[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

[netCDF #KCB-778033]: trouble shooting while installing NCO

> Hi Ed,
>
> Thanks for your suggestion. I tried the following
>
> *CFLAGS=-fPIC ./configure --prefix=/home/sandeep/NETCDF/netcdf-3.6.2
> --enable-shared && make check
> *
> But gave me a following errors (Error A) while installing...

This is a problem with your C++ API. Are you going to use the C++ API? If not,
I would just retry, with the --disable-cxx option to configure.

>
> Then tried the following options
>
> *C**FLAGS=-fPIC ./configure --prefix=/home/sandeep/NETCDF/netcdf-3.6.2
> -with-pic && make check*
>
> It gave me the following errors (Error B) while installing.

These are NCO errors. NCO is a different package. First make sure you have
netCDF working by running make check. If make check succeeds, then go on to
NCO.

The problem in error B is not from netCDF, so I can't tell you much. Sorry. :-(

>
> Please let me know if you find any clue or suspect anything which is
> messing up the compilation.
>

Maybe your netCDF build already worked, if it completed OK. Run "make check" to
be sure.

Then try a "make distclean" on the NCO package, and start over again clean, and
see if it works...

Good luck!

Ed
> *ErrroA:*
>
> make  check-TESTS
> make[4]: Entering directory `/home/sandeep/NCO/nco-3.9.2/src/nco'
> make[4]: Leaving directory `/home/sandeep/NCO/nco-3.9.2/src/nco'
> make[3]: Leaving directory `/home/sandeep/NCO/nco-3.9.2/src/nco'
> Making check in nco_c++
> make[3]: Entering directory `/home/sandeep/NCO/nco-3.9.2/src/nco_c++'
> if /bin/sh ../../libtool --tag=CXX --tag=CXX --mode=compile g++
> -DHAVE_CONFIG_H -I. -I. -I../..  -DABORT_ON_ERROR   -g -O2 -MT
> libnco_c___la-nco_att.lo -MD -MP -MF ".deps/libnco_c___la-nco_att.Tpo"
> -c -o libnco_c___la-nco_att.lo `test -f 'nco_att.cc' || echo
> './'`nco_att.cc; \
> then mv -f ".deps/libnco_c___la-nco_att.Tpo"
> ".deps/libnco_c___la-nco_att.Plo"; else rm -f
> ".deps/libnco_c___la-nco_att.Tpo"; exit 1; fi
> mkdir .libs
> g++ -DHAVE_CONFIG_H -I. -I. -I../.. -DABORT_ON_ERROR -g -O2 -MT
> libnco_c___la-nco_att.lo -MD -MP -MF .deps/libnco_c___la-nco_att.Tpo -c
> nco_att.cc  -fPIC -DPIC -o .libs/libnco_c___la-nco_att.o
> In file included from nco_att.cc:9:
> nco_att.hh:23:42: netcdf.h: No such file or directory
> In file included from nco_att.hh:26,
> from nco_att.cc:9:
> nco_utl.hh:31:42: netcdf.h: No such file or directory
> In file included from nco_att.hh:26,
> from nco_att.cc:9:
> nco_utl.hh:37: `NC_NOERR' was not declared in this scope
> In file included from nco_utl.hh:58,
> from nco_att.hh:26,
> from nco_att.cc:9:
> nco_dmn.hh:22:42: netcdf.h: No such file or directory
> In file included from nco_utl.hh:58,
> from nco_att.hh:26,
> from nco_att.cc:9:
> nco_dmn.hh:58: `NC_NOERR' was not declared in this scope
> nco_dmn.hh:68: `NC_NOERR' was not declared in this scope
> nco_dmn.hh:85: `NC_NOERR' was not declared in this scope
> In file included from nco_utl.hh:59,
> from nco_att.hh:26,
> from nco_att.cc:9:
> nco_var.hh:24:42: netcdf.h: No such file or directory
> In file included from nco_utl.hh:59,
> from nco_att.hh:26,
> from nco_att.cc:9:
> nco_var.hh:43: syntax error before `&' token
> nco_var.hh:53: syntax error before `&' token
> nco_var.hh:66: type specifier omitted for parameter `nc_type'
> nco_var.hh:66: syntax error before `&' token
