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Encountered an issue while compiling RegCM5.0 #35

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lymelody opened this issue Jul 19, 2023 · 7 comments
Open

Encountered an issue while compiling RegCM5.0 #35

lymelody opened this issue Jul 19, 2023 · 7 comments

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@lymelody
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I reported an error while compiling RegCM5.0. Configure: error: NetCDF library not found, but my NetCDF has been installed and my environment variables have also been configured. I don't know why? awaiting for a reply.Thanks.
@graziano-giuliani
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After configuring environment variable, can you find the nf-config? On my development machine:

nf-config --all

This netCDF-Fortran 4.6.0 has been built with the following features:

--cc -> gcc
--cflags -> -I/home/netapp-clima/users/ggiulian/m20/include -I/home/netapp-clima/users/ggiulian/m20/include

--fc -> gfortran
--fflags -> -I/home/netapp-clima/users/ggiulian/m20/include -I/home/netapp-clima/users/ggiulian/m20/include
--flibs -> -L/home/netapp-clima/users/ggiulian/m20/lib -lnetcdff -L/home/netapp-clima/users/ggiulian/m20/lib -lnetcdf -lnetcdf -ldl -lm
--has-f90 ->
--has-f03 -> yes

--has-nc2 -> yes
--has-nc4 -> yes

--prefix -> /home/netapp-clima/users/ggiulian/m20
--includedir-> /home/netapp-clima/users/ggiulian/m20/include
--version -> netCDF-Fortran 4.6.0

Path will be different on your system, obviously, but is the nf-config script available in the path?

@lymelody
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Thank you very much for your answer. Based on your guidance, I gave it a try and my computer output is as follows: [root@localhost RegCM5]# nf-config --all

This netCDF-Fortran 4.4.4 has been built with the following features:

--cc -> gcc --cflags -> -I/data/user/local/netcdf4-needed/include -I/data/user/local/netcdf4-needed/include

--fc -> gfortran --fflags -> -I/data/user/local/netcdf4-needed/include --flibs -> -L/data/user/local/netcdf4-needed/lib -lnetcdff -L/data/user/local/netcdf4-needed/lib -lnetcdf -lnetcdf --has-f90 -> no --has-f03 -> yes

--has-nc2 -> yes --has-nc4 -> yes

--prefix -> /data/user/local/netcdf4-needed --includedir-> /data/user/local/netcdf4-needed/include --version -> netCDF-Fortran 4.4.4

Thank you very much for your answer. Based on your guidance, I gave it a try and my computer output is as follows:
[root@localhost RegCM5]# nf-config --all

This netCDF-Fortran 4.4.4 has been built with the following features:

--cc -> gcc
--cflags -> -I/data/user/local/netcdf4-needed/include -I/data/user/local/netcdf4-needed/include

--fc -> gfortran
--fflags -> -I/data/user/local/netcdf4-needed/include
--flibs -> -L/data/user/local/netcdf4-needed/lib -lnetcdff -L/data/user/local/netcdf4-needed/lib -lnetcdf -lnetcdf
--has-f90 -> no
--has-f03 -> yes

--has-nc2 -> yes
--has-nc4 -> yes

--prefix -> /data/user/local/netcdf4-needed
--includedir-> /data/user/local/netcdf4-needed/include
--version -> netCDF-Fortran 4.4.4

@graziano-giuliani
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Can you post the config.log?

@lymelody
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Can you post the config.log?

