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
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
|
<!-- $Header$
Purpose: Build_Hints archive
URL:
http://nco.sf.net/build_hints.shtml
http://dust.ess.uci.edu/nco/build_hints.shtml
file:///home/zender/nco/doc/build_hints.shtml
Usage:
/usr/bin/scp ~/nco/doc/build_hints.shtml zender,nco@web.sf.net:/home/project-web/nco/htdocs
scp -p ~/nco/doc/build_hints.shtml dust.ess.uci.edu:Sites/nco
-->
<!doctype html public "-//W3C//DTD HTML 3.2//EN">
<html>
<head>
<title>NCO Homepage</title>
<meta name="GENERATOR" content="Mozilla/3.04Gold (X11; I; Linux 2.0.0 i686) [Netscape]">
<meta name="Author" content="Charles S. Zender">
<meta name="Keywords" content="NCO Homepage, netCDF, netCDF operator, GCM, HDF, scientific data">
</head>
<body bgcolor="#FFFFFF" text="#000000" link="#0000FF" vlink="#008080" alink="#FF0000">
<dt><a name="Makefile"></a></dt> <!-- http://nco.sf.net#Makefile -->
<dt><a name="hnt"></a></dt> <!-- http://nco.sf.net#hnt -->
<dt><a name="bld_hnt"></a></dt> <!-- http://nco.sf.net#bld_hnt -->
<h2>Hints to Build-from-Source:</h2>
<ul><b>Generic Build Hints:</b>
<a name="bld_cnf"></a> <!-- http://nco.sf.net#bld_cnf -->
<li><i>The two NCO build mechanisms:</i>
NCO has two build mechanisms: (1) GNU configure and
(2) a custom Makefile (<tt>nco/bld/Makefile</tt>)
designed for hand-editing.
Try the traditional GNU <tt>configure</tt> method first, i.e.,
<tt>./configure;make;make check;make install</tt>.
This method involves no hand-editing of makefiles, but trouble-free
builds with it are less common than we would like.
The file <tt>nco/configure.eg</tt> contains a table which describes the
success you can expect building NCO with the <tt>configure</tt>
mechanism.
If the simple <tt>configure</tt> recipe above does not work, savvy
users may find it straightforward to modify and use the following, more
advanced <tt>configure</tt> recipe:
<tt>
<pre class="example">
# gcc/g++ Sysadmins use/modify this to install/update NCO in /usr/local, based on netCDF4 also in /usr/local (works on givre 20100727):
export GNU_TRP=`~/nco/autobld/config.guess`
cd ~/nco;/bin/rm -f *.${GNU_TRP}.foo;make distclean
CPPFLAGS='-DHAVE_NETCDF4_H -I/usr/local/include' LDFLAGS='-L/usr/local/lib' ./configure --prefix='/usr/local' --enable-ncap2 --enable-netcdf4 > nco.configure.${GNU_TRP}.foo 2>&1
/bin/cp -f config.log nco.config.log.${GNU_TRP}.foo
/bin/cp -f libtool nco.libtool.${GNU_TRP}.foo
make clean;make > nco.make.${GNU_TRP}.foo 2>&1
make check >> nco.make.${GNU_TRP}.foo 2>&1
sudo make install >> nco.make.${GNU_TRP}.foo 2>&1
</pre>
</tt>
This is the recipe that the developers use to test <tt>configure</tt>
on their machines.
Please contribute patches required to get the <tt>configure</tt>
mechanism working properly for NCO on your platform.
The <a href="http://dust.ess.uci.edu/nco/rgr">regressions archive</a>
contains gory details of successful (and failed) builds for many platforms.
Plaform-specific build hints (CentOS, Mac OS X, RHEL, Solaris)
are listed <a href="#bld_plt_spc">below</a>.
