Unless I am reading this wrongly, you did
2 fs dt, nstlim=2000000 --> 4 ns/10.6 hours
4fs dt , nstlim=2000000 --> 8 ns/11.5 hours
So, basically in the same wallclock time, you DOUBLED the simulation
time. That is exactly what is supposed to happen, right ?
adrian
On 8/5/15 7:28 PM, George Green wrote:
> I set-up a system using hydrogen mass repartitioning (HMR) using a 4fs
> timestep and ran using 24 processors for 4 ns simulation time (total time =
> 11.5 hours). When comparing it against the 2fs simulation it took longer
> (total time = 10.6 hours). A setting might be wrong somewhere, but it is
> not obvious.
>
> Main changes from 4 fs sims from 2 fs sims:
> 1. Identical box size and number of waters added.
> original 2fs Box size =
> Total vdw box size: 67.818 91.065 92.217 angstroms.
> Volume: 569515.132 A^3
>
> new 4fs Box size:
> Total vdw box size: 67.818 91.065 92.217 angstroms.
> Volume: 569515.132 A^3
>
> 2. Use of new montecarlo barostat
> 3. changing dt from 0.002 to 0.004
> 4. change cut from 8.0 to 9.0
> 5. setting ntave to 0
> 6. some changes to print such as NTPR and NTWR
>
> >From the timings, I think this might be an issue with the mpi configuration
> as the average ns/day seems to indicate a speed up, but the wallclock tells
> a different story. However, I would like to make sure that my settings are
> correct. Particularly for ntave and mcbarint. If anyone has any ideas, that
> would be great
>
> ######################
> #HMR input file:
> &cntrl
>
> nstlim=2000000, dt=0.004, ntx=5, irest=1,
> ntpr=1000, ntwr=2000000, ntwx=500,
> temp0=300.0, ntt=1, tautp=2.0, ioutfm=1, ntxo=2, ig=-1, cut=9.0,
>
>
>
> barostat=2, mcbarint=100, ntave=0,
>
>
>
> ntb=2, ntp=1,
>
>
>
> ntc=2, ntf=2,
>
>
>
> nrespa=1,
>
> &end
> ######################
> #
> #
> ######################
> #normal 2 fs input file:
> &cntrl
>
> nstlim=2000000, dt=0.002, ntx=5, irest=1,
> ntpr=500, ntwr=1000000, ntwx=500,
> temp0=300.0, ntt=1, tautp=2.0, ioutfm=1, ntxo=2, ig=-1,
>
>
>
> ntb=2, ntp=1,
>
>
>
> ntc=2, ntf=2,
>
>
>
> nrespa=1,
>
> &end
>
> ######################
> ######################
> ######################
> ######################
>
> Timings for 2 fs:
> | NonSetup CPU Time in Major Routines, Average for All Tasks:
> |
> | Routine Sec %
> | ------------------------------
> | DataDistrib 6023.97 15.84
> | Nonbond 30754.53 80.88
> | Bond 6.45 0.02
> | Angle 73.44 0.19
> | Dihedral 250.79 0.66
> | Shake 199.60 0.52
> | RunMD 712.39 1.87
> | Other 2.04 0.01
> | ------------------------------
> | Total 38023.21
>
> | PME Nonbond Pairlist CPU Time, Average for All Tasks:
> |
> | Routine Sec %
> | ---------------------------------
> | Set Up Cit 344.21 0.91
> | Build List 3158.82 8.31
> | ---------------------------------
> | Total 3503.03 9.21
>
> | PME Direct Force CPU Time, Average for All Tasks:
> |
> | Routine Sec %
> | ---------------------------------
> | NonBonded Calc 21337.98 56.12
> | Exclude Masked 458.01 1.20
> | Other 1239.56 3.26
> | ---------------------------------
> | Total 23035.55 60.58
>
> | PME Load Balancing CPU Time, Average for All Tasks:
> |
> | Routine Sec %
> | ------------------------------------
> | Atom Reassign 2.96 0.01
> | Image Reassign 6.25 0.02
> | FFT Reassign 0.01 0.00
> | ------------------------------------
> | Total 9.22 0.02
>
