mkdir build
$ cd build
$ ../configure --prefix=${WRF_INSTALL}/openmpi-${OPENMPI_VERSION} --enable-mpirun-prefix-by-default
$ make -j$(nproc) && make install

4. 安装 ZLIB 

$ source /fsx/wrf-arm/wrf-install.env
$ cd $DOWNLOAD
$ wget -N http://www.zlib.net/zlib-1.2.11.tar.gz
$ tar -xzvf zlib-1.2.11.tar.gz
$ cd zlib-1.2.11
$ ./configure --prefix=${WRF_INSTALL}/zlib
$ make check && make install

5. 安装 HDF5

浏览器打开 https://www.hdfgroup.org/downloads/hdf5/source-code/ 查看最新版本的 HDF5 源码的下载地址，例如 hdf5-1.12.0 的下载地址为 https://www.hdfgroup.org/package/hdf5-1-12-0-tar-gz/?wpdmdl=14582

$ source /fsx/wrf-arm/wrf-install.env
$ cd $DOWNLOAD
$ curl -o hdf5-1.12.0.tar.gz -J -L https://www.hdfgroup.org/package/hdf5-1-12-0-tar-gz/?wpdmdl=14582
$ tar -xzvf hdf5-1.12.0.tar.gz
$ cd hdf5-1.12.0
$ ./configure --prefix=${WRF_INSTALL}/hdf5 --with-zlib=${WRF_INSTALL}/zlib --enable-parallel --enable-shared --enable-hl --enable-fortran
$ make -j$(nproc) && make install

6. 安装 Parallel-NETCDF

Parallel-NETCDF 可在官网 https://parallel-netcdf.github.io/wiki/Download.html 下载最新版本。

$ source /fsx/wrf-arm/wrf-install.env
$ cd $DOWNLOAD
$ wget -N https://parallel-netcdf.github.io/Release/pnetcdf-1.12.2.tar.gz
$ tar -xzvf pnetcdf-1.12.2.tar.gz
$ cd pnetcdf-1.12.2
$ ./configure --prefix=${WRF_INSTALL}/pnetcdf --enable-fortran --enable-large-file-test --enable-shared
$ make -j$(nproc) && make install

7. 安装 NETCDF

NETCDF 可在官网 https://www.unidata.ucar.edu/downloads/netcdf/ 下载最新版本。

7.1 安装NetCDF-C 

$ source /fsx/wrf-arm/wrf-install.env
$ cd $DOWNLOAD
$ wget -N https://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-c-4.7.4.tar.gz
$ tar -xzvf netcdf-c-4.7.4.tar.gz
$ cd netcdf-c-4.7.4
$ ./configure --prefix=$NCDIR CPPFLAGS="-I$HDF5/include -I$PNET/include" CFLAGS="-DHAVE_STRDUP -O3 -march=armv8.2-a+crypto+fp16+rcpc+dotprod" LDFLAGS="-L$HDF5/lib -L$PNET/lib" --enable-pnetcdf --enable-large-file-tests --enable-largefile  --enable-parallel-tests --enable-shared --enable-netcdf-4  --with-pic --disable-doxygen --disable-dap
$ make -j$(nproc) && make install

7.2 安装 NetCDF-F 

$ source /fsx/wrf-arm/wrf-install.env
$ wget -N https://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-fortran-4.5.3.tar.gz
$ tar -xzvf netcdf-fortran-4.5.3.tar.gz
$ cd netcdf-fortran-4.5.3
$ ./configure --prefix=$NCDIR --disable-static --enable-shared --with-pic --enable-parallel-tests --enable-large-file-tests --enable-largefile
$ make -j$(nproc) && make install

8. 安装 WRF

8.1 下载 WRF

WRF 可以在 Github 上下载 https://github.com/wrf-model/WRF/tree/master

$ source /fsx/wrf-arm/wrf-install.env
$ cd ${WRF_INSTALL}
$ curl -o WRF-v4.2.2.zip -J -L https://github.com/wrf-model/WRF/archive/v4.2.2.zip
$ unzip WRF-v4.2.2.zip
$ cd WRF-4.2.2

8.2 编译配置文件

使用你熟悉的编辑器，例如 view 编辑文件arch/configure.defaults，在行 #insert new stanza here 与 #ARCH Fujitsu FX10/FX100... 之间添加以下内容：

