From 31ed3f7178a349b5d47827eb8fefea90b034e7cd Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Mon, 27 Aug 2018 17:09:59 -0600
Subject: [PATCH] more changes to insure each triplet IJK computed exactly once
---
...og.23Aug18.atm.g++.1 => log.27Aug18.g++.1} | 32 +++++------
...og.23Aug18.atm.g++.4 => log.27Aug18.g++.4} | 32 +++++------
src/MANYBODY/pair_atm.cpp | 54 ++++++++-----------
3 files changed, 53 insertions(+), 65 deletions(-)
rename examples/atm/{log.23Aug18.atm.g++.1 => log.27Aug18.g++.1} (69%)
rename examples/atm/{log.23Aug18.atm.g++.4 => log.27Aug18.g++.4} (69%)
diff --git a/examples/atm/log.23Aug18.atm.g++.1 b/examples/atm/log.27Aug18.g++.1
similarity index 69%
rename from examples/atm/log.23Aug18.atm.g++.1
rename to examples/atm/log.27Aug18.g++.1
index 3373846b31..46215e108c 100644
--- a/examples/atm/log.23Aug18.atm.g++.1
+++ b/examples/atm/log.27Aug18.g++.1
@@ -26,7 +26,7 @@ Created orthogonal box = (0 0 0) to (18.3252 18.3252 18.3252)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
- Time spent = 0.00126314 secs
+ Time spent = 0.00139618 secs
pair_style hybrid/overlay lj/cut 4.5 atm 4.5 2.5
pair_coeff * * lj/cut 1.0 1.0
@@ -60,26 +60,26 @@ Neighbor list info ...
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.47 | 11.47 | 11.47 Mbytes
Step Temp E_pair E_mol TotEng Press
- 0 1.033 -4.8899813 0 -3.3408686 -4.2298176
- 5 1.0337853 -4.8928208 0 -3.3425304 -4.2233154
- 10 1.0358056 -4.8953304 0 -3.3420104 -4.1897183
- 15 1.0380938 -4.8990457 0 -3.3422942 -4.1310148
- 20 1.0389566 -4.9014345 0 -3.3433892 -4.0406616
- 25 1.0358313 -4.8989663 0 -3.3456079 -3.9093019
-Loop time of 12.2062 on 1 procs for 25 steps with 4000 atoms
+ 0 1.033 -4.8404387 0 -3.291326 -4.1332095
+ 5 1.0337247 -4.8402263 0 -3.290027 -4.1207962
+ 10 1.0355935 -4.8425889 0 -3.2895869 -4.0870158
+ 15 1.0376519 -4.84599 0 -3.2899013 -4.0278711
+ 20 1.0382257 -4.8478854 0 -3.2909361 -3.9368052
+ 25 1.0347886 -4.84473 0 -3.2929351 -3.8044469
+Loop time of 15.95 on 1 procs for 25 steps with 4000 atoms
-Performance: 353.920 tau/day, 2.048 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 270.846 tau/day, 1.567 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 12.202 | 12.202 | 12.202 | 0.0 | 99.96
+Pair | 15.946 | 15.946 | 15.946 | 0.0 | 99.97
Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.0015621 | 0.0015621 | 0.0015621 | 0.0 | 0.01
-Output | 0.00020814 | 0.00020814 | 0.00020814 | 0.0 | 0.00
-Modify | 0.0019698 | 0.0019698 | 0.0019698 | 0.0 | 0.02
-Other | | 0.0007734 | | | 0.01
+Comm | 0.0015042 | 0.0015042 | 0.0015042 | 0.0 | 0.01
+Output | 0.00013781 | 0.00013781 | 0.00013781 | 0.0 | 0.00
+Modify | 0.0017776 | 0.0017776 | 0.0017776 | 0.0 | 0.01
+Other | | 0.0006771 | | | 0.00
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -97,4 +97,4 @@ Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
-Total wall time: 0:00:13
+Total wall time: 0:00:16
diff --git a/examples/atm/log.23Aug18.atm.g++.4 b/examples/atm/log.27Aug18.g++.4
similarity index 69%
rename from examples/atm/log.23Aug18.atm.g++.4
rename to examples/atm/log.27Aug18.g++.4
index d5edfe32ba..d84f17ee2b 100644
--- a/examples/atm/log.23Aug18.atm.g++.4
+++ b/examples/atm/log.27Aug18.g++.4
@@ -26,7 +26,7 @@ Created orthogonal box = (0 0 0) to (18.3252 18.3252 18.3252)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 atoms
- Time spent = 0.000785112 secs
+ Time spent = 0.000900984 secs
pair_style hybrid/overlay lj/cut 4.5 atm 4.5 2.5
pair_coeff * * lj/cut 1.0 1.0
@@ -60,26 +60,26 @@ Neighbor list info ...
