fantastic, thanks for your report. Cheers.
Hai
On Tue, Dec 20, 2016 at 4:24 PM, Susan Chacko <susanc.helix.nih.gov> wrote:
> Thank you! This gave me some idea of what to look for. We normally load
> the intel compiler via an environment module, and looking at that
> module, I discovered that it sets CC, FC etc. to their full paths.
>
> So instead of loading the Intel module, I just added the ifort/icc
> directory to $PATH, and added the location of the Intel libraries to
> $LD_LIBRARY_PATH. i.e. the minimum required for the configure. After
> this the build chugged along nicely and I had no further problems.
>
> Thanks again,
>
> Susan
>
> On 12/20/16 2:04 PM, Daniel Roe wrote:
> > Hi,
> >
> > On Tue, Dec 20, 2016 at 1:45 PM, Susan Chacko <susanc.helix.nih.gov>
> wrote:
> >> % ./nf-config --all
> >>
> >> This netCDF-Fortran 4.2 has been built with the following features:
> >>
> >> --cc -> /usr/local/intel/composer_xe_
> 2015.1.133/bin/intel64/icc
> >> --cflags -> -I/usr/local/apps/amber/amber16/include
> -I/usr/local/apps/amber/amber16/include
> >> --libs -> -L/usr/local/apps/amber/amber16/lib
> -L/usr/local/apps/amber/amber16/lib -shared-intel -lnetcdf -lnetcdff
> -lnetcdf
> > Not sure how you got here but this 'libs' line might be your problem.
> > For some reason you have a '-lnetcdff' flag in there, which shouldn't
> > be needed when linking a non-Fortran program. It's also in the wrong
> > place; '-lnetcdff' needs to come *before* '-lnetcdf' since the latter
> > contains the symbols the former needs. Note that your 'flibs' line
> > looks OK:
> >
> >> --flibs -> -L/usr/local/apps/amber/amber16/lib -lnetcdff
> -L/usr/local/apps/amber/amber16/lib -shared-intel -lnetcdf -lnetcdff
> -lnetcdf
> > Contrast this output from nf-config with one of my Intel compiles:
> >
> > --libs -> -L/v/apps/amber/amber16/intel_17.0.0-mvapich2_2.2/lib
> > -L/v/apps/amber/amber16/intel_17.0.0-mvapich2_2.2/lib -shared-intel
> > -lnetcdf -lnetcdf
> > --flibs -> -L/v/apps/amber/amber16/intel_17.0.0-mvapich2_2.2/lib
> > -lnetcdff -L/v/apps/amber/amber16/intel_17.0.0-mvapich2_2.2/lib
> > -shared-intel -lnetcdf -lnetcdf
> >
> > The output of your configure message makes it look like you might have
> > some environment variables relating to the compiler name set, like
> > CC/FC etc, and what's more it looks like they may contain the full
> > path to the compiler binaries. Is that the case? If so, try unsetting
> > them (or just setting them to the compiler name, e.g. CC=icc etc) and
> > run configure again.
> >
> > -Dan
> >
> >> --has-f90 -> yes
> >>
> >> --has-nc2 -> yes
> >> --has-nc4 -> no
> >>
> >> --prefix -> /usr/local/apps/amber/amber16
> >> --includedir-> /usr/local/apps/amber/amber16/include
> >> --version -> netCDF-Fortran 4.2
> >>
> >>
> >> But then, when I go back to the top level of amber16, and type
> >>
> >> ./configure --with-netcdf /usr/local/apps/amber/amber16/ intel
> >>
> >> I still get the same flurry of 'undefined reference' errors.
> >>
> >> Susan.
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
> --
> Susan Chacko, Ph.D.
> HPC . NIH Staff
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Dec 20 2016 - 13:30:03 PST
