[gmx-users] GPU g_energy problem

[Andrei Neamtu]

Dear Justin,

Many thanks for your reply!

I have performed the simulation with 4.6.1 and then I installed 4.6.4 and
run again the simulations from the beginning.
But indeed, as in  the log you have sent me, I have multiple (4) energy
groups. This is probably the cause for the zeroes in my edr file.
Thank you,
Andrei




 ------------------------
 Dr. Andrei Neamtu, PhD, Lecturer
 Dept. of Physiology
"Gr. T. Popa" Iasi University of Medicine and Pharmacy
 http://www.umfiasi.ro/
 str. Universitatii nr. 16
 IASI, Jud. Iasi
 ROMANIA
 ----------------------



On Tue, Nov 26, 2013 at 2:26 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On Mon, Nov 25, 2013 at 3:40 AM, Andrei Neamtu <neamtuandrei at gmail.com
> >wrote:
>
> > Dear GMX users,
> >
> > I am simulating a system of two proteins in TIP4P water box. The
> > simulations are performed on a system with 3 servers each containing 16
> CPU
> > cores and 2 Tesla 2090 GPU.
> > The problem thai I encounter is related to the saved interaction energies
> > in the .edr file and read with g_energy.
> >
> > It seems that when using the GPU acceleration none of the interaction
> > energies are saved for the short-range non-bonded interaction computed on
> > the GPU.
> > The SOL (solvent) - SOL LJ-SR and Coul-SR are all ZERO. Also Protein -
> SOL
> > are all zero.
> > When using CPU only accceleration these energies are saved correctly!
> > Despite the zeroes in the energy file the simulations seems to proceed
> > correctly when visually inspected.
> >
> > I wonder in I do not miss something obvious.
> >
> > I am asking if anybody observed a similar behaviour and what should be
> the
> > solution to this problem.
> >
> >
> > I upgraded to 4.6.4 version but also on 4.6.1 the problem was still
> > present.
> >
> >
> Can you clarify if you have re-run the simulation under 4.6.4, not just
> re-analyzed the energies with 4.6.4 g_energy?  Doing the latter will have
> no effect if the energies were not saved correctly in the original .edr
> file.  http://redmine.gromacs.org/issues/1293 seems relevant here; perhaps
> multiple energygrps still are not supported on GPU.
>
> -Justin
>
> --
>
> ==========================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
>
> ==========================================
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