Looks Great! Thanks Dave and Taisung!
Dan
On Dec 23, 2017 10:35 AM, "David Cerutti" <dscerutti.gmail.com> wrote:
> I think this is some great work from Taisung, and he has taught me a number
> of things about CUDA and C++. I think that the gpuContext consolidation is
> definitely something that should be carried through to master, and I
> believe that the linking will help debugging (the CUDA debugger has
> requirements about things be compiled simultaneously).
>
> While I am not yet ready to take a side on which TI implementation, I will
> say that I've managed to integrate the AFE code from SDSC into some of my
> new code and it has been cleanly integrated. Having a separate part of the
> program handle TI and perform transactions with the equilibrium MD code (as
> opposed to embedding the calculations in the workflow) will impose a
> cost--no one can reach in and extract information for additional
> computations as quickly as they could be done within the context of the
> primary MD kernels--but that cost appears to be small, and an apparatus
> that reaches in and extracts such information would serve as a model for
> future program extensions. There are features of each code not found in
> the other: the Berendsen barostat is supported by pmemd-GTI while MBAR is
> supported by the AFE code.
>
> Merry Christmas all,
>
> Dave
>
>
> On Sat, Dec 23, 2017 at 1:11 PM, David Cerutti <dscerutti.gmail.com>
> wrote:
>
> > Hi all:
> >
> > In an effort to evaluate and prepare to ultimately merge
> > our GPU-accelerated TI implementation with the master branch, we created
> > the “gti” branch that is synced to the current master branch, but that
> > enabled both TI implementations - the pmemdGTI implementation from the
> > Laboratory for Biomolecular Simulation Research (LBSR) at Rutgers, and
> the
> > AFE implementation from Ross' group which is in the current master
> branch -
> > to co-exist. This allows head to head tests and comparisons, code
> > evaluation, consolidation and discussion of how we want to move forward
> in
> > the next official release. I am sure we can learn a lot from looking at
> > both code bases, and adopt best practices from each.
> >
> > Here is a summary of main changes from current main branch:
> >
> > *Major program changes—for cuda developers*
> >
> > *1. **all*
> >
> > The cSim and gpuContext objects are now wrapped as base classes. All
> > variable definitions and initializations are done in base_gpuCpntext.{h,
> > cpp} and base_simulationConst.{h, cpp}.
> >
> > *2. **Configured with –gti flag:*
> >
> > a. The current pmemd.cuda is compiled as a combination of several
> > compiled cuda units. All units need to keep its own copy of cSim and
> that
> > means ~10 copies of cSim are in the program at the same time and they
> need
> > to share the GPU constant memory (64KB). *As a result, cSim is limited
> > to size of ~5KB*. Furthermore, any change in cSim on the host needs to
> > be passed to all copies of cSim’s on GPU.
> >
> > With –gti configured, the cuda kernels are compiled as portable units
> and
> > linked as one cuda unit—hence there is only one copy of cSim at
> runtime. *The
> > cSim now has the size limit of ~64KB. *And coping cSim from host to GPU
> > only needs to be done once. You will be able to start putting much more
> > things into cSim.
> >
> > b. The gpu context object is a local variable created in the heap
> > space (gpu = new _gpuContext;). With –gti configured. It is now handled
> > as a singleton object and can be accessed from anywhere by
> >
> > “gpu = theGPUContext::GetPointer(); “.
> >
> >
> >
> > *Test results*
> >
> > *1.without -git flag*
> >
> > Without turning on GTI (i.e., configured without –gti),
> > test_cuda_serial.sh gave
> >
> > 171 file comparisons passed
> >
> > 0 file comparison failed
> >
> > 0 test experienced an error
> >
> > *2. with -git flag*
> >
> > With -gti turned on (i.e., configured with), test_cuda_serial.sh gave
> >
> > 161 file comparisons passed
> >
> > 10 file comparison failed
> >
> > 0 test experienced an error
> >
> > The “file comparison failed” is small numerical differences in the
> > cellulose case and all AFE cases (due to different TI implementations).
> >
> >
> > We will update all GTI functionalities and test cases after this initial
> > merge.
> >
> > Please take a look at the “gti” branch and let us any problems:
> especially
> > the AFE part: we need to modify some parts so that the “#ifdef GTI” can
> > effectively distinguish the AFE and the GTI implementations. It seems
> > there is no problem—all AFE tests are passed when –gti is not configured.
> >
> > Best,
> >
> > Taisung and Darrin
> >
> >
> >
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Received on Sat Dec 23 2017 - 11:00:04 PST
