J. Swails wrote: I'm not familiar with REMD in NAMD. I know NAMD uses
charm++, which is a
different parallelization scheme (although it can optionally be compiled
using MPI as its message-passing back-end, I believe), and it also takes
advantage of shared memory parallelism, if available.
For remd, namd must be compiled with MPI. I did that some time ago with
namd2.9. However, although MPI relates to processes, namd/remd requires
physical nodes. Can not be run on a shared mem machine, even with multiple
680 cards, like my machine.
francesco
On Wed, Sep 11, 2013 at 1:58 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Wed, Sep 11, 2013 at 4:34 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> > On Wed, Sep 11, 2013 at 2:03 AM, Francesco Pietra <chiendarret.gmail.com
> >
> > wrote:
> > > Hello Hai:
> > > Can a debug trial be carried out on a shared memory GPU machine (the
> one
> > I
> > > use currently) or are multiple physical nodes required? With NAMD,
> > physical
> > > nodes are needed.
> >
>
> MPI allows for distributed computing because each thread is given its own
> chunk of memory, with none shared between the different threads. [1] While
> this allows MPI to be spread across multiple nodes, there is certainly no
> rule against providing separate memory to multiple threads from the same
> source of RAM.
>
> As far as Amber (or any MPI program) is concerned, there is no difference
> between running 8 threads on 1 node with shared memory or 8 threads on 8
> nodes with no shared memory.
>
> I'm not familiar with REMD in NAMD. I know NAMD uses charm++, which is a
> different parallelization scheme (although it can optionally be compiled
> using MPI as its message-passing back-end, I believe), and it also takes
> advantage of shared memory parallelism, if available.
>
> Hopefully this answers your question,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Sep 11 2013 - 07:00:03 PDT
