wrf安装摘要.docx

摘要： 本文档简要介绍在曙光HPC集群上部署WRF/ARPS气象模式时软件环境的准备及模式安装的方法步骤。1 曙光集群基础软件环境1.1 操作系统所有节点统一安装Red Hat Enterprise Linux Server release 6.2 64位操作系统1.2 编译器要求安装GNU、Intel、PGI三套编译器。默认情况下，推荐使用Intel编译器，运行效率较高。1.2.1 GNU编译器编译器类型编译器命令版本安装路径C编译器gcc4.4.6/usr/bin/gccC+编译器g+4.4.6/usr/bin/g+Fortran 77编译器gfortran4.4.6/usr/bin/gfortranFortran 90编译器gfortran4.4.6/usr/bin/gfortran备注：GNU编译器为Red Hat Linux系统自带。1.2.2 Intel编译器编译器类型编译器命令版本安装路径C编译器icc12.1.0/public/software/intel/composer_xe_2011_sp1.7.256/bin/intel64/iccC+编译器icpc12.1.0/public/software/intel/composer_xe_2011_sp1.7.256/bin/intel64/icpcFortran 77编译器ifort12.1.0/public/software/intel/composer_xe_2011_sp1.7.256/bin/intel64/ifortFortran 90编译器ifort12.1.0/public/software/intel/composer_xe_2011_sp1.7.256/bin/intel64/ifortIntel编译器环境变量脚本：/public/software/profile.d/intel-env.sh1.2.3 PGI编译器编译器类型编译器命令版本安装路径C编译器pgcc10.2/public/software/pgi/linux86-64/10.2/bin/pgccC+编译器pgCC10.2/public/software/pgi/linux86-64/10.2/bin/pgCCFortran 77编译器pgf7710.2/public/software/pgi/linux86-64/10.2/bin/pgf77Fortran 90编译器pgf9010.2/public/software/pgi/linux86-64/10.2/bin/pgf90PGI编译器环境变量脚本：/public/software/profile.d/pgi-env.sh1.3 MPI并行环境1.3.1 mvapich2MVAPICH2是基于MPICH2的一个MPI拓展实现，提供了对IB，iWARP，RcCE，PSM，uDAPL等新型高性能通信设备和协议的支持，同时也支持TCP/IP协议和共享内存，还支持Nvidia GPU并行任务。MVAPICH2支持的通信接口（10种）如下图所示：MVAPICH2由美国俄亥俄大学开发，最新版本已到MVAPICH2 1.9+，基于MPICH2-1.5+开发，支持MPI-1和MPI2.2标准，并已初步支持MPI-3标准。官方网站为：/overview/mvapich2/。 Intel编译器版本(默认MPI) 版本：mvapich2-1.8 安装路径：/public/software/mpi/mvapich2-18-intel 环境变量脚本：/public/software/profile.d/mvapich2-intel-env.sh MPI编译器：编译器类型编译器命令安装路径C编译器mpicc/public/software/mpi/mvapich2-18-intel/bin/mpiccC+编译器mpicxx/public/software/mpi/mvapich2-18-intel/bin/mpicxxFortran 77编译器mpif77/public/software/mpi/mvapich2-18-intel/bin/mpif77Fortran 90编译器mpif90/public/software/mpi/mvapich2-18-intel/bin/mpif90 MPI运行方式：#mpirun f hostfile n 32 ./mpi_exec其中hostfile格式如下：node1:16node2:16 从源码安装mvapich2方法：#tar zxvf mvapich2-1.8.tar.gz#cd mvapich2-1.8#./configure -prefix=/public/software/mpi/mvapich2-18-intel -with-device=ch3:nemesis:ib,tcp CC=icc CXX=icpc FC=ifort F77=ifort#make#make install GNU编译器版本 版本：mvapich2-1.8 安装路径：/public/software/mpi/mvapich2-18-gnu 环境变量脚本：/public/software/profile.d/mvapich2-gnu-env.sh MPI编译器：编译器类型编译器命令安装路径C编译器mpicc/public/software/mpi/mvapich2-18-gnu/bin/mpiccC+编译器mpicxx/public/software/mpi/mvapich2-18-gnu/bin/mpicxxFortran 77编译器mpif77/public/software/mpi/mvapich2-18-gnu/bin/mpif77Fortran 90编译器mpif90/public/software/mpi/mvapich2-18-gnu/bin/mpif90 MPI运行方式：#mpirun f hostfile n 32 ./mpi_exec其中hostfile格式如下：node1:16node2:16 从源码安装mvapich2方法：#tar zxvf mvapich2-1.8.tar.gz#cd mvapich2-1.8#./configure -prefix=/public/software/mpi/mvapich2-18-gnu -with-device=ch3:nemesis:ib,tcp CC=gcc CXX=g+ FC=gfortran F77=gfortran#make#make install1.3.2 OpenMPIOpenMPI是一个免费的、开源的MPI实现，兼容MPI-1和MPI-2标准。