捣鼓了两天，终于在msys2上安装了GMT4.5.6，下载msys2安装以后，安装netcdf，解压GMT4.5.6至/home/xiaok目录下，然后生成配置文件
./configure mingw32 shared --prefix=/home/xiaok/gmt/GMT4.5.6 --bindir=/home/xiaok/gmt/GMT4.5.6/bin --libdir=/home/xiaok/gmt/GMT4.5.6/lib --includedir=/home/xiaok/gmt/GMT4.5.6/include --enable-netcdf=/ mingw32/bin
在Src/configure.mk的文件中修改netcdf的INC和LIB文件目录
NETCDF_INC = -I/mingw32/include
然后运行make，出现很多错误，比如找不到pwd.h，O_BINARY等，冲突错误 error: conflicting types for 'mode_t'，非常不好解决，幸亏在cygwin里配置和运行GMT4.5.6是没有问题的，坚信应该是库函数没安装完成的原因，后来集中安装了msys的库文件以及其它跟编译和运行的库文件
mingw32,mingw-w64-i686-binutils,2.30-3
mingw32,mingw-w64-i686-brotli,1.0.4-1
mingw32,mingw-w64-i686-bzip2,1.0.6-6
mingw32,mingw-w64-i686-c-ares,1.14.0-1
mingw32,mingw-w64-i686-ca-certificates,20170211-2
mingw32,mingw-w64-i686-cmake,3.11.1-2
mingw32,mingw-w64-i686-crt-git,6.0.0.5136.897300fe-1
mingw32,mingw-w64-i686-curl,7.59.0-2
mingw32,mingw-w64-i686-expat,2.2.5-1
mingw32,mingw-w64-i686-gcc,7.3.0-2
mingw32,mingw-w64-i686-gcc-libgfortran,7.3.0-2
mingw32,mingw-w64-i686-gcc-libs,7.3.0-2
mingw32,mingw-w64-i686-gettext,0.19.8.1-3
mingw32,mingw-w64-i686-gmp,6.1.2-1
mingw32,mingw-w64-i686-hdf5,1.8.20-1
mingw32,mingw-w64-i686-headers-git,6.0.0.5136.897300fe-1
mingw32,mingw-w64-i686-isl,0.19-1
mingw32,mingw-w64-i686-jansson,2.11-1
mingw32,mingw-w64-i686-jsoncpp,1.8.4-1
mingw32,mingw-w64-i686-l-smash,2.14.5-1
mingw32,mingw-w64-i686-libarchive,3.3.2-1
mingw32,mingw-w64-i686-libffi,3.2.1-4
mingw32,mingw-w64-i686-libiconv,1.15-2
mingw32,mingw-w64-i686-libidn2,2.0.5-1
mingw32,mingw-w64-i686-libmetalink,0.1.3-3
mingw32,mingw-w64-i686-libogg,1.3.3-1
mingw32,mingw-w64-i686-libpng,1.6.34-1
mingw32,mingw-w64-i686-libshout,2.4.1-1
mingw32,mingw-w64-i686-libsquish,1.15-1
mingw32,mingw-w64-i686-libssh,0.7.5-1
mingw32,mingw-w64-i686-libssh2,1.8.0-1
mingw32,mingw-w64-i686-libsystre,1.0.1-4
mingw32,mingw-w64-i686-libtasn1,4.13-1
mingw32,mingw-w64-i686-libtheora,1.1.1-4
mingw32,mingw-w64-i686-libtre-git,r128.6fb7206-2
mingw32,mingw-w64-i686-libunistring,0.9.9-2
mingw32,mingw-w64-i686-libuv,1.20.3-1
mingw32,mingw-w64-i686-libvorbis,1.3.6-1
mingw32,mingw-w64-i686-libwinpthread-git,6.0.0.5134.2416de71-1
mingw32,mingw-w64-i686-lz4,1.8.2-1
mingw32,mingw-w64-i686-lzo2,2.10-1
mingw32,mingw-w64-i686-make,4.2.1-2
mingw32,mingw-w64-i686-mpc,1.1.0-1
mingw32,mingw-w64-i686-mpfr,4.0.1-1
mingw32,mingw-w64-i686-netcdf,4.6.1-1
mingw32,mingw-w64-i686-nettle,3.4-1
mingw32,mingw-w64-i686-nghttp2,1.31.1-1
mingw32,mingw-w64-i686-openssl,1.0.2.o-1
mingw32,mingw-w64-i686-p11-kit,0.23.12-1
mingw32,mingw-w64-i686-rhash,1.3.6-1
mingw32,mingw-w64-i686-speex,1.2.0-1
mingw32,mingw-w64-i686-speexdsp,1.2rc3-3
mingw32,mingw-w64-i686-szip,2.1.1-1
mingw32,mingw-w64-i686-windows-default-manifest,6.4-3
mingw32,mingw-w64-i686-winpthreads-git,6.0.0.5134.2416de71-1
mingw32,mingw-w64-i686-xz,5.2.4-1
mingw32,mingw-w64-i686-zlib,1.2.11-1
msys,bash,4.4.019-3
msys,bash-completion,2.8-1