<br>
All platforms continue to work fine with the <tt>nco/bld/Makefile</tt>
method:
<tt>
<pre class="example">
export MY_BIN_DIR='/home/username/bin' # Executables installed here
export MY_OBJ_DIR='/home/username/obj' # Object files placed here
export MY_LIB_DIR='/home/username/lib' # Libraries built here
mkdir -p ${MY_BIN_DIR} ${MY_OBJ_DIR} ${MY_LIB_DIR}
cd ~/nco/bld
make dir
make all
make ncap2
make test
</pre>
</tt>
Disadvantages are that <tt>nco/bld/Makefile</tt> (1) Usually requires
editing to fix your platforms paths; (2) Does not support shared
libraries; and (3) Requires a degree from Hogwarts to understand.
</li>
<!-- http://nco.sf.net#dpl_sym -->
<a name="dpl_sym"></a>
<li><i>Duplicate symbols errors:</i>
When building NCO with the netCDF4 library and headers, some compilers
emit errors due to duplicate symbol definitions.
This arises because of the complexity of the build system.
Essentially, NCO has to define some netCDF API prototypes itself
to handle the corner case where the netCDF4 distribution is used
to build netCDF3 libraries.
We have tried to address this issue using <tt>autoconf/configure</tt>
but it is beyond our abilities.
The fix is to manually tell NCO that the netCDF4 header
file <tt>netcdf.h</tt> is in fact being used so that NCO should
not attempt to define these prototypes.
Do this, e.g., with <tt>CPPFLAGS='-DHAVE_NETCDF4_H'</tt> or
<tt>USR_TKN='-DHAVE_NETCDF4_H'</tt> if you use <tt>configure</tt>.
</li>
<!-- http://nco.sf.net#bld_chn -->
<a name="bld_chn"></a>
<li><i>Build Chain Version Incompatibilities:</i>
NCO requires GNU <tt>make</tt> version ≥ 3.78.1 to support target-specific variable values in <tt>bld/Makefile</tt>.
NCO most often fails to build because <tt>ncap</tt> fails to build.
Two of the most common reasons that <tt>ncap</tt> fails to build are
(1) GNU <tt>bison</tt> is out-of-date (upgrade <tt>bison</tt>)
and (2) <tt>--enable-optimize-*</tt> is specified to
<tt>configure</tt> (do not specify it).<br>
</li>
<!-- http://nco.sf.net#bld_c99 -->
<a name="bld_c99"></a>
<li><i>C99-compliance & old compilers:</i>
NCO versions ≥ 2.9.8 require the compiler to
support the 1999 ISO C-Standard called C99.
NCO takes advantage of two C99 features, restricted pointers and
designated initializers.
To build NCO versions ≥ 2.9.8 without a C99-compliant
compiler, simply undefine the <tt>restrict</tt> type qualifier
before compiling NCO.
Do this, e.g., with <tt>CPPFLAGS='-Drestrict='</tt>.
More details on C99 compatibility are in the header file
<a href="http://nco.cvs.sf.net/nco/nco/src/nco/nco.h"><tt>nco/src/nco/nco.h</tt></a>.<br>
</li>
<!-- http://nco.sf.net#bld_netcdf -->
<a name="bld_netcdf"></a>
<li><i>Old netCDF libraries:</i>
NCO versions ≥ 3.0.0 require netCDF versions
≥ 3.6 to take advantage of the new 64-bit offset file type.
The library <i>and</i> include directories (e.g., <tt>/usr/lib</tt> and
<tt>/usr/include</tt>, respectively) for netCDF version ≥ 3.6
must be on the path searched by the compiler, and must precede the
locations of any older netCDF installations.
To build NCO versions ≥ 3.0.0 with older netCDF versions
< 3.6, simply define the pre-processor token
<tt>NC_64BIT_OFFSET</tt> to <tt>0</tt> before compiling NCO.
Do this, e.g., with <tt>CPPFLAGS='-DNC_64BIT_OFFSET=0'</tt> or
<tt>USR_TKN='-DNC_64BIT_OFFSET=0'</tt> if you use <tt>configure</tt>
or <tt>bld/Makefile</tt>, respectively.
Users attempting to build NCO with OPeNDAP versions ≤ 3.6.x may
need this workaround because OPeNDAP did not fully support netCDF
version 3.6.x functionality until OPeNDAP versions ≥ 3.7.0.
