這里提供兩種方法來安裝 netcdf：
一是 yum 安裝，yum 安裝時采用的是系統自帶的 gfortran 編譯器，版本較舊；
二是采用源碼來 Makefile 編譯安裝的方式，它可以下載最新版的源碼，並自行指定 Intel 或 PGI 編譯器，適合自定義的需求。
O 系統環境
centOS 64位系統：CentOS Linux release 7.6.1810 (Core), 3.10.0-957.el7.x86_64 #1 SMP Thu Nov 8 23:39:32 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
PGI 2019：PGI Compilers and Tools 19.4-0 64-bit target on x86-64 Linux -tp sandybridge
一 yum 安裝 netcdf
在CentOS 下安裝比較簡單，兩句命令即可：
[She@she-centos7 netcdf-cxx4-4.3.0]$ sudo yum install netcdf ...========================================================================== Package 架構 版本 源 大小 ========================================================================== 正在安裝: netcdf x86_64 4.3.3.1-5.el7 epel 693 k 為依賴而安裝: hdf5 x86_64 1.8.12-8.el7 epel 1.6 M 事務概要 ========================================================================== 安裝 1 軟件包 (+1 依賴軟件包) ... 完畢！ [She@she-centos7 netcdf-cxx4-4.3.0]$ sudo yum install netcdf-devel ... 依賴關系解決 ========================================================================== Package 架構 版本 源 大小 ========================================================================== 正在安裝: netcdf-devel x86_64 4.3.3.1-5.el7 epel 67 k 為依賴而安裝: hdf5-devel x86_64 1.8.12-8.el7 epel 642 k libcurl-devel x86_64 7.29.0-35.el7.centos base 299 k 事務概要 ========================================================================== 安裝 1 軟件包 (+2 依賴軟件包) ... 完畢！
以上方法安裝的 netcdf 版本為 4.3.3.1，是2015年的版本，比較老。
二 從源碼編譯安裝 netcdf
下面采用編譯安裝的方式，保證每個模塊都使用當前最新的版本。
(1). http://www.zlib.net/zlib-1.2.11.tar.gz
(2). ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4/szip-2.1.tar.gz
(3) https://curl.haxx.se/download/curl-7.64.1.tar.gz
(4). https://www.hdfgroup.org/downloads/hdf5/source-code/
(5). ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.6.1.tar.gz。
(6). ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-c-4.7.0.tar.gz
(7). https://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-fortran-4.4.5.tar.gz
(8). https://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-cxx4-4.3.0.tar.gz
截止netcdf 4.1.3版本，C lib和fortran lib沒有分開，從4.2版本開始分開。這就導致了netcdf-fortran-4.2的安裝麻煩了一點。
需要依次安裝 zlib，hdf5，netcdf，netcdf-c，netcdf-fortran。
1 安裝 zlib
$ wget http://www.zlib.net/zlib-1.2.11.tar.gz $ tar -xvf ./zlib-1.2.11.tar.gz $ cd ./zlib-1.2.11$ env CC="pgcc -fPIC" CFLAGS="-O3" CXX="pgc++ -fPIC" CXXFLAGS="-O3" ./configure \ --prefix=/usr/local/netcdf4 --sharedlibdir=/opt/pgi/linux86-64/19.4/lib ... ... Checking for shared library support... Building shared library libz.so.1.2.11 with pgcc -fPIC. Checking for size_t... Yes. Checking for off64_t... Yes. Checking for fseeko... Yes. Checking for strerror... Yes. Checking for unistd.h... Yes. Checking for stdarg.h... Yes. Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf(). Checking for vsnprintf() in stdio.h... Yes. Checking for return value of vsnprintf()... Yes. Checking for attribute(visibility) support... Yes. $ make
$ make check
$ sudo make install
$ echo "/usr/local/netcdf4/lib/" >> /etc/ld.so.conf $ make clean
2 安裝 szip
$ wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4/szip-2.1.tar.gz $ tar -xvf szip-2.1.tar.gz $ cd ./szip-2.1 $ env CC="pgcc" CFLAGS="-O2 -fPIC" CXX="pgc++" CXXFLAGS="-O2 -fPIC" ./configure 、
--prefix=/usr/local/netcdf4 --libdir=/opt/pgi/linux86-64/19.4/lib $ make $ make check $ sudo make install $ make clean
3 安裝 curl
$ wget https://curl.haxx.se/download/curl-7.64.1.tar.gz
$ tar -xvf ./curl-7.64.1.tar.gz
$ cd ./curl-7.64.1
$ env CC="pgcc" CFLAGS="-O2 -fPIC" CXX="pgc++" CXXFLAGS="-O2 -fPIC" ./configure \
--prefix=/usr/local/netcdf4 --libdir=/opt/pgi/linux86-64/19.4/lib ... SSPI: no (--enable-sspi) ca cert bundle: no ca cert path: ca fallback: LDAP: no (--enable-ldap / --with-ldap-lib / --with-lber-lib) LDAPS: no (--enable-ldaps) RTSP: enabled RTMP: no (--with-librtmp) Metalink: no (--with-libmetalink) PSL: no (libpsl not found) Alt-svc: no (--enable-alt-svc) HTTP2: disabled (--with-nghttp2) Protocols: DICT FILE FTP GOPHER HTTP IMAP POP3 RTSP SMTP TELNET TFTP Features: IPv6 UnixSockets libz AsynchDNS $ make
$ make check ...