msys,bash-devel,4.4.019-3
msys,binutils,2.28-1
msys,bsdcpio,3.3.2-1
msys,bsdtar,3.3.2-1
msys,bzip2,1.0.6-2
msys,ca-certificates,20170717-2
msys,cmake,3.10.2-1
msys,coreutils,8.26-3
msys,curl,7.58.0-1
msys,dash,0.5.9.1-1
msys,db,5.3.28-2
msys,dtc,1.4.4-1
msys,file,5.33-1
msys,filesystem,2018.04-1
msys,findutils,4.6.0-1
msys,flex,2.6.4-1
msys,gawk,4.2.0-1
msys,gcc,7.3.0-1
msys,gcc-libs,7.3.0-1
msys,gdbm,1.11-3
msys,getent,2.18.90-2
msys,gettext,0.19.8.1-1
msys,glib2,2.48.2-1
msys,gmp,6.1.2-1
msys,gnupg,1.4.22-3
msys,grep,3.0-1
msys,gzip,1.9-1
msys,heimdal,1.5.3-9
msys,heimdal-libs,1.5.3-9
msys,icu,60.2-1
msys,inetutils,1.9.4-1
msys,info,6.3-1
msys,isl,0.18-1
msys,jsoncpp,1.8.3-1
msys,less,529-1
msys,libarchive,3.3.2-1
msys,libargp,20110921-1
msys,libasprintf,0.19.8.1-1
msys,libassuan,2.4.3-1
msys,libbz2,1.0.6-2
msys,libcrypt,2.1-1
msys,libcurl,7.58.0-1
msys,libdb,5.3.28-2
msys,libedit,3.1-20170329
msys,libexpat,2.2.5-1
msys,libffi,3.2.1-1
msys,libgcrypt,1.8.1-1
msys,libgdbm,1.11-3
msys,libgettextpo,0.19.8.1-1
msys,libgpg-error,1.27-1
msys,libgpgme,1.6.0-1
msys,libiconv,1.15-1
msys,libidn2,2.0.4-2
msys,libintl,0.19.8.1-1
msys,liblzma,5.2.3-1
msys,liblzo2,2.10-1
msys,libmetalink,0.1.3-2
msys,libnettle,3.3-1
msys,libnghttp2,1.30.0-1
msys,libopenssl,1.0.2.m-1
msys,libp11-kit,0.23.9-1
msys,libpcre,8.40-2
msys,libpcre16,8.40-2
msys,libpcre32,8.40-2
msys,libpcrecpp,8.40-2
msys,libpcreposix,8.40-2
msys,libpsl,0.19.1-1
msys,libreadline,7.0.003-2
msys,librhash,1.3.6-1
msys,librhash-devel,1.3.6-1
msys,libsqlite,3.21.0-2
msys,libssh2,1.8.0-1
msys,libssh2-devel,1.8.0-1
msys,libtasn1,4.13-1
msys,libunistring,0.9.7-2
msys,libutil-linux,2.26.2-1
msys,libuv,1.19.1-1
msys,libxml2,2.9.7-2
msys,libxslt,1.1.32-1
msys,lndir,1.0.3-1
msys,m4,1.4.18-1
msys,make,4.2.1-1
msys,mintty,1~2.8.5-1
msys,mksh,56.c-1
msys,mosh,1.3.2-1
msys,mpc,1.1.0-1
msys,mpfr,4.0.1-1
msys,msys2-keyring,r9.397a52e-1
msys,msys2-launcher-git,0.3.32.56c2ba7-2
msys,msys2-runtime,2.10.0-2
msys,msys2-runtime-devel,2.10.0-2
msys,msys2-w32api-headers,6.0.0.5097.36d7b92b-1
msys,msys2-w32api-runtime,6.0.0.5097.36d7b92b-1
msys,ncurses,6.1.20180526-1
msys,openssh,7.6p1-2
msys,openssl,1.0.2.m-1
msys,openssl-devel,1.0.2.m-1
msys,p11-kit,0.23.9-1
msys,pacman,5.0.1-7
msys,pacman-mirrors,20180419-1
msys,pactoys-git,r2.07ca37f-1
msys,pax-git,20161104.2-1
msys,pcre,8.40-2
msys,perl,5.24.4-1
msys,pkg-config,0.29.2-1
msys,pkgfile,1月17日
msys,protobuf,2.6.1-1
msys,pwgen,2.07-1
msys,rebase,4.4.2-1
msys,rhash,1.3.6-1
msys,rsync2,3.1.3dev_msys2.7.0_r3-0
msys,sed,4.4-2
msys,sharutils,4.15.2-1
msys,sshpass,1.06-1
msys,tar,1.30-1
msys,tcsh,6.20.00-2
msys,texinfo,6.3-1
msys,tftp-hpa,5.2-2
msys,time,1.7-1
msys,ttyrec,1.0.8-1
msys,tzcode,2018.c-1
msys,util-linux,2.26.2-1
msys,wget,1.19.4-1
msys,which,2.21-2
msys,windows-default-manifest,6.4-1
msys,xz,5.2.3-1
msys,zlib,1.2.11-1
msys,zlib-devel,1.2.11-1
msys,zsh,5.5.1-1