On Wed, Apr 23, 2014 at 7:21 PM, Eugene Yedvabny <eyedvabny.berkeley.edu>wrote:
> Hello Amber community,
>
> I am compiling Amber14 with gcc/gfortran and want to build the OpenMP
> version of cpptraj. It seems that GNU OpenMP and MKL libs are not mutually
> compatible, so I was wondering if cpptraj used MKL
Yes. It uses MKL routines in the rotdif (rotational diffusion), and
matrix diagonalization routines. But as far as I can tell, that's it.
(Basically I tried compiling WITHOUT linking the MKL libraries and just
took note of the unresolved symbols, which just came from action_rotdif and
dataset_mods).
and if compiling an
> OpenMP version would have an impact on the speed of non-threaded parts of
> cpptraj?
>
It might for the rotdif and diagonalization routines if the MKL speeds
those calculations up (on my AMD-based machine, MKL actually runs _slower_
than several standard ifort-optimized blas/lapack/arpack routines). Other
than that, there won't be any impact on using OpenMP parallelization.
(Where threading is not supported, it's not used and simply defaults to
the serial code).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Apr 23 2014 - 20:00:03 PDT