PASS: check-easy PASS: check-multi ============================================================================ Testsuite summary for curl - ============================================================================ # TOTAL: 2 # PASS: 2 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory `/home/She/Software/LINUX/NetCDF/curl-7.64.1/docs/libcurl' make[3]: Leaving directory `/home/She/Software/LINUX/NetCDF/curl-7.64.1/docs/libcurl' make[2]: Leaving directory `/home/She/Software/LINUX/NetCDF/curl-7.64.1/docs/libcurl' make[1]: Leaving directory `/home/She/Software/LINUX/NetCDF/curl-7.64.1/docs/libcurl'
$ sudo make install
$ make clean
4 安裝 hdf5
下載地址：在網頁 https://www.hdfgroup.org/downloads/hdf5/source-code/ 中選擇版本 1.10.5，下載 .tar.gz 格式的文件。
$ tar -xvf ./hdf5-1.10.5.tar.gz
$ cd ./hdf5-1.10.5
$ env CC="pgcc" CFLAGS="-O3 -fPIC" FC="pgfortran" FCFLAGS="-O3 -fPIC" CXX="pgc++" \
CXXFLAGS="-O3 -fPIC" CPPFLAGS=-I/opt/pgi/linux86-64/19.4/include \
LDFLAGS=-L/opt/pgi/linux86-64/19.4/lib ./configure \
--with-zlib=/usr/local/netcdf4 --with-szlib=/usr/local/netcdf4 \
--prefix=/usr/local/netcdf4 --libdir=/opt/pgi/linux86-64/19.4/lib \
--enable-fortran=yes
$ make$ make check
$ make install
$ make clean
5 安裝netcdf
下載地址位於UCAR網站 https://www.unidata.ucar.edu/downloads/netcdf/index.jsp，也可以從UCAR的FTP直接下載 ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4，選擇其中的*.tar.gz格式的文件，目前的最新版本如下：
(1) NetCDF-4.6.0: ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.6.1.tar.gz
(2) netcdf-c-4.7.0: ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-c-4.7.0.tar.gz
(3) netcdf-fortran-4.4.5: https://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-fortran-4.4.5.tar.gz
(4) netcdf-cxx4-4.3.0: https://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-cxx4-4.3.0.tar.gz
$ wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.6.1.tar.gz
$ tar -xvf ./netcdf-4.6.1.tar.gz
$ cd netcdf-4.6.1 $ env CC="pgcc" CFLAGS="-O3 -fPIC" FC="pgf90" FCFLAGS="-O3 -fPIC" CXX="pgc++" CXXFLAGS="-O3 -fPIC" \
CPPFLAGS=-I/usr/local/netcdf4/include LDFLAGS=-L/usr/local/netcdf4/lib ./configure \
--disable-dap --with-zlib=/usr/local/netcdf4 --with-szlib=/usr/local/netcdf4 \
--libdir=/opt/pgi/linux86-64/19.4/lib --prefix=/usr/local/netcdf4 $ make
$ make check ... ============================================================================ Testsuite summary for netCDF 4.6.1 ============================================================================ # TOTAL: 2 # PASS: 2 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ $ sudo make install ... +-------------------------------------------------------------+ | Congratulations! You have successfully installed netCDF! | | | | You can use script "nc-config" to find out the relevant | | compiler options to build your application. Enter | | | | nc-config --help | | | | for additional information. | | | | CAUTION: | | | | If you have not already run "make check", then we strongly | | recommend you do so. It does not take very long. | | | | Before using netCDF to store important data, test your | | build with "make check". | | | | NetCDF is tested nightly on many platforms at Unidata | | but your platform is probably different in some ways. | | | | If any tests fail, please see the netCDF web site: | | http://www.unidata.ucar.edu/software/netcdf/ | | | | NetCDF is developed and maintained at the Unidata Program | | Center. Unidata provides a broad array of data and software | | tools for use in geoscience education and research. | | http://www.unidata.ucar.edu | +-------------------------------------------------------------+ $ make clean