[root@localhost RegCM5]# cat -n config.log
1 This file contains any messages produced by compilers while
2 running configure, to aid debugging if configure makes a mistake.
3
4 It was created by RegCM configure 5.0.0, which was
5 generated by GNU Autoconf 2.69. Invocation command line was
6
7 $ ./configure CC=gcc LDFLAGS=-L/data/user/local/netcdf4-needed/lib CPPFLAGS=-I/data/user/local/netcdf4-needed/include FC=gfortran --no-create --no-recursion
8
9 ## --------- ##
10 ## Platform. ##
11 ## --------- ##
12
13 hostname = localhost.localdomain
14 uname -m = x86_64
15 uname -r = 3.10.0-862.el7.x86_64
16 uname -s = Linux
17 uname -v = #1 SMP Fri Apr 20 16:44:24 UTC 2018
18
19 /usr/bin/uname -p = x86_64
20 /bin/uname -X = unknown
21
22 /bin/arch = x86_64
23 /usr/bin/arch -k = unknown
24 /usr/convex/getsysinfo = unknown
25 /usr/bin/hostinfo = unknown
26 /bin/machine = unknown
27 /usr/bin/oslevel = unknown
28 /bin/universe = unknown
29
30 PATH: /data/user/local/netcdf4-needed/bin
31 PATH: /data/user/local/ncl/bin
32 PATH: /data/user/local/mpi/bin
33 PATH: /usr/local/sbin
34 PATH: /usr/local/bin
35 PATH: /usr/sbin
36 PATH: /usr/bin
37 PATH: /root/bin
38
39
40 ## ----------- ##
41 ## Core tests. ##
42 ## ----------- ##
43
44 configure:2468: checking build system type
45 configure:2482: result: x86_64-unknown-linux-gnu
46 configure:2502: checking host system type
47 configure:2515: result: x86_64-unknown-linux-gnu
48 configure:2556: checking how to print strings
49 configure:2583: result: printf
50 configure:2652: checking for gcc
51 configure:2679: result: gcc
52 configure:2908: checking for C compiler version
53 configure:2917: gcc --version >&5
54 gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)
55 Copyright (C) 2015 Free Software Foundation, Inc.
56 This is free software; see the source for copying conditions. There is NO
57 warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
58
59 configure:2928: $? = 0
60 configure:2917: gcc -v >&5
61 Using built-in specs.
62 COLLECT_GCC=gcc
63 COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper
64 Target: x86_64-redhat-linux
65 Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux
66 Thread model: posix
67 gcc version 4.8.5 20150623 (Red Hat 4.8.5-44) (GCC)
68 configure:2928: $? = 0
69 configure:2917: gcc -V >&5
70 gcc: error: unrecognized command line option '-V'
71 gcc: fatal error: no input files
72 compilation terminated.
73 configure:2928: $? = 4
74 configure:2917: gcc -qversion >&5
75 gcc: error: unrecognized command line option '-qversion'
76 gcc: fatal error: no input files
77 compilation terminated.
78 configure:2928: $? = 4
79 configure:2948: checking whether the C compiler works
80 configure:2970: gcc -I/data/user/local/netcdf4-needed/include -L/data/user/local/netcdf4-needed/lib conftest.c >&5
81 configure:2974: $? = 0
82 configure:3022: result: yes
83 configure:3025: checking for C compiler default output file name
84 configure:3027: result: a.out
85 configure:3033: checking for suffix of executables
86 configure:3040: gcc -o conftest -I/data/user/local/netcdf4-needed/include -L/data/user/local/netcdf4-needed/lib conftest.c >&5
87 configure:3044: $? = 0
88 configure:3066: result:
89 configure:3088: checking whether we are cross compiling
90 configure:3096: gcc -o conftest -I/data/user/local/netcdf4-needed/include -L/data/user/local/netcdf4-needed/lib conftest.c >&5
91 configure:3100: $? = 0
92 configure:3107: ./conftest
93 configure:3111: $? = 0
94 configure:3126: result: no
95 configure:3131: checking for suffix of object files
96 configure:3153: gcc -c -I/data/user/local/netcdf4-needed/include conftest.c >&5
97 configure:3157: $? = 0
98 configure:3178: result: o
99 configure:3182: checking whether we are using the GNU C compiler
100 configure:3201: gcc -c -I/data/user/local/netcdf4-needed/include conftest.c >&5
101 configure:3201: $? = 0
102 configure:3210: result: yes
103 configure:3219: checking whether gcc accepts -g
104 configure:3239: gcc -c -g -I/data/user/local/netcdf4-needed/include conftest.c >&5
105 configure:3239: $? = 0
106 configure:3280: result: yes
107 configure:3297: checking for gcc option to accept ISO C89
108 configure:3360: gcc -c -g -O2 -I/data/user/local/netcdf4-needed/include conftest.c >&5
109 configure:3360: $? = 0
110 configure:3373: result: none needed
111 configure:3393: checking for a sed that does not truncate output
112 configure:3457: result: /usr/bin/sed
113 configure:3475: checking for grep that handles long lines and -e
114 configure:3533: result: /usr/bin/grep
115 configure:3538: checking for egrep
116 configure:3600: result: /usr/bin/grep -E
117 configure:3605: checking for fgrep
118 configure:3667: result: /usr/bin/grep -F
119 configure:3702: checking for ld used by gcc
120 configure:3769: result: /usr/bin/ld
121 configure:3776: checking if the linker (/usr/bin/ld) is GNU ld
122 configure:3791: result: yes
123 configure:3803: checking for BSD- or MS-compatible name lister (nm)
124 configure:3852: result: /usr/bin/nm -B
125 configure:3982: checking the name lister (/usr/bin/nm -B) interface
126 configure:3989: gcc -c -g -O2 -I/data/user/local/netcdf4-needed/include conftest.c >&5
127 configure:3992: /usr/bin/nm -B "conftest.o"
128 configure:3995: output
129 0000000000000000 B some_variable
130 configure:4002: result: BSD nm
131 configure:4005: checking whether ln -s works
132 configure:4009: result: yes
133 configure:4017: checking the maximum length of command line arguments
134 configure:4147: result: 1572864
135 configure:4164: checking whether the shell understands some XSI constructs
136 configure:4174: result: yes
137 configure:4178: checking whether the shell understands "+="
138 configure:4184: result: yes
139 configure:4219: checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format
140 configure:4259: result: func_convert_file_noop
141 configure:4266: checking how to convert x86_64-unknown-linux-gnu file names to toolchain format
142 configure:4286: result: func_convert_file_noop
143 configure:4293: checking for /usr/bin/ld option to reload object files
144 configure:4300: result: -r
145 configure:4374: checking for objdump
146 configure:4390: found /usr/bin/objdump
147 configure:4401: result: objdump
148 configure:4433: checking how to recognize dependent libraries
149 configure:4635: result: pass_all
150 configure:4720: checking for dlltool
151 configure:4750: result: no
152 configure:4780: checking how to associate runtime and link libraries
153 configure:4807: result: printf %s\n
154 configure:4868: checking for ar
155 configure:4884: found /usr/bin/ar
156 configure:4895: result: ar
157 configure:4932: checking for archiver @file support
158 configure:4949: gcc -c -g -O2 -I/data/user/local/netcdf4-needed/include conftest.c >&5
159 configure:4949: $? = 0
160 configure:4952: ar cru libconftest.a @conftest.lst >&5
161 configure:4955: $? = 0
162 configure:4960: ar cru libconftest.a @conftest.lst >&5
163 ar: conftest.o: No such file or directory
164 configure:4963: $? = 1
165 configure:4975: result: @
166 configure:5033: checking for strip
167 configure:5049: found /usr/bin/strip
168 configure:5060: result: strip
169 configure:5132: checking for ranlib
170 configure:5148: found /usr/bin/ranlib
171 configure:5159: result: ranlib
172 configure:5236: checking for gawk
173 configure:5252: found /usr/bin/gawk