> nco_var.hh:80: `NC_NOERR' was not declared in this scope
> nco_var.hh:97: `NC_NOERR' was not declared in this scope
> nco_var.hh:113: type specifier omitted for parameter `nc_type'
> nco_var.hh:113: syntax error before `&' token
> nco_var.hh:119: syntax error before `int'
> nco_var.hh:125: syntax error before `int'
> nco_var.hh:137: `NC_NOERR' was not declared in this scope
> nco_var.hh:145: `NC_NOERR' was not declared in this scope
> nco_var.hh:168: `NC_NOERR' was not declared in this scope
> nco_var.hh:190: `NC_NOERR' was not declared in this scope
> In file included from nco_att.hh:26,
> from nco_att.cc:9:
> nco_utl.hh:101: `NC_NOERR' was not declared in this scope
> nco_utl.hh:106: syntax error before `&' token
> nco_utl.hh:111: syntax error before `&' token
> nco_utl.hh:116: syntax error before `&' token
> nco_utl.hh:121: syntax error before `&' token
> nco_utl.hh:132: syntax error before `float'
> nco_utl.hh:137: syntax error before `double'
> In file included from nco_att.cc:9:
> nco_att.hh:44: syntax error before `&' token
> nco_att.hh:53: syntax error before `&' token
> nco_att.hh:63: syntax error before `&' token
> nco_att.hh:72: syntax error before `&' token
> nco_att.hh:82: syntax error before `&' token
> nco_att.hh:90: syntax error before `&' token
> nco_att.hh:100: syntax error before `&' token
> nco_att.hh:108: syntax error before `&' token
> nco_att.hh:118: syntax error before `&' token
> nco_att.hh:126: syntax error before `&' token
> nco_att.hh:151: syntax error before `&' token
> nco_att.hh:162: type specifier omitted for parameter `nc_type'
> nco_att.hh:162: syntax error before `&' token
> nco_att.hh:176: `NC_NOERR' was not declared in this scope
> nco_att.hh:185: `NC_NOERR' was not declared in this scope
> nco_att.hh:211: `NC_NOERR' was not declared in this scope
> nco_att.hh:236: type specifier omitted for parameter `nc_type'
> nco_att.hh:236: syntax error before `&' token
> nco_att.hh:242: syntax error before `int'
> nco_att.hh:256: `NC_NOERR' was not declared in this scope
> nco_att.cc:39: syntax error before `&' token
> nco_att.cc: In function `int nco_put_att(...)':
> nco_att.cc:42: `nc_id' undeclared (first use this function)
> nco_att.cc:42: (Each undeclared identifier is reported only once for each
> function it appears in.)
> nco_att.cc:42: `var_id' undeclared (first use this function)
> nco_att.cc:42: `att_nm' undeclared (first use this function)
> nco_att.cc:42: `att_typ' undeclared (first use this function)
> nco_att.cc:42: `att_sz' undeclared (first use this function)
> nco_att.cc:42: `att_val' undeclared (first use this function)
> nco_att.cc:42: `nc_put_att_float' undeclared (first use this function)
> nco_att.cc:43: `NC_NOERR' undeclared (first use this function)
> nco_att.cc: At global scope:
> nco_att.cc:53: syntax error before `&' token
> nco_att.cc: In function `int nco_put_att(...)':
> nco_att.cc:54: redefinition of `int nco_put_att(...)'
> nco_att.cc:40: `int nco_put_att(...)' previously defined here
> nco_att.cc:54: redefinition of `int nco_put_att(...)'
> nco_att.cc:40: `int nco_put_att(...)' previously defined here
> nco_att.cc: At global scope:
> nco_att.cc:74: syntax error before `&' token
> nco_att.cc: In function `int nco_put_att(...)':
> nco_att.cc:75: redefinition of `int nco_put_att(...)'
> nco_att.cc:54: `int nco_put_att(...)' previously defined here