(The indicator for this problem is a build error like
<tt>"nco_fl_utl.c", line 30.20: 1506-045 (S) Undeclared identifier
NC_64BIT_OFFSET</tt>.)
All modern NCO versions require netCDF versions ≥ 3.5.0 to
support <tt>nc_type NC_NAT</tt> in NCO source code.
NCO versions 3.9.0 and greater (May, 2007) require netCDF versions
≥ 3.6.0 to resolve the <tt>nc_inq_format()</tt> function.
</li>
<!-- http://nco.sf.net#bld_ncap -->
<a name="bld_ncap"></a>
<li><i><tt>ncap</tt> build hints:</i>
<tt>ncap</tt> is a sophisticated and somewhat fragile program.
<tt>ncap</tt> requires <tt>flex</tt> to build correctly.
AT&T <tt>lex</tt> will not work because it does not understand
<tt>EOF</tt> rules used in <tt>ncap_lex.l</tt>.
<tt>bison</tt> version 1.29 (the default version on early
Mac OS X) is buggy and does not parse <tt>ncap_yacc.y</tt>
correctly; previous and later <tt>bison</tt>'s work
correctly.
<tt>bison</tt> version 1.25 will not build <tt>ncap</tt> on Solaris.
Please upgrade <tt>bison</tt> to the latest version (e.g., 1.875+)
before reporting <tt>ncap</tt> build problems.
If <tt>ncap</tt> keeps you from building NCO, and you do not need
<tt>ncap</tt>, configure with <tt>--disable-ncap</tt> (and know that
<tt>ncwa</tt> will fail to build as a result).
</li>
<!-- http://nco.sf.net#bld_GSL -->
<a name="bld_gsl"></a><a name="bld_GSL"></a>
<li><i>Build Hints with GSL:</i><br>
NCO versions 3.9.6— support automatic building and linking
for <a href="http://www.gnu.org/software/gsl">GSL</a>
versions 1.4—.
Earlier GSL versions are not supported.<br>
</li>
<!-- http://nco.sf.net#bld_DAP -->
<a name="bld_dap"></a><a name="bld_DAP"></a><a name="bld_DODS"></a><a name="bld_OPeNDAP"></a>
<li><i>Build Hints with DAP:</i><br>
NCO versions 3.9.9— support automatic building and linking
for DAP supplied from <a href="http://www.unidata.ucar.edu/software/netcdf/docs/netcdf/DAP-Support.html">libnetcdf</a> versions 4.1-beta1 and beyond<br>
NCO versions 3.1.3— support automatic building and linking
for <a href="http://opendap.org">OPeNDAP</a> versions 3.6.x and
GCC versions 4.0+.<br>
NCO versions 3.0.1—3.1.2 support automatic building and linking
for <a href="http://opendap.org">OPeNDAP</a> versions 3.5.x and
GCC versions 3.4+.<br>
NCO versions 2.8.5—3.0.0 support automatic building and linking
for <a href="http://opendap.org">OPeNDAP</a> versions 3.4.x and
GCC versions 3.3+.<br>
NCO versions ?.?.?—2.8.4 support automatic building and linking
for <a href="http://opendap.org">DODS</a> versions 3.2.x and
GCC versions 3.2+.<br>
No other version combinations are supported.
</li>
<!-- http://nco.sf.net#bld_nco_c++ -->
<a name="bld_nco_c++"></a>
<li><i><tt>libnco_c++</tt> build hints:</i>
<tt>libnco_c++</tt> requires a good C++ compiler to build correctly.
Few people need <tt>libnco_c++</tt>, so the workaround is not to build it.
This is done by configuring with <tt>--disable-nco_cplusplus</tt>.
</li>
</ul>
<!-- http://nco.sf.net#bld_plt_spc -->
<a name="bld_plt_spc"></a>
<ul><b>Platform-Specific Build Hints:</b>
<!-- http://nco.sf.net#bld_aix -->
<a name="bld_aix"></a>
<li><i>AIX build hints:</i>
NCO versions 2.8.7+ do not build with autotools under AIX when
<tt>--enable-optimize-*</tt> is selected.