174 configure:5263: result: gawk
175 configure:5303: checking command to parse /usr/bin/nm -B output from gcc object
176 configure:5423: gcc -c -g -O2 -I/data/user/local/netcdf4-needed/include conftest.c >&5
177 configure:5426: $? = 0
178 configure:5430: /usr/bin/nm -B conftest.o | sed -n -e 's/^.[ ]([ABCDGIRSTW][ABCDGIRSTW])[ ][ ]([_A-Za-z][_A-Za-z0-9])$/\1 \2 \2/p' | sed '/ __gnu_lto/d' > conftest.nm
179 configure:5433: $? = 0
180 configure:5499: gcc -o conftest -g -O2 -I/data/user/local/netcdf4-needed/include -L/data/user/local/netcdf4-needed/lib conftest.c conftstm.o >&5
181 configure:5502: $? = 0
182 configure:5540: result: ok
183 configure:5577: checking for sysroot
184 configure:5607: result: no
185 configure:5684: gcc -c -g -O2 -I/data/user/local/netcdf4-needed/include conftest.c >&5
186 configure:5687: $? = 0
187 configure:5863: checking for mt
188 configure:5893: result: no
189 configure:5913: checking if : is a manifest tool
190 configure:5919: : '-?'
191 configure:5927: result: no
192 configure:6569: checking how to run the C preprocessor
193 configure:6600: gcc -E -I/data/user/local/netcdf4-needed/include conftest.c
194 configure:6600: $? = 0
195 configure:6614: gcc -E -I/data/user/local/netcdf4-needed/include conftest.c
196 conftest.c:9:28: fatal error: ac_nonexistent.h: No such file or directory
197 #include <ac_nonexistent.h>
198 ^
199 compilation terminated.
200 configure:6614: $? = 1
201 configure: failed program was:
202 | /* confdefs.h /
203 | #define PACKAGE_NAME "RegCM"
204 | #define PACKAGE_TARNAME "regcm"
205 | #define PACKAGE_VERSION "5.0.0"
206 | #define PACKAGE_STRING "RegCM 5.0.0"
207 | #define PACKAGE_BUGREPORT "[email protected]"
208 | #define PACKAGE_URL ""
209 | / end confdefs.h. /
210 | #include <ac_nonexistent.h>
211 configure:6639: result: gcc -E
212 configure:6659: gcc -E -I/data/user/local/netcdf4-needed/include conftest.c
213 configure:6659: $? = 0
214 configure:6673: gcc -E -I/data/user/local/netcdf4-needed/include conftest.c
215 conftest.c:9:28: fatal error: ac_nonexistent.h: No such file or directory
216 #include <ac_nonexistent.h>
217 ^
218 compilation terminated.
219 configure:6673: $? = 1
220 configure: failed program was:
221 | / confdefs.h /
222 | #define PACKAGE_NAME "RegCM"
223 | #define PACKAGE_TARNAME "regcm"
224 | #define PACKAGE_VERSION "5.0.0"
225 | #define PACKAGE_STRING "RegCM 5.0.0"
226 | #define PACKAGE_BUGREPORT "[email protected]"
227 | #define PACKAGE_URL ""
228 | / end confdefs.h. /
229 | #include <ac_nonexistent.h>
230 configure:6702: checking for ANSI C header files
231 configure:6722: gcc -c -g -O2 -I/data/user/local/netcdf4-needed/include conftest.c >&5
232 configure:6722: $? = 0
233 configure:6795: gcc -o conftest -g -O2 -I/data/user/local/netcdf4-needed/include -L/data/user/local/netcdf4-needed/lib conftest.c >&5
234 configure:6795: $? = 0
235 configure:6795: ./conftest
236 configure:6795: $? = 0
237 configure:6806: result: yes
238 configure:6819: checking for sys/types.h
239 configure:6819: gcc -c -g -O2 -I/data/user/local/netcdf4-needed/include conftest.c >&5
240 configure:6819: $? = 0
241 configure:6819: result: yes
242 configure:6819: checking for sys/stat.h
243 configure:6819: gcc -c -g -O2 -I/data/user/local/netcdf4-needed/include conftest.c >&5
244 configure:6819: $? = 0
245 configure:6819: result: yes
246 configure:6819: checking for stdlib.h
247 configure:6819: gcc -c -g -O2 -I/data/user/local/netcdf4-needed/include conftest.c >&5
248 configure:6819: $? = 0
249 configure:6819: result: yes
250 configure:6819: checking for string.h
251 configure:6819: gcc -c -g -O2 -I/data/user/local/netcdf4-needed/include conftest.c >&5
252 configure:6819: $? = 0
253 configure:6819: result: yes
254 configure:6819: checking for memory.h
255 configure:6819: gcc -c -g -O2 -I/data/user/local/netcdf4-needed/include conftest.c >&5
256 configure:6819: $? = 0
257 configure:6819: result: yes
258 configure:6819: checking for strings.h
259 configure:6819: gcc -c -g -O2 -I/data/user/local/netcdf4-needed/include conftest.c >&5
260 configure:6819: $? = 0
261 configure:6819: result: yes
262 configure:6819: checking for inttypes.h
263 configure:6819: gcc -c -g -O2 -I/data/user/local/netcdf4-needed/include conftest.c >&5
264 configure:6819: $? = 0
265 configure:6819: result: yes
266 configure:6819: checking for stdint.h
267 configure:6819: gcc -c -g -O2 -I/data/user/local/netcdf4-needed/include conftest.c >&5
268 configure:6819: $? = 0
269 configure:6819: result: yes
270 configure:6819: checking for unistd.h
271 configure:6819: gcc -c -g -O2 -I/data/user/local/netcdf4-needed/include conftest.c >&5
272 configure:6819: $? = 0
273 configure:6819: result: yes
274 configure:6833: checking for dlfcn.h
275 configure:6833: gcc -c -g -O2 -I/data/user/local/netcdf4-needed/include conftest.c >&5
276 configure:6833: $? = 0
277 configure:6833: result: yes
278 configure:7039: checking for objdir
279 configure:7054: result: .libs
280 configure:7321: checking if gcc supports -fno-rtti -fno-exceptions
281 configure:7339: gcc -c -g -O2 -I/data/user/local/netcdf4-needed/include -fno-rtti -fno-exceptions conftest.c >&5
282 cc1: warning: command line option '-fno-rtti' is valid for C++/ObjC++ but not for C [enabled by default]
283 configure:7343: $? = 0
284 configure:7356: result: no
285 configure:7683: checking for gcc option to produce PIC
286 configure:7690: result: -fPIC -DPIC
287 configure:7698: checking if gcc PIC flag -fPIC -DPIC works
288 configure:7716: gcc -c -g -O2 -I/data/user/local/netcdf4-needed/include -fPIC -DPIC -DPIC conftest.c >&5
289 configure:7720: $? = 0
290 configure:7733: result: yes
291 configure:7762: checking if gcc static flag -static works
292 configure:7790: result: no
293 configure:7805: checking if gcc supports -c -o file.o
294 configure:7826: gcc -c -g -O2 -I/data/user/local/netcdf4-needed/include -o out/conftest2.o conftest.c >&5
295 configure:7830: $? = 0
296 configure:7852: result: yes
297 configure:7860: checking if gcc supports -c -o file.o
298 configure:7907: result: yes
299 configure:7940: checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
300 configure:9093: result: yes
301 configure:9130: checking whether -lc should be explicitly linked in
302 configure:9138: gcc -c -g -O2 -I/data/user/local/netcdf4-needed/include conftest.c >&5
303 configure:9141: $? = 0
304 configure:9156: gcc -shared -fPIC -DPIC conftest.o -v -Wl,-soname -Wl,conftest -o conftest 2>&1 | /usr/bin/grep -lc >/dev/null 2>&1
305 configure:9159: $? = 0
306 configure:9173: result: no
307 configure:9333: checking dynamic linker characteristics
308 configure:9844: gcc -o conftest -g -O2 -I/data/user/local/netcdf4-needed/include -L/data/user/local/netcdf4-needed/lib -Wl,-rpath -Wl,/foo conftest.c >&5
309 configure:9844: $? = 0
310 configure:10070: result: GNU/Linux ld.so
311 configure:10177: checking how to hardcode library paths into programs
312 configure:10202: result: immediate
313 configure:10742: checking whether stripping libraries is possible
314 configure:10747: result: yes
315 configure:10782: checking if libtool supports shared libraries
316 configure:10784: result: yes
317 configure:10787: checking whether to build shared libraries
318 configure:10808: result: yes
319 configure:10811: checking whether to build static libraries
320 configure:10815: result: yes
321 configure:10869: checking for a BSD-compatible install