> nco_att.cc:75: redefinition of `int nco_put_att(...)'
> nco_att.cc:54: `int nco_put_att(...)' previously defined here
> nco_att.cc:75: redefinition of `int nco_put_att(...)'
> nco_att.cc:40: `int nco_put_att(...)' previously defined here
> nco_att.cc:77: `nc_put_att_double' undeclared (first use this function)
> nco_att.cc: At global scope:
> nco_att.cc:88: syntax error before `&' token
> nco_att.cc: In function `int nco_put_att(...)':
> nco_att.cc:89: redefinition of `int nco_put_att(...)'
> nco_att.cc:75: `int nco_put_att(...)' previously defined here
> nco_att.cc:89: redefinition of `int nco_put_att(...)'
> nco_att.cc:75: `int nco_put_att(...)' previously defined here
> nco_att.cc:89: redefinition of `int nco_put_att(...)'
> nco_att.cc:54: `int nco_put_att(...)' previously defined here
> nco_att.cc:89: redefinition of `int nco_put_att(...)'
> nco_att.cc:40: `int nco_put_att(...)' previously defined here
> nco_att.cc: At global scope:
> nco_att.cc:103: syntax error before `&' token
> nco_att.cc: In function `int nco_put_att(...)':
> nco_att.cc:104: redefinition of `int nco_put_att(...)'
> nco_att.cc:89: `int nco_put_att(...)' previously defined here
> nco_att.cc:104: redefinition of `int nco_put_att(...)'
> nco_att.cc:89: `int nco_put_att(...)' previously defined here
> nco_att.cc:104: redefinition of `int nco_put_att(...)'
> nco_att.cc:75: `int nco_put_att(...)' previously defined here
> nco_att.cc:104: redefinition of `int nco_put_att(...)'
> nco_att.cc:54: `int nco_put_att(...)' previously defined here
> nco_att.cc:104: redefinition of `int nco_put_att(...)'
> nco_att.cc:40: `int nco_put_att(...)' previously defined here
> nco_att.cc:106: `nc_put_att_int' undeclared (first use this function)
> nco_att.cc: At global scope:
> nco_att.cc:116: syntax error before `&' token
> nco_att.cc: In function `int nco_put_att(...)':
> nco_att.cc:117: redefinition of `int nco_put_att(...)'
> nco_att.cc:104: `int nco_put_att(...)' previously defined here
> nco_att.cc:117: redefinition of `int nco_put_att(...)'
> nco_att.cc:104: `int nco_put_att(...)' previously defined here
> nco_att.cc:117: redefinition of `int nco_put_att(...)'
> nco_att.cc:89: `int nco_put_att(...)' previously defined here
> nco_att.cc:117: redefinition of `int nco_put_att(...)'
> nco_att.cc:75: `int nco_put_att(...)' previously defined here
> nco_att.cc:117: redefinition of `int nco_put_att(...)'
> nco_att.cc:54: `int nco_put_att(...)' previously defined here
> nco_att.cc:117: redefinition of `int nco_put_att(...)'
> nco_att.cc:40: `int nco_put_att(...)' previously defined here
> nco_att.cc: At global scope:
> nco_att.cc:131: syntax error before `&' token
> nco_att.cc: In function `int nco_put_att(...)':
> nco_att.cc:132: redefinition of `int nco_put_att(...)'
> nco_att.cc:117: `int nco_put_att(...)' previously defined here
> nco_att.cc:132: redefinition of `int nco_put_att(...)'
> nco_att.cc:117: `int nco_put_att(...)' previously defined here
> nco_att.cc:132: redefinition of `int nco_put_att(...)'
> nco_att.cc:104: `int nco_put_att(...)' previously defined here
> nco_att.cc:132: redefinition of `int nco_put_att(...)'
> nco_att.cc:89: `int nco_put_att(...)' previously defined here
> nco_att.cc:132: redefinition of `int nco_put_att(...)'
> nco_att.cc:75: `int nco_put_att(...)' previously defined here
> nco_att.cc:132: redefinition of `int nco_put_att(...)'
