Hi,
I'm not sure that your numbers are that strange given the file that
you've put in attachment. It says:
ntpr = 100, ntwx = 100, ntwr = 1000,
(in contracdiction with your saying below, are you sure that you use the
right mdin?)
and NATOM=265294
So your system is rather big and your save every 100 steps
(recommendation for GPU run is to save at least every 1000 steps,
meaning ntpr, ntwx and ntwr should be >= 1000). With a GTX760 card, that
doesn't seem strange to me. Try increasing ntwx and ntpr, and see how it
goes.
Gerald.
On 06/04/2015 10:13 AM, Chinh Su Tran To wrote:
> Dear AMBER users, especially GPU experts,
>
> I am running a 432-residue protein in explicit (amber12) on GPU (installed
> in a desktop Ubuntu 12.04, 64bit). What confuses me is that it runs so slow
> (and I think it should not have been).
>
> My mdinfo (equilibrium for 20ns) says:
>
> ------------------------------------------------------------------------------
> | Current Timing Info
> | -------------------
> | Total steps : 10000000 | Completed : 50000 | Remaining : 9950000
> |
> | Average timings for last 50000 steps:
> | Elapsed(s) = 2803.57 Per Step(ms) = 56.07
> | ns/day = 3.08 seconds/ns = 28035.65
> |
> | Average timings for all steps:
> | Elapsed(s) = 2803.57 Per Step(ms) = 56.07
> | ns/day = 3.08 seconds/ns = 28035.65
> |
> |
> | Estimated time remaining: 155.0 hours.
> ------------------------------------------------------------------------------
>
> The rate of 3ns/day for GPU (pmemd.cuda) may be not right here.
>
> When I checked "nvidia-smi" for the GPU info, it gives:
>
> +------------------------------------------------------+
>
> | NVIDIA-SMI 346.72 Driver Version: 346.72
> |
> |-------------------------------+----------------------+----------------------+
> | GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr.
> ECC |
> | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute
> M. |
> |===============================+======================+======================|
> | 0 GeForce GTX 760 Off | 0000:01:00.0 N/A |
> N/A |
> | 80% 73C P0 N/A / N/A | 1267MiB / 2047MiB | N/A
> Default |
> +-------------------------------+----------------------+----------------------+
>
>
> +-----------------------------------------------------------------------------+
> | Processes: GPU
> Memory |
> | GPU PID Type Process name
> Usage |
> |=============================================================================|
> | 0 C+G Not
> Supported |
> +-----------------------------------------------------------------------------+
>
> May I ask if there is anything wrong about the card or the system?
> Or if I made any mistakes during the set-up?
>
> Attached is the results from the heating stage, and it seems ok.
>
> Thank you. Please help.
>
> My input file (eq.in):
> &cntrl
> imin=0, irest=1, ntx=7,
> ntxo=2
> ig=-1, ntb=2,
> pres0=1.0, ntp=1, taup=2.0,
> cut=10.0,
> ntr=0, ntc=2, ntf=2,
> tempi=300.0, temp0=300.0,
> ntt=3, gamma_ln=1.0,
> nstlim=10000000, dt=0.002,
> ntpr=50000, ntwx=50000, ntwr=50000
> /
>
> Thanks and regards,
> Chinh
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
____________________________________________________________________________
Prof. Gerald MONARD
SRSMC, Université de Lorraine, CNRS
Boulevard des Aiguillettes B.P. 70239
F-54506 Vandoeuvre-les-Nancy, FRANCE
e-mail : Gerald.Monard.univ-lorraine.fr
tel. : +33 (0)383.684.381
fax : +33 (0)383.684.371
web : http://www.monard.info
____________________________________________________________________________
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 04 2015 - 03:00:04 PDT