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.532 | 5.532 | 5.532 Mbytes
Step Temp E_pair E_mol TotEng Press
- 0 1.033 -4.8921547 0 -3.343042 -4.2340557
- 5 1.0337949 -4.8947881 0 -3.3444835 -4.2271456
- 10 1.0358286 -4.8973178 0 -3.3439632 -4.1935779
- 15 1.0381322 -4.9010593 0 -3.3442503 -4.134913
- 20 1.0390107 -4.9034854 0 -3.3453589 -4.0446162
- 25 1.0358988 -4.9010506 0 -3.3475908 -3.9133006
-Loop time of 3.20632 on 4 procs for 25 steps with 4000 atoms
+ 0 1.033 -4.8404387 0 -3.291326 -4.1332095
+ 5 1.0337247 -4.8402263 0 -3.290027 -4.1207962
+ 10 1.0355935 -4.8425889 0 -3.2895869 -4.0870158
+ 15 1.0376519 -4.84599 0 -3.2899013 -4.0278711
+ 20 1.0382257 -4.8478854 0 -3.2909361 -3.9368052
+ 25 1.0347886 -4.84473 0 -3.2929351 -3.8044469
+Loop time of 4.34636 on 4 procs for 25 steps with 4000 atoms
-Performance: 1347.340 tau/day, 7.797 timesteps/s
-100.0% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 993.935 tau/day, 5.752 timesteps/s
+99.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 3.1207 | 3.1553 | 3.1859 | 1.5 | 98.41
+Pair | 3.9977 | 4.1036 | 4.209 | 4.9 | 94.41
Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.019466 | 0.05009 | 0.084602 | 12.0 | 1.56
-Output | 7.1049e-05 | 8.2076e-05 | 0.00011325 | 0.0 | 0.00
-Modify | 0.00056338 | 0.00057292 | 0.00058413 | 0.0 | 0.02
-Other | | 0.0003092 | | | 0.01
+Comm | 0.13588 | 0.24134 | 0.34722 | 20.4 | 5.55
+Output | 0.00013757 | 0.00015104 | 0.00016761 | 0.0 | 0.00
+Modify | 0.00087953 | 0.00091547 | 0.00095582 | 0.0 | 0.02
+Other | | 0.0003656 | | | 0.01
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -97,4 +97,4 @@ Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
-Total wall time: 0:00:03
+Total wall time: 0:00:04
diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp
index b63407dfe9..a6e52faeba 100644
--- a/src/MANYBODY/pair_atm.cpp
+++ b/src/MANYBODY/pair_atm.cpp
@@ -98,9 +98,15 @@ void PairATM::compute(int eflag, int vflag)
numneigh = list->numneigh;
firstneigh = list->firstneigh;
- int count1 = 0;
- int count2 = 0;
- int count3 = 0;
+ // triple loop over local atoms and neighbors twice
+ // must compute each IJK triplet interaction exactly once
+ // by proc that owns the triplet atom with smallest x coord
+ // special logic to break ties if multiple atoms have same x or y coords
+ // inner two loops for jj=1,Jnum and kk=jj+1,Jnum insure
+ // the pair of other 2 non-minimum-x atoms is only considered once
+ // triplet geometry criteria for calculation:
+ // each pair distance <= cutoff
+ // produce of 3 pair distances <= cutoff_triple^3
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
@@ -112,12 +118,10 @@ void PairATM::compute(int eflag, int vflag)
jnum = numneigh[i];
jnumm1 = jnum - 1;
- // for (jj = 0; jj < jnumm1; jj++) {
- // replace with this line:
- for (jj = 0; jj < jnum; jj++) {
-
+ for (jj = 0; jj < jnumm1; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
+
rij[0] = x[j][0] - xi;
if (rij[0] < 0.0) continue;
rij[1] = x[j][1] - yi;
@@ -125,40 +129,33 @@ void PairATM::compute(int eflag, int vflag)
rij[2] = x[j][2] - zi;
if (rij[0] == 0.0 and rij[1] == 0.0 and rij[2] < 0.0) continue;
rij2 = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2];
- count1++;
if (rij2 > cutoff_squared) continue;
- count2++;
-
- //for (kk = jj+1; kk < jnum; kk++) {
- // replace with these two lines:
- for (kk = 0; kk < jnum; kk++) {
- if (kk == jj) continue;
+ for (kk = jj+1; kk < jnum; kk++) {
k = jlist[kk];
k &= NEIGHMASK;
- rjk[0] = x[k][0] - x[j][0];
- if (rjk[0] < 0.0) continue;
- rjk[1] = x[k][1] - x[j][1];
- if (rjk[0] == 0.0 and rjk[1] < 0.0) continue;
- rjk[2] = x[k][2] - x[j][2];
- if (rjk[0] == 0.0 and rjk[1] == 0.0 and rjk[2] < 0.0) continue;
- rjk2 = rjk[0]*rjk[0] + rjk[1]*rjk[1] + rjk[2]*rjk[2];
- if (rjk2 > cutoff_squared) continue;
-
rik[0] = x[k][0] - xi;
+ if (rik[0] < 0.0) continue;
rik[1] = x[k][1] - yi;
+ if (rik[0] == 0.0 and rik[1] < 0.0) continue;
rik[2] = x[k][2] - zi;
+ if (rik[0] == 0.0 and rik[1] == 0.0 and rik[2] < 0.0) continue;
rik2 = rik[0]*rik[0] + rik[1]*rik[1] + rik[2]*rik[2];
if (rik2 > cutoff_squared) continue;
+ rjk[0] = x[k][0] - x[j][0];
+ rjk[1] = x[k][1] - x[j][1];
+ rjk[2] = x[k][2] - x[j][2];
+ rjk2 = rjk[0]*rjk[0] + rjk[1]*rjk[1] + rjk[2]*rjk[2];
+ if (rjk2 > cutoff_squared) continue;
+
double r6 = rij2*rjk2*rik2;
if (r6 > cutoff_triple_sixth) continue;
nu_local = nu[type[i]][type[j]][type[k]];
if (nu_local == 0.0) continue;
- count3++;
interaction_ddd(nu_local,
r6,rij2,rik2,rjk2,rij,rik,rjk,fj,fk,eflag,evdwl);
@@ -177,15 +174,6 @@ void PairATM::compute(int eflag, int vflag)
}
}
- int count = count1;
- MPI_Allreduce(&count,&count1,1,MPI_INT,MPI_SUM,world);
- count = count2;
- MPI_Allreduce(&count,&count2,1,MPI_INT,MPI_SUM,world);
- count = count3;
- MPI_Allreduce(&count,&count3,1,MPI_INT,MPI_SUM,world);
- printf("FORCE %g %d %d %d\n",cutoff_squared,count1,count2,count3);
-
-
if (vflag_fdotr) virial_fdotr_compute();
}