AMBER Archive (2008)

Subject: RE: AMBER: MKL libraries/Amber10

From: Ross Walker (
Date: Fri May 16 2008 - 13:25:36 CDT

Hi Francesco,

> Before performing tests, may I ask why during the compilation both g++ and
> g77 were used. In particular about g77, should I have indicated ifort as
> compiler (as I'll do for Amber10 and openmpi)? I was unable to see an
> option for ifort in place of g77 for the above compilation.

Ambertools always uses g77 for the Fortran compiler. There is no performance sensitive code in there that would benefit from ifort so in short don't worry about it. If it all compiled correctly and the tests pass you are good to go.
> When all that is in order, I understand to unpack Amber10.tar.bz2 into
> /usr/local/amber10
> and proceed to compile.

Yes and here you would benefit from specifying ifort since this is for the compilation of the MD engine code which is more computationally intensive.
> Incidentally (which I forgot to mention in my original post), are MKL
> libraries of help even for a NUMA-type machine with dual-opterons?

Yes they can although it depends very much on the type of simulation you are running. QMMM runs (especially if you specify diag_routine=0 in &qmmm) can benefit enormously from MKL. GB runs can also benefit quite a bit. For regular classical PME MD simulations the difference is much smaller, on the order of 5 to 10% or so but if you have MKL available you might as well use it.

Good luck,

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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