[netCDF #VUQ-446360]: netcdf 4.1.1 installation errors

Pavel,

> In addition to my yesterday message (below), today I have reinstalled netcdf
> 4.1.1
> in order to put the output to a specified place:
> ./configure --prefix=/usr/local/netcdf411
> 
> The installation was successful as you can see in the attached file
> make_check_install_110328.log.
> 
> However, when I tried to compile the WRF v.3.2.1 program, I got the output
> that many references in netcdf libraries were undefined (see examples
> below).
> I know that you are responsible only for netcdf and not for WRF. But maybe
> you can explain to me where the problem is.

It looks like your successful installation did not use shared libraries 
(which have the ".so" shared object extension, but instead used static
libraries with a ".a" extension.  However, if you had previously installed
shared libraries in the same directory /usr/local/netcdf411/lib/, these
may be interfering with your ability to link to the static libraries.  I
suggest that you delete (or rename or move to another directory that won't
be searched) the file /usr/local/netcdf411/lib/libnetcdff.so, and then try
the WRF link step again.  WRF should then find the functions with the right
names in /usr/local/netcdf411/lib/libnetcdf.a, which appears to be where the
successful install archived them.

--Russ

> Examples of WRF installation errors:
> /usr/local/netcdf411/lib/libnetcdff.so: undefined reference to
> `nf_get_varm_double_'
> /usr/local/netcdf411/lib/libnetcdff.so: undefined reference to
> `nf_put_varm_int1_'
> /usr/local/netcdf411/lib/libnetcdff.so: undefined reference to
> `nf_put_vars_int1_'
> /usr/local/netcdf411/lib/libnetcdff.so: undefined reference to `nf__create_'
> /usr/local/netcdf411/lib/libnetcdff.so: undefined reference to `nf_inq_dim_'
> /usr/local/netcdf411/lib/libnetcdff.so: undefined reference to
> `nf_put_varm_text_'
> /usr/local/netcdf411/lib/libnetcdff.so: undefined reference to
> `nf__open_mp_'
> /usr/local/netcdf411/lib/libnetcdff.so: undefined reference to
> `nf_get_varm_real_'
> /usr/local/netcdf411/lib/libnetcdff.so: undefined reference to
> `nf_get_var1_real_'
> /usr/local/netcdf411/lib/libnetcdff.so: undefined reference to
> `nf_put_varm_double_'
> /usr/local/netcdf411/lib/libnetcdff.so: undefined reference to
> `nf_get_vara_int2_'
> /usr/local/netcdf411/lib/libnetcdff.so: undefined reference to
> `nf_put_vara_int2_'
> /usr/local/netcdf411/lib/libnetcdff.so: undefined reference to
> `nf_put_var1_int2_'
> /usr/local/netcdf411/lib/libnetcdff.so: undefined reference to
> `nf_get_varm_text_'
> /usr/local/netcdf411/lib/libnetcdff.so: undefined reference to
> `nf_put_att_int2_'
> /usr/local/netcdf411/lib/libnetcdff.so: undefined reference to
> `nf_rename_var_'
> /usr/local/netcdf411/lib/libnetcdff.so: undefined reference to
> `nf_inq_libvers_'
> /usr/local/netcdf411/lib/libnetcdff.so: undefined reference to
> `nf_put_att_int1_'
> /usr/local/netcdf411/lib/libnetcdff.so: undefined reference to `nf_abort_'
> /usr/local/netcdf411/lib/libnetcdff.so: undefined reference to
> `nf_get_var1_int2_'
> /usr/local/netcdf411/lib/libnetcdff.so: undefined reference to
> `nf_put_vars_int_'
> /usr/local/netcdf411/lib/libnetcdff.so: undefined reference to
> `nf_get_var1_double_'
> /usr/local/netcdf411/lib/libnetcdff.so: undefined reference to
> `nf_get_vars_double_'
> /usr/local/netcdf411/lib/libnetcdff.so: undefined reference to
> `nf_inq_attname_'
> /usr/local/netcdf411/lib/libnetcdff.so: undefined reference to
> `nf_put_vara_int1_'
> /usr/local/netcdf411/lib/libnetcdff.so: undefined reference to
> `nf_inq_format_'
> /usr/local/netcdf411/lib/libnetcdff.so: undefined reference to
> `nf_get_vara_int1_'
> /usr/local/netcdf411/lib/libnetcdff.so: undefined reference to
> `nf__create_mp_'
> /usr/local/netcdf411/lib/libnetcdff.so: undefined reference to
> `nf_get_var1_int1_'
> /usr/local/netcdf411/lib/libnetcdff.so: undefined reference to `nf__enddef_'
> 
> 
> 
> 
> On Sun, Mar 27, 2011 at 5:34 PM, Pavel Kishcha <address@hidden>wrote:
> 
> > Russ,
> >
> > Ignor my previous message.
> > Now I have set the following environmental variables (see attached file
> > env_110327):
> > export FC=gfortran44
> > export CC=gcc44
> > export CFLAGS="-DgFortran"
> >
