[CIG-SHORT] NetCDF error when attempting to build git version

Brad Aagaard baagaard at usgs.gov
Fri Oct 17 10:13:27 PDT 2014 

Eric,

You need to rebuild all the Fortran object files after adding the PIC 
flags. Do a "make clean" and then "make" in the NetCDF build directory.

Brad


On 10/17/14, 10:04 AM, Eric Lindsey wrote:
> Ok, I looked through the INSTALL file and see the options it is telling
> me to add (pic_flag=-fPIC and wl=-Wl,). These variables are defined
> several times in libtool; I found that the section labeled # ### BEGIN
> LIBTOOL TAG CONFIG: FC was missing the pic_flag=-fPIC option, but adding
> it there had no effect on the error I'm getting. Maybe I did not
> understand those instructions correctly. Here is a larger context for
> the error:
>
> /bin/sh ../libtool --tag=FC   --mode=link mpif90    -version-number
> 5:1:0  -L/home/class239/software/pylith-git/pylith/lib  -o libnetcdff.la
> <http://libnetcdff.la> -rpath
> /home/class239/software/pylith-git/pylith/lib fort-attio.lo
> fort-control.lo fort-dim.lo fort-genatt.lo fort-geninq.lo fort-genvar.lo
> fort-lib.lo fort-misc.lo fort-v2compat.lo fort-vario.lo fort-var1io.lo
> fort-varaio.lo fort-varmio.lo fort-varsio.lo fort-nc4.lo
> ../liblib/libnetcdf.la <http://libnetcdf.la> ../f90/libnetcdff90.la
> <http://libnetcdff90.la> -lhdf5_hl -lhdf5 -lm -lz
> libtool: link: mpif90 -shared   .libs/fort-attio.o .libs/fort-control.o
> .libs/fort-dim.o .libs/fort-genatt.o .libs/fort-geninq.o
> .libs/fort-genvar.o .libs/fort-lib.o .libs/fort-misc.o
> .libs/fort-v2compat.o .libs/fort-vario.o .libs/fort-var1io.o
> .libs/fort-varaio.o .libs/fort-varmio.o .libs/fort-varsio.o
> .libs/fort-nc4.o   --whole-archive ../f90/.libs/libnetcdff90.a
> --no-whole-archive  -rpath
> /home/class239/software/pylith-git/build/netcdf-build/liblib/.libs
> -rpath /home/class239/software/pylith-git/pylith/lib -rpath
> /home/class239/software/pylith-git/pylith/lib
> -L/home/class239/software/pylith-git/pylith/lib
> ../liblib/.libs/libnetcdf.so
> /home/class239/software/pylith-git/pylith/lib/libhdf5_hl.so
> /home/class239/software/pylith-git/pylith/lib/libhdf5.so -lrt -lz
> -L/opt/intel/composer_xe_2013.0.079/compiler/lib/intel64
> -L/opt/intel/composer_xe_2013.0.079/ipp/../compiler/lib/intel64
> -L/opt/intel/composer_xe_2013.0.079/ipp/lib/intel64
> -L/opt/intel/composer_xe_2013.0.079/tbb/lib/intel64
> -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/
> -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64
> -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/
> -L/lib/../lib64 -L/lib/../lib64/ -L/usr/lib/../lib64
> -L/usr/lib/../lib64/
> -L/opt/intel/composer_xe_2013.0.079/compiler/lib/intel64/
> -L/opt/intel/composer_xe_2013.0.079/ipp/../compiler/lib/intel64/
> -L/opt/intel/composer_xe_2013.0.079/ipp/lib/intel64/
> -L/opt/intel/composer_xe_2013.0.079/tbb/lib/intel64/
> -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../ -L/lib64 -L/lib/
> -L/usr/lib64 -L/usr/lib
> /home/class239/software/pylith-git/pylith/lib/libmpi_f90.so
> /home/class239/software/pylith-git/pylith/lib/libmpi_f77.so
> /home/class239/software/pylith-git/pylith/lib/libmpi.so
> /home/class239/software/pylith-git/pylith/lib/libopen-rte.so
> /home/class239/software/pylith-git/pylith/lib/libopen-pal.so -lnsl
> -lutil -lifport -lifcoremt -limf -lm -lipgo -lintlc -lpthread -lsvml
> -lgcc -lgcc_s -lirc_s -ldl -lc    -pthread -soname libnetcdff.so.5 -o
> .libs/libnetcdff.so.5.1.0
> ifort: command line warning #10006: ignoring unknown option
