NetCDF  4.6.0
install.md
1 Getting and Building netCDF {#getting_and_building_netcdf}
2 =============================
3 
4 [TOC]
5 
6 This document is for getting and building the netCDF C library and utilities for the most recent released version. Other libraries that depend on the netCDF C library, such as the Fortran, Python, Java, and C++ libraries, are available as separate distributions that can be optionally built and installed after the C library is successfully installed. The netCDF-Java library is independent of the netCDF C library unless writing netCDF-4 files from Java is required.
7 
8 Getting netCDF-C {#getting}
9 =========================
10 
11 * For information regarding the netCDF-Fortran libraries, see \subpage building_netcdf_fortran.
12 * Functionality to make it easier to build netcdf-fortran as part of the netcdf-c build for *non-MSVC* builds may be enabled at configure time by using the following **Highly Experimental** options:
13 
14  * Autotools: `--enable-remote-fortran-bootstrap`
15  * CMake: `-DENABLE_REMOTE_FORTRAN_BOOTSTRAP=ON`
16 
17 For more details, see the <a href="https://github.com/Unidata/netcdf-c/blob/master/RELEASE_NOTES.md">draft instructions</a> in the Release Notes under the `4.3.3-rc3` section.
18 
19 Getting pre-built netCDF-C libraries. {#sec_get_pre_built}
20 -------------------------------------
21 
22 The easiest way to get netCDF is through a package management program,
23 such as rpm, yum, homebrew, macports, adept, and others. NetCDF is
24 available from many different repositories, including the default Red
25 Hat and Ubuntu repositories.
26 
27 When getting netCDF from a software repository, you should get a
28 development version that includes the netcdf.h header file. A
29 development version will typically have a name such as "netcdf-devel"
30 or "libnetcdf-dev".
31 
32 Instructions for installing and using pre-built libraries for Windows may be found here: \ref winbin.
33 
34 Getting the latest netCDF-C Source Code {#sec_get_source}
35 ----------------------------------------
36 
37 The netCDF-C source code is hosted from the <a href="http://github.com/Unidata/netcdf-c" >Unidata GitHub repository</a>.
38 
39 
40 Two options are available for building from source:
41 
42 * The latest release.
43 * The developer snapshot.
44 
45 ### The latest release {#sec_latest_release}
46 
47 The latest full release may be <a href="http://github.com/Unidata/netcdf-c/releases" >downloaded from GitHub</a>.
48 
49 Source files are available in `.tar.gz` and `.zip` formats.
50 
51 ### The developer snapshot {#sec_dev_snapshot}
52 
53 The developer snapshot may be cloned from GitHub directly by using the `git` command.
54 
55 > $ git clone http://github.com/Unidata/netcdf-c netcdf-c
56 
57 **Note:**
58 
59 *The developer snapshot release contains bug-fixes and new features added since the last full release, but may also contain new bugs, as it is not tested as extensively as the full release.*
60 
61 Building netCDF-C {#building}
62 ===========================
63 
64 The netCDF-C library and utilities require third-party libraries for
65 full functionality. (See \ref architecture).
66 * \ref build_default
67 * \ref build_classic
68 * \ref build_hdf4
69 * \ref build_parallel
70 * \ref building_netcdf_fortran
71 * \ref configure_options
72 
73 Requirements {#netcdf_requirements}
74 ----------------------------------
75 
76 * For netCDF-4 support
77  * HDF5 1.8.9 or later.
78  * HDF5 1.10.1 or later.
79 * zlib 1.2.5 or later (for netCDF-4 compression)
80 * curl 7.18.0 or later (for DAP remote access client support)
81 
82 
83 CMake and Windows support {#sub}
84 --------------------------------
85 
86 * \ref netCDF-CMake
87 * \subpage winbin
88 
89 Building with netCDF-4 and the Remote Data Client {#build_default}
90 --------------------------------
91 
92 The usual way of building netCDF requires the HDF5, zlib, and curl libraries. Versions required are at least HDF5 1.8.9, zlib 1.2.5, and curl 7.18.0 or later.
