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Re: [lammps-users] Fix Addforce Slow Down the Computational Efficiency
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Re: [lammps-users] Fix Addforce Slow Down the Computational Efficiency


From: Wei Peng <pengwrpi2@...24...>
Date: Mon, 16 Apr 2018 20:28:43 -0400

Dear Axel,

Thank you so much for your prompt response!

Can you tell me how to correctly merge all the reduction?

I tried this:

compute ftotal all reduce sum v_fx1 v_fy1 v_fz1 v_fx2 v_fy2 v_fz2 v_fx3 v_fy3 v_fz3 v_fx4 v_fy4 v_fz4 v_fx5 v_fy5 v_fz5 v_fx6 v_fy6 v_fz6 v_fx7 v_fy7 v_fz7 v_fx8 v_fy8 v_fz8

And I found c_ftotal[1] is wrong, not the same as c_fxsum1 ( which is from "compute fxsum1 half1 reduce sum v_fx1"). Ideally, I hope v_fx1 can be only defined for group half1, but I don't know how to limit scope of per-atom variable to a fraction of atoms in the simulation box.

I am thinking about set fx1 value for all other atoms to be zero explicitly (but I still don't know how), and do the merge of reduction as I posted above. But this is clearly not an elegant solution. What advice do you have for either defining v_fx1 exclusively on atoms of half1 group or doing the merge of reduction differently?

Thanks again,
Wei
 

Wei Peng
Graduate Student at Rensselaer Polytechnic Institute
Department of Materials Science and Engineering
110 8th Street, Troy, NY 12180

On Mon, Apr 16, 2018 at 5:59 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:
On Mon, Apr 16, 2018 at 4:58 PM, Wei Peng <pengwrpi2@...24...> wrote:
> Dear LAMMPS administrators or users,
>
> I am simulating a system with 8 nanoparticles containing Lennard-Jones atoms
> connected by FENE bonds. Every step, I applied a force to each atom that are
> contained in half of each nanoparticle. The force applied to every atom all
> points to the center of the mass of the whole nanoparticle. To conserve the
> momentum, I added an opposite force that is applied to the rest of the
> system. To take the additional energy out of the system, I used Nose-Hoover
> thermostat.
>
> I used fix addforce command to apply the extra force. It turns out it works
> very well, and it can give the expected result. However, the efficiency of
> the computation is significantly slowed down by this additional force (~20
> times slower). I guess the low efficiency is mainly caused by the
> communication cost, but it turns out not the case (according to the output
> file produced by LAMMPS).

that output only includes cost of communication for regular known
communication points
does not include time spend in communication that is included in
variable updates or computes.

the obvious cost is for compute reduce. you should be able to cut this
cost by a significant margin by doing one reduction over three values
instead of three reductions over one value.
...and since you have seven more nanoparticles, you can reduce that
cost even by combining all reductions into one.
so right now you seem to be doing 24 reductions, which can be handled
by just one compute reduce.

another "hidden" reduction operation is in the count(groupID)
function. if the number doesn't change over the course of a run, you
can cache it with something like this:

variable nliquid equal $(ncount(liquid))

so by avoiding redundant reductions you should be able to
significantly reduce the computational effort.

axel.

>
> I have attached the input file and the output file here. The version of
> LAMMPS is Aug. 2017.
>
> Can you give me any advice on accelerating the computation. Thank you for
> your help!
>
> Below is the input file:
>
>
> compute          coord1 np1 property/atom xu yu zu
> compute          c1 np1 com
>
> # np1 is the group id of nanoparticle 1.
>
> variable         famp equal "0.1"
>
> variable         dirx1 atom "c_coord1[1]-c_c1[1]"
> variable         diry1 atom "c_coord1[2]-c_c1[2]"
> variable         dirz1 atom "c_coord1[3]-c_c1[3]"
> variable         diramp1 atom "sqrt(v_dirx1^2 + v_diry1^2 + v_dirz1^2)"
> variable         fx1 atom "v_famp*v_dirx1/v_diramp1"
> variable         fy1 atom "v_famp*v_diry1/v_diramp1"
> variable         fz1 atom "v_famp*v_dirz1/v_diramp1"
> compute          fxsum1 half1 reduce sum v_fx1
> compute          fysum1 half1 reduce sum v_fy1
> compute          fzsum1 half1 reduce sum v_fz1
> fix              addfnp1 half1 addforce v_fx1 v_fy1 v_fz1
>
> # "half1" is the group id of the half of nanoparticle 1 that was applied a
> force to
> # I did the same thing for other 7 nanoparticles, which was not posted here.
>
> variable         fxliquid equal "-1.0
> *(c_fxsum1+c_fxsum2+c_fxsum3+c_fxsum4+c_fxsum5+c_fxsum6+c_fxsum7+c_fxsum8)/count(liquid)"
>
> variable         fyliquid equal "-1.0 *
> (c_fysum1+c_fysum2+c_fysum3+c_fysum4+c_fysum5+c_fysum6+c_fysum7+c_fysum8)/count(liquid)"
>
> variable         fzliquid equal "-1.0 *
> (c_fzsum1+c_fzsum2+c_fzsum3+c_fzsum4+c_fzsum5+c_fzsum6+c_fzsum7+c_fzsum8)/count(liquid)"
>
> fix              addliquid liquid addforce v_fxliquid v_fyliquid v_fzliquid
>
> # I summed up the forces applied to the 8 nanoparticles and take the
> opposite and then add it to every atom in group "liquid".
>
> Here is the performance report in the output file:
>
> Loop time of 2228.15 on 1024 procs for 100000 steps with 53432 atoms
>
> Performance: 38776.610 tau/day, 44.880 timesteps/s
> 100.0% CPU use with 1024 MPI tasks x 1 OpenMP threads
>
> MPI task timing breakdown:
> Section |  min time  |  avg time  |  max time  |%varavg| %total
> ---------------------------------------------------------------
> Pair    | 3.1147     | 3.4368     | 3.6571     |   4.7 |  0.15
> Bond    | 0.14084    | 0.74264    | 5.9983     | 113.4 |  0.03
> Neigh   | 152.64     | 153.88     | 154.96     |   4.0 |  6.91
> Comm    | 39.216     | 47.364     | 63.729     |  80.0 |  2.13
> Output  | 8.1437     | 8.8403     | 9.5221     |  13.4 |  0.40
> Modify  | 1982.8     | 1999.6     | 2007.8     |  12.5 | 89.74
> Other   |            | 14.33      |            |       |  0.64
>
> Nlocal:    52.1797 ave 478 max 40 min
> Histogram: 1010 6 2 2 0 2 0 1 0 1
> Nghost:    236.358 ave 1235 max 204 min
> Histogram: 993 16 4 2 3 3 1 1 0 1
> Neighs:    261.92 ave 343 max 63 min
> Histogram: 2 3 4 4 5 66 355 429 145 11
>
> Total # of neighbors = 268206
> Ave neighs/atom = 5.01958
> Ave special neighs/atom = 0.63243
> Neighbor list builds = 22088
> Dangerous builds = 0
> Total wall time: 0:37:10
>
>
> Sincerely,
> Wei
>
>
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--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.