[gmx-users] Fwd: Bad performance in free energy calulations

[Mark Abraham]

Hi,

mdrun doesn't see any problems, but if something else is reporting 25%
utilization then that probably means you have something else running on
your machine, which is a terrible idea for running mdrun. You should expect
some slowdown wrt to the non-free-energy version of the run - the
implementation of the short-ranged loops for the perturbed atoms is not as
great as the rest.

Mark

On Tue, May 19, 2015 at 3:13 PM Julian Zachmann <
FrankJulian.Zachmann at uab.cat> wrote:

> Dear Gromacs users,
>
> I want to do free energy calculations following this
> <
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html
> >
> tutorial.
> My system contains a GPCR, membrane, small ligand, solvate - in total
> 60.000 atoms. I want to perturb the ligand (31 atoms, 3 hydrogen atoms get
> converted to dummy atoms, one carbon atom get converted to a carbon atom,
> the other 27 ligand atoms just change slightly their charges). Apart from
> the perturbation and an extra simulated annealing step in the
> equilibration, I am following the tutorial as close as possible.
>
> My calculations work, but the computer performance is really bad. I am
> using only 8 processors for each Lambda, so domain decomposition is not
> really an issue (see below) but the CPUs run with only 25% load. Which
> could be the reason? Any ideas?
>
> I have made all files available under this link
> <
> https://drive.google.com/folderview?id=0B2M9aqeJrxnYfjRLbzZ0VkFBTlFraEJaWWJ3MzVSaHlUN2cyVzV6X2ZibjRkek81UVM5S0k&usp=sharing
> >
> .
>
> Thank you very much for your help!!
>
> Julian
>
>
>     D O M A I N   D E C O M P O S I T I O N   S T A T I S T I C S
>
>  av. #atoms communicated per step for force:  2 x 74451.3
>  av. #atoms communicated per step for LINCS:  2 x 4495.3
>
>  Average load imbalance: 2.9 %
>  Part of the total run time spent waiting due to load imbalance: 1.4 %
>  Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 2
> %
>
>
>      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 8 MPI ranks
>
>  Computing:          Num   Num      Call    Wall time         Giga-Cycles
>                      Ranks Threads  Count      (s)         total sum    %
>
> -----------------------------------------------------------------------------
>  Domain decomp.         8    1        150       3.136         65.226   0.3
>  DD comm. load          8    1        150       0.208          4.335   0.0
>  DD comm. bounds        8    1        150       0.257          5.355   0.0
>  Neighbor search        8    1        151      11.329        235.608   1.2
>  Comm. coord.           8    1       4850      11.368        236.425   1.2
>  Force                  8    1       5001     466.392       9699.934  50.6
>  Wait + Comm. F         8    1       5001      10.598        220.418   1.2
>  PME mesh               8    1       5001     386.976       8048.244  42.0
>  NB X/F buffer ops.     8    1      14701       1.670         34.724   0.2
>  Write traj.            8    1          3       0.133          2.768   0.0
>  Update                 8    1       5001       1.474         30.664   0.2
>  Constraints            8    1      10002      20.387        423.998   2.2
>  Comm. energies         8    1        501       2.255         46.891   0.2
>  Rest                                           4.983        103.631   0.5
>
> -----------------------------------------------------------------------------
>  Total                                        921.165      19158.221 100.0
>
> -----------------------------------------------------------------------------
>  Breakdown of PME mesh computation
>
> -----------------------------------------------------------------------------
>  PME redist. X/F        8    1      15003     134.013       2787.183  14.5
>  PME spread/gather      8    1      20004     179.277       3728.576  19.5
>  PME 3D-FFT             8    1      20004      22.603        470.092   2.5
>  PME 3D-FFT Comm.       8    1      20004      47.072        979.004   5.1
>  PME solve Elec         8    1      10002       3.941         81.965   0.4
>
> -----------------------------------------------------------------------------
>
>                Core t (s)   Wall t (s)        (%)
>        Time:     3693.315      921.165      400.9
>                  (ns/day)    (hour/ns)
> Performance:        0.938       25.583
> Finished mdrun on rank 0 Tue May 19 14:01:45 2015
> --
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