93 
94 HDF5 and zlib packages are available from the <a href="http://www.hdfgroup.org/downloads/">HDF5 downloads site</a> and the <a href="http://www.zlib.net/">zlib home site</a>. If you wish to use the remote data client code, then you will also need libcurl, which can be obtained from the <a href="http://curl.haxx.se/download.html">curl website</a>.
95 
96 > Note that for building netCDF, it is not necessary to build the HDF5 Fortran, C++, or Java API's. Only the HDF5 C library is used, even for netCDF Fortran or C++ libraries.
97 
98 ### Optional: szip support {#op_szip_support}
99 
100 *Optionally*, you can also build netCDF-4 with the szip library (a.k.a. szlib). If building with szlib, get szip 2.0 or later. Technically, we mean that
101 the HDF5 library is built with szip support. The netcdf build will then
102 inherit szip support from the HDF5 library.
103 If you intend to write files with szip compression, then we suggest that you
104 use [libaec](https://gitlab.dkrz.de/k202009/libaec.git)
105 to avoid patent problems. That library can be used as a
106 drop-in replacement for the standard szip library.
107 If you plan to use the standard szip library,
108 then determine whether license restrictions on the use of szip apply to your situation. See the <a href="http://www.hdfgroup.org/doc_resource/SZIP/">web page on szip compression in HDF products</a>.
109 
110 If `make check` fails for either `zlib` or `HDF5`, the problem must be resolved before the netCDF-4 installation can continue. For HDF5 problems, see the <a href="http://www.hdfgroup.org/services/support.html">HDF5 help services</a>.
111 
112 ### Building zlib from source {#build_zlib_from_source}
113 
114 To build zlib from source, specify where you want to install zlib in a shell variable you will also use later (ZDIR, for example), and build it like this from the top-level zlib source directory
115 
116 ~~~~{.py}
117  $ # Build and install zlib
118  $ ZDIR=/usr/local
119  $ ./configure --prefix=${ZDIR}
120  $ make check
121  $ make install # or sudo make install, if root permissions required
122 ~~~~
123 
124 ### Building hdf5 from source {#build_hdf5_from_source}
125 
126 Next, specify where you want to install HDF5 in another shell variable, for example H5DIR, and build it from the HDF5 top-level source directory:
127 
128 ~~~~{.py}
129  $ # Build and install HDF5
130  $ H5DIR=/usr/local
131  $ ./configure --with-zlib=${ZDIR} --prefix=${H5DIR} --eanble-hl
132  $ make check
133  $ make install # or sudo make install, if root permissions required
134 ~~~~
135 
136 If you are building HDF5 with the optional szip library, include the `--with-szlib=` option to specify where it was installed.
137 
138 In all cases, the installation location specified with the `--prefix` option *must be different* from the source directory where the software is being built.
139 
140 ### Building netCDF-4 and the Remote Data Client from source {#build_nc4_dap_from_source}
141 
142 Before building netCDF, you may need to add `${H5DIR}/lib` to the LD_LIBRARY_PATH environment variable if that lib directory is not searched by default. See the <a href="http://www.unidata.ucar.edu/netcdf/docs/faq.html#Shared%20Libraries">netCDF FAQ</a> for more details on using shared libraries.
143 
144 Indicate where you want to install netCDF in another shell variable, for example NCDIR. Then run the netCDF configure script, specifying where HDF5 was installed using the CPPFLAGS and LDFLAGS environment variables. For example, from the top-level netCDF source directory:
145 
146 ~~~~{.py}
147  $ # Build and install netCDF-4
148  $ NCDIR=/usr/local
149  $ CPPFLAGS=-I${H5DIR}/include LDFLAGS=-L${H5DIR}/lib ./configure --prefix=${NCDIR}
150  $ make check
151  $ make install # or sudo make install
152 ~~~~
153 
154 If you don't provide a `--prefix` option, installation will be in `/usr/local/`, in subdirectories lib/, include/, and bin/. The installation location specified with the `--prefix` option must be different from the source directory where the software is being built.