OpenMPI由开源社区开发维护，支持大多数类型的HPC平台，并具有很高的性能。OpenMPI目前最新版本为openmpi-1.6+，官方网站：/，可从官网免费下载Openmpi源码安装包。 Intel编译器版本 版本：OpenMPI 1.6 安装路径：/public/software/mpi/openmpi-16-intel 环境变量脚本：/public/software/profile.d/openmpi-intel-env.sh MPI编译器：编译器类型编译器命令安装路径C编译器mpicc/public/software/mpi/openmpi-16-intel/bin/mpiccC+编译器mpicxx/public/software/mpi/openmpi-16-intel/bin/mpicxxFortran 77编译器mpif77/public/software/mpi/openmpi-16-intel/bin/mpif77Fortran 90编译器mpif90/public/software/mpi/openmpi-16-intel/bin/mpif90 MPI运行方式：#mpirun np 32 -hostfile hostfile ./mpi_exec其中hostfile格式如下：node1 slots=16node2 slots=16 从源码安装Openmpi方法：#tar zxvf openmpi-1.6.tar.gz#cd openmpi-1.6#./configure -prefix=/public/software/mpi/openmpi-16-intel -enable-mpirun-prefix-by-default CC=icc CXX=icpc FC=ifort F77=ifort#make#make install GNU编译器版本 版本：OpenMPI 1.6 安装路径：/public/software/mpi/openmpi-16-gnu 环境变量脚本：/public/software/profile.d/openmpi-gnu-env.sh MPI编译器：编译器类型编译器命令安装路径C编译器mpicc/public/software/mpi/openmpi-16-gnu/bin/mpiccC+编译器mpicxx/public/software/mpi/openmpi-16-gnu/bin/mpicxxFortran 77编译器mpif77/public/software/mpi/openmpi-16-gnu/bin/mpif77Fortran 90编译器mpif90/public/software/mpi/openmpi-16-gnu/bin/mpif90 MPI运行方式：#mpirun np 32 -hostfile hostfile ./mpi_exec其中hostfile格式如下：node1 slots=16node2 slots=16 从源码安装Openmpi方法：#tar zxvf openmpi-1.6.tar.gz#cd openmpi-1.6#./configure -prefix=/public/software/mpi/openmpi-16-gnu -enable-mpirun-prefix-by-default CC=gcc CXX=g+ FC=gfortran F77=gfortran#make#make install2 常用气象函数库安装2.1 系统自带函数库2.1.1 zlibzlib是一个用于数据压缩的通用函数库，红帽Linux默认已经安装zlib。 版本：1.2.3 安装路径：/usr 库文件路径：/usr/lib64/libz.so2.1.2 libpnglibpng是一个处理PNG格式图像的库，可调用zlib函数库对图像进行无损压缩，红帽Linux默认已经安装libpng。 版本：1.2.46 安装路径：/usr 库文件路径：/usr/lib64/libpng.so2.1.3 libjpegjpeg是一个通用的数字图像有损压缩程序，红帽Linux默认已经安装libjpeg。 版本：6b 安装路径：/usr 库文件路径：/usr/lib64/libjpeg.so2.1.4 ImageMagickImageMagick是一套功能强大、稳定而且免费的工具集和开发包，可以用来读、写和处理超过89种基本格式的图片文件，包括流行的TIFF、JPEG、GIF、 PNG、PDF以及PhotoCD等格式。ImageMagick 是一个用来创建、编辑、合成图片的软件。它可以读取、转换、写入多种格式的图片。 版本：6.5.4 安装路径：/usr 可执行文件路径：/usr/bin，如/usr/bin/convert2.2 hdf4HDF是一个用于科学数据存储和管理的函数库和文件格式，有两个版本：HDF-4和HDF-5。两个版本不兼容，需分别安装。本小节说明hdf-4.2.9的安装配置方法。# cd /public/sourcecode/# tar jxvf hdf-4.2.9.tar.bz2# cd hdf-4.2.9# ./configure -prefix=/public/software/hdf4 -includedir=/public/software/hdf4/include/hdf CC=icc CXX=icpc FC=ifort F77=ifort# make# make install设置环境变量：# cat /public/software/profile.d/hdf4-env.shexport HDFPATH=/public/software/hdf4export LD_LIBRARY_PATH=$HDFPATH/lib:$LD_LIBRARY_PATHexport INCLUDE=$HDFPATH/include/hdf:$INCLUDEexport PATH=$HDFPATH/bin:$PATH2.3 hdf5本小节说明hdf5-1.8.9的安装配置方法。