###########################################################
#ARCH    Linux aarch64, GCC compiler OpenMPI # serial smpar dmpar dm+sm
#
DESCRIPTION     =      GCC ($SFC/$SCC): Aarch64
DMPARALLEL      =
OMPCPP          =      -fopenmp
OMP             =      -fopenmp
OMPCC           =      -fopenmp
SFC             =      gfortran
SCC             =      gcc
CCOMP           =      gcc
DM_FC           =      mpif90
DM_CC           =      mpicc -DMPI2_SUPPORT
FC              =      CONFIGURE_FC
CC              =      CONFIGURE_CC
LD              =      $(FC)
RWORDSIZE       =      CONFIGURE_RWORDSIZE
PROMOTION       =
ARCH_LOCAL      =
CFLAGS_LOCAL    =      -w -O3 -c
LDFLAGS_LOCAL   =      -fopenmp
FCOPTIM         =      -Ofast -march=armv8.2-a+fp16+rcpc+dotprod+crypto -fopenmp -frecursive -funroll-loops
FCREDUCEDOPT    =      $(FCOPTIM)
FCNOOPT         =      -O0 -fopenmp -frecursive
FCDEBUG         =      -g $(FCNOOPT)
FORMAT_FIXED    =      -ffixed-form -ffixed-line-length-0 -fallow-argument-mismatch -fallow-invalid-boz
FORMAT_FREE     =      -ffree-form -ffree-line-length-0 -fallow-argument-mismatch -fallow-invalid-boz
FCSUFFIX        =
BYTESWAPIO      =      -fconvert=big-endian -frecord-marker=4
FCBASEOPTS      =      -w $(FORMAT_FREE) $(BYTESWAPIO)
MODULE_SRCH_FLAG=      -I$(WRF_SRC_ROOT_DIR)/main
TRADFLAG        =      -traditional-cpp
CPP             =      /lib/cpp CONFIGURE_CPPFLAGS
AR              =      ar
ARFLAGS         =      ru
M4              =      m4 -B 14000
RANLIB          =      ranlib
RLFLAGS         =
CC_TOOLS        =      $(SCC)

8.3 编译选项 

$ ./configure
编译选项选择
8. (dm+sm) GCC (gfortran/gcc): Aarch64
Select Option 1 -Compile for nesting? (1=basic, 2=preset moves, 3=vortex following) [default 1]:

8.4 执行编译 

$ ./compile -j $(nproc) em_real 2>&1 | tee compile_wrf.out

编译成功后，你可以在main目录下 WRF-4.2.2/main 找到WRF的EXE文件
  main/ndown.exe
main/real.exe
main/tc.exe
main/wrf.exe

9.安装 WPS 4.2

9.1 安装 Jasper

下载 Jasper

$ source /fsx/wrf-arm/wrf-install.env
$ cd $DOWNLOAD
$ wget https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compile_tutorial/tar_files/jasper-1.900.1.tar.gz
$ tar -xzvf jasper-1.900.1.tar.gz

在编译之前,我们需要从 http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD 下载config.guess文件并覆盖目录 jasper-1.900.1 下的 acaux/config.guess
  执行以下命令进行下载并覆盖原config.guess文件

$ cd $DOWNLOAD/jasper-1.900.1
$ wget -N -O acaux/config.guess "http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD"

安装 Jasper 

$ cd $DOWNLOAD/jasper-1.900.1
$ ./configure --prefix=${WRF_INSTALL}/jasper
$ make -j$(nproc) install

9.2 安装 WPS

下载最新版本的 WPS https://github.com/wrf-model/WPS/releases/ 以下示例下载并安装4.2版本

$ source /fsx/wrf-arm/wrf-install.env
$ cd $DOWNLOAD
$ curl -o WPS-v4.2.tar.gz -J -L https://github.com/wrf-model/WPS/archive/refs/tags/v4.2.tar.gz
$ tar -xzvf WPS-v4.2.tar.gz -C ${WRF_INSTALL}
$ cd ${WRF_INSTALL}/WPS-4.2

使用文本编辑器在文件 arch/configure.defaults 顶部添加以下内容 

########################################################################################################################
#ARCH Linux aarch64, Arm compiler OpenMPI # serial smpar dmpar dm+sm#
COMPRESSION_LIBS    = CONFIGURE_COMP_L
COMPRESSION_INC     = CONFIGURE_COMP_I
FDEFS               = CONFIGURE_FDEFS
SFC                 = gfortran
SCC                 = gcc
DM_FC               = mpif90
DM_CC               = mpicc
FC                  = CONFIGURE_FC
CC                  = CONFIGURE_CC
LD                  = $(FC)
FFLAGS              = -ffree-form -O -fconvert=big-endian -frecord-marker=4 -ffixed-line-length-0 -fallow-argument-mismatch -fallow-invalid-boz
F77FLAGS            = -ffixed-form -O -fconvert=big-endian -frecord-marker=4 -ffree-line-length-0 -fallow-argument-mismatch -fallow-invalid-boz
FCSUFFIX            =
FNGFLAGS            = $(FFLAGS)
LDFLAGS             =
CFLAGS              =
CPP                 = /usr/bin/cpp -P -traditional
CPPFLAGS            = -D_UNDERSCORE -DBYTESWAP -DLINUX -DIO_NETCDF -DBIT32 -DNO_SIGNAL CONFIGURE_MPI
RANLIB              = ranlib

编译安装

$ ./configure

编译选项选择 

Linux aarch64, Arm compiler OpenMPI (dmpar)

若遇到如下的输出提示，忽略即可。

Your versions of Fortran and NETCDF are not consistent.