> > Then, I run the following commands: make clean; ./configure; make check
> > compile.
> > It looks like the compilation was successful. But I am not sure. Could you
> > check the attached files, config.log and   make_check_install_110327.log,
> > for details?
> >
> > According to you suggestion, I also run the following commands:
> >
> > root@cyclone netcdf-4.1.1# cd
> > /home/pavel/WRF_v321/netcdf-4.1.1/fortran/.libs
> > root@cyclone .libs# file fort-lib.o libnetcdff.a
> > fort-lib.o:   ERROR: cannot open `fort-lib.o' (No such file or directory)
> >
> > libnetcdff.a: current ar archive
> > root@cyclone .libs# nm -a libnetcdff.a | grep nf_open
> > 0000000000000546 T nf_open_
> >                  U nf_open_
> >
> >
> > What is your opinion?
> >
> > Thank you,
> > Pavel
> >
> >
> >
> > On Fri, Mar 25, 2011 at 11:04 AM, Pavel Kishcha <address@hidden>wrote:
> >
> >> Russ,
> >>
> >> First, here is the output for your commands:
> >>
> >> root@cyclone fortran# cd /home/pavel/WRF_v321/netcdf-4.1.1/fortran
> >> root@cyclone fortran# file fort-lib.o libnetcdff.a
> >> fort-lib.o:   ELF 64-bit LSB relocatable, AMD x86-64, version 1 (SYSV),
> >> not stripped
> >> libnetcdff.a: ERROR: cannot open `libnetcdff.a' (No such file or
> >> directory)
> >> root@cyclone fortran# nm -a libnetcdff.a | grep nf_open
> >> nm: 'libnetcdff.a': No such file
> >>
> >> Second, I tried "make clean", then I specified the environment variable
> >> CFLAGS="-DgFortran" (see attached file env_110325), and then "make check
> >> install". Here is the output (see attached files for details):
> >>
> >> *** Test: varm on URL:
> >> http://test.opendap.org/opendap/data/nc/coads_climatology.nc
> >> *** Testing: stride case 1
> >> *** nc function failure: -33 NetCDF: Not a valid ID
> >> FAIL: test_varm3
> >> ================================================
> >> 3 of 4 tests failed
> >> Please report to address@hidden
> >> ================================================
> >> make[3]: *** [check-TESTS] Error 1
> >> make[3]: Leaving directory `/home/pavel/WRF_v321/netcdf-4.1.1/ncdap_test'
> >> make[2]: *** [check-am] Error 2
> >> make[2]: Leaving directory `/home/pavel/WRF_v321/netcdf-4.1.1/ncdap_test'
> >> make[1]: *** [check-recursive] Error 1
> >> make[1]: Leaving directory `/home/pavel/WRF_v321/netcdf-4.1.1/ncdap_test'
> >> make: *** [check-recursive] Error 1
> >>
> >>
> >> Finally, after all changes, I run again your commands:
> >>
> >> root@cyclone netcdf-4.1.1# cd /home/pavel/WRF_v321/netcdf-4.1.1/fortran
> >> root@cyclone fortran# file fort-lib.o libnetcdff.a
> >> fort-lib.o:   ELF 64-bit LSB relocatable, AMD x86-64, version 1 (SYSV),
> >> not stripped
> >> libnetcdff.a: ERROR: cannot open `libnetcdff.a' (No such file or
> >> directory)
> >> root@cyclone fortran# nm -a libnetcdff.a | grep nf_open
> >> nm: 'libnetcdff.a': No such file
> >>
> >>
> >> Thank you very much for your support,
> >> Pavel
> >>
> >>
> >> address@hidden> wrote:
> >>
> >>> Pavel,
> >>>
> >>>
> >>> OK, the output is puzzling, because the gfortran44 compiler is still
> >>> not finding the C functions it needs to call from Fortran.  Could you
> >>> please run the following commands and send me the output.  I've also
> >>> provided the output I get when running the analogous commands (in my
> >>> build directory) for comparison:
> >>>
> >>>  $ cd /home/pavel/WRF_v321/netcdf-4.1.1/fortran/.libs
> >>>  $ file fort-lib.o libnetcdff.a
> >>>  fort-lib.o:   ELF 64-bit LSB relocatable, x86-64, version 1 (SYSV), not
> >>> stripped
> >>>  libnetcdff.a: current ar archive
> >>>  $ nm -a libnetcdff.a | grep nf_open
> >>>  0000000000000270 T nf_open_
> >>>  0000000000000170 T nf_open_par_
> >>>                   U nf_open_
> >>>                   U nf_open_par_
> >>>
> >>> Thanks.
> >>>
> >>> --Russ
> >>>
> >>>
> >>> Russ Rew                                         UCAR Unidata Program
> >>> address@hidden                      http://www.unidata.ucar.edu
> >>>
> >>>
> >>>
> >>> Ticket Details
> >>> ===================
> >>> Ticket ID: VUQ-446360
> >>> Department: Support netCDF
> >>> Priority: Normal
> >>> Status: Closed
> >>>
> >>>
> >>
> >
> 
> 

Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: VUQ-446360
Department: Support netCDF
Priority: Normal
Status: Closed