155 
156 > WARNING: you should be able to use parallel 'make all'. But 'make check' will probably fail if you use parallel make. This is because historically, there are inter-dependencies between test programs. It is unlikely that this will be fixed any time soon, if ever.
157 
158 Building netCDF with Classic Library Only {#build_classic}
159 ---------------------------------------
160 
161 It is possible to build the netCDF C libraries and utilities so that
162 only the netCDF classic and 64-bit offset formats are supported, or
163 the remote data access client is not built. (See \ref netcdf_format
164 for more information about the netCDF format variants. See the <a
165 href="http://www.opendap.org/documentation">DAP documentation and
166 support site</a> for more information about remote client access to
167 data on OPeNDAP servers.)
168 
169 If necessary, set the NCDIR shell variable to indicate where netCDF should be
170 installed. Then to build a netCDF-3 library without support for the
171 netCDF-4 formats or functions, but with remote client access, use:
172 
173 ~~~~{.py}
174  $ # Build and install netCDF-3 from netCDF-4 source
175  $ ./configure --prefix=${NCDIR} --disable-netcdf-4
176  $ make check install
177 ~~~~
178 
179 To build with full support for netCDF-4 API's and format but without
180 remote client access, use:
181 
182 ~~~~{.py}
183  $ # Build and install netCDF-4 without DAP client support
184  $ ./configure --prefix=${NCDIR} --disable-dap
185  $ make check install
186 ~~~~
187 
188 To build without netCDF-4 support or remote client access, use:
189 
190 ~~~~{.py}
191  $ # Build and install minimal netCDF-3 with no DAP client support
192  $ ./configure --prefix=${NCDIR} --disable-netcdf-4 --disable-dap
193  $ make check install
194 ~~~~
195 
196 If you get the message that netCDF installed correctly, then you are
197 done!
198 
199 Building with HDF4 Support {#build_hdf4}
200 ---------------------
201 
202 The netCDF-4 library can read HDF4 data files, if they were created
203 with the SD (Scientific Data) API.
204 
205 For this to work, you must build the HDF4 library with the
206 configure option `--disable-netcdf`
207 to prevent it from building an HDF4 version of the netCDF-2 library
208 that conflicts with the netCDF-2 functions that are built into the Unidata
209 netCDF library.
210 
211 Then, when building netCDF-4, use the `--enable-hdf4`.
212 option to configure. The location for the HDF4 header files and
213 library must be specified in the CPPFLAGS and LDFLAGS environment variables
214 or configure options.
215 
216 For HDF4 access to work, the library must be built with netCDF-4
217 features.
218 
219 Here's an example, assuming the HDF5 library has been built and
220 installed in H5DIR and you will build and install the HDF4 library in
221 H4DIR (which could be the same as H5DIR). From the top-level HDF4
222 source directory:
223 
224 ~~~~{.py}
225  $ # Build and install HDF4
226  $ ./configure --enable-shared --disable-netcdf --disable-fortran --prefix=${H4DIR}
227  $ make check
228  $ make install
229 ~~~~
230 
231 Then from the top-level netCDF directory:
232 
233 ~~~~{.py}
234  $ # Build and install netCDF-4 with HDF4 access enabled
235  $ CPPFLAGS="-I${H5DIR}/include -I${H4DIR}/include" \
236  LDFLAGS="-L${H5DIR}/lib -L${H4DIR}/lib" \
237  ./configure --enable-hdf4 --enable-hdf4-file-tests
238  $ make check
239  $ make install
240 ~~~~
241 
242 Building with Parallel I/O Support {#build_parallel}
243 --------------
244 
245 For parallel I/O to work, HDF5 must be installed with
246 â€“enable-parallel, and an MPI library (and related libraries) must be
247 made available to the HDF5 configure. This can be accomplished with
248 an mpicc wrapper script.
