git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7497 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
77
examples/gpu/log.gpu.melt.2.5.9Jan12.linux.1
Normal file
77
examples/gpu/log.gpu.melt.2.5.9Jan12.linux.1
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@ -0,0 +1,77 @@
|
||||
LAMMPS (10 Jan 2012)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
newton off
|
||||
package gpu force/neigh 0 1 1
|
||||
|
||||
variable x index 2
|
||||
variable y index 2
|
||||
variable z index 2
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*2
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*2
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*2
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 40 0 ${yy} 0 ${zz}
|
||||
region box block 0 40 0 40 0 ${zz}
|
||||
region box block 0 40 0 40 0 40
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 256000 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut/gpu 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
Memory usage per processor = 46.8382 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733685 0 -4.6133769 -5.0196738
|
||||
100 0.75865618 -5.760326 0 -4.6223462 0.19586078
|
||||
200 0.75643081 -5.7572862 0 -4.6226445 0.22641252
|
||||
300 0.74927357 -5.7463992 0 -4.6224932 0.2973801
|
||||
400 0.7404924 -5.7329247 0 -4.6221905 0.37767073
|
||||
500 0.73092032 -5.7182616 0 -4.6218854 0.46900679
|
||||
600 0.72315678 -5.706314 0 -4.621583 0.5348031
|
||||
700 0.71597165 -5.6952207 0 -4.6212675 0.59549602
|
||||
800 0.71194748 -5.6889042 0 -4.6209871 0.63784817
|
||||
900 0.70596464 -5.6796285 0 -4.6206857 0.68573109
|
||||
1000 0.70323336 -5.67534 0 -4.6204941 0.7069076
|
||||
Loop time of 20.1772 on 1 procs for 1000 steps with 256000 atoms
|
||||
|
||||
Pair time (%) = 12.8361 (63.6167)
|
||||
Neigh time (%) = 7.34329e-05 (0.00036394)
|
||||
Comm time (%) = 1.08434 (5.3741)
|
||||
Outpt time (%) = 0.0102942 (0.051019)
|
||||
Other time (%) = 6.24641 (30.9578)
|
||||
|
||||
Nlocal: 256000 ave 256000 max 256000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 69905 ave 69905 max 69905 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 50
|
||||
Dangerous builds = 0
|
||||
77
examples/gpu/log.gpu.melt.2.5.9Jan12.linux.4
Normal file
77
examples/gpu/log.gpu.melt.2.5.9Jan12.linux.4
Normal file
@ -0,0 +1,77 @@
|
||||
LAMMPS (10 Jan 2012)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
newton off
|
||||
package gpu force/neigh 0 1 1
|
||||
|
||||
variable x index 2
|
||||
variable y index 2
|
||||
variable z index 2
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*2
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*2
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*2
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 40 0 ${yy} 0 ${zz}
|
||||
region box block 0 40 0 40 0 ${zz}
|
||||
region box block 0 40 0 40 0 40
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 256000 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut/gpu 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
Memory usage per processor = 14.5128 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733685 0 -4.6133769 -5.0196738
|
||||
100 0.75865619 -5.7603258 0 -4.622346 0.19586113
|
||||
200 0.75643076 -5.7572857 0 -4.6226439 0.22641355
|
||||
300 0.74927365 -5.7463989 0 -4.6224928 0.29738053
|
||||
400 0.74049513 -5.7329265 0 -4.6221881 0.37765479
|
||||
500 0.73092165 -5.7182628 0 -4.6218846 0.46899675
|
||||
600 0.72307341 -5.7061845 0 -4.6215786 0.53536825
|
||||