322 configure:10937: result: /usr/bin/install -c
323 configure:10948: checking whether build environment is sane
324 configure:11003: result: yes
325 configure:11154: checking for a thread-safe mkdir -p
326 configure:11193: result: /usr/bin/mkdir -p
327 configure:11196: checking whether make sets $(MAKE)
328 configure:11218: result: yes
329 configure:11248: checking for style of include used by make
330 configure:11276: result: GNU
331 configure:11310: checking whether make supports nested variables
332 configure:11327: result: yes
333 configure:11412: checking dependency style of gcc
334 configure:11523: result: gcc3
335 configure:11583: checking for ranlib
336 configure:11610: result: ranlib
337 configure:11680: checking for gcc
338 configure:11707: result: gcc
339 configure:11936: checking for C compiler version
340 configure:11945: gcc --version >&5
341 gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)
342 Copyright (C) 2015 Free Software Foundation, Inc.
343 This is free software; see the source for copying conditions. There is NO
344 warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
345
346 configure:11956: $? = 0
347 configure:11945: gcc -v >&5
348 Using built-in specs.
349 COLLECT_GCC=gcc
350 COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper
351 Target: x86_64-redhat-linux
352 Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux
353 Thread model: posix
354 gcc version 4.8.5 20150623 (Red Hat 4.8.5-44) (GCC)
355 configure:11956: $? = 0
356 configure:11945: gcc -V >&5
357 gcc: error: unrecognized command line option '-V'
358 gcc: fatal error: no input files
359 compilation terminated.
360 configure:11956: $? = 4
361 configure:11945: gcc -qversion >&5
362 gcc: error: unrecognized command line option '-qversion'
363 gcc: fatal error: no input files
364 compilation terminated.
365 configure:11956: $? = 4
366 configure:11960: checking whether we are using the GNU C compiler
367 configure:11988: result: yes
368 configure:11997: checking whether gcc accepts -g
369 configure:12058: result: yes
370 configure:12075: checking for gcc option to accept ISO C89
371 configure:12151: result: none needed
372 configure:12277: checking for Fortran compiler version
373 configure:12286: gfortran --version >&5
374 GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)
375 Copyright (C) 2015 Free Software Foundation, Inc.
376
377 GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
378 You may redistribute copies of GNU Fortran
379 under the terms of the GNU General Public License.
380 For more information about these matters, see the file named COPYING
381
382 configure:12297: $? = 0
383 configure:12286: gfortran -v >&5
384 Using built-in specs.
385 COLLECT_GCC=gfortran
386 COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper
387 Target: x86_64-redhat-linux
388 Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux
389 Thread model: posix
390 gcc version 4.8.5 20150623 (Red Hat 4.8.5-44) (GCC)
391 configure:12297: $? = 0
392 configure:12286: gfortran -V >&5
393 gfortran: error: unrecognized command line option '-V'
394 gfortran: fatal error: no input files
395 compilation terminated.
396 configure:12297: $? = 4
397 configure:12286: gfortran -qversion >&5
398 gfortran: error: unrecognized command line option '-qversion'
399 gfortran: fatal error: no input files
400 compilation terminated.
401 configure:12297: $? = 4
402 configure:12306: checking whether we are using the GNU Fortran compiler
403 configure:12319: gfortran -c conftest.F >&5
404 configure:12319: $? = 0
405 configure:12328: result: yes
406 configure:12334: checking whether gfortran accepts -g
407 configure:12345: gfortran -c -g conftest.f >&5
408 configure:12345: $? = 0
409 configure:12353: result: yes
410 configure:12502: checking if libtool supports shared libraries
411 configure:12504: result: yes
412 configure:12507: checking whether to build shared libraries
413 configure:12527: result: yes
414 configure:12530: checking whether to build static libraries
415 configure:12534: result: yes
416 configure:12568: gfortran -c -g -O2 conftest.f >&5
417 configure:12571: $? = 0
418 configure:13018: checking for gfortran option to produce PIC
419 configure:13025: result: -fPIC
420 configure:13033: checking if gfortran PIC flag -fPIC works
421 configure:13051: gfortran -c -g -O2 -fPIC conftest.f >&5
422 configure:13055: $? = 0
423 configure:13068: result: yes
424 configure:13091: checking if gfortran static flag -static works
425 configure:13119: result: no
426 configure:13131: checking if gfortran supports -c -o file.o
427 configure:13152: gfortran -c -g -O2 -o out/conftest2.o conftest.f >&5
428 configure:13156: $? = 0
429 configure:13178: result: yes
430 configure:13183: checking if gfortran supports -c -o file.o
431 configure:13230: result: yes
432 configure:13260: checking whether the gfortran linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
433 configure:14363: result: yes
434 configure:14504: checking dynamic linker characteristics
435 configure:15169: result: GNU/Linux ld.so
436 configure:15222: checking how to hardcode library paths into programs
437 configure:15247: result: immediate
438 configure:15595: checking if nf-config program is present
439 configure:15608: result: yes
440 configure:15620: checking if nc-config program is present
441 configure:15633: result: yes
442 configure:15727: checking whether byte ordering is bigendian
443 configure:15742: gcc -c -g -O2 -I/data/user/local/netcdf4-needed/include conftest.c >&5
444 conftest.c:24:9: error: unknown type name 'not'
445 not a universal capable compiler
446 ^
447 conftest.c:24:15: error: expected '=', ',', ';', 'asm' or 'attribute' before 'universal'
448 not a universal capable compiler
449 ^
450 conftest.c:24:15: error: unknown type name 'universal'
451 configure:15742: $? = 1
452 configure: failed program was:
453 | / confdefs.h /
454 | #define PACKAGE_NAME "RegCM"
455 | #define PACKAGE_TARNAME "regcm"
456 | #define PACKAGE_VERSION "5.0.0"
457 | #define PACKAGE_STRING "RegCM 5.0.0"
458 | #define PACKAGE_BUGREPORT "[email protected]"
459 | #define PACKAGE_URL ""
460 | #define STDC_HEADERS 1
461 | #define HAVE_SYS_TYPES_H 1
462 | #define HAVE_SYS_STAT_H 1
463 | #define HAVE_STDLIB_H 1
464 | #define HAVE_STRING_H 1
465 | #define HAVE_MEMORY_H 1
466 | #define HAVE_STRINGS_H 1
467 | #define HAVE_INTTYPES_H 1
468 | #define HAVE_STDINT_H 1
469 | #define HAVE_UNISTD_H 1
470 | #define HAVE_DLFCN_H 1
471 | #define LT_OBJDIR ".libs/"
472 | #define PACKAGE "regcm"
473 | #define VERSION "5.0.0"
474 | / end confdefs.h. /
475 | #ifndef APPLE_CC
476 | not a universal capable compiler
477 | #endif
478 | typedef int dummy;
479 |
480 configure:15787: gcc -c -g -O2 -I/data/user/local/netcdf4-needed/include conftest.c >&5
481 configure:15787: $? = 0
482 configure:15805: gcc -c -g -O2 -I/data/user/local/netcdf4-needed/include conftest.c >&5
483 conftest.c: In function 'main':
484 conftest.c:30:4: error: unknown type name 'not'
485 not big endian
486 ^
487 conftest.c:30:12: error: expected '=', ',', ';', 'asm' or 'attribute' before 'endian'
488 not big endian
489 ^
490 configure:15805: $? = 1
491 configure: failed program was:
492 | / confdefs.h /
493 | #define PACKAGE_NAME "RegCM"
494 | #define PACKAGE_TARNAME "regcm"
495 | #define PACKAGE_VERSION "5.0.0"
496 | #define PACKAGE_STRING "RegCM 5.0.0"