6 安裝 netcdf-c 庫
$ wget https://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-c-4.7.0.tar.gz
$ tar -xvf ./netcdf-c-4.7.0.tar.gz
$ cd netcdf-c-4.7.0 $ env CC="pgcc" CFLAGS="-O3 -fPIC" FC="pgf90" FCFLAGS="-O3 -fPIC" CXX="pgc++" CXXFLAGS="-O3 -fPIC" \
CPPFLAGS=-I/usr/local/netcdf4/include LDFLAGS=-L/usr/local/netcdf4/lib ./configure \
--disable-dap --with-zlib=/usr/local/netcdf4 --with-szlib=/usr/local/netcdf4 \
--libdir=/opt/pgi/linux86-64/19.4/lib --includedir=/opt/pgi/linux86-64/19.4/include \
--prefix=/usr/local/netcdf4
$ make
$ make check
$ sudo make install
$ make clean ...
============================== # General ------- NetCDF Version: 4.7.0 Configured On: Mon May 13 14:54:33 CST 2019 Host System: x86_64-pc-linux-gnu Build Directory: /home/She/Software/LINUX/NetCDF/netcdf-c-4.7.0 Install Prefix: /usr/local/netcdf4 # Compiling Options ----------------- C Compiler: /opt/pgi/linux86-64/19.4/bin/pgcc CFLAGS: -O3 -fPIC CPPFLAGS: -I/usr/local/netcdf4/include LDFLAGS: -L/usr/local/netcdf4/lib AM_CFLAGS: AM_CPPFLAGS: AM_LDFLAGS: Shared Library: yes Static Library: yes Extra libraries: -lsz -lhdf5_hl -lhdf5 -lm -ldl -lz # Features -------- NetCDF-2 API: yes HDF4 Support: no HDF5 Support: yes NetCDF-4 API: yes NC-4 Parallel Support: no PnetCDF Support: no DAP2 Support: no DAP4 Support: no Byte-Range Support: no Diskless Support: yes MMap Support: no JNA Support: no CDF5 Support: yes ERANGE Fill Support: no Relaxed Boundary Check: yes $ make check ... ============================================================================ Testsuite summary for netCDF 4.7.0 ============================================================================ # TOTAL: 3 # PASS: 3 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0
$ sudo make install ... +-------------------------------------------------------------+ | Congratulations! You have successfully installed netCDF! | | | | You can use script "nc-config" to find out the relevant | | compiler options to build your application. Enter | | | | nc-config --help | | | | for additional information. | | | | CAUTION: | | | | If you have not already run "make check", then we strongly | | recommend you do so. It does not take very long. | | | | Before using netCDF to store important data, test your | | build with "make check". | | | | NetCDF is tested nightly on many platforms at Unidata | | but your platform is probably different in some ways. | | | | If any tests fail, please see the netCDF web site: | | http://www.unidata.ucar.edu/software/netcdf/ | | | | NetCDF is developed and maintained at the Unidata Program | | Center. Unidata provides a broad array of data and software | | tools for use in geoscience education and research. | | http://www.unidata.ucar.edu | +-------------------------------------------------------------+ $ make clean
7 添加 netcdf 的環境變量
$ vi ~/env_netcdf_LD.sh #!/bin/bash # setting for netcdf, edit by She export LD_LIBRARY_PATH=/usr/local/netcdf4/lib:${LD_LIBRARY_PATH} $ sudo cp ~/env_netcdf_LD.sh /etc/profile.d $ source /etc/profile.d/env_netcdf_LD.sh $ echo $LD_LIBRARY_PATH /usr/local/netcdf4/lib:/usr/lib64/openmpi/lib
8 安裝netcdf-fortran 庫
$ wget https://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-fortran-4.4.5.tar.gz $ tar -xvf ./netcdf-fortran-4.4.5.tar.gz $ cd netcdf-fortran-4.4.5 $ env CC="pgcc" CFLAGS="-O3 -fPIC" FC="pgf90" FCFLAGS="-O3 -fPIC" CXX="pgc++" CXXFLAGS="-O3 -fPIC" \.... ...
