Re: [AMBER-Developers] Dear Professor Case, I would like to enquiry whether the current amber will still support gcc4.1.2 in the future release. Thank you.

From: Jason Swails <>
Date: Wed, 14 Dec 2011 14:18:12 -0500

On Wed, Dec 14, 2011 at 11:39 AM, David A Case <>wrote:

> On Wed, Dec 14, 2011, Lin Fu wrote:
> >
> Thanks for your note(Below). These points should be posted on the Amber
> developers list; and I am cc-ing this there.
> I think we are still trying to support gcc 4.1.2, mainly because Ross has
> noted that such compilers are still prevalent at supercomputer sites, and
> there are other machines in the same boat. I'd love to get past that
> however,
> and I wonder if supercomputer users don't have access to other compilers
> (e.g.
> Intel, pathscale, etc.) that would avoid this problem. There are many
> other
> places that would benefit from not being tied to gcc 4.1.2, and most
> developers (including me) don't have such machines; (instructions for
> setting
> up a virutal machine with whatever OS this is [RHEL x??] might help.

FWIW, I found what I think is a good distro for testing. I set up Gentoo
on a machine (and as a VM on my Mac) that uses portage as the package
manager (builds everything from source). It makes it easy to install
multiple GCCs which can be switched between much like "port select" works
on the Mac:

$ gcc-config -l
 [1] i686-pc-linux-gnu-4.1.2
 [2] i686-pc-linux-gnu-4.2.4
 [3] i686-pc-linux-gnu-4.3.6
 [4] i686-pc-linux-gnu-4.4.6
 [5] i686-pc-linux-gnu-4.5.3 *
 [6] i686-pc-linux-gnu-4.6.2

(It actually goes back as far as GCC-2.95.3, ca. 2001). Interestingly (and
I think it's unique among Linux distributions in this regard), it has
AmberTools as an available install through its package manager:

$ emerge --search AmberTools
[ Results for search key : AmberTools ]
[ Applications found : 1 ]

* sci-chemistry/ambertools [ Masked ]
      Latest version available: 1.5-r1
      Latest version installed: [ Not Installed ]
      Size of files: 118,256 kB
      Description: A suite for carrying out complete molecular mechanics
      License: GPL-2

I haven't tried it yet, but that's kind of neat. It's also good for
testing other things, like linking to a customized system NetCDF, FFTW, etc.

All the best,

Gentoo has LiveDVD's that I think can be used to install the OS, but the
primary method for installation is from source (including the desktop
environment and the kernel itself), which is the avenue I took.

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER-Developers mailing list
Received on Wed Dec 14 2011 - 11:30:03 PST
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