> | Final Performance Info:
> | -----------------------------------------------------
> | Average timings for last 2000 steps:
> | Elapsed(s) = 36.86 Per Step(ms) = 18.43
> | ns/day = 9.38 seconds/ns = 9214.24
> |
> | Average timings for all steps:
> | Elapsed(s) = 38042.45 Per Step(ms) = 19.02
> | ns/day = 9.08 seconds/ns = 9510.61
> | -----------------------------------------------------
>
> | Master Setup CPU time: 4.10 seconds
> | Master NonSetup CPU time: 37949.66 seconds
> | Master Total CPU time: 37953.76 seconds 10.54 hours
>
> | Master Setup wall time: 6 seconds
> | Master NonSetup wall time: 38043 seconds
> | Master Total wall time: 38049 seconds 10.57 hours
>
> #####################################################################
> #####################################################################
> #####################################################################
> #####################################################################
> Timings for 4 fs:
>
> | NonSetup CPU Time in Major Routines, Average for All Tasks:
> |
> | Routine Sec %
> | ------------------------------
> | DataDistrib 6016.64 14.50
> | Nonbond 34083.64 82.12
> | Bond 6.95 0.02
> | Angle 75.69 0.18
> | Dihedral 257.11 0.62
> | Shake 209.68 0.51
> | RunMD 732.79 1.77
> | Other 122.96 0.30
> | ------------------------------
> | Total 41505.46
>
> | PME Nonbond Pairlist CPU Time, Average for All Tasks:
> |
> | Routine Sec %
> | ---------------------------------
> | Set Up Cit 731.30 1.76
> | Build List 7938.13 19.13
> | ---------------------------------
> | Total 8669.43 20.89
>
> | PME Direct Force CPU Time, Average for All Tasks:
> |
> | Routine Sec %
> | ---------------------------------
> | NonBonded Calc 20390.62 49.13
> | Exclude Masked 523.13 1.26
> | Other 1535.61 3.70
> | ---------------------------------
> | Total 22449.36 54.09
>
> | PME Reciprocal Force CPU Time, Average for All Tasks:
> |
> | Routine Sec %
> | ---------------------------------
> | 1D bspline 319.85 0.77
> | Grid Charges 410.92 0.99
> | Scalar Sum 93.01 0.22
> | Gradient Sum 651.85 1.57
> | FFT 1459.25 3.52
> | ---------------------------------
> | Total 2934.88 7.07
>
> | PME Load Balancing CPU Time, Average for All Tasks:
> |
> | Routine Sec %
> | ------------------------------------
> | Atom Reassign 8.20 0.02
> | Image Reassign 15.61 0.04
> | FFT Reassign 0.01 0.00
> | ------------------------------------
> | Total 23.82 0.06
>
> | Final Performance Info:
> | -----------------------------------------------------
> | Average timings for last 1000 steps:
> | Elapsed(s) = 20.75 Per Step(ms) = 20.75
> | ns/day = 16.66 seconds/ns = 5187.32
> |
> | Average timings for all steps:
> | Elapsed(s) = 41536.36 Per Step(ms) = 20.77
> | ns/day = 16.64 seconds/ns = 5192.05
> | -----------------------------------------------------
>
> | Master Setup CPU time: 6.76 seconds
> | Master NonSetup CPU time: 41457.54 seconds
> | Master Total CPU time: 41464.30 seconds 11.52 hours
>
> | Master Setup wall time: 8 seconds
> | Master NonSetup wall time: 41537 seconds
> | Master Total wall time: 41545 seconds 11.54 hours
> _______________________________________________
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--
Dr. Adrian E. Roitberg
Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Wed Aug 05 2015 - 17:00:02 PDT
