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

[Eric Lindsey]

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 -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 ../f90/
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] 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> 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] 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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>>
>>
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