Re: [AMBER] Issues Compiling AmberTools13

From: Jason Swails <>
Date: Wed, 2 Jul 2014 12:54:20 -0700

On Wed, Jul 2, 2014 at 12:20 PM, Malachi Phillips <> wrote:

> Hello,
> I am having issues installing AmberTools 13. After successfully compiling
> it with the command ./compile gnu, whenever I use the make install command
> I get this error message that seems to point to a programming error in a
> filenames vardata.c:

What version compilers are you using? What Linux version are you using?
 This is a problem with the bundled NetCDF library (which is not actually
our code).

Some ideas to work around this:

1) Upgrade to AmberTools 14. It uses a newer NetCDF release that may not
suffer from this problem.
2) Install a version of NetCDF locally and use that instead.

I would recommend #1, but to do #2, you would need to install both netcdf
and netcdf-fortran (your package manager should have those packages), then
reconfigure using

./configure --with-netcdf /path/to/netcdf gnu

If you install NetCDF from your package manager, /path/to/netcdf is simply


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Wed Jul 02 2014 - 13:00:02 PDT
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