249 
250 The following works from the top-level HDF5 source directory to build
251 HDF5 with parallel I/O:
252 
253 ~~~~{.py}
254  $ # Build and install HDF5 with parallel support
255  $ CC=mpicc ./configure --enable-parallel --prefix=${H5DIR}
256  $ make check
257  $ make install
258 ~~~~
259 
260 If the HDF5 used by netCDF has been built with parallel I/O, then netCDF will also be built with inherited support for parallel I/O. This allows parallel I/O access to netCDF-4/HDF5 files. (See /ref netcdf_formats for more information about the netCDF format variants.)
261 
262 From the top-level netCDF-4 source directory, the following builds netCDF-4 with parallel I/O, assuming H5DIR specifies where parallel HDF5 was installed:
263 
264 ~~~~{.py}
265  $ # Build, test, and install netCDF-4 with HDF5 parallel support
266  $ CC=mpicc CPPFLAGS=-I${H5DIR}/include LDFLAGS=-L${H5DIR}/lib \
267  ./configure --disable-shared --enable-parallel-tests --prefix=${NCDIR}
268  $ make check
269  $ make install
270 ~~~~
271 
272 If parallel I/O access to netCDF classic and 64-bit offset files is
273 needed, an alternate
274 [parallel-netcdf library](https://trac.mcs.anl.gov/projects/parallel-netcdf/wiki/WikiStart),
275 referred to as "PnetCDF", must also be installed. Assume it was
276 installed in the directory named by the PNDIR shell variable.
277 Then, from the top-level netCDF-4 source directory, configure netCDF
278 with the "--enable-pnetcdf" option:
279 
280 ~~~~{.py}
281  $ # Build, test, and install netCDF-4 with pnetcdf support
282  $ CC=mpicc CPPFLAGS="-I${H5DIR}/include -I${PNDIR}/include" \
283  LDFLAGS="-L${H5DIR}/lib -L${PNDIR}/lib" ./configure \
284  --disable-shared --enable-pnetcdf --enable-parallel-tests \
285  --prefix=${NCDIR}
286  $ make check
287  $ make install
288 ~~~~
289 
290 Linking to netCDF-C {#linking}
291 -------------------
292 
293 For static builds of applications that use netCDF-4 you must link to all the libraries,
294 netCDF, HDF5, zlib, szip (if used with HDF5 build), and curl (if the
295 remote access client has not been disabled). This will require -L options
296 to your build for the locations of the libraries, and -l (lower-case
297 L) for the names of the libraries.
298 
299 For example, you might build other applications with netCDF-4 by
300 setting the LIBS environment variable, assuming NCDIR, H5DIR, and ZDIR
301 indicate where netCDF, HDF5, and zlib are installed:
302 
303 ~~~~{.py}
304  LIBS="-L${NCDIR}/lib -lnetcdf -L${H5DIR}/lib -lhdf5_hl -lhdf5 -L${ZDIR}/lib -lz -lm"
305 ~~~~
306 
307 For shared builds, only `-L${NCDIR}/lib -lnetcdf` is
308 needed. All other libraries will be found automatically.
