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

> Russ,
> 
> To let you know, I have again reinstalled netcdf with the option of the use
> of shared libraries.
> Then I was able to installed WRF without compilation errors and to obtain
> exe-files.

Great, I'm glad to hear it!  We're making shared libraries the default for 
version
4.1.2 and greater, so maybe things like this will get easier.

--Russ

> Thank you very much indeed for your support,
> Pavel
> 
> 
> On Mon, Mar 28, 2011 at 7:41 PM, Pavel Kishcha <address@hidden>wrote:
> 
> > Russ,
> >
> > Thank you for your suggestion.
> > I have deleted all files *.so in the directory /usr/local/netcdf411/lib
> > and reinstalled netcdf 4.1.1. anew.
> > After compiling WRF, I found that the number of installation errors reduced
> > significantly.
> > However, some errors relating to netcdf libraries remain on hand. See the
> > attached file for details. Below are some examples.
> >
> > Thank you,
> > Pavel
> >
> > Examples of errors
> >
> > /usr/local/netcdf411/lib/libnetcdf.a(liboc_la-ocinternal.o): In function
> > `ocinitialize':
> > ocinternal.c:(.text+0x2b9): undefined reference to `curl_version_info'
> > /usr/local/netcdf411/lib/libnetcdf.a(liboc_la-http.o): In function
> > `ocfetchhttpcode':
> > http.c:(.text+0x29): undefined reference to `curl_easy_getinfo'
> > /usr/local/netcdf411/lib/libnetcdf.a(liboc_la-http.o): In function
> > `ocfetchurl_file':
> > http.c:(.text+0xa4): undefined reference to `curl_easy_setopt'
> > http.c:(.text+0xcc): undefined reference to `curl_easy_setopt'
> > http.c:(.text+0xf3): undefined reference to `curl_easy_setopt'
> > http.c:(.text+0x11b): undefined reference to `curl_easy_setopt'
> > http.c:(.text+0x13a): undefined reference to `curl_easy_perform'
> > http.c:(.text+0x17c): undefined reference to `curl_easy_getinfo'
> > http.c:(.text+0x1a4): undefined reference to `curl_easy_strerror'
> > /usr/local/netcdf411/lib/libnetcdf.a(liboc_la-http.o): In function
> > `ocfetchurl':
> > http.c:(.text+0x222): undefined reference to `curl_easy_setopt'
> > http.c:(.text+0x24a): undefined reference to `curl_easy_setopt'
> > http.c:(.text+0x271): undefined reference to `curl_easy_setopt'
> > http.c:(.text+0x299): undefined reference to `curl_easy_setopt'
> > http.c:(.text+0x2a8): undefined reference to `curl_easy_perform'
> > http.c:(.text+0x2bb): undefined reference to `curl_easy_strerror'
> > http.c:(.text+0x300): undefined reference to `curl_easy_getinfo'
> > http.c:(.text+0x368): undefined reference to `curl_easy_strerror'
> >
> >
> >
> >
> > address@hidden> wrote:
> >
> >> 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
> >> > >
> >> > >
> >> > >
> >> 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
> >>
> >>
> >
> 
> 

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