Re: [AMBER] AmberTools 1.4 parallel programs

From: Jason Swails <>
Date: Mon, 7 Feb 2011 17:45:39 -0500


On Mon, Feb 7, 2011 at 4:44 PM, Martin M. Ossowski <
> wrote:

> Hello,
> I noticed that parallel AmberTools 1.4 programs do not have an *.MPI
> suffixes while parallel Amber 11 programs have. Is there a reason for
> this -- in other words, is it safe to rename parallel nab and nab2c to
> nab.MPI and nab2c.MPI while also keeping the serial versions of these
> programs in the same directory?

I may be mistaken here, but I believe the answer is *no*. Note that I
believe nab is the *only* AmberTools package that makes use of MPI but
overwrites the serial build with executables that are the same name. The
other parallel tool, ptraj, should create a ptraj.MPI executable.

The problem with just *renaming* nab and nab2c with a .MPI suffix is that it
links to other libraries (like libsff.a). A quick "grep" in that directory
shows me that there are MPI calls in the sff source files, so libsff.a will
also be dependent on MPI as well. As far as I can tell, this approach will
require you to rename *all* of the libraries nab links to (I'm not sure what
all of them are) with the .MPI suffix and link to those explicitly.

The safest way I can think of doing this is to have a separate directory
where you compile just AmberTools in parallel if you have some need for
having both versions, so that you can keep them sufficiently separated.

Hope this helps,

> -Thank you,
> -Martin.
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Mon Feb 07 2011 - 15:00:10 PST
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