497 | #define PACKAGE_BUGREPORT "[email protected]"
498 | #define PACKAGE_URL ""
499 | #define STDC_HEADERS 1
500 | #define HAVE_SYS_TYPES_H 1
501 | #define HAVE_SYS_STAT_H 1
502 | #define HAVE_STDLIB_H 1
503 | #define HAVE_STRING_H 1
504 | #define HAVE_MEMORY_H 1
505 | #define HAVE_STRINGS_H 1
506 | #define HAVE_INTTYPES_H 1
507 | #define HAVE_STDINT_H 1
508 | #define HAVE_UNISTD_H 1
509 | #define HAVE_DLFCN_H 1
510 | #define LT_OBJDIR ".libs/"
511 | #define PACKAGE "regcm"
512 | #define VERSION "5.0.0"
513 | / end confdefs.h. /
514 | #include <sys/types.h>
515 | #include <sys/param.h>
516 |
517 | int
518 | main ()
519 | {
520 | #if BYTE_ORDER != BIG_ENDIAN
521 | not big endian
522 | #endif
523 |
524 | ;
525 | return 0;
526 | }
527 configure:15933: result: no
528 configure:15956: checking for Fortran name-mangling scheme
529 configure:15969: gfortran -c -g -O2 conftest.f >&5
530 configure:15969: $? = 0
531 configure:16002: gcc -o conftest -g -O2 -I/data/user/local/netcdf4-needed/include -L/data/user/local/netcdf4-needed/lib conftest.c cfortran_test.o >&5
532 /tmp/ccgTZSru.o: In function main': 533 /root/RegCM5/conftest.c:34: undefined reference to foobar'
534 collect2: error: ld returned 1 exit status
535 configure:16002: $? = 1
536 configure: failed program was:
537 | / confdefs.h /
538 | #define PACKAGE_NAME "RegCM"
539 | #define PACKAGE_TARNAME "regcm"
540 | #define PACKAGE_VERSION "5.0.0"
541 | #define PACKAGE_STRING "RegCM 5.0.0"
542 | #define PACKAGE_BUGREPORT "[email protected]"
543 | #define PACKAGE_URL ""
544 | #define STDC_HEADERS 1
545 | #define HAVE_SYS_TYPES_H 1
546 | #define HAVE_SYS_STAT_H 1
547 | #define HAVE_STDLIB_H 1
548 | #define HAVE_STRING_H 1
549 | #define HAVE_MEMORY_H 1
550 | #define HAVE_STRINGS_H 1
551 | #define HAVE_INTTYPES_H 1
552 | #define HAVE_STDINT_H 1
553 | #define HAVE_UNISTD_H 1
554 | #define HAVE_DLFCN_H 1
555 | #define LT_OBJDIR ".libs/"
556 | #define PACKAGE "regcm"
557 | #define VERSION "5.0.0"
558 | / end confdefs.h. /
559 |
560 | / Override any GCC internal prototype to avoid an error.
561 | Use char because int might match the return type of a GCC
562 | builtin and then its argument prototype would still apply. /
563 | #ifdef __cplusplus
564 | extern "C"
565 | #endif
566 | char foobar ();
567 | int
568 | main ()
569 | {
570 | return foobar ();
571 | ;
572 | return 0;
573 | }
574 configure:16002: gcc -o conftest -g -O2 -I/data/user/local/netcdf4-needed/include -L/data/user/local/netcdf4-needed/lib conftest.c cfortran_test.o >&5
575 configure:16002: $? = 0
576 configure:16052: gcc -o conftest -g -O2 -I/data/user/local/netcdf4-needed/include -L/data/user/local/netcdf4-needed/lib conftest.c cfortran_test.o >&5
577 configure:16052: $? = 0
578 configure:16094: result: lower case, underscore, no extra underscore
579 configure:16118: checking for NetCDF...
580 configure:16139: checking for netcdf.h...
581 configure:16141: checking netcdf.h usability
582 configure:16141: gcc -c -g -O2 -I/data/user/local/netcdf4-needed/include -I/data/user/local/netcdf4-needed/include -I/data/user/local/netcdf4-needed/include -I/data/user/local/netcdf4-needed/include conftest.c >&5
583 configure:16141: $? = 0
584 configure:16141: result: yes
585 configure:16141: checking netcdf.h presence
586 configure:16141: gcc -E -I/data/user/local/netcdf4-needed/include -I/data/user/local/netcdf4-needed/include -I/data/user/local/netcdf4-needed/include -I/data/user/local/netcdf4-needed/include conftest.c
587 configure:16141: $? = 0
588 configure:16141: result: yes
589 configure:16141: checking for netcdf.h
590 configure:16141: result: yes
591 configure:16154: checking for libnetcdf.a...
592 configure:16156: checking for nc_close in -lnetcdf
593 configure:16181: gcc -o conftest -g -O2 -I/data/user/local/netcdf4-needed/include -I/data/user/local/netcdf4-needed/include -I/data/user/local/netcdf4-needed/include -I/data/user/local/netcdf4-needed/include -L/data/user/local/netcdf4-needed/lib -L/data/user/local/netcdf4-needed/lib -L/data/user/local/netcdf4-needed/lib conftest.c -lnetcdf -L/data/user/local/netcdf4-needed/lib -lnetcdf -L/data/user/local/netcdf4-needed/lib -lnetcdff -L/data/user/local/netcdf4-needed/lib -lnetcdf -lnetcdf >&5
594 /data/user/local/netcdf4-needed/lib/libnetcdff.so: undefined reference to `nc_open_mem'
595 collect2: error: ld returned 1 exit status
596 configure:16181: $? = 1
597 configure: failed program was:
598 | / confdefs.h /
599 | #define PACKAGE_NAME "RegCM"
600 | #define PACKAGE_TARNAME "regcm"
601 | #define PACKAGE_VERSION "5.0.0"
602 | #define PACKAGE_STRING "RegCM 5.0.0"
603 | #define PACKAGE_BUGREPORT "[email protected]"
604 | #define PACKAGE_URL ""
605 | #define STDC_HEADERS 1
606 | #define HAVE_SYS_TYPES_H 1
607 | #define HAVE_SYS_STAT_H 1
608 | #define HAVE_STDLIB_H 1
609 | #define HAVE_STRING_H 1
610 | #define HAVE_MEMORY_H 1
611 | #define HAVE_STRINGS_H 1
612 | #define HAVE_INTTYPES_H 1
613 | #define HAVE_STDINT_H 1
614 | #define HAVE_UNISTD_H 1
615 | #define HAVE_DLFCN_H 1
616 | #define LT_OBJDIR ".libs/"
617 | #define PACKAGE "regcm"
618 | #define VERSION "5.0.0"
619 | / end confdefs.h. /
620 |
621 | / Override any GCC internal prototype to avoid an error.
622 | Use char because int might match the return type of a GCC
623 | builtin and then its argument prototype would still apply. /
624 | #ifdef __cplusplus
625 | extern "C"
626 | #endif
627 | char nc_close ();
628 | int
629 | main ()
630 | {
631 | return nc_close ();
632 | ;
633 | return 0;
634 | }
635 configure:16190: result: no
636 configure:16199: checking if we need to link jpeg library for HDF4...
637 configure:16203: checking for nc_enddef in -lnetcdf
638 configure:16228: gcc -o conftest -g -O2 -I/data/user/local/netcdf4-needed/include -I/data/user/local/netcdf4-needed/include -I/data/user/local/netcdf4-needed/include -I/data/user/local/netcdf4-needed/include -L/data/user/local/netcdf4-needed/lib -L/data/user/local/netcdf4-needed/lib -L/data/user/local/netcdf4-needed/lib -L/data/user/local/netcdf4-needed/lib -L/data/user/local/netcdf4-needed/lib conftest.c -lnetcdf -L/data/user/local/netcdf4-needed/lib -lnetcdf -L/data/user/local/netcdf4-needed/lib -lnetcdff -L/data/user/local/netcdf4-needed/lib -lnetcdf -lnetcdf -ljpeg >&5
639 /usr/bin/ld: cannot find -ljpeg
640 collect2: error: ld returned 1 exit status
641 configure:16228: $? = 1
642 configure: failed program was:
643 | / confdefs.h /
644 | #define PACKAGE_NAME "RegCM"
645 | #define PACKAGE_TARNAME "regcm"
646 | #define PACKAGE_VERSION "5.0.0"
647 | #define PACKAGE_STRING "RegCM 5.0.0"
648 | #define PACKAGE_BUGREPORT "[email protected]"
649 | #define PACKAGE_URL ""
650 | #define STDC_HEADERS 1
651 | #define HAVE_SYS_TYPES_H 1
652 | #define HAVE_SYS_STAT_H 1
653 | #define HAVE_STDLIB_H 1
654 | #define HAVE_STRING_H 1
655 | #define HAVE_MEMORY_H 1
656 | #define HAVE_STRINGS_H 1
657 | #define HAVE_INTTYPES_H 1
658 | #define HAVE_STDINT_H 1
659 | #define HAVE_UNISTD_H 1
660 | #define HAVE_DLFCN_H 1
661 | #define LT_OBJDIR ".libs/"
662 | #define PACKAGE "regcm"
663 | #define VERSION "5.0.0"
664 | / end confdefs.h. /
665 |
666 | / Override any GCC internal prototype to avoid an error.
667 | Use char because int might match the return type of a GCC
668 | builtin and then its argument prototype would still apply. /
669 | #ifdef __cplusplus
670 | extern "C"
671 | #endif