309 
310 The `pkg-config` or `nc-config` utilities can be
311 used to specify build options for software that uses netCDF. For
312 example, to compile and link an application named myapp.c with a
313 netCDF-C libraries, whether shared or static, you can use
314 
315 ~~~~{.py}
316  $ cc -o myapp myapp.c `nc-config --cflags --libs`
317 ~~~~
318 
319 or
320 
321 ~~~~{.py}
322  $ PKG_CONFIG_PATH=${NCDIR}/lib/pkgconfig:$PKG_CONFIG_PATH
323  $ export PKG_CONFIG_PATH
324  $ cc -o myapp myapp.c `pkg-config --cflags --libs netcdf`
325 ~~~~
326 
327 configure options {#configure_options}
328 -----------------------------
329 
330 These options are used for `autotools`-based builds.yup
331 
332 Note: `--disable` prefix indicates that the option is normally enabled.
333 <table>
334 <tr><th>Option<th>Description<th>Dependencies
335 <tr><td>--disable-doxygen<td>Disable generation of documentation.<td>doxygen
336 <tr><td>--disable-fsync<td>disable fsync support<td>kernel fsync support
337 
338 <tr><td>--disable-netcdf-4<td>build netcdf-3 without HDF5 and zlib<td>
339 <tr><td>--disable-netcdf4<td>synonym for disable-netcdf-4
340 <tr><td>--enable-hdf4<td>build netcdf-4 with HDF4 read capability<td>HDF4, HDF5 and zlib
341 <tr><td>--enable-hdf4-file-tests<td>test ability to read HDF4 files<td>selected HDF4 files from Unidata ftp site
342 <tr><td>--enable-pnetcdf<td>build netcdf-4 with parallel I/O for classic and
343  64-bit offset files using parallel-netcdf
344 <tr><td>--enable-extra-example-tests<td>Run extra example tests<td>--enable-netcdf-4,GNU sed
345 <tr><td>--disable-filter-testing<td>Run filter example<td>--enable-shared --enable-netcdf-4
346 <tr><td>--enable-parallel-tests <td>run extra parallel IO tests<td>--enable-netcdf-4, parallel IO support
347 <tr><td>--enable-logging<td>enable logging capability<td>--enable-netcdf-4
348 <tr><td>--disable-dap<td>build without DAP client support.<td>libcurl
349 <tr><td>--disable-dap-remote-tests<td>disable dap remote tests<td>--enable-dap
350 <tr><td>--enable-dap-long-tests<td>enable dap long tests<td>
351 <tr><td>--enable-extra-tests<td>run some extra tests that may not pass because of known issues<td>
352 <tr><td>--enable-ffio<td>use ffio instead of posixio (ex. on the Cray)<td>
353 <tr><td>--disable-examples<td>don't build the netCDF examples during make check
354  (examples are treated as extra tests by netCDF)<td>
355 <tr><td>--disable-v2<td>turn off the netCDF version 2 API<td>
356 <tr><td>--disable-utilities<td>don't build netCDF utilities ncgen, ncdump, and nccopy<td>
357 <tr><td>--disable-testsets<td>don't build or run netCDF tests<td>
358 <tr><td>--enable-large-file-tests <td>Run tests which create very large data
359  files<td>~13 GB disk space required, but recovered when
360  tests are complete). See option --with-temp-large to
361  specify temporary directory
362 <tr><td>--enable-benchmarks<td>Run benchmarks. This is an experimental feature.
363  The benchmarks are extra tests, used to check netCDF performance.
364  <td>sample data files from the Unidata ftp site
365 <tr><td>--disable-extreme-numbers
366 <td>don't use extreme numbers during testing, such as MAX_INT - 1<td>
367 <tr><td>--disable-shared<td>don't build shared libraries<td>
368 <tr><td>--disable-static<td>don't build static libraries<td>
369 <tr><td>--disable-largefile<td>omit support for files larger than 2GB<td>
370 <tr><td>--enable-mmap<td>Use mmap to implement NC_DISKLESS<td>System-provided `mmap` or `mremap` functions
371 <tr><td>--enable-valgrind-tests <td>build with valgrind-tests; static builds only<td>valgrind
372 </table>
373 
374 Build Instructions for netCDF-C using CMake {#netCDF-CMake}
375 ===========================================
376 
377 ## Overview {#cmake_overview}
378 
379 Starting with netCDF-C 4.3.0, we are happy to announce the inclusion of CMake support. CMake will allow for building netCDF on a wider range of platforms, include Microsoft Windows with Visual Studio. CMake support also provides robust unit and regression testing tools. We will also maintain the standard autotools-based build system in parallel.
380 
381 In addition to providing new build options for netCDF-C, we will also provide pre-built binary downloads for the shared versions of netCDF for use with Visual Studio.
382 
383 
384 ## Requirements {#cmake_requirements}
385 The following packages are required to build netCDF-C using CMake.
386 
387 * netCDF-C Source Code
388 * CMake version 2.8.12 or greater.
389 * Optional Requirements:
390  * HDF5 Libraries for netCDF4/HDF5 support.
