On Fri, 2014-01-24 at 10:27 -0800, Andreas Goetz wrote:
> On Jan 23, 2014, at 5:21 AM, Jason Swails wrote:
>
> > On Thu, 2014-01-23 at 15:54 +0800, Jheng Wei Li wrote:
> >> Hello, all
> >> The version of Amber is 12.
> >> I am running few testings for pure_QM_MD_GAUSSIAN_PIMD.
> >>
> >> The original setting is nprocs=2, ng=2 and GAU_NCPUS=1.
> >> ( mpirun -np 2 $sander -ng 2 -groupfile gf_pimd ).
> >>
> >> If I change into nprocs=4, ng=2 and GAU_NCPUS=2, it doesn't work!!
> >> ( mpirun -np 4 $sander -ng 2 -groupfile gf_pimd )
> >> ***************************************************************************************
> >> Running multisander version of sander Amber12
> >> Total processors = 4
> >> Number of groups = 2
> >>
> >> --------------------------------------------------------------------------
> >> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> >> with errorcode 1.
> >> ***************************************************************************************
> >> Is there any way to use 2 processors for 1 group?
> >
> > This simulation is set up to run pure QM entirely with the external QM
> > package (in this case, Gaussian). Since only one thread can launch a
> > Gaussian job, it doesn't make any sense to use 2 threads for sander for
> > each group, since one thread will simply sit there and wait while the
> > other one runs Gaussian.
> >
> > Note that the input you provided above actually requests the use of 6
> > processors. Each PIMD bead will be run using 2 CPUs (for a total of 4
> > CPUs), but the processor in each bead that runs Gaussian (there will be
> > 2 of those processors total) will each run Gaussian with 2 cores. This
> > is clearly not what you want.
>
> This is not correct - only the master process of each process group launches Gaussian:
That's what I said -- 2 groups with 2 processors each give 4 total
processors for sander (which dies), and of these 4 processors only 2 of
them will run Gaussian (namely the master of each group) ;). Since each
of the 2 threads that run Gaussian will run with 2 threads, 6 CPUs may
be used in total (assuming the slave sander nodes are doing some work
while the masters run the QM program). My description may certainly
have been confusing, though (as is what actually happens with hybrid
parallelization schemes like this one)...
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Jan 24 2014 - 13:30:02 PST