> nco_att.cc:54: `int nco_put_att(...)' previously defined here
> nco_att.cc:132: redefinition of `int nco_put_att(...)'
> nco_att.cc:40: `int nco_put_att(...)' previously defined here
> nco_att.cc:134: `nc_put_att_short' undeclared (first use this function)
> nco_att.cc: At global scope:
> nco_att.cc:144: syntax error before `&' token
> nco_att.cc: In function `int nco_put_att(...)':
> nco_att.cc:145: redefinition of `int nco_put_att(...)'
> nco_att.cc:132: `int nco_put_att(...)' previously defined here
> nco_att.cc:145: redefinition of `int nco_put_att(...)'
> nco_att.cc:132: `int nco_put_att(...)' previously defined here
> nco_att.cc:145: redefinition of `int nco_put_att(...)'
> nco_att.cc:117: `int nco_put_att(...)' previously defined here
> nco_att.cc:145: redefinition of `int nco_put_att(...)'
> nco_att.cc:104: `int nco_put_att(...)' previously defined here
> nco_att.cc:145: redefinition of `int nco_put_att(...)'
> nco_att.cc:89: `int nco_put_att(...)' previously defined here
> nco_att.cc:145: redefinition of `int nco_put_att(...)'
> nco_att.cc:75: `int nco_put_att(...)' previously defined here
> nco_att.cc:145: redefinition of `int nco_put_att(...)'
> nco_att.cc:54: `int nco_put_att(...)' previously defined here
> nco_att.cc:145: redefinition of `int nco_put_att(...)'
> nco_att.cc:40: `int nco_put_att(...)' previously defined here
> nco_att.cc: At global scope:
> nco_att.cc:159: syntax error before `&' token
> nco_att.cc: In function `int nco_put_att(...)':
> nco_att.cc:160: redefinition of `int nco_put_att(...)'
> nco_att.cc:145: `int nco_put_att(...)' previously defined here
> nco_att.cc:160: redefinition of `int nco_put_att(...)'
> nco_att.cc:145: `int nco_put_att(...)' previously defined here
> nco_att.cc:160: redefinition of `int nco_put_att(...)'
> nco_att.cc:132: `int nco_put_att(...)' previously defined here
> nco_att.cc:160: redefinition of `int nco_put_att(...)'
> nco_att.cc:117: `int nco_put_att(...)' previously defined here
> nco_att.cc:160: redefinition of `int nco_put_att(...)'
> nco_att.cc:104: `int nco_put_att(...)' previously defined here
> nco_att.cc:160: redefinition of `int nco_put_att(...)'
> nco_att.cc:89: `int nco_put_att(...)' previously defined here
> nco_att.cc:160: redefinition of `int nco_put_att(...)'
> nco_att.cc:75: `int nco_put_att(...)' previously defined here
> nco_att.cc:160: redefinition of `int nco_put_att(...)'
> nco_att.cc:54: `int nco_put_att(...)' previously defined here
> nco_att.cc:160: redefinition of `int nco_put_att(...)'
> nco_att.cc:40: `int nco_put_att(...)' previously defined here
> nco_att.cc:162: `nc_put_att_long' undeclared (first use this function)
> nco_att.cc: At global scope:
> nco_att.cc:172: syntax error before `&' token
> nco_att.cc: In function `int nco_put_att(...)':
> nco_att.cc:173: redefinition of `int nco_put_att(...)'
> nco_att.cc:160: `int nco_put_att(...)' previously defined here
> nco_att.cc:173: redefinition of `int nco_put_att(...)'
> nco_att.cc:160: `int nco_put_att(...)' previously defined here
> nco_att.cc:173: redefinition of `int nco_put_att(...)'
> nco_att.cc:145: `int nco_put_att(...)' previously defined here
> nco_att.cc:173: redefinition of `int nco_put_att(...)'
> nco_att.cc:132: `int nco_put_att(...)' previously defined here
> nco_att.cc:173: redefinition of `int nco_put_att(...)'
> nco_att.cc:117: `int nco_put_att(...)' previously defined here