391  * libcurl for DAP support.
392 
393 <center>
394 <img src="deptree.jpg" height="250px" />
395 </center>
396 
397 ## The CMake Build Process {#cmake_build}
398 
399 There are four steps in the Build Process when using CMake
400 
401 1. Configuration: Before compiling, the software is configured based on the desired options.
402 2. Building: Once configuration is complete, the libraries are compiled.
403 3. Testing: Post-build, it is possible to run tests to ensure the functionality of the netCDF-C libraries.
404 4. Installation: If all tests pass, the libraries can be installed in the location specified during configuration.
405 
406 For users who prefer pre-built binaries, installation packages are available at \ref winbin
407 
408 ### Configuration {#cmake_configuration}
409 
410 The output of the configuration step is a project file based on the appropriate configurator specified. Common configurators include:
411 
412 * Unix Makefiles
413 * Visual Studio
414 * CodeBlocks
415 * ... and others
416 
417 ### Common CMake Options {#cmake_common_options}
418 
419 | **Option** | **Autotools** | **CMake** |
420 | :------- | :---- | :----- |
421 Specify Install Location | --prefix=PREFIX | -D"CMAKE_INSTALL_PREFIX=PREFIX"
422 Enable/Disable netCDF-4 | --enable-netcdf-4<br>--disable-netcdf-4 | -D"ENABLE_NETCDF_4=ON" <br> -D"ENABLE_NETCDF_4=OFF"
423 Enable/Disable DAP | --enable-dap <br> --disable-dap | -D"ENABLE_DAP=ON" <br> -D"ENABLE_DAP=OFF"
424 Enable/Disable Utilities | --enable-utilities <br> --disable-utilities | -D"BUILD_UTILITIES=ON" <br> -D"BUILD_UTILITIES=OFF"
425 Specify shared/Static Libraries | --enable-shared <br> --enable-static | -D"BUILD_SHARED_LIBS=ON" <br> -D"BUILD_SHARED_LIBS=OFF"
426 Enable/Disable Tests | --enable-testsets <br> --disable-testsets | -D"ENABLE_TESTS=ON" <br> -D"ENABLE_TESTS=OFF"
427 Specify a custom library location | Use *CFLAGS* and *LDFLAGS* | -D"CMAKE_PREFIX_PATH=/usr/custom_libs/"
428 
429 A full list of *basic* options can be found by invoking `cmake [Source Directory] -L`. To enable a list of *basic* and *advanced* options, one would invoke `cmake [Source Directory] -LA`.
430 
431 ### Configuring your build from the command line. {#cmake_command_line}
432 
433 The easiest configuration case would be one in which all of the dependent libraries are installed on the system path (in either Unix/Linux or Windows) and all the default options are desired. From the build directory (often, but not required to be located within the source directory):
434 
435 > $ cmake [Source Directory]
436 
437 If you have libraries installed in a custom directory, you may need to specify the **CMAKE\_PREFIX_PATH** variable to tell cmake where the libraries are installed. For example:
438 
439 > $ cmake [Source Directory] -DCMAKE\_PREFIX\_PATH=/usr/custom_libraries/
440 
441 ## Building {#cmake_building}
442 
443 The compiler can be executed directly with 'make' or the appropriate command for the configurator which was used.
444 
445 > $ make
446 
447 Building can also be executed indirectly via cmake:
448 
449 > $ cmake --build [Build Directory]
450 
451 ## Testing {#cmake_testing}
452 
453 Testing can be executed several different ways:
454 
455 > $ make test
456 
457 or
458 
459 > $ ctest
460 
461 or
462 
463 > $ cmake --build [Build Directory] --target test
464 
465 ### Installation {#cmake_installation}
466 
467 Once netCDF has been built and tested, it may be installed using the following commands:
468 
469 > $ make install
470 
471 or
472 
473 > $ cmake --build [Build Directory] --target install
474 
475 ## See Also {#cmake_see_also}
476 
477 For further information regarding netCDF and CMake, see \ref cmake_faq.
478 

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