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

Pavel,

> This is a good idea to make shared libraries the default.
> In addition, it is worth doing the command "make clean" to be able to remove
> all netcdf libraries (both with ".so" and ".a" extensions) from  previous
> installations.

Thanks for the suggestion.  We have a "make uninstall" that's supposed to do 
that, but it hasn't
been tested extensively.  I think "make clean" should be something that can be 
run by an
ordinary user to clean the source directories from a build, whereas you may 
need root
or sudo privileges to run "make uninstall".

--Russ

> address@hidden> wrote:
> 
> > > 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_'
> > > >> >
> > > >> >
> > > >> >
> > > >> >
> > 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
> >
> >
> 
> 

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