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
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Received on Tue Dec 20 2016 - 13:30:02 PST