安装HDF5之前需要先确认系统安装zlib库，由于本集群Linux自带zlib库，所以无需单独再安装。如果系统无zlib库，需要首先从源码编译zlib。# cd /public/sourcecode/# tar zxvf hdf5-1.8.9.tar.gz# cd hdf5-1.8.9# ./configure -prefix=/public/software/hdf5 -enable-cxx -enable-fortran -enable-fortran2003 -disable-dap CC=icc CXX=icpc FC=ifort F77=ifort# make# make install设置环境变量：# cat /public/software/profile.d/hdf5-env.shexport HDF5=/public/software/hdf5export LD_LIBRARY_PATH=$HDF5/lib:$LD_LIBRARY_PATHexport INCLUDE=$HDF5/include:$INCLUDEexport PATH=$HDF5/bin:$PATH2.4 netcdf3netCDF（network Common Data Format）即“网络通用数据格式”，跟PNG、JPEG、BMP一样，是一种文件格式标准，最初的目的是用于存储气象科学中的数据，现在已经成为许多数据采集软件的生成文件的格式。NETCDF分为classic netcdf和netcdf-4两种格式，而且两种格式互不兼容。推荐单独安装。本小节说明netcdf 3.6.3（即classic netcdf格式）的安装配置方法。安装步骤：# cd /public/sourcecode/# tar zxvf netcdf-3.6.3.tar.gz# cd netcdf-3.6.3# ./configure prefix=/public/software/netcdf CC=icc CXX=icpc FC=ifort F77=ifort# make# make install设置环境变量：# cat /public/software/profile.d/netcdf-env.shexport NETCDF=/public/software/netcdfexport NETCDF_LIB=$NETCDF/libexport NETCDF_INC=$NETCDF/includeexport PATH=$NETCDF/bin:$PATH2.5 netcdf4本小节说明netcdf （即netcdf-4格式）的安装配置方法。注意，NETCDF自从4.1.3版本后，C版本和Fortran版本不再合成在一个tar包里面，所以需要单独安装。需要先安装HDF5，参考2.3。# cd /public/sourcecode/# tar zxvf netcdf-.tar.gz# tar zxvf netcdf-fortran-4.2.tar.gz# cd netcdf-#./configure -prefix=/public/software/netcdf4 -enable-netcdf4 -disable-dap CPPFLAGS=-I/public/software/hdf5/include LDFLAGS=-L/public/software/hdf5/lib CC=icc CXX=icpc FC=ifort F77=ifort# make# make install# cd ./netcdf-fortran-4.2#./configure -prefix=/public/software/netcdf4 CPPFLAGS=-I/public/software/netcdf4/include LDFLAGS=-L/public/software/netcdf4/lib CC=icc CXX=icpc FC=ifort F77=ifort# make# make install设置环境变量：# cat /public/software/profile.d/netcdf4-env.shexport NETCDF4=1export NETCDF=/public/software/netcdf4export LD_LIBRARY_PATH=$NETCDF/lib:$LD_LIBRARY_PATHexport INCLUDE=$NETCDF/include:$INCLUDEexport PATH=$NETCDF/bin:$PATH如果需要安装classic netcdf格式，在C语言版本netcdf的configure步骤加入-disable-netcdf-4选项即可。2.6 jasperJasPer是处理JPEG-2000图像格式的函数库，JPEG-2000是基于小波变换的新一代图像压缩标准，支持无损和有损压缩，由于比JPEG有更优的压缩性能，在医学影像、数字遥感、气象科学等领域得到了应用。安装步骤：# cd /public/sourcecode/# tar zxvf jasper-1.701.0.tar.gz# cd jasper-1.701.0./configure prefix=/public/software/jasper CC=icc CXX=icpc F77=ifort# make# make install设置环境变量：# cat /public/software/profile.d/jasper-env.shexport JASPER=/public/software/jasperexport JASPERLIB=$JASPER/libexport JASPERINC=$JASPER/includeexport PATH=$JASPER/bin:$PATH2.7 ncl/ncargNCL(The NCAR Command Language)是一种专门为科学数据处理以及数据可视化设计的高级语言，很适合用在气象数据的处理和可视化上。NCL包含了现代编程语言的许多常见功能：条件语句、循环、数组运算等。