CentOS 7系统上添加netcdf库

这里提供两种方法来安装 netcdf：

一是 yum 安装，yum 安装时采用的是系统自带的 gfortran 编译器，版本较旧；

二是采用源码来 Makefile 编译安装的方式，它可以下载最新版的源码，并自行指定 Intel 或 PGI 编译器，适合自定义的需求。

O  系统环境

centOS 64位系统：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 安装 netcdf

在CentOS 下安装比较简单，两句命令即可：

[She@she-centos7 netcdf-cxx4-4.3.]$ sudo yum install netcdf
...==========================================================================
 Package        架构           版本                    源            大小
==========================================================================
正在安装:
 netcdf         x86_64         4.3.3.1-.el7           epel          k
为依赖而安装:
 hdf5           x86_64         1.8.-.el7            epel         1.6 M

事务概要
==========================================================================
安装   软件包 (+ 依赖软件包)
...
完毕！

[She@she-centos7 netcdf-cxx4-4.3.]$ sudo yum install netcdf-devel
...
依赖关系解决

==========================================================================
 Package            架构        版本                      源         大小
==========================================================================
正在安装:
 netcdf-devel       x86_64      4.3.3.1-.el7             epel        k
为依赖而安装:
 hdf5-devel         x86_64      1.8.-.el7              epel       k
 libcurl-devel      x86_64      7.29.-.el7.centos      base       k

事务概要
==========================================================================
安装   软件包 (+ 依赖软件包)
...
完毕！

以上方法安装的 netcdf 版本为 4.3.3.1，是2015年的版本，比较老。

二 从源码编译安装 netcdf

下面采用编译安装的方式，保证每个模块都使用当前最新的版本。

(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没有分开，从4.2版本开始分开。这就导致了netcdf-fortran-4.2的安装麻烦了一点。

需要依次安装 zlib，hdf5，netcdf，netcdf-c，netcdf-fortran。

1  安装 zlib

$ wget http://www.zlib.net/zlib-1.2.11.tar.gz
$ tar -xvf ./zlib-1.2..tar.gz
$ cd ./zlib-1.2.$ env CC="pgcc -fPIC" CFLAGS="-O3" CXX="pgc++ -fPIC" CXXFLAGS="-O3" ./configure \
  --prefix=/usr/local/netcdf4 --sharedlibdir=/opt/pgi/linux86-/19.4/lib
...
...
Checking for shared library support...
Building shared library libz.so.1.2. 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 安装 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-/19.4/lib
$ make
$ make check
$ sudo make install
$ make clean

3 安装 curl

$ wget https://curl.haxx.se/download/curl-7.64.1.tar.gz
$ tar -xvf ./curl-7.64..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-/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:
# PASS:
# SKIP:
# XFAIL:
# FAIL:
# XPASS:
# ERROR:
============================================================================
make[]: Leaving directory `/home/She/Software/LINUX/NetCDF/curl-7.64./docs/libcurl'
make[]: Leaving directory `/home/She/Software/LINUX/NetCDF/curl-7.64./docs/libcurl'
make[]: Leaving directory `/home/She/Software/LINUX/NetCDF/curl-7.64./docs/libcurl'
make[]: Leaving directory `/home/She/Software/LINUX/NetCDF/curl-7.64./docs/libcurl'

$ sudo make install
$ make clean

4 安装 hdf5

下载地址：在网页 https://www.hdfgroup.org/downloads/hdf5/source-code/ 中选择版本 1.10.5，下载 .tar.gz 格式的文件。

$ tar -xvf ./hdf5-1.10..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-/19.4/include \
    LDFLAGS=-L/opt/pgi/linux86-/19.4/lib ./configure \
    --with-zlib=/usr/local/netcdf4 --with-szlib=/usr/local/netcdf4 \
    --prefix=/usr/local/netcdf4 --libdir=/opt/pgi/linux86-/19.4/lib \
    --enable-fortran=yes

$ make$ make check

$ make install

$ make clean

5 安装netcdf

下载地址位于UCAR网站　https://www.unidata.ucar.edu/downloads/netcdf/index.jsp，也可以从UCAR的FTP直接下载　ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4，选择其中的*.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..tar.gz
$ cd netcdf-4.6.

$ 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-/19.4/lib --prefix=/usr/local/netcdf4

$ make
$ make check
...
============================================================================
Testsuite summary for netCDF 4.6.
============================================================================
# TOTAL:
# PASS:
# SKIP:
# XFAIL:
# FAIL:
# XPASS:
# ERROR:
============================================================================

$ 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 安装 netcdf-c 库

$ wget https://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-c-4.7.0.tar.gz
$ tar -xvf ./netcdf-c-4.7..tar.gz
$ cd netcdf-c-4.7.

$ 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-/19.4/lib --includedir=/opt/pgi/linux86-/19.4/include \
    --prefix=/usr/local/netcdf4

$ make

$ make check
$ sudo make install
$ make clean

...
==============================

# General
-------
NetCDF Version:        4.7.
Configured On:        Mon May  :: CST
Host System:        x86_64-pc-linux-gnu
Build Directory:     /home/She/Software/LINUX/NetCDF/netcdf-c-4.7.
Install Prefix:         /usr/local/netcdf4

# Compiling Options
-----------------
C Compiler:        /opt/pgi/linux86-/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- API:        yes
HDF4 Support:        no
HDF5 Support:        yes
NetCDF- API:        yes
NC- 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.
============================================================================
# TOTAL:
# PASS:
# SKIP:
# XFAIL:
# FAIL:
# XPASS:
# ERROR: 

$ 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 的环境变量

$ 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 安装netcdf-fortran 库

$ wget https://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-fortran-4.4.5.tar.gz
$ tar -xvf ./netcdf-fortran-4.4..tar.gz
$ cd netcdf-fortran-4.4.

$ 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-/19.4/lib --includedir=/opt/pgi/linux86-/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 时，可能会提示ftst_rengrps.F文件的一个小错误，错误内容如下：

$ 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

解决办法是，在源路径中找到文件“ftst_rengrps.F”，在第13行的开头增加一个空格，重新编译即可。

$ cat /home/She/Software/LINUX/NetCDF/netcdf-fortran-4.4./nf_test/ftst_rengrps.F | grep nclude
    include "netcdf.inc"
        include "netcdf.inc"
$ head -n  /home/She/Software/LINUX/NetCDF/netcdf-fortran-4.4./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：错误的句子，不符合固定格式的写法)
      include "netcdf.inc" (修改后：正确)

9 再次添加 netcdf 终版的环境变量

$ 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 参考文献

1. 【CESM】1.2.0环境搭建扩充版

2. HDF5 Source Code

3. zlib download

4. curl release and download

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

8. CentOS 7 编译安装 WRF 3.8

9. 在linux下用fortran读取netcdf文件(以WRF模式输出的数据为例)

10. 延伸阅读：NCL基础讲解（一）——NCL简介

11. 延伸阅读：NCL基础讲解（二）——NCL安装与运行