128 / 8 = 16 CPUs for each replica (which is a MD run).
(vs 108 CPUs for a single MD run (assume that you have good CPU scaling)
Hai
On Tue, Jan 24, 2017 at 6:11 PM, Thakur, Abhishek <axt651.miami.edu> wrote:
> I am sorry
>
> I have use 108 processor for MD and aMD and have got around 7-8 and 6-7
> ns/day respectively.
>
>
> Here for REMD I am using 8 replicas on 128 processors.
>
> ________________________________
> From: Adrian Roitberg <roitberg.ufl.edu>
> Sent: Tuesday, January 24, 2017 10:09:35 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] REMD_just_1.10ns/day
>
> Thakur, you need togive us much better data if we are to help youy.
>
> What does "somewhat less processor" means?
>
> You said you used 128 cores for REMD. How many replicas ?
>
> How many cores did you use to run without REMD?
>
> adrian
>
> On 1/24/17 3:58 PM, Thakur, Abhishek wrote:
> > Hi Dr.Simmerling,
> >
> > I have ran with same mdind file MD with some what less processor but ot
> gave me around 7-8ns/day.
> >
> > than is why I am more shocked that REMD is giving so slow.
> >
> > With aMD I have got 6ns/day.
> >
> > ________________________________
> > From: Carlos Simmerling <carlos.simmerling.gmail.com>
> > Sent: Tuesday, January 24, 2017 9:50:28 AM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] REMD_just_1.10ns/day
> >
> > I would suggest doing the benchmarking without REMD. Do your MD speeds
> > match published benchmarks for similar size systems? REMD should not add
> > much overhead but can add complications if your computer system is not
> > configured well. It's best to try to isolate the factors and test MD
> alone.
> >
> > On Tue, Jan 24, 2017 at 1:53 PM, Thakur, Abhishek <axt651.miami.edu>
> wrote:
> >
> >> Hi every one,
> >>
> >> I am running REMD on 128 processors with 10706 atoms implicitly and just
> >> getting 1.1ns/day.
> >>
> >> Is it normal that such calculation run so slow?
> >>
> >> Or can there be a possibility of some fault in my script?
> >>
> >> Here is what I am using
> >>
> >>
> >> &cntrl
> >> irest=1, ntx=5,
> >> nstlim=100, dt=0.004,
> >> ntt=3, gamma_ln=50.0,
> >> temp0=XXXXX, ig=RANDOM_NUMBER,
> >> ntc=2, ntf=2, nscm=1000,
> >> ntb=0, igb=5,
> >> cut=999.0, rgbmax=15.0,
> >> ntpr=100, ntwx=1000, ntwr=100000,
> >> nmropt=1,
> >> numexchg=100000,
> >> saltcon=0.2,
> >> /
> >> &wt TYPE='END'
> >> /
> >> DISANG=WT_chir.dat
> >>
> >>
> >> Thanking you,
> >>
> >> -AT
> >> _______________________________________________
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> --
> Dr. Adrian E. Roitberg
> University of Florida Research Foundation Professor.
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
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Received on Tue Jan 24 2017 - 15:30:03 PST
