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简介
FVCOM是无结构三角形网格架构、有限体积、自由表面、三维原始方程海洋数值模型,包含了多种物理、水质、生态计算模块。FVCOM模型输入输出基于标准化NETCDF格式,具有平台通用兼容性,并能使用VISIT可视化软件是输入输出结构进行快速二维/三维可视化。该模型基于Fortran 90/95标准,且在MPI(Message Passing Interface)的框架下实现计算并行化,可以在共享内存及分布式内存多计算节点的 高性能计算 机上实现并行快速模拟。 配置流程1.获取源代码和测试数据 本文档所测试版本为:FVCOM v4.1 软件获取路径为:官网注册申请,获取授权后下载 FVCOM官网:http://fvcom.smast.umassd.edu/ METIS组件补丁包下载地址:https://www.math-linux.com/IMG/patch/metis-4.0.patch 本文以FVCOM v4.1为例,编译安装FVCOM。 1)执行以下步骤获取主程序源码: 通过官方网址注册(http://fvcom.smast.umassd.edu/wp-login.php?action=register) 注册成功后登陆(http://fvcom.smast.umassd.edu/wp-login.php) 点击下图红框链接 访问受限 获取授权后可通过如下方式执行主程序和补丁包文件下载: wget http://fvcom.smast.umassd.edu/releases/fvcom-4.1.tar.gz wget https://www.math-linux.com/IMG/patch/metis-4.0.patch2.基础环境安装 1)执行如下命令,安装必要的系统组件 yum install-y curl-devel libcurl-devel zlib-devel2)执行如下命令下载基础环境软件包 wget https://ftp.gnu.org/gnu/gcc/gcc-9.1.0/gcc-9.1.0.tar.gz wget https://download.open-mpi.org/release/open-mpi/v3.1/openmpi-3.1.4.tar.gz wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.5/src/hdf5-1.10.5.tar.gz wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-c-4.7.0.tar.gz wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-4.4.5.tar.gz3)依次执行如下命令升级安装最新版gcc编译器(当前为gcc v9.1.0) tar-zxvf gcc-9.1.0.tar.gz cd gcc-9.1.0 ./contrib/download_prerequisites ./configure--prefix=/usr/local/gcc/9.1.0 make-j 4 make install cd-4)依次执行如下命令安装并行库OpenMPI(v3.1.4) export GCC_HOME=/usr/local/gcc/9.1.0/ export PATH=$GCC_HOME/bin:$PATH export LD_LIBRARY_PATH=$GCC_HOME/lib:$GCC_HOME/lib64:$LD_LIBRARY_PATH export INCLUDE=$GCC_HOME/include:$INCLUDE tar-zxvf openmpi-3.1.4.tar.gz cd openmpi-3.1.4 ./configure--prefix=/usr/local/openmpi3--enable-orterun-prefix-by-default make-j 4 make install cd-5)依次执行如下命令安装数据格式库HDF5(v1.10.5) export MPI_HOME=/usr/local/openmpi3 export PATH=$MPI_HOME/bin:$PATH export LD_LIBRARY_PATH=$MPI_HOME/lib:$LD_LIBRARY_PATH export INCLUDE=$MPI_HOME/include:$INCLUDE tar-zxvf hdf5-1.10.5.tar.gz cd hdf5-1.10.5 ./configure--prefix=/usr/local//hdf5--enable-fortran--enable-parallel CC=mpicc FC=mpif90 CXX=mpicxx make-j 4 make install cd-6)依次执行如下命令安装数据格式库NetCDF(v4.x.x) export HDF5=/usr/local/hdf5 export PATH=$HDF5/bin:$PATH export LD_LIBRARY_PATH=$HDF5/lib:$LD_LIBRARY_PATH export INCLUDE=$HDF5/include:$INCLUDE tar-zxvf netcdf-c-4.7.0.tar.gz cd netcdf-c-4.7.0 ./configure--prefix=/usr/local/netcdf LDFLAGS="-L$HDF5/lib"CPPFLAGS="-I$HDF5/include"CC=mpicc--disable-dap make-j 4 make install cd- export NETCDF=/usr/local/netcdf export PATH=$NETCDF/bin:$PATH export LD_LIBRARY_PATH=$NETCDF/lib:$LD_LIBRARY_PATH export INCLUDE=$NETCDF/include:$INCLUDE tar-zxvf netcdf-fortran-4.4.5.tar.gz cd netcdf-fortran-4.4.5 ./configure--prefix=/usr/local/netcdf CPPFLAGS="-I$HDF5/include-I$NETCDF/include"LDFLAGS="-L$HDF5/lib-L$NETCDF/lib"CC=mpicc FC=mpif90 F77=mpif90 make-j 4 make install cd-3.