> '-fwhole-archive'
> ifort: command line warning #10006: ignoring unknown option
> '-fno-whole-archive'
> ifort: command line warning #10006: ignoring unknown option '-rpath'
> ifort: command line warning #10006: ignoring unknown option '-rpath'
> ifort: command line warning #10006: ignoring unknown option '-rpath'
> ifort: command line remark #10010: option '-pthread' is deprecated and
> will be removed in a future release. See '-help deprecated'
> ifort: command line warning #10006: ignoring unknown option '-soname'
> ifort: error #10236: File not found:  'libnetcdff.so.5'
> ifort: command line remark #10010: option '-pthread' is deprecated and
> will be removed in a future release. See '-help deprecated'
> make[6]: *** [libnetcdff.la <http://libnetcdff.la>] Error 1
> make[6]: Leaving directory
> `/home/class239/software/pylith-git/build/netcdf-build/fortran'
> make[5]: *** [all] Error 2
> make[5]: Leaving directory
> `/home/class239/software/pylith-git/build/netcdf-build/fortran'
> make[4]: *** [all-recursive] Error 1
> make[4]: Leaving directory
> `/home/class239/software/pylith-git/build/netcdf-build'
> make[3]: *** [all] Error 2
> make[3]: Leaving directory
> `/home/class239/software/pylith-git/build/netcdf-build'
> make[2]: *** [netcdf] Error 2
> make[2]: Leaving directory `/home/class239/software/pylith-git/build'
> make[1]: *** [installed_netcdf] Error 2
> make[1]: Leaving directory `/home/class239/software/pylith-git/build'
> make: *** [installed_pylith] Error 2
>
>
>
> On Tue, Oct 14, 2014 at 4:05 PM, Brad Aagaard <baagaard at usgs.gov
> <mailto:baagaard at usgs.gov>> wrote:
>
>     Eric,
>
>     It looks like the linker is unable to create the NetCDF shared
>     library. You need to examine the error message to see what the
>     linkiner is complaining about. Feel free to send the error message.
>
>     At the bottom of the INSTALL file, there are some notes on manually
>     patching libtool (this will be at the top-level of the build
>     directory for NetCDF) so that the NetCDF shared library can be
>     built. The notes are a bit cryptic, so let me know if they need more
>     explanation.
>
>     Regards,
>     Brad
>
>
>
>     On 10/14/2014 03:41 PM, Eric Lindsey wrote:
>
>         Greetings,
>
>         I've been trying to build the latest version of Pylith from the git
>         repository, but am failing on the netcdf build step. I used the
>         pylith-installer, with the configure command:
>
>         /home/class239/software/__pylith-git/pylith-installer-2.__0.3-0/configure
>         --with-pylith-git=master --with-make-threads=2
>         --prefix=/home/class239/__software/pylith-git/pylith --enable-python
>         --enable-mpi=openmpi --enable-force-install
>
>         A different version of netcdf is already installed on this
>         system, but it
>         is not an option for me to remove it (hence enable-force-install).
>
>         The configure runs successfully, but 'make' fails with:
>
>         ifort: error #10236: File not found:  'libnetcdff.so.5'
>         make[6]: *** [libnetcdff.la <http://libnetcdff.la>] Error 1
>         make[6]: Leaving directory
>         `/home/class239/software/__pylith-git/build/netcdf-build/__fortran'
>
>         Am I doing something wrong? Or is this a result of my having a prior
>         installation of netcdf? Any hints would be appreciated.
>
>         Thanks,
>         Eric
>
>
>
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