672 | char nc_enddef ();
673 | int
674 | main ()
675 | {
676 | return nc_enddef ();
677 | ;
678 | return 0;
679 | }
680 configure:16237: result: no
681 configure:16246: checking if we need to link hdf5 library...
682 configure:16251: checking for nc_sync in -lnetcdf
683 configure:16276: gcc -o conftest -g -O2 -I/data/user/local/netcdf4-needed/include -I/data/user/local/netcdf4-needed/include -I/data/user/local/netcdf4-needed/include -I/data/user/local/netcdf4-needed/include -L/data/user/local/netcdf4-needed/lib -L/data/user/local/netcdf4-needed/lib -L/data/user/local/netcdf4-needed/lib -L/data/user/local/netcdf4-needed/lib -L/data/user/local/netcdf4-needed/lib -L/data/user/local/netcdf4-needed/lib -L/data/user/local/netcdf4-needed/lib -L/lib conftest.c -lnetcdf -L/data/user/local/netcdf4-needed/lib -lnetcdf -L/data/user/local/netcdf4-needed/lib -lnetcdff -L/data/user/local/netcdf4-needed/lib -lnetcdf -lnetcdf -ljpeg -lhdf5 -lhdf5_hl >&5
684 /usr/bin/ld: cannot find -ljpeg
685 collect2: error: ld returned 1 exit status
686 configure:16276: $? = 1
687 configure: failed program was:
688 | / confdefs.h /
689 | #define PACKAGE_NAME "RegCM"
690 | #define PACKAGE_TARNAME "regcm"
691 | #define PACKAGE_VERSION "5.0.0"
692 | #define PACKAGE_STRING "RegCM 5.0.0"
693 | #define PACKAGE_BUGREPORT "[email protected]"
694 | #define PACKAGE_URL ""
695 | #define STDC_HEADERS 1
696 | #define HAVE_SYS_TYPES_H 1
697 | #define HAVE_SYS_STAT_H 1
698 | #define HAVE_STDLIB_H 1
699 | #define HAVE_STRING_H 1
700 | #define HAVE_MEMORY_H 1
701 | #define HAVE_STRINGS_H 1
702 | #define HAVE_INTTYPES_H 1
703 | #define HAVE_STDINT_H 1
704 | #define HAVE_UNISTD_H 1
705 | #define HAVE_DLFCN_H 1
706 | #define LT_OBJDIR ".libs/"
707 | #define PACKAGE "regcm"
708 | #define VERSION "5.0.0"
709 | / end confdefs.h. /
710 |
711 | / Override any GCC internal prototype to avoid an error.
712 | Use char because int might match the return type of a GCC
713 | builtin and then its argument prototype would still apply. /
714 | #ifdef __cplusplus
715 | extern "C"
716 | #endif
717 | char nc_sync ();
718 | int
719 | main ()
720 | {
721 | return nc_sync ();
722 | ;
723 | return 0;
724 | }
725 configure:16285: result: no
726 configure:16294: checking if we need to link szlib library...
727 configure:16299: checking for nc_inq_libvers in -lnetcdf
728 configure:16324: gcc -o conftest -g -O2 -I/data/user/local/netcdf4-needed/include -I/data/user/local/netcdf4-needed/include -I/data/user/local/netcdf4-needed/include -I/data/user/local/netcdf4-needed/include -L/data/user/local/netcdf4-needed/lib -L/data/user/local/netcdf4-needed/lib -L/data/user/local/netcdf4-needed/lib -L/data/user/local/netcdf4-needed/lib -L/data/user/local/netcdf4-needed/lib -L/data/user/local/netcdf4-needed/lib -L/data/user/local/netcdf4-needed/lib -L/lib -L/data/user/local/netcdf4-needed/lib -L/data/user/local/netcdf4-needed/lib -L/lib -L/lib conftest.c -lnetcdf -L/data/user/local/netcdf4-needed/lib -lnetcdf -L/data/user/local/netcdf4-needed/lib -lnetcdff -L/data/user/local/netcdf4-needed/lib -lnetcdf -lnetcdf -ljpeg -lhdf5 -lhdf5_hl -lsz >&5
729 /usr/bin/ld: cannot find -ljpeg
730 collect2: error: ld returned 1 exit status
731 configure:16324: $? = 1
732 configure: failed program was:
733 | / confdefs.h /
734 | #define PACKAGE_NAME "RegCM"
735 | #define PACKAGE_TARNAME "regcm"
736 | #define PACKAGE_VERSION "5.0.0"
737 | #define PACKAGE_STRING "RegCM 5.0.0"
738 | #define PACKAGE_BUGREPORT "[email protected]"
739 | #define PACKAGE_URL ""
740 | #define STDC_HEADERS 1
741 | #define HAVE_SYS_TYPES_H 1
742 | #define HAVE_SYS_STAT_H 1
743 | #define HAVE_STDLIB_H 1
744 | #define HAVE_STRING_H 1
745 | #define HAVE_MEMORY_H 1
746 | #define HAVE_STRINGS_H 1
747 | #define HAVE_INTTYPES_H 1
748 | #define HAVE_STDINT_H 1
749 | #define HAVE_UNISTD_H 1
750 | #define HAVE_DLFCN_H 1
751 | #define LT_OBJDIR ".libs/"
752 | #define PACKAGE "regcm"
753 | #define VERSION "5.0.0"
754 | / end confdefs.h. /
755 |
756 | / Override any GCC internal prototype to avoid an error.
757 | Use char because int might match the return type of a GCC
758 | builtin and then its argument prototype would still apply. /
759 | #ifdef __cplusplus
760 | extern "C"
761 | #endif
762 | char nc_inq_libvers ();
763 | int
764 | main ()
765 | {
766 | return nc_inq_libvers ();
767 | ;
768 | return 0;
769 | }
770 configure:16333: result: no
771 configure:16344: error: NetCDF library not found
772
773 ## ---------------- ##
774 ## Cache variables. ##
775 ## ---------------- ##
776
777 ac_cv_build=x86_64-unknown-linux-gnu
778 ac_cv_c_bigendian=no
779 ac_cv_c_compiler_gnu=yes
780 ac_cv_env_CC_set=set
781 ac_cv_env_CC_value=gcc
782 ac_cv_env_CFLAGS_set=
783 ac_cv_env_CFLAGS_value=
784 ac_cv_env_CPPFLAGS_set=set
785 ac_cv_env_CPPFLAGS_value=-I/data/user/local/netcdf4-needed/include
786 ac_cv_env_CPP_set=
787 ac_cv_env_CPP_value=
788 ac_cv_env_FCFLAGS_set=
789 ac_cv_env_FCFLAGS_value=
790 ac_cv_env_FC_set=set
791 ac_cv_env_FC_value=gfortran
792 ac_cv_env_LDFLAGS_set=set
793 ac_cv_env_LDFLAGS_value=-L/data/user/local/netcdf4-needed/lib
794 ac_cv_env_LIBS_set=
795 ac_cv_env_LIBS_value=
796 ac_cv_env_MPIFC_set=
797 ac_cv_env_MPIFC_value=
798 ac_cv_env_build_alias_set=
799 ac_cv_env_build_alias_value=
800 ac_cv_env_host_alias_set=
801 ac_cv_env_host_alias_value=
802 ac_cv_env_target_alias_set=
803 ac_cv_env_target_alias_value=
804 ac_cv_fc_compiler_gnu=yes
805 ac_cv_fc_mangling='lower case, underscore, no extra underscore'
806 ac_cv_header_dlfcn_h=yes
807 ac_cv_header_inttypes_h=yes
808 ac_cv_header_memory_h=yes
809 ac_cv_header_netcdf_h=yes
810 ac_cv_header_stdc=yes
811 ac_cv_header_stdint_h=yes
812 ac_cv_header_stdlib_h=yes
813 ac_cv_header_string_h=yes
814 ac_cv_header_strings_h=yes
815 ac_cv_header_sys_stat_h=yes
816 ac_cv_header_sys_types_h=yes
817 ac_cv_header_unistd_h=yes
818 ac_cv_host=x86_64-unknown-linux-gnu
819 ac_cv_lib_netcdf_nc_close=no
820 ac_cv_lib_netcdf_nc_enddef=no
821 ac_cv_lib_netcdf_nc_inq_libvers=no
822 ac_cv_lib_netcdf_nc_sync=no
823 ac_cv_objext=o
824 ac_cv_path_EGREP='/usr/bin/grep -E'
825 ac_cv_path_FGREP='/usr/bin/grep -F'
826 ac_cv_path_GREP=/usr/bin/grep
827 ac_cv_path_SED=/usr/bin/sed
828 ac_cv_path_install='/usr/bin/install -c'
829 ac_cv_path_mkdir=/usr/bin/mkdir
830 ac_cv_prog_AWK=gawk
831 ac_cv_prog_CPP='gcc -E'
832 ac_cv_prog_ac_ct_AR=ar
833 ac_cv_prog_ac_ct_CC=gcc
834 ac_cv_prog_ac_ct_OBJDUMP=objdump
835 ac_cv_prog_ac_ct_RANLIB=ranlib
836 ac_cv_prog_ac_ct_STRIP=strip
837 ac_cv_prog_cc_c89=
838 ac_cv_prog_cc_g=yes
839 ac_cv_prog_fc_g=yes
840 ac_cv_prog_make_make_set=yes
841 am_cv_CC_dependencies_compiler_type=gcc3
842 am_cv_make_support_nested_variables=yes
843 ax_cv_prog_nc_config=yes
844 ax_cv_prog_nf_config=yes
845 lt_cv_ar_at_file=@
846 lt_cv_archive_cmds_need_lc=no
847 lt_cv_deplibs_check_method=pass_all
848 lt_cv_file_magic_cmd='$MAGIC_CMD'
849 lt_cv_file_magic_test_file=
850 lt_cv_ld_reload_flag=-r
851 lt_cv_nm_interface='BSD nm'
852 lt_cv_objdir=.libs
853 lt_cv_path_LD=/usr/bin/ld
854 lt_cv_path_NM='/usr/bin/nm -B'
855 lt_cv_path_mainfest_tool=no
856 lt_cv_prog_compiler_c_o=yes
857 lt_cv_prog_compiler_c_o_FC=yes
858 lt_cv_prog_compiler_pic='-fPIC -DPIC'
859 lt_cv_prog_compiler_pic_FC=-fPIC
860 lt_cv_prog_compiler_pic_works=yes
861 lt_cv_prog_compiler_pic_works_FC=yes
862 lt_cv_prog_compiler_rtti_exceptions=no
863 lt_cv_prog_compiler_static_works=no