> nco_att.cc:173: redefinition of `int nco_put_att(...)'
> nco_att.cc:104: `int nco_put_att(...)' previously defined here
> nco_att.cc:173: redefinition of `int nco_put_att(...)'
> nco_att.cc:89: `int nco_put_att(...)' previously defined here
> nco_att.cc:173: redefinition of `int nco_put_att(...)'
> nco_att.cc:75: `int nco_put_att(...)' previously defined here
> nco_att.cc:173: redefinition of `int nco_put_att(...)'
> nco_att.cc:54: `int nco_put_att(...)' previously defined here
> nco_att.cc:173: redefinition of `int nco_put_att(...)'
> nco_att.cc:40: `int nco_put_att(...)' previously defined here
> nco_att.cc: In function `int nco_put_att(const int&, const int&, const
> std::string&, const std::string&)':
> nco_att.cc:188: `nc_put_att_text' undeclared (first use this function)
> nco_att.cc: At global scope:
> nco_att.cc:211: syntax error before `&' token
> nco_att.cc: In function `int nco_put_att(...)':
> nco_att.cc:212: redefinition of `int nco_put_att(...)'
> nco_att.cc:173: `int nco_put_att(...)' previously defined here
> nco_att.cc:212: redefinition of `int nco_put_att(...)'
> nco_att.cc:173: `int nco_put_att(...)' previously defined here
> nco_att.cc:212: redefinition of `int nco_put_att(...)'
> nco_att.cc:160: `int nco_put_att(...)' previously defined here
> nco_att.cc:212: redefinition of `int nco_put_att(...)'
> nco_att.cc:145: `int nco_put_att(...)' previously defined here
> nco_att.cc:212: redefinition of `int nco_put_att(...)'
> nco_att.cc:132: `int nco_put_att(...)' previously defined here
> nco_att.cc:212: redefinition of `int nco_put_att(...)'
> nco_att.cc:117: `int nco_put_att(...)' previously defined here
> nco_att.cc:212: redefinition of `int nco_put_att(...)'
> nco_att.cc:104: `int nco_put_att(...)' previously defined here
> nco_att.cc:212: redefinition of `int nco_put_att(...)'
> nco_att.cc:89: `int nco_put_att(...)' previously defined here
> nco_att.cc:212: redefinition of `int nco_put_att(...)'
> nco_att.cc:75: `int nco_put_att(...)' previously defined here
> nco_att.cc:212: redefinition of `int nco_put_att(...)'
> nco_att.cc:54: `int nco_put_att(...)' previously defined here
> nco_att.cc:212: redefinition of `int nco_put_att(...)'
> nco_att.cc:40: `int nco_put_att(...)' previously defined here
> nco_att.cc: At global scope:
> nco_att.cc:228: type specifier omitted for parameter `nc_type'
> nco_att.cc:228: syntax error before `&' token
> nco_att.cc: In function `int nco_inq_att(...)':
> nco_att.cc:234: `nc_inq_att' undeclared (first use this function)
> nco_att.cc:235: `rcd_opt' undeclared (first use this function)
> nco_att.cc: In function `int nco_inq_attid(const int&, const int&, const
> std::string&, int&, const int&)':
> nco_att.cc:252: `nc_inq_attid' undeclared (first use this function)
> nco_att.cc: In function `int nco_inq_attname(const int&, const int&, const
> int&, std::string&, const int&)':
> nco_att.cc:312: `NC_MAX_NAME' undeclared (first use this function)
> nco_att.cc:313: `att_nm_chr' undeclared (first use this function)
> nco_att.cc:313: `nc_inq_attname' undeclared (first use this function)
> nco_att.cc: At global scope:
> nco_att.cc:353: type specifier omitted for parameter `nc_type'
> nco_att.cc:353: syntax error before `&' token
> nco_att.cc: In function `int nco_inq_atttype(...)':
> nco_att.cc:358: `nc_inq_atttype' undeclared (first use this function)
> nco_att.cc: At global scope:
> nco_att.cc:365: syntax error before `int'
> nco_att.cc:371: `var_nm' was not declared in this scope
> nco_att.cc:372: syntax error before `+=' token
> nco_att.cc: In function `int nco_inq_attlen(const int&, const int&, const
> std::string&, size_t&, const int&)':
> nco_att.cc:390: `nc_inq_attlen' undeclared (first use this function)
> nco_att.cc: In function `int nco_get_att(const int&, const int&, const
> std::string&, std::string&)':
> nco_att.cc:449: `nc_get_att_text' undeclared (first use this function)
> nco_att.cc: In function `int nco_get_att(const int&, const int&, const
> std::string&, float*&)':
> nco_att.cc:471: `nc_get_att_float' undeclared (first use this function)
> nco_att.cc: In function `int nco_get_att(const int&, const int&, const
> std::string&, double*&)':
> nco_att.cc:487: `nc_get_att_double' undeclared (first use this function)
> make[3]: *** [libnco_c___la-nco_att.lo] Error 1
> make[3]: Leaving directory `/home/sandeep/NCO/nco-3.9.2/src/nco_c++'
> make[2]: *** [check-recursive] Error 1
> make[2]: Leaving directory `/home/sandeep/NCO/nco-3.9.2/src'
> make[1]: *** [check-recursive] Error 1
> make[1]: Leaving directory `/home/sandeep/NCO/nco-3.9.2'
> make: *** [test] Error 2
>
>
> *Error B*
>
> gcc -std=gnu99 -g -O2 -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -o
> .libs/ncap ncap_utl.o ncap.o ncap_yacc.o ncap_lex.o
> -L/home/sandeep/NETCDF/netcdf-3.6.2/lib ./.libs/libnco.so -lnsl -lm
> /home/sandeep/NETCDF/netcdf-3.6.2/lib/libnetcdf.a -Wl,--rpath
> -Wl,/home/sandeep/NCO/nco-3.9.2/lib
> ./.libs/libnco.so: undefined reference to `for_len_trim'
> ./.libs/libnco.so: undefined reference to `for_trim'
> ./.libs/libnco.so: undefined reference to `for_contig_array'
> ./.libs/libnco.so: undefined reference to `for_cpystr'
> collect2: ld returned 1 exit status
> make[3]: *** [ncap] Error 1
> make[3]: Leaving directory `/home/sandeep/NCO/nco-3.9.2/src/nco'
>
>
>
> Unidata netCDF Support wrote:
> >> Hi Russ,
> >>
> >> Thanks for the response. I need one help from you i.e. how to compile
> >> NETCDF-3.6.2 version
> >> with -fPIC option or how to validate that the libraries obtained from
> >> certain compilation has been
> >> compiled with -fPIC options.
> >>
> >> Once i can confirm myself about this, i might fix the problem with the
> >> other software which is
> >> using NETCDF libraries.
> >>
> >> regards
> >> sandeep
> >>
> >>
> >
> > Howdy Sandeep!
> >
> > Set the CFLAGS env variable before running configure.
> >
> > Make sure you do a "make distclean" first. Like this in the borne shell:
> >
> > make distclean; CFLAGS=-fPIC ./configure --enable-shared && make check
> >
> > Also, you probably want to use the --disable-f77 --disable-cxx options to
turn off the building of the Fortran 77, Fortran 90, and C++ APIs. They are not
used by NCO. Otherwise you may have to set FFLAGS, F90FLAGS, and CXXFLAGS as
well.
> >
> > Good luck!
> >
> > Ed
> >
> > Ticket Details
> > ===================
> > Ticket ID: KCB-778033
> > Department: Support netCDF
> > Priority: Normal
> > Status: Closed
> >
> >
>
>
> --
> Dr. Sandeep Pattnaik
> Research Associate
> Department of Meteorology
> Florida State University
> Tallahassee,Fl,32306-4502
> Ph: 850-644-2232(W)
> 850-575-9238(R)
> Fax:850-644-9642
>
>
>


Ticket Details
===================
Ticket ID: KCB-778033
Department: Support netCDF
Priority: Normal
Status: Closed