此外，NCL还包括许多有用的内置函数和过程用来进行处理和操作数据，其中包括统计函数、插值、EOF分析、波谱分析等。NCL包含NCAR Graphic画图函数库，可以用来绘制精美的气象产品图像。ncl推荐使用官方提供的二进制版本。# mkdir p /public/software/ncl# cd /public/sourcecode/# tar zxvf ncl_ncarg-6.1.2.Linux_RHEL6.2_x86_64_gcc446.tar.gz -C /public/software/ncl设置环境变量：# cat /public/software/profile.d/ncl-env.shexport NCARG_ROOT=/public/software/nclexport NCARG_LIB=/public/software/ncl/libexport NCARG_INC=/public/software/ncl/includeexport PATH=/public/software/ncl/bin:$PATH3 气象模式安装3.1 WRF .1 安装前要求源码包目录：/public/sourcecode/wrf341l WPSV3.4.1.TAR.gz：WPS 3.4.1源码包l WRFV3.4.1.TAR.gz：WRF 3.4.1源码包l ARWpost_V3.tar.gz：ARWpost后处理程序源码包l RIP4.tar.gz：RIP4后处理程序源码包l WRFDA_V3.4.1.tar.gz：WRFDA 3.4.1源码包安装WRF前，除了要求Intel编译器、MPI（如mvapich2，openmpi）外，还需要先安装好netcdf 3.6.3、jasper-1.701.0、NCL等函数库，安装方法请参考2.4，2.6，2.7等章节。设置环境变量：# source /public/software/profile.d/intel-env.sh# source /public/software/profile.d/mvapich2-intel-env.sh# source /public/software/profile.d/jasper-env.sh# source /public/software/profile.d/netcdf-env.sh# source /public/software/profile.d/ncl-env.sh# export WRFIO_NCD_LARGE_FILE_SUPPORT=1(支持超过2GB的NETCDF文件)# export WRF_HOME=/public/software/WRF3413.1.2 安装WRF解压WRFV3.4.1.tar.gz# mkdir p $WRF_HOME# cd $WRF_HOME# tar zxvf /public/sourcecode/wrf341/WRFV3.4.1.TAR.gz# cd WRFV3修改arch/Config_new.pl，将第188行FALSE改为TRUE，如下：188 $I_really_want_to_output_grib2_from_WRF = TRUE ;执行configure自动检测和设置编译环境，编译选项选择第15项（即采用Intel Ifort+MPI，不同WRF版本此序号不一致，请注意）：# ./configurechecking for perl5. nochecking for perl. found /usr/bin/perl (perl)Will use NETCDF in dir: /public/software/netcdfPHDF5 not set in environment. Will configure WRF for use without.which: no timex in (/public/soft/mpi/openmpi-164-intel/bin:/usr/bin/:/usr/lib64/qt-3.3/bin:/public/soft/mpi/openmpi-164-intel/bin:/usr/kerberos/sbin:/usr/kerberos/bin:/public/soft/intel/composer_xe_2013.1.117/bin/intel64:/public/soft/intel/composer_xe_2013.1.117/mpirt/bin/intel64:/public/soft/intel/composer_xe_2013.1.117/bin/intel64:/public/soft/intel/composer_xe_2013.1.117/bin/intel64_mic:/public/soft/intel/composer_xe_2013.1.117/debugger/gui/intel64:/opt/gridview/pbs/dispatcher-sched/bin:/opt/gridview/pbs/dispatcher-sched/sbin:/opt/gridview/pbs/dispatcher/bin:/opt/gridview/pbs/dispatcher/sbin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin)Configuring to use jasper library to build Grib2 I/O. $JASPERLIB = /public/software/jasper/lib $JASPERINC = /public/software/jasper/include-Please select from among the following supported platforms. 