700 0.71593631 -5.6951696 0 -4.6212694 0.59644919
|
||||
800 0.71106107 -5.6875486 0 -4.6209611 0.6450072
|
||||
900 0.70789378 -5.6825117 0 -4.6206752 0.67079907
|
||||
1000 0.70324302 -5.6753075 0 -4.6204471 0.71004301
|
||||
Loop time of 8.45152 on 4 procs for 1000 steps with 256000 atoms
|
||||
|
||||
Pair time (%) = 5.1208 (60.5903)
|
||||
Neigh time (%) = 5.52535e-05 (0.00065377)
|
||||
Comm time (%) = 1.60643 (19.0076)
|
||||
Outpt time (%) = 0.032979 (0.390213)
|
||||
Other time (%) = 1.69126 (20.0113)
|
||||
|
||||
Nlocal: 64000 ave 64090 max 63900 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
Nghost: 30521 ave 30604 max 30461 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 50
|
||||
Dangerous builds = 0
|
||||
77
examples/gpu/log.gpu.melt.5.0.9Jan12.linux.1
Normal file
77
examples/gpu/log.gpu.melt.5.0.9Jan12.linux.1
Normal file
@ -0,0 +1,77 @@
|
||||
LAMMPS (10 Jan 2012)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
newton off
|
||||
package gpu force/neigh 0 1 1 threads_per_atom 8
|
||||
|
||||
variable x index 2
|
||||
variable y index 2
|
||||
variable z index 2
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*2
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*2
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*2
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 40 0 ${yy} 0 ${zz}
|
||||
region box block 0 40 0 40 0 ${zz}
|
||||
region box block 0 40 0 40 0 40
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 256000 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut/gpu 5.0
|
||||
pair_coeff 1 1 1.0 1.0 5.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
Memory usage per processor = 58.5637 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -7.1616924 0 -5.0017009 -5.6743468
|
||||
100 0.7599844 -6.1430228 0 -5.0030506 -0.43702259
|
||||
200 0.75772866 -6.1397323 0 -5.0031437 -0.40563905
|
||||
300 0.7502998 -6.1286575 0 -5.0032122 -0.33104598
|
||||
400 0.73999173 -6.1132483 0 -5.003265 -0.24002836
|
||||
500 0.73224837 -6.101694 0 -5.0033257 -0.16523366
|
||||
600 0.72448052 -6.0900828 0 -5.0033662 -0.099466624
|
||||
700 0.71878723 -6.0815904 0 -5.0034138 -0.044361885
|
||||
800 0.71444388 -6.0751019 0 -5.0034403 -0.0083893389
|
||||
900 0.70949961 -6.0676978 0 -5.0034525 0.032534654
|
||||
1000 0.70480647 -6.0606748 0 -5.0034693 0.067358025
|
||||
Loop time of 43.8997 on 1 procs for 1000 steps with 256000 atoms
|
||||
|
||||
Pair time (%) = 35.1574 (80.0858)
|
||||
Neigh time (%) = 8.29697e-05 (0.000188998)
|
||||
Comm time (%) = 1.61756 (3.68467)
|
||||
Outpt time (%) = 0.011915 (0.0271413)
|
||||
Other time (%) = 7.1127 (16.2022)
|
||||
|
||||
Nlocal: 256000 ave 256000 max 256000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 141753 ave 141753 max 141753 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 50
|
||||
Dangerous builds = 0
|
||||
77
examples/gpu/log.gpu.melt.5.0.9Jan12.linux.4
Normal file
77
examples/gpu/log.gpu.melt.5.0.9Jan12.linux.4
Normal file
@ -0,0 +1,77 @@
|
||||
LAMMPS (10 Jan 2012)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
newton off
|
||||
package gpu force/neigh 0 1 1 threads_per_atom 8
|
||||
|
||||
variable x index 2
|
||||
variable y index 2
|
||||
variable z index 2
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*2
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*2
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*2
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 40 0 ${yy} 0 ${zz}
|
||||
region box block 0 40 0 40 0 ${zz}
|
||||
