[gmx-developers] Gromacs-2016: Win64 quasi-portable

Justin Lemkul jalemkul at vt.edu
Mon Oct 3 00:01:27 CEST 2016

On 10/2/16 5:42 PM, Boris Timofeev wrote:
> Good afternoon to all!
> I did a great job on compilation of the "portable" Gromacs-2016 version on the
> Win64  platform without cygwin with OpenCL support and  AVX_256/AVX2_256
> expansions. The project is builded on VS-2015. By small changes in CMakeLists, I
> managed to achieve that both the "embedded" tests, and regressiontests, are
> executed after assembly immediately from VS IDE. It was tested on Windows7/
> Windows10  with IntelCore i3, i5, i7  processors and video cards from Nvidia and
> AMD. So far it was not succeeded to win  - against the video card from Intel -
> Intel OpenCL compiler preprocessor is left unfinished, does not recognize
> directive "-I" and have buggy concatention (##) implementation.
> It was necessary to realize a primitive preprocessor,  became successful, but
> all the same calculations (tests and regressiontests) are wrong as it was
> already metioned here (https://bugs.freedesktop.org/show_bug.cgi?
> id=94265#add_comment).
> If it is interesting to community, I am ready to report about some necessary
> changes in progect and to provide the main CMake-file.
> There are several questions to developers.
> 1. The nbnxn_ocl_kernel_nvidia.clh, nbnxn_ocl_kernel_nowarp.clh and
> nbnxn_ocl_kernel_amd.clh files, if to compare their with kdiff, differ only in
> comments and lack of unroll pragma for Nvidia. Why not to unite them in one?
> Where the promised optimization?
> 2. Why in the Gromacs'a code so many paths to files are embedded up? To start
> tests without development environment on other computer it is necessary to copy
> practically all project.
> 3. A question "on science". When performing an example of
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html,
>  pdb2gmx for the aminoacid residue  HIS ("HIZE-branch" on stdout ), unlike all
> others residue,  gives a nonintegral charge 0.883,  inexplicable with round-off
> errors.
> Whether there is no program mistake here?

I can't speak to points 1 and 2, but here: what is HIZE-branch?  I've never 
heard of that.  Note, too, that if you're working with a single amino acid with 
OPLS-AA, you can't rely on the default terminus selection.  You need to choose 
the zwitterion termini, otherwise the charges will be junk because OPLS-AA makes 
changes to CA depending on whether the residue is a zwitterion or in a polypeptide.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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