1. Linux x86_64, PGI compiler with gcc (serial) 2. Linux x86_64, PGI compiler with gcc (smpar) 3. Linux x86_64, PGI compiler with gcc (dmpar) 4. Linux x86_64, PGI compiler with gcc (dm+sm) 5. Linux x86_64, PGI compiler with pgcc, SGI MPT (serial) 6. Linux x86_64, PGI compiler with pgcc, SGI MPT (smpar) 7. Linux x86_64, PGI compiler with pgcc, SGI MPT (dmpar) 8. Linux x86_64, PGI compiler with pgcc, SGI MPT (dm+sm) 9. Linux x86_64, PGI accelerator compiler with gcc (serial) 10. Linux x86_64, PGI accelerator compiler with gcc (smpar) 11. Linux x86_64, PGI accelerator compiler with gcc (dmpar) 12. Linux x86_64, PGI accelerator compiler with gcc (dm+sm) 13. Linux x86_64 i486 i586 i686, ifort compiler with icc (serial) 14. Linux x86_64 i486 i586 i686, ifort compiler with icc (smpar) 15. Linux x86_64 i486 i586 i686, ifort compiler with icc (dmpar) 16. Linux x86_64 i486 i586 i686, ifort compiler with icc (dm+sm) 17. Linux x86_64 i486 i586 i686, ifort compiler with icc, SGI MPT (serial) 18. Linux x86_64 i486 i586 i686, ifort compiler with icc, SGI MPT (smpar) 19. Linux x86_64 i486 i586 i686, ifort compiler with icc, SGI MPT (dmpar) 20. Linux x86_64 i486 i586 i686, ifort compiler with icc, SGI MPT (dm+sm) 21. Linux i486 i586 i686 x86_64, PathScale compiler with pathcc (serial) 22. Linux i486 i586 i686 x86_64, PathScale compiler with pathcc (dmpar) 23. x86_64 Linux, gfortran compiler with gcc (serial) 24. x86_64 Linux, gfortran compiler with gcc (smpar) 25. x86_64 Linux, gfortran compiler with gcc (dmpar) 26. x86_64 Linux, gfortran compiler with gcc (dm+sm) 27. Cray XT CLE/Linux x86_64, PGI compiler with gcc (serial) 28. Cray XT CLE/Linux x86_64, PGI compiler with gcc (smpar) 29. Cray XT CLE/Linux x86_64, PGI compiler with gcc (dmpar) 30. Cray XT CLE/Linux x86_64, PGI compiler with gcc (dm+sm) 31. Cray XT CLE/Linux x86_64, Cray CCE compiler with gcc (serial) 32. Cray XT CLE/Linux x86_64, Cray CCE compiler with gcc (smpar) 33. Cray XT CLE/Linux x86_64, Cray CCE compiler with gcc (dmpar) 34. Cray XT CLE/Linux x86_64, Cray CCE compiler with gcc (dm+sm)Enter selection 1-34 : 15-Compile for nesting? (1=basic, 2=preset moves, 3=vortex following) default 1: 1Configuration successful. To build the model type compile .编译WRF：# ./compile em_real 2&1|tee c.log# ./compile em_real 2&1|tee a c.log (执行两遍，第一遍无法生成real.exe)编译成功后，会在main/目录下有real.exe和wrf.exe等可执行文件，如果没有生成，请检查c.log日志文件排错。# ls main/*.exemain/ndown.exe main/nup.exe main/real.exe main/tc.exe main/wrf.exe注意的问题(史小康添加): OpenMPIs mpicc doesnt support the -cc flag so it just passes it to pgcc, which doesnt support it either. The easy way to fix it is recompiling OpenMPI with gcc and pgf ./configure CC=gcc CXX=g+ F77=pgf. FC=pgf. . After that, edit the WRF configure.wrf and remove every instance of -cc=$SOMEVAR I think there should be two, but I dont have access to mine at the moment to tell you the exact names.3.1.3 安装WPS确保NETCDF、JASPERINC、JASPERLIB、NCARG_ROOT等环境变量设置正确，见上述WRF安装步骤。