Re: [AMBER] Problems compiling pmemd.cuda - undefined reference to ...

From: Jason Swails <>
Date: Sat, 24 Mar 2012 12:06:43 -0400


On Fri, Mar 23, 2012 at 1:22 PM, Adam Jion <> wrote:

> Hi!
> All the bugfixes have been applied. Below is the config.h file.
> AmberTools 1.5 (serial + parallel) and Amber 11 (serial + parallel) were
> compiled without error using gcc-4.6.1. and gfortran. However, they cannot
> be compiled using a gcc-4.4.6 compiler (It will lead to a cannot find
> 'lgfortran' error)
> Because pmemd.cuda required a gcc-4.4 and below compiler, I changed the
> compiler to gcc-4.4.6 but got an error message about not finding
> 'lgfortran' That is,

As Dan has already said, Amber builds fine with GCC 4.4.6 (that's what I've
used on my machine for ages). I've also tested, at one point, 4.3, 4.4,
4.5, and 4.6 all on the same machine -- all of which worked.

The trickiest thing about using multiple GCC installations on the same
machine is how to properly toggle between them (this is what you're having
troubles with, I think). The operating systems where I regularly switch
GCC versions (Mac OS X and Gentoo) have scripts that do this for you. If
this is the case for you, then use those scripts. If it's not, you're
probably best off using only the version that came with your OS unless you
really know what you're doing.

All that said, the original error looks like an issue with your CUDA
compiler, not your C/F90 compilers, so we can't help you unless you provide
information about your CUDA setup.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Sat Mar 24 2012 - 09:30:03 PDT
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