I am running the example with my current branch and I do not see the
behavior that you describe. I did recently patch the master about that bug
I mentioned; you might try merging in the most recent changes to see if
that fixes the behavior. I do find that the Fortran and extern "C"
functions are writing to different places--the Fortran output is going to
mdout, the C output is going to the terminal window. If I correlate the
outputs, they match exactly.
Dave
On Fri, Nov 3, 2017 at 3:13 PM, Yinglong Miao <yinglong.miao.gmail.com>
wrote:
> Hi Dave,
>
> The test system is alanine dipeptide as attached. I have been working on my
> own mods, with the master branch checked out about one month ago. But the
> problem should be detected in Amber16 also.
>
> It would be great if you are able to fix it as you clean the code, and
> figure out what's the cause ... thanks!
>
> Yinglong
>
>
> On Fri, Nov 3, 2017 at 1:53 PM, David Cerutti <dscerutti.gmail.com> wrote:
>
> > Can you provide the system on which this occurs? I am doing a major
> sweep
> > of the code and am nearly finished rebuilding the way bonded interactions
> > are computed. As such, the GaMD routines are on my list of things to
> > incorporate. We spotted a bug earlier, which has since been patched,
> that
> > involved sending values to extern "C" functions as literals, not
> pointers,
> > but that doesn't seem to be the case here. However, that problem was
> only
> > detected after I tried to pass additional arguments to the function,
> which
> > then got turned to gobbledegook. Are you using code from Amber16, master
> > branch, or your own mods?
> >
> > Dave
> >
> >
> > On Fri, Nov 3, 2017 at 10:35 AM, Yinglong Miao <yinglong.miao.gmail.com>
> > wrote:
> >
> > > Hi All,
> > >
> > > I run into this problem with the Fortran-CUDA interface. Basically, in
> > the
> > > pme_force.F90, I called a function in the cuda/gpu.cpp as shown below.
> > The
> > > calculations inside the gpu function run fine, but it seems the
> potential
> > > energies got changed *strangely* in the first place when they are
> passed
> > > for calling the function:
> > >
> > > pme_force.F90:
> > > write(*,'(a,2f22.12)') "Debug-p1) (pot_ene%total,
> > pot_ene%dihedral)
> > > = ", &
> > > pot_ene%total, pot_ene%dihedral
> > > call gpu_calculate_and_apply_gamd_weights(pot_ene%total,
> > > pot_ene%dihedral, &
> > >
> > pot_ene%gamd_boost,num_gamd_
> > > lag)
> > > ...
> > >
> > > cuda/gpu.cpp:
> > > extern "C" void gpu_calculate_and_apply_gamd_weights_(double*
> > > pot_ene_tot, double* dih_ene_tot,
> > > double*
> > gamd_ene_tot,
> > > double*
> > num_gamd_lag)
> > > {
> > > PRINTMETHOD("gpu_calculate_and_apply_gamd_weights");
> > > double tboost = 0.0;
> > > double fwgtd = 1.0;
> > > double fwgt = 1.0;
> > > double tboostall = 0.0;
> > > double temp0 = gpu->sim.gamd_temp0;
> > > double ONE_KB = 1.0 / (temp0 * KB);
> > > printf("Debug-GPU-p0) (pot_ene_tot, dih_ene_tot) = (%12.5f,
> %12.5f)\n",
> > > *pot_ene_tot, *dih_ene_tot);
> > > ...
> > >
> > > Output:
> > > Debug-p1) (pot_ene%total, pot_ene%dihedral) = -5991.862400868107
> > > 9.501277353615
> > > Debug-GPU-p0) (pot_ene_tot, dih_ene_tot) = ( -5988.16828, 9.89661)
> > > =========
> > >
> > > As you can see, the energy values before and after they are passed are
> > > different. And this problem appeared to depend on the simulation
> length.
> > > The energy differences are negligible when I test the code with several
> > > thousand steps, but get larger with hundreds of thousand steps or more
> > like
> > > the above. Has anyone come across similar issues before? My workstation
> > has
> > > a new NVIDIA Quadro P5000 GPU card. Could this be related to the
> > hardware?
> > > If not, how may I fix it?
> > >
> > > Any suggestions will be much appreciated,
> > > Yinglong
> > >
> > > Yinglong Miao, Ph.D.
> > > Assistant Professor
> > > Center for Computational Biology and
> > > Department of Molecular Biosciences
> > > University of Kansas
> > > http://miao.compbio.ku.edu
> > >
> > > _______________________________________________
> > > AMBER-Developers mailing list
> > > AMBER-Developers.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber-developers
> > >
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> >
>
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Received on Fri Nov 03 2017 - 14:30:02 PDT