编译之前, 我们还需要修改WPS-4.2目录下的文件 configure.wps 中的 WRF_LIB 值，将 -L$(NETCDF)/lib -lnetcdf 更改成 -L$(NETCDF)/lib -lnetcdff -lnetcdf -lgomp
  如下所示:

WRF_LIB = -L$(WRF_DIR)/external/io_grib1 -lio_grib1 \
-L$(WRF_DIR)/external/io_grib_share -lio_grib_share \
-L$(WRF_DIR)/external/io_int -lwrfio_int \
-L$(WRF_DIR)/external/io_netcdf -lwrfio_nf \
-L$(NETCDF)/lib -lnetcdff -lnetcdf -lgomp

执行编译 

$ ./compile | tee compile_wps.out

编译成功后，可以在当前目录下看到3个可执行文件:
geogrid.exe → geogrid/src/geogrid.exe
ungrib.exe → ungrib/src/ungrib.exe
metgrid.exe → metgrid/src/metgrid.exe

10. 安装 WRFDA

WRFDA 是一个统一的模型空间数据同化系统，可以全球或区域，多模型，3/4D-Var。其组成及各组成间的联系如图所示。 

在4.0之后的版本，WRFDA 的编译安装可以在 WRF 源码上进行。
解压WRF到目录 WRFDA-4.2.2

$ source /fsx/wrf-arm/wrf-install.env
$ cd ${WRF_INSTALL}
$ unzip -d /tmp WRF-v4.2.2.zip
$ mv /tmp/WRF-4.2.2 ${WRF_INSTALL}/WRFDA-4.2.2
$ cd ${WRF_INSTALL}/WRFDA-4.2.2

编译

$ ./configure wrfda

编译选项选择

3. (dmpar)

执行编译

$ ./compile all_wrfvar 2>&1 | tee compile_wrfda.out

编译成功后，你可以在 ${WRF_INSTALL}/WRFDA-4.2.2/var/build/ 目录下找到WRFDA的EXE文件
  da_wrfvar.exe

11. 安装 OBSGRID

下载 OBSGRID

OBSGRID 可以在 Github 下载 https://github.com/wrf-model/OBSGRID

$ source /fsx/wrf-arm/wrf-install.env
$ cd ${WRF_INSTALL}
$ git clone https://github.com/wrf-model/OBSGRID
$ cd ${WRF_INSTALL}/OBSGRID

编译配置文件
使用你熟悉的编辑器，例如 view 编辑文件 arch/configure.defaults，在顶部添加以下内容：

###########################################################
#ARCH Linux aarch64,  gfortran compiler
#
FC              =       gfortran
FFLAGS          = -ffree-form -O -fconvert=big-endian -frecord-marker=4 -ffixed-line-length-0 -fallow-argument-mismatch -fallow-invalid-boz
F77FLAGS        = -ffixed-form -O -fconvert=big-endian -frecord-marker=4 -ffree-line-length-0 -fallow-argument-mismatch -fallow-invalid-boz
FNGFLAGS        =       $(FFLAGS)
LDFLAGS         =
CC              =       gcc
CFLAGS          =
CPP             =       /usr/bin/cpp -P -traditional
CPPFLAGS        = -D_UNDERSCORE -DBYTESWAP -DLINUX -DIO_NETCDF -DBIT32 -DNO_SIGNAL

编译

$ ./configure

选择

Select 1. Linux aarch64, gfortran compiler

修改文件 configure.oa 中 NETCDF_LIBS 的值 

NETCDF_LIBS = -L${NETCDF}/lib -lnetcdff -lnetcdf

执行编译 

$ ./compile 2>&1 | tee -a compile_oa.out

目前缺乏NCAR Graphics Library, 所以编译plot的程序时会收到失败的信息(但不影响OBSGRID的编译)
gfortran -o plot_soundings.exe plot_soundings.o module_mapinfo.o module_report.o module_skewt.o date_pack_module.o -L/lib -lncarg -lncarg_gks -lncarg_c -lX11 -lm -lcairo -L/fsx/wrf-arm/netcdf/lib -lnetcdff -lnetcdf -I/fsx/wrf-arm/netcdf/include
/usr/bin/ld: cannot find -lncarg
/usr/bin/ld: cannot find -lncarg_gks
/usr/bin/ld: cannot find -lncarg_c
/usr/bin/ld: cannot find -lcairo
collect2: error: ld returned 1 exit status
编译成功后，你可以在 OBSGRID 当前目录下${WRF_INSTALL}/OBSGRID找到 OBSGRID 的EXE文件 obsgrid.exe 

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