Dear all,
I can use the intel compiler (version 17.0.0 ) to install amber16. Maybe,
you can update the intel compiler.
good luck
YT
2016-12-21 3:04 GMT+08:00 Daniel Roe <daniel.r.roe.gmail.com>:
> 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
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Dec 20 2016 - 11:30:02 PST