864 lt_cv_prog_compiler_static_works_FC=no
865 lt_cv_prog_gnu_ld=yes
866 lt_cv_sharedlib_from_linklib_cmd='printf %s\n'
867 lt_cv_shlibpath_overrides_runpath=no
868 lt_cv_sys_global_symbol_pipe='sed -n -e '''s/^.[ ]([ABCDGIRSTW][ABCDGIRSTW])[ ][ ]([_A-Za-z][_A-Za-z0-9])$/\1 \2 \2/p''' | sed '''/ __gnu_lto/d''''
869 lt_cv_sys_global_symbol_to_c_name_address='sed -n -e '''s/^: ([^ ])[ ]$/ {"\1", (void ) 0},/p''' -e '''s/^[ABCDGIRSTW] ([^ ]) ([^ ])$/ {"\2", (void ) &\2},/p''''
870 lt_cv_sys_global_symbol_to_c_name_address_lib_prefix='sed -n -e '''s/^: ([^ ])[ ]$/ {"\1", (void ) 0},/p''' -e '''s/^[ABCDGIRSTW] ([^ ]) (lib[^ ])$/ {"\2", (void ) &\2},/p''' -e '''s/^[ABCDGIRSTW] ([^ ]) ([^ ])$/ {"lib\2", (void ) &\2},/p''''
871 lt_cv_sys_global_symbol_to_cdecl='sed -n -e '''s/^T . (.)$/extern int \1();/p''' -e '''s/^[ABCDGIRSTW] .* (.)$/extern char \1;/p''''
872 lt_cv_sys_max_cmd_len=1572864
873 lt_cv_to_host_file_cmd=func_convert_file_noop
874 lt_cv_to_tool_file_cmd=func_convert_file_noop
875
876 ## ----------------- ##
877 ## Output variables. ##
878 ## ----------------- ##
879
880 ACLOCAL='${SHELL} /root/RegCM5/missing aclocal-1.13'
881 AMDEPBACKSLASH=''
882 AMDEPFLAGS=' -I/data/user/local/netcdf4-needed/include -I/data/user/local/netcdf4-needed/include -I/data/user/local/netcdf4-needed/include'
883 AMDEP_FALSE='#'
884 AMDEP_TRUE=''
885 AMTAR='$${TAR-tar}'
886 AM_BACKSLASH=''
887 AM_CPPFLAGS=''
888 AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)'
889 AM_DEFAULT_VERBOSITY='1'
890 AM_LDFLAGS=''
891 AM_V='$(V)'
892 AR='ar'
893 AUTOCONF='${SHELL} /root/RegCM5/missing autoconf'
894 AUTOHEADER='${SHELL} /root/RegCM5/missing autoheader'
895 AUTOMAKE='${SHELL} /root/RegCM5/missing automake-1.13'
896 AWK='gawk'
897 CC='gcc'
898 CCDEPMODE='depmode=gcc3'
899 CFLAGS='-g -O2'
900 COMPILER_CRAY_FALSE=''
901 COMPILER_CRAY_TRUE=''
902 COMPILER_G95_FALSE=''
903 COMPILER_G95_TRUE=''
904 COMPILER_GNU_FALSE=''
905 COMPILER_GNU_TRUE=''
906 COMPILER_IBM_FALSE=''
907 COMPILER_IBM_TRUE=''
908 COMPILER_INTEL_FALSE=''
909 COMPILER_INTEL_TRUE=''
910 COMPILER_PGI_FALSE=''
911 COMPILER_PGI_TRUE=''
912 COMPILER_SUN_FALSE=''
913 COMPILER_SUN_TRUE=''
914 CPP='gcc -E'
915 CPPFLAGS='-I/data/user/local/netcdf4-needed/include -I/data/user/local/netcdf4-needed/include -I/data/user/local/netcdf4-needed/include -I/data/user/local/netcdf4-needed/include'
916 CPRDEF=''
917 CYGPATH_W='echo'
918 DEFS=''
919 DEPDIR='.deps'
920 DLLTOOL='false'
921 DO_COMPILE_CPL_FALSE=''
922 DO_COMPILE_CPL_TRUE='#'
923 DO_COMPILE_LIBCLM45_FALSE=''
924 DO_COMPILE_LIBCLM45_TRUE='#'
925 DO_COMPILE_LIBCLM_FALSE=''
926 DO_COMPILE_LIBCLM_TRUE='#'
927 DSYMUTIL=''
928 DUMPBIN=''
929 ECHO_C=''
930 ECHO_N='-n'
931 ECHO_T=''
932 EGREP='/usr/bin/grep -E'
933 EXEEXT=''
934 F90FLAGS=''
935 FC='gfortran'
936 FCFLAGS='-g -O2'
937 FCPROG=''
938 FGREP='/usr/bin/grep -F'
939 FORT_SIZE=''
940 GREP='/usr/bin/grep'
941 INSTALL_DATA='${INSTALL} -m 644'
942 INSTALL_PROGRAM='${INSTALL}'
943 INSTALL_SCRIPT='${INSTALL}'
944 INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
945 LD='/usr/bin/ld -m elf_x86_64'
946 LDFLAGS='-L/data/user/local/netcdf4-needed/lib -L/data/user/local/netcdf4-needed/lib -L/data/user/local/netcdf4-needed/lib -L/data/user/local/netcdf4-needed/lib -L/data/user/local/netcdf4-needed/lib -L/data/user/local/netcdf4-needed/lib -L/data/user/local/netcdf4-needed/lib -L/lib -L/data/user/local/netcdf4-needed/lib -L/data/user/local/netcdf4-needed/lib -L/lib -L/lib'
947 LIBOBJS=''
948 LIBS=' -L/data/user/local/netcdf4-needed/lib -lnetcdf -L/data/user/local/netcdf4-needed/lib -lnetcdff -L/data/user/local/netcdf4-needed/lib -lnetcdf -lnetcdf -ljpeg -lhdf5 -lhdf5_hl -lsz'
949 LIBTOOL='$(SHELL) $(top_builddir)/libtool'
950 LIPO=''
951 LN_S='ln -s'
952 LTLIBOBJS=''
953 MAKEINFO='${SHELL} /root/RegCM5/missing makeinfo'
954 MANIFEST_TOOL=':'
955 MKDIR_P='/usr/bin/mkdir -p'
956 MPEUCFLAGS=''
957 MPEUFCFLAGS=''
958 MPIFC=''
959 MPILIBS=''
960 NC_INCLUDES='-I/data/user/local/netcdf4-needed/include -I/data/user/local/netcdf4-needed/include -I/data/user/local/netcdf4-needed/include'
961 NC_LDFLAGS='-L/data/user/local/netcdf4-needed/lib -L/data/user/local/netcdf4-needed/lib -L/lib -L/lib'
962 NC_LIBS='-L/data/user/local/netcdf4-needed/lib -lnetcdf -L/data/user/local/netcdf4-needed/lib -lnetcdff -L/data/user/local/netcdf4-needed/lib -lnetcdf -lnetcdf'
963 NC_PREFIX='/data/user/local/netcdf4-needed'
964 NF_PREFIX='/data/user/local/netcdf4-needed'
965 NM='/usr/bin/nm -B'
966 NMEDIT=''
967 NOOPTFC=''
968 OBJDUMP='objdump'
969 OBJEXT='o'
970 OMPFLAGS=''
971 OSNAME=''
972 OSNAME_AIX_FALSE=''
973 OSNAME_AIX_TRUE=''
974 OSNAME_LINUX_FALSE=''
975 OSNAME_LINUX_TRUE=''
976 OTOOL64=''
977 OTOOL=''
978 PACKAGE='regcm'
979 PACKAGE_BUGREPORT='[email protected]'
980 PACKAGE_NAME='RegCM'
981 PACKAGE_STRING='RegCM 5.0.0'
982 PACKAGE_TARNAME='regcm'
983 PACKAGE_URL='https://github.com/ICTP/RegCM'
984 PACKAGE_VERSION='5.0.0'
985 PATH_SEPARATOR=':'
986 RANLIB='ranlib'
987 REGCM_PARALLEL_FALSE=''
988 REGCM_PARALLEL_TRUE=''
989 REGCM_ROOT=''
990 SED='/usr/bin/sed'
991 SET_MAKE=''
992 SHELL='/bin/sh'
993 STRIP='strip'
994 SYSLIBS=''
995 VERSION='5.0.0'
996 ac_ct_AR='ar'
997 ac_ct_CC='gcc'
998 ac_ct_DUMPBIN=''
999 ac_ct_FC=''
1000 am__EXEEXT_FALSE=''
1001 am__EXEEXT_TRUE=''
1002 am__fastdepCC_FALSE='#'
1003 am__fastdepCC_TRUE=''
1004 am__include='include'
1005 am__isrc=''
1006 am__leading_dot='.'
1007 am__nodep='_no'
1008 am__quote=''
1009 am__tar='$${TAR-tar} chof - "$$tardir"'
1010 am__untar='$${TAR-tar} xf -'
1011 bindir='${exec_prefix}/bin'
1012 build='x86_64-unknown-linux-gnu'
1013 build_alias=''
1014 build_cpu='x86_64'
1015 build_os='linux-gnu'
1016 build_vendor='unknown'
1017 datadir='${datarootdir}'
1018 datarootdir='${prefix}/share'
1019 docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
1020 dvidir='${docdir}'
1021 exec_prefix='NONE'
1022 host='x86_64-unknown-linux-gnu'
1023 host_alias=''
1024 host_cpu='x86_64'
1025 host_os='linux-gnu'
1026 host_vendor='unknown'
1027 htmldir='${docdir}'
1028 includedir='${prefix}/include'
1029 infodir='${datarootdir}/info'
1030 install_sh='${SHELL} /root/RegCM5/install-sh'
1031 libdir='${exec_prefix}/lib'
1032 libexecdir='${exec_prefix}/libexec'
1033 localedir='${datarootdir}/locale'
1034 localstatedir='${prefix}/var'
1035 mandir='${datarootdir}/man'
1036 mkdir_p='$(MKDIR_P)'
1037 oldincludedir='/usr/include'
1038 pdfdir='${docdir}'
1039 prefix='NONE'
1040 program_transform_name='s,x,x,'
1041 psdir='${docdir}'
1042 sbindir='${exec_prefix}/sbin'
1043 sharedstatedir='${prefix}/com'
1044 sysconfdir='${prefix}/etc'
1045 target_alias=''
1046
1047 ## ----------- ##
1048 ## confdefs.h. ##
1049 ## ----------- ##
1050
1051 / confdefs.h */
1052 #define PACKAGE_NAME "RegCM"
1053 #define PACKAGE_TARNAME "regcm"
1054 #define PACKAGE_VERSION "5.0.0"
1055 #define PACKAGE_STRING "RegCM 5.0.0"
1056 #define PACKAGE_BUGREPORT "[email protected]"
1057 #define PACKAGE_URL ""
1058 #define STDC_HEADERS 1
1059 #define HAVE_SYS_TYPES_H 1
1060 #define HAVE_SYS_STAT_H 1
1061 #define HAVE_STDLIB_H 1
1062 #define HAVE_STRING_H 1
1063 #define HAVE_MEMORY_H 1
1064 #define HAVE_STRINGS_H 1
1065 #define HAVE_INTTYPES_H 1
1066 #define HAVE_STDINT_H 1
1067 #define HAVE_UNISTD_H 1
1068 #define HAVE_DLFCN_H 1
1069 #define LT_OBJDIR ".libs/"
1070 #define PACKAGE "regcm"
1071 #define VERSION "5.0.0"
1072
1073 configure: exit 1

