[gmx-users] md.log interpretation

[Mark Abraham]

Hi,

I am not familiar with the implementation details, but I would assume there
is a dependency on rcoulomb of the cost of the Born force chain rule. You
can check this by trying different values. It might be faster to use
infinite cutoffs (see manual) so that the algorithm does not need to search.

Mark

On Tue, Nov 4, 2014 at 1:34 AM, Nizar Masbukhin <nizar.fkub08 at gmail.com>
wrote:

> Dear gromacs users,
> I've just finished my NVT equilibration in implicit solvent. From md.log, i
> see that most of time were used to calculate Forces (of Born force chain
> rule). Could someone explain to me why calculating it takes so long?
>
> mdp setting:
>
> integrator=md
> dt=0.004
> nstep=2500000
> bd-frict=50
> rlist=5
> rvdw=5
> rcoulomb=5
> nstlist=40
> implicit-solvent=GBSA
> gb-alogarithm=still
> nstgbradii=40
> gbradii=5
> gb-epsilon-solvent=80
> gb-salt-conc=0.2
> sa-algorithm=ace-approximation
> sa-surface-tension=2.05
> constraints=all-bonds
> constraints-algorithm=LINCS
> lincs-order=12
>
>
> md.log
>
> M E G A - F L O P S   A C C O U N T I N G
>
>  NB=Group-cutoff nonbonded kernels    NxN=N-by-N cluster Verlet kernels
>  RF=Reaction-Field  VdW=Van der Waals  QSTab=quadratic-spline table
>  W3=SPC/TIP3p  W4=TIP4p (single or pairs)
>  V&F=Potential and force  V=Potential only  F=Force only
>
>  Computing:                               M-Number         M-Flops  % Flops
>
> -----------------------------------------------------------------------------
>  NB VdW [V&F]                         32677.013279       32677.013     0.0
>  NB VdW [F]                         1740991.575264     1740991.575     0.3
>  NB VdW & Elec. [V&F]               1192677.312698     1192677.313     0.2
>  NB VdW & Elec. [F]               106409048.599622   106409048.600    17.9
>  1,4 nonbonded interactions           20035.628466     1803206.562     0.3
>  Born radii (Still)                 1999216.232742    93963162.939    15.8
>  Born force chain rule             25548182.811729   *383222742.176*
> 64.4
>  NS-Pairs                             64906.572700     1363038.027     0.2
>  CG-CoM                                 205.506576         616.520     0.0
>  Propers                              15168.313980     3473543.901     0.6
>  Impropers                              637.980588      132699.962     0.0
>  Pos. Restr.                           3830.053530      191502.676     0.0
>  Virial                                  82.695471        1488.518     0.0
>  Stop-CM                                 82.214752         822.148     0.0
>  Calc-Ekin                              822.011152       22194.301     0.0
>  Lincs                                 4696.969329      281818.160     0.0
>  Lincs-Mat                           229529.791548      918119.166     0.2
>  Constraint-V                          9393.938658       75151.509     0.0
>  Constraint-Vir                          46.973979        1127.375     0.0
>  Virtual Site 3                         615.868824       22787.146     0.0
>  Virtual Site 3fd                       791.205144       75164.489     0.0
>  Virtual Site 3fad                      168.761208       29701.973     0.0
>  Virtual Site 3out                     1893.632256      164746.006     0.0
>  Virtual Site 4fdn                      576.418152      146410.211     0.0
>  (null)                                 476.315439           0.000     0.0
>
> -----------------------------------------------------------------------------
>  Total                                               595265438.267   100.0
>
> -----------------------------------------------------------------------------
>
>
>      R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
>
> On 1 MPI rank
>
>  Computing:          Num   Num      Call    Wall time         Giga-Cycles
>                      Ranks Threads  Count      (s)         total sum    %
>
> -----------------------------------------------------------------------------
>  Vsite constr.          1    1    1085001      96.421        385.432   0.2
>  Neighbor search        1    1      27126     915.964       3661.462   2.1
>  Force                  1    1    1085001   *39317.742*     157168.118
> 91.3
>  Vsite spread           1    1    1095852     142.563        569.880   0.3
>  Write traj.            1    1      11030     425.764       1701.942   1.0
>  Update                 1    1    1085001      96.742        386.714   0.2
>  Constraints            1    1    1085001    1311.720       5243.449   3.0
>  Rest                                         766.404       3063.612   1.8
>
> -----------------------------------------------------------------------------
>  Total                                      43073.320     172180.608 100.0
>
> -----------------------------------------------------------------------------
>
>                Core t (s)   Wall t (s)        (%)
>        Time:    41985.828    43073.320       97.5
>                          11h57:53
>                  (ns/day)    (hour/ns)
> Performance:        8.706        2.757
> Finished mdrun on rank 0 Tue Nov  4 03:27:26 2014
>
>
> I know, for someone this question is less important, but for me performance
> is important.
>
> --
> Thanks
> My Best Regards, Nizar
> Medical Faculty of Brawijaya University
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>