The workaround is to not use <tt>--enable-optimize-*</tt>.
NCO versions 2.9.7+ do not build shared libraries with AIX xlc
compilers because of silly AIX library dependencies activated
by OpenMP directives.
The workaround is to configure with <tt>--disable-shared</tt>.
</li>
<!-- http://nco.sf.net#bld_irix -->
<a name="bld_irix"></a>
<li><i>IRIX build hints:</i>
The most common problem with building on SGI IRIX is an out-of-date toolchain.
</li>
<!-- http://nco.sf.net#bld_osx -->
<a name="bld_osx"></a>
<li><i>Mac OS X build hints:</i>
Mac OS X users report success building NCO without patches so
long as they (1) Install the latest version of <tt>bison</tt>,
(2) Disable shared libraries and (3) Disable extended regular
expressions. This is done with
<tt>./configure --disable-regex --disable-shared</tt>
Building NCO with shared libraries on Mac OS X on may be possible.
To try, first re-build and re-install the netCDF library using
<tt>CFLAGS=-fno-common</tt>.
Apparently netCDF, unlike most codes, does not set this automatically.
Then build NCO normally.
Mac OS X ships with a broken version of the POSIX <tt>cut</tt>
utility which causes many NCO regression tests to appear to fail.
In fact the NCO commands succeed, but the <tt>cut</tt> output fails.
The workaround is not to heed the regression tests, or to install a
working <tt>cut</tt>, e.g., from the GNU <tt>coreutils</tt> package.
</li>
<!-- http://nco.sf.net#bld_rhel -->
<a name="bld_rhel"></a>
<a name="bld_centos"></a> <!-- http://nco.sf.net#bld_centos -->
<li><i>RHEL build hints:</i>
Scripts for generating executables for recent (4.0.x, ~2011) versions of NCO for RedHat Enterprise Linux 5 (RHEL5) and CentOS5 platforms are described <a href="http://sf.net/projects/nco/forums/forum/9830/topic/4089501">here</a>.
Older information on building x86_64 RPMs is available <a href="http://dust.ess.uci.edu/wangd/s9y">here</a>.
</li>
<!-- http://nco.sf.net#bld_slr -->
<a name="bld_slr"></a>
<li><i>Solaris build hints:</i>
All recent NCO versions build with autotools on Solaris 2.7—2.9.
The most common problem with building on Solaris with
<tt>cc</tt>/<tt>CC</tt> is that <tt>bison</tt> may be out-of-date.
Install an up-to-date <tt>bison</tt> (e.g., 1.875+).
Solaris 2.10, i.e., Solaris10, had the audacity to change the
prototype of the <tt>ctime_r()</tt> function and so does not build
NCO 3.0.1.
The fix is to upgrade to the current NCO version.
</li>
<!-- http://nco.sf.net#bld_sx -->
<a name="bld_sx"></a>
<li><i>SX build hints:</i>
NEC SX does not understand the <tt>S_ISLNK</tt> macro,
preferring instead the (non-POSIX) <tt>S_IFLNK</tt> macro.
This macro appears in the file
<a href="http://nco.cvs.sf.net/nco/nco/src/nco/nco_fl_utl.c"><tt>nco_fl_utl.c</tt></a>.
The patch I wrote for this may be broken.
Will someone with NEC SX please send us a working patch?
</li>
<!-- http://nco.sf.net#bld_wnd -->
<a name="bld_wnd"></a>
<li><i>Windows build hints:</i>
Building on Microsoft Windows is possible with Cygwin.
The resulting executables will behave normally on local files,
but will not have some (most?) of NCO's network functionality
(e.g., <tt>scp</tt>, <a href="http://opendap.org">OPeNDAP</a>).
See the <a href="http://nco.sf.net/nco.html#wnd">User's Guide</a>
for more details.
</li>
</ul>
<hr></p>
</body>
</html>
|