@graziano-giuliani
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The problem is this one:
[...]
594 /data/user/local/netcdf4-needed/lib/libnetcdff.so: undefined reference to `nc_open_mem'
[...]

I think your netcdf Fortran + netcdf C library is not in shape. My guess is that you compiled the Fortran library against a system present netcdf C library somewhere else in in the system. This is error comes usually in trying to link against conflicting versions of netCDF libraries. Have you used the install_prereq.sh script?

@lymelody
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lymelody commented Aug 1, 2023 •
edited
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Thank you very much for your support. I did not use the install_prereq.sh scripts, and each one was installed separately. I replaced the versions of netcdf-c and netcdf-fortran, but encountered a problem during reinstallation. An error was reported when installing netcdf-fortran for compilation, as follows，The version of netcdf-c is 4.7.4 and the version of netcdf-fortran is 4.6.1:

gfortran -DPACKAGE_NAME="netCDF-Fortran" -DPACKAGE_TARNAME="netcdf-fortran" -DPACKAGE_VERSION="4.6.1" -DPACKAGE_STRING="netCDF-Fortran\ 4.6.1" -DPACKAGE_BUGREPORT="[email protected]" -DPACKAGE_URL="" -DPACKAGE="netcdf-fortran" -DVERSION="4.6.1" -DNF_RELAX_COORD_BOUND=1 -DENABLE_CDF5=1 -DHAVE_F2008=1 -DHAVE_TS29113_SUPPORT=1 -DTEMP_LARGE="." -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TIME_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=".libs/" -DNF_INT1_T=byte -DNF_INT2_T=integer*2 -DNF_INT8_T=integer*8 -DNF_INT1_IS_C_SIGNED_CHAR=1 -DNF_INT2_IS_C_SHORT=1 -DNF_INT8_IS_C_LONG_LONG=1 -DNF_INT_IS_C_INT=1 -DNF_REAL_IS_C_FLOAT=1 -DNF_DOUBLEPRECISION_IS_C_DOUBLE=1 -DNCBYTE_T=byte -DNCSHORT_T=integer*2 -DHAVE_LIBM=1 -DHAVE_NETCDF_H=1 -DHAVE_NC_DEF_OPAQUE=1 -DHAVE_NCCREATE=1 -DHAVE_NC_SET_LOG_LEVEL=1 -DHAVE_NC_DEF_VAR_SZIP=1 -DUSE_NETCDF4=1 -DLOGGING=1 -DHAVE_SYS_PARAM_H=1 -DHAVE_LOCALE_H=1 -DHAVE_STDIO_H=1 -DHAVE_STDARG_H=1 -DHAVE_ERRNO_H=1 -DHAVE_CTYPE_H=1 -DHAVE_FCNTL_H=1 -DHAVE_MALLOC_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_STRINGS_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_GETOPT_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_DIRENT_H=1 -DHAVE_SYS_WAIT_H=1 -DTIME_WITH_SYS_TIME=1 -DHAVE_VPRINTF=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_ALLOCA_H=1 -DHAVE_ALLOCA=1 -DHAVE_SSIZE_T=1 -DHAVE_PTRDIFF_T=1 -DSIZEOF_SHORT=2 -DSIZEOF_INT=4 -DSIZEOF_LONG=8 -DSIZEOF_FLOAT=4 -DSIZEOF_DOUBLE=8 -DSIZEOF_OFF_T=8 -DSIZEOF_SIZE_T=8 -DSIZEOF_PTRDIFF_T=8 -I. -I/data/user/local/netcdf4-needed/include -I../fortran -g -O2 -c -o module_tests.o module_tests.F90
module_tests.F90:35.11:

   USE netcdf4_f03
       1

Fatal Error: File 'netcdf4_f03.mod' opened at (1) is not a GNU Fortran module file
make[1]: *** [module_tests.o] Error 1
make[1]: Leaving directory `/data/user/software/netcdf-fortran-4.6.1/nf_test'
make: *** [all-recursive] Error 1

@graziano-giuliani
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My take is that on your system you have multiple fortran compilers, and the build system is using both messing up the compilation. Try forcing the values of FC,CC in the environment. Take a look at the prereq_install.sh script and try adopting a similar strategy. Note the use also of of CPPFLAGS, FCFLAGS and LD_FLAGS and the setup of PATH, LD_LIBRARY_PATH. If you use cmake, I think it may be CMAKE_SYSTEM_PREFIX_PATH that you want to set. I don't have access to your system to sort things out for you, though, and I am guessing the problem from the symptoms without the means for a sure remedy.

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@graziano-giuliani @lymelody