Re: [AMBER-Developers] Adding fortran module into nab with some catches.

From: Ray Luo <>
Date: Wed, 10 Feb 2010 18:58:46 -0800


You have to focus on the numerical solver in the profiling analysis.
Initialization is indeed not significant. Also, DMP is probably too
small to be representative.

All the best,

Ray Luo, Ph.D.
Associate Professor in Computational
Biochemistry and Molecular Biophysics
Dept of Molecular Biology and Biochemistry
Dept of Biomedical Engineering
University of California, Irvine, CA 92697-3900
Email: Phones: (949) 824-9528, 9562

Mengjuei Hsieh wrote:
> On Wed, Feb 10, 2010 at 08:55:48AM -0500, case wrote:
>> On Tue, Feb 09, 2010, Mengjuei Hsieh wrote:
>>> Yet another issues for pbsa integration is that I am still doing
>>> single point calculation for every step of the nab minimization.
>>> I.e. redundant initialization and deallocation will definitely
>>> slow down the performance.
>> OK...something to have on the to-do list. But you might want to check about
>> how big the performance hit is.
> Hi,
> I went to check the profile of the whole calculation, the initialization
> cost is not even significant enough to show up in the list.
> figure:
> So I'll just forget this, unless other people show me otherwise.
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Received on Wed Feb 10 2010 - 19:00:03 PST
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