解压WPS压缩源码包：# cd $WRF_HOME# tar zxvf /public/sourcecode/wrf341/WPSV3.4.1.TAR.gz# cd WPS执行configure设置编译环境，选择第19项ifort/icc/dmparWill use NETCDF in dir: /public/software/netcdfFound Jasper environment variables for GRIB2 support. $JASPERLIB = /public/software/jasper/lib $JASPERINC = /public/software/jasper/include-Please select from among the following supported platforms. 1. Linux x86_64, gfortran (serial) 2. Linux x86_64, gfortran (serial_NO_GRIB2) 3. Linux x86_64, gfortran (dmpar) 4. Linux x86_64, gfortran (dmpar_NO_GRIB2) 5. Linux x86_64, PGI compiler (serial) 6. Linux x86_64, PGI compiler (serial_NO_GRIB2) 7. Linux x86_64, PGI compiler (dmpar) 8. Linux x86_64, PGI compiler (dmpar_NO_GRIB2) 9. Linux x86_64, PGI compiler, SGI MPT (serial) 10. Linux x86_64, PGI compiler, SGI MPT (serial_NO_GRIB2) 11. Linux x86_64, PGI compiler, SGI MPT (dmpar) 12. Linux x86_64, PGI compiler, SGI MPT (dmpar_NO_GRIB2) 13. Linux x86_64, IA64 and Opteron (serial) 14. Linux x86_64, IA64 and Opteron (serial_NO_GRIB2) 15. Linux x86_64, IA64 and Opteron (dmpar) 16. Linux x86_64, IA64 and Opteron (dmpar_NO_GRIB2) 17. Linux x86_64, Intel compiler (serial) 18. Linux x86_64, Intel compiler (serial_NO_GRIB2) 19. Linux x86_64, Intel compiler (dmpar) 20. Linux x86_64, Intel compiler (dmpar_NO_GRIB2) 21. Linux x86_64 g95 compiler (serial) 22. Linux x86_64 g95 compiler (serial_NO_GRIB2) 23. Linux x86_64 g95 compiler (dmpar) 24. Linux x86_64 g95 compiler (dmpar_NO_GRIB2) 25. Cray XT/XE Linux x86_64 (Opteron), PGI compiler 5.2 or higher (serial) 26. Cray XT/XE Linux x86_64 (Opteron), PGI compiler 5.2 or higher (serial_NO_GRIB2) 27. Cray XT/XE Linux x86_64 (Opteron), PGI compiler 5.2 or higher (dmpar) 28. Cray XT/XE Linux x86_64 (Opteron), PGI compiler 5.2 or higher (dmpar_NO_GRIB2) 29. Cray XT/XE Linux x86_64 (Opteron), Cray CCE compiler 7.0 or higher (dmpar) 30. Cray XT/XE Linux x86_64 (Opteron), Cray CCE compiler 7.0 or higher (dmpar_NO_GRIB2)Enter selection 1-30 : 19-Configuration successful. To build the WPS, type: compile修改configure.wps第18行，添加-lgfortran lcairo，如下所示：18 NCARG_LIBS = -L$(NCARG_ROOT)/lib -lncarg -lncarg_gks -lncarg_c -lgfortran -lcairo 编译WPS：# ./compile 2&1|tee c.log编译成功后，在WPS目录下会生成geogrid.exe、ungrib.exe或metgrid.exe三个可执行文件，如果没有生成，请检查c.log日志文件排错。3.1.4 安装ARWpost解压ARWpost压缩源码包：# cd $WRF_HOME# tar zxvf /public/sourcecode/wrf341/ARWpost_V3.tar.gz# cd ARWpost确保NETCDF路径设置正确，然后执行configure选择编译环境：# ./configureWill use NETCDF in dir: /public/software/netcdf-Please select from among the following support