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

[Boris Timofeev]

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/Pa ges/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?
Sincerely,
Boris Timofeev
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