F90="pgf90" FCFLAGS="-O3 -fPIC" CPPFLAGS=-I/usr/local/netcdf4/include LDFLAGS=-L/usr/local/netcdf4/lib \
./configure --libdir=/opt/pgi/linux86-64/19.4/lib --includedir=/opt/pgi/linux86-64/19.4/include \
--prefix=/usr/local/netcdf4 $ make
$ make check
$ sudo make install
+-------------------------------------------------------------+
| Congratulations! You have successfully installed the netCDF |
| Fortran libraries. |
| |
| You can use script "nf-config" to find out the relevant |
| compiler options to build your application. Enter |
| |
| nf-config --help |
| |
| for additional information. |
| |
| CAUTION: |
| |
| If you have not already run "make check", then we strongly |
| recommend you do so. It does not take very long. |
| |
| Before using netCDF to store important data, test your |
| build with "make check". |
| |
| NetCDF is tested nightly on many platforms at Unidata |
| but your platform is probably different in some ways. |
| |
| If any tests fail, please see the netCDF web site: |
| http://www.unidata.ucar.edu/software/netcdf/ |
| |
| NetCDF is developed and maintained at the Unidata Program |
| Center. Unidata provides a broad array of data and software |
| tools for use in geoscience education and research. |
| http://www.unidata.ucar.edu |
+-------------------------------------------------------------+
$ make clean
在 make check 時，可能會提示ftst_rengrps.F文件的一個小錯誤，錯誤內容如下：
$ make check
...
... pgfortran -DHAVE_CONFIG_H -I. -I.. -I../libsrc -I../fortran -I../fortran -I/usr/local/netcdf4/include -I../fortran -g -c -o ftst_rengrps.o ftst_rengrps.F PGF90-S-0034-Syntax error at or near identifier nclude (ftst_rengrps.F: 13) PGF90/x86-64 Linux 19.4-0: compilation completed with severe errors make[2]: *** [ftst_rengrps.o] Error 2 make[2]: Leaving directory `/home/xxx/Software/LINUX/NetCDF/netcdf-fortran-4.4.5/nf_test' make[1]: *** [check-am] Error 2 make[1]: Leaving directory `/home/xxx/Software/LINUX/NetCDF/netcdf-fortran-4.4.5/nf_test' make: *** [check-recursive] Error 1
解決辦法是，在源路徑中找到文件“ftst_rengrps.F”，在第13行的開頭增加一個空格，重新編譯即可。
$ cat /home/She/Software/LINUX/NetCDF/netcdf-fortran-4.4.5/nf_test/ftst_rengrps.F | grep nclude include "netcdf.inc" include "netcdf.inc" $ head -n 15 /home/She/Software/LINUX/NetCDF/netcdf-fortran-4.4.5/nf_test/ftst_rengrps.F
C This is part of the netCDF package.
C Copyright 2006 University Corporation for Atmospheric Research/Unidata.
C See COPYRIGHT file for conditions of use.
C This program tests netCDF-4 variable functions from fortran.
C $Id: ftst_rengrps.F,v 1.3 2010/02/03 14:35:21 ed Exp $
program ftst_rengrps
C use typeSizes
C use netcdf
C use netcdf4_f03
implicit none
include "netcdf.inc" (修改前：錯誤的句子，不符合固定格式的寫法)
include "netcdf.inc" (修改后：正確)
9 再次添加 netcdf 終版的環境變量
$ vi ~/env_netcdf_final.sh #!/bin/bash # setting for netcdf, edit by She export NETCDF=/usr/local/netcdf4 export PATH=$PATH:$NETCDF/bin:$NETCDF/include:$NETCDF/lib export MANPATH=$MANPATH:$NETCDF/share/man$ sudo cp ~/env_netcdf_final.sh /etc/profile.d $ source /etc/profile.d/env_netcdf_final.sh
三 參考文獻
5. netcdf-4.4.1 FTP source download
6. netcdf-cxx4-4.3.0.tar.gz FTP source download
7. netcdf-fortran-4.4.4.tar.gz FTP source download
9. 在linux下用fortran讀取netcdf文件(以WRF模式輸出的數據為例)
10. 延伸閱讀：NCL基礎講解（一）——NCL簡介
11. 延伸閱讀：NCL基礎講解（二）——NCL安裝與運行