1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
|
************************************************************************
HDF5 Build and Install Instructions for Cygwin
************************************************************************
Preconditions:
--------------
1. Installed Cygwin 1.7.5 or higher
To install the Cygwin net release, go to http://www.cygwin.com and
click on "Install or update now!" icon. This will download a GUI
installer called setup.txt which can be run to download a complete
Cygwin installation via the internet. Then follow the instructions
on each screen to install Cygwin.
Cygwin uses packages to manage installing various software. Users can
choose to install or uninstall certain packages by running setup.exe.
http://www.cygwin.com/packages/ provides detailed information about
Cygwin packages.
To build HDF5 on Cygwin, Devel package (including gcc,gcc-g++,
gcc-g77, and gcc-java compiles, and gdb tool) should be installed.
2. Compilers Installed
2.1 C/C++ Compilers HDF5-1.8 Supported
gcc (4.3.4), which includes:
gcc4-core : C compiler
gcc4-g++ : C++ compiler
gcc4-fortran : fortran compiler
2.2 Using Compilers Not Supported
The compilers in 2.1 are supported and tested by HDF
group. Any other compilers may still work but they are not
guaranteed by HDF group.
If users want to use other compilers except those in 2.1,
try to set the following variables to override the default
choices.
CXX : C++ compiler command
FC : Fortran compiler command
For example, if users want to use pgf90 as fortran compiler, then
setenv FC pgf90
3. HDF5 Dependencies
3.1 Zlib
zlib-1.2.2 or later is supported and tested on Cygwin.
3.2 Szip
The HDF5 library has a predefined compression filter that uses
the extended-Rice lossless compression algorithm for chunked
datatsets. For more information about Szip compression and
license terms see
http://hdfgroup.org/HDF5/doc_resource/SZIP/index.html.
The latest supported public release of SZIP is available from
ftp://ftp.hdfgroup.org/lib-external/szip/2.0. Binary distribution can be
found under ftp://ftp.hdfgroup.org/lib-external/szip/2.0/bin/cygwin
Install HDF5 on Cygwin
----------------------
1. Get HDF5 source code package
Users can download HDF5 source code package from HDF website
(http://hdfgroup.org).
2. Unpacking the distribution
The HDF5 source code is distributed in a variety of formats which
can be unpacked with the following commands, each of which creates
an `hdf5-1.8.5' directory.
2.1 Non-compressed tar archive (*.tar)
$ tar xf hdf5-1.8.5.tar
2.2 Gzip'd tar archive (*.tar.gz)
$ gunzip < hdf5-1.8.5.tar.gz | tar xf -
2.3 Bzip'd tar archive (*.tar.bz2)
$ bunzip2 < hdf5-1.8.5.tar.bz2 | tar xf -
2. Setup Environment
In Cygwin, most compilers and setting are automatically detected during
the configure script. However, if you are building Fortran we recommend
that you explicitly set the "FC" variable in your environment to use the
gfortran compiler. For example, issue the command:
$ export FC=gfortran
4. Configuring
Notes: See detailed information in hdf5/release_docs/INSTALL,
part 5. Full installation instructions for source
distributions
The host configuration file for cygwin i686-pc-cygwin is located
in the `config' directory and are based on architecture name,
vendor name, and operating system which are displayed near the
beginning of the `configure' output. The host config file influences
the behavior of configure by setting or augmenting shell variables.
In short,
To configure HDF5 C Library, using
$ ./configure
To configure HDF5 C/C++ Library, using
$ ./configure --enable-cxx
To configure HDF5 C/Fortran Library, using
$ ./configure --enable-fortran
To configure HDF5 C with Szip library, using
$ ./configure --with-szlib="path to szlib"
For example, if szip library was installed in the directory
/cygdrive/c/szip, which is parent directory of "include" and
"lib", then the following command will configure HDF5 C library
with szip enabled:
$ ./configure --with-szlib=/cygdrive/c/szip
To configure HDF5 C without Zlib,
To disable zlib, using
$ ./configure --without-zlib
Two ways to configure HDF5 C with specified Zlib
Using
$ ./configure --with-zlib=INCDIR,LIBDIR
For example, if the zlib library is installed in
/cygdrive/c/usr, which is the parent directory of directories
"include" and "lib",
$ ./configure --with-zlib=/cygdrive/c/usr/include,/cygdrive/c/usr/lib
Through the CPPFLAGS and LDFLAGS Variables
For example, if zlib was installed in the directory
/cygdrive/c/usr then using the following command to configure
HDF5 with zib
$ CPPFLAGS=-I/cygdrive/c/usr/include \
$ LDFLAGS=-L/cygdrive/c/usr/lib \
$ ./configure
To specify the installation directories, using
$ ./configure --prefix="path for installation"
By default, HDF5 library, header files, examples, and
support programs will be installed in /usr/local/lib,
/usr/local/include, /usr/local/doc/hdf5/examples, and
/usr/local/bin. To use a path other than /usr/local specify
the path with the `--prefix=PATH' switch as in the above
command.
Combination of Switches
All of the above switches can be combined together. For
example, if users want to configure HDF5 C/C++/Fortran
library with szip library enabled, with zlib library at
/cygdrive/c/usr/, and install HDF5 into directory
/cygdrive/c/hdf5 using gcc/g++ as C/C++ compiler and g95
as fortran compiler
$ ./configure
--with-szlib=/cygdrive/c/szip
--with-zlib=/cygdrive/c/usr/include,/cygdrive/c/usr/lib
--prefix=/cygdrive/c/hdf5
--enable-cxx
--enable-fortran
<"If no more switches, then hit Enter">
Notes: The command format above is for readilibity. In practice,
please type in the command above with at least one
space between each line, No "Enter" until users finish
the switches and want to run the configure.
or do it through CPPFLAGS and LDFLAGS variables:
$ CPPFLAGS=-I/cygdrive/c/usr/include \
$ LDFLAGS=-L/cygdrive/c/usr/lib \
$ ./configure
--with-szlib=/cygdrive/c/szip
--prefix=/cygdrive/c/hdf5
--enable-cxx
--enable-fortran
<"If no more switches, then hit Enter">
5. Make and Make Check
After configuration is done successfully, run the following series of
commands to build, test and install HDF5
$ make > "output file name"
$ make check > "output file name"
Before run "make install", check output file for "make check", there
should be no failures at all.
6. Make Install
$ make install > "output file name"
7. Check installed HDF5 library
After step 6, go to your installation directory, there should be
three subdirectories: "bin" "include" and "lib".
8. Known Problems
Shared libraries can not be built on Cygwin In release 1.8.
-----------------------------------------------------------------------
Need Further assistance, email help@hdfgroup.org
|