主程序安装 1)依次执行如下命令,创建主程序安装目录,并解压缩FVCOM源码和METIS组件补丁至安装目录 mkdir-p/usr/local/fvcom tar xvf fvcom-4.1.tar.gz-C/usr/local/fvcom cp metis-4.0.patch/usr/local/fvcom/FVCOM4.1/METIS_source/2)依次使用如下命令,创建依赖组件环境变量加载脚本 vim/usr/local/fvcom/env-fvcom.sh依次输入如下行: export GCC_HOME=/usr/local/gcc/9.1.0/ export PATH=$GCC_HOME/bin:$PATH export LD_LIBRARY_PATH=$GCC_HOME/lib:$GCC_HOME/lib64:$LD_LIBRARY_PATH export INCLUDE=$GCC_HOME/include:$INCLUDE export MPI_HOME=/usr/local/openmpi3 export PATH=$MPI_HOME/bin:$PATH export LD_LIBRARY_PATH=$MPI_HOME/lib:$LD_LIBRARY_PATH export INCLUDE=$MPI_HOME/include:$INCLUDE export HDF5=/usr/local/hdf5 export PATH=$HDF5/bin:$PATH export LD_LIBRARY_PATH=$HDF5/lib:$LD_LIBRARY_PATH export INCLUDE=$HDF5/include:$INCLUDE export NETCDF=/usr/local/netcdf export PATH=$NETCDF/bin:$PATH export LD_LIBRARY_PATH=$NETCDF/lib:$LD_LIBRARY_PATH export INCLUDE=$NETCDF/include:$INCLUDE保存并退出vim。 3)依次执行如下命令,进入安装目录并配置相关文件 cd/usr/local/fvcom/FVCOM4.1 cp Examples/Estuary/make.inc_example FVCOM_source/make.inc ln-sf FVCOM_source/make.inc./ vim make.inc修改TOPDIR变量值为源码目录,注意行尾不能出现空格,如: TOPDIR=/usr/local/fvcom/FVCOM4.1/FVCOM_source修改“#LOCAL INSTAL”行下边的“LIBDIR”和“INCDIR”变量值,如: #LOCAL INSTAL LIBDIR=-L$(INSTALLDIR)/lib-L../METIS_source/metis-L./libs/julian INCDIR=-I$(INSTALLDIR)/include-I../METIS_source/metis-I./libs/julian完善“IOLIBS”和“IOINCS”变量中HDF5和NetCDF的路径,如: IOLIBS=-L/usr/local/netcdf/lib-L/usr/local/hdf5/lib-lnetcdff-lnetcdf-lhdf5_hl-lhdf5-lz-lcurl-lm IOINCS=-I/usr/local/netcdf/include-I/usr/local/hdf5/include注释“Intel/MPI Compiler Definitions(SMAST)”段落变量,如: #Intel/MPI Compiler Definitions(SMAST) #-------------------------------------------------------------------------- #CPP=/usr/bin/cpp #COMPILER=-DIFORT #CC=mpicc #CXX=mpicxx #CFLAGS=-O3 #FC=mpif90 #DEBFLGS=-check all–traceback #Use'OPT=-O0-g'for fast compile to test the make #Use'OPT=-xP'for fast run on em64t(Hydra and Guppy) #Use'OPT=-xN'for fast run on ia32(Salmon and Minke) #OPT=-O0–g #OPT=-axN–xN #OPT=-O3在下方编辑和增加“gfortran defs”段落相关变量,如: #gfortran defs #-------------------------------------------------------------------------- CPP=/usr/bin/cpp COMPILER=-DGFORTRAN CC=mpicc CXX=mpicxx FC=mpif90 DEBFLGS= OPT=-O3 CLIB=保存并退出vim。 4)依次执行如下命令,编译METIS库 cd./METIS_source tar-zxvf metis.tgz cd metis patch-p2 |
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