region box block 0 40 0 40 0 40
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 256000 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut/gpu 5.0
|
||||
pair_coeff 1 1 1.0 1.0 5.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
Memory usage per processor = 20.3741 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -7.1616924 0 -5.0017009 -5.6743468
|
||||
100 0.75998442 -6.1430228 0 -5.0030506 -0.4370226
|
||||
200 0.75772866 -6.1397323 0 -5.0031437 -0.40563885
|
||||
300 0.75029998 -6.1286577 0 -5.0032121 -0.33104745
|
||||
400 0.73999268 -6.1132497 0 -5.003265 -0.24002923
|
||||
500 0.73223459 -6.1016733 0 -5.0033257 -0.16512674
|
||||
600 0.72450196 -6.0901153 0 -5.0033666 -0.099408327
|
||||
700 0.71915302 -6.0821406 0 -5.0034153 -0.045922554
|
||||
800 0.71398822 -6.0744174 0 -5.0034392 -0.0064880998
|
||||
900 0.70918338 -6.0672194 0 -5.0034485 0.032885247
|
||||
1000 0.70513415 -6.0611556 0 -5.0034585 0.063293271
|
||||
Loop time of 20.8409 on 4 procs for 1000 steps with 256000 atoms
|
||||
|
||||
Pair time (%) = 14.4203 (69.1925)
|
||||
Neigh time (%) = 5.91874e-05 (0.000283997)
|
||||
Comm time (%) = 4.66054 (22.3625)
|
||||
Outpt time (%) = 0.0455028 (0.218335)
|
||||
Other time (%) = 1.71444 (8.22633)
|
||||
|
||||
Nlocal: 64000 ave 64103 max 63848 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
Nghost: 64409.2 ave 64479 max 64338 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 50
|
||||
Dangerous builds = 0
|
||||
74
examples/gpu/log.gpu.phosphate.9Jan12.linux.1
Normal file
74
examples/gpu/log.gpu.phosphate.9Jan12.linux.1
Normal file
@ -0,0 +1,74 @@
|
||||
LAMMPS (10 Jan 2012)
|
||||
# GI-System
|
||||
|
||||
units metal
|
||||
newton off
|
||||
package gpu force/neigh 0 1 1
|
||||
|
||||
atom_style charge
|
||||
read_data data.phosphate
|
||||
orthogonal box = (33.0201 33.0201 33.0201) to (86.9799 86.9799 86.9799)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
10950 atoms
|
||||
10950 velocities
|
||||
|
||||
replicate 3 3 3
|
||||
orthogonal box = (33.0201 33.0201 33.0201) to (194.899 194.899 194.899)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
295650 atoms
|
||||
|
||||
pair_style lj/cut/coul/long/gpu 15.0
|
||||
|
||||
pair_coeff 1 1 0.0 0.29
|
||||
pair_coeff 1 2 0.0 0.29
|
||||
pair_coeff 1 3 0.000668 2.5738064
|
||||
pair_coeff 2 2 0.0 0.29
|
||||
pair_coeff 2 3 0.004251 1.91988674
|
||||
pair_coeff 3 3 0.012185 2.91706967
|
||||
|
||||
kspace_style pppm/gpu 1e-5
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
thermo 100
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all npt temp 400 400 0.01 iso 1000.0 1000.0 1.0
|
||||
run 200
|
||||
PPPM initialization ...
|
||||
G vector = 0.210111
|
||||
grid = 108 108 108
|
||||
stencil order = 5
|
||||
RMS precision = 8.76251e-06
|
||||
using double precision FFTs
|
||||
brick FFT buffer size/proc = 1520875 1259712 158700
|
||||
Memory usage per processor = 266.913 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 400.30257 -2381941.5 0 -2366643.7 -449.93537 4242016.4
|
||||
100 411.69679 -2392428.5 0 -2376695.2 7046.7022 4308883.6
|
||||
200 401.28406 -2394152.4 0 -2378817.1 3243.2514 4334284.6
|
||||
Loop time of 174.691 on 1 procs for 200 steps with 295650 atoms
|
||||
|
||||
Pair time (%) = 12.053 (6.89962)
|
||||
Kspce time (%) = 80.9936 (46.3638)
|
||||
Neigh time (%) = 0.013356 (0.00764546)
|
||||
Comm time (%) = 0.347907 (0.199155)
|
||||
Outpt time (%) = 0.00172615 (0.000988114)
|
||||
Other time (%) = 81.2818 (46.5288)
|
||||
|
||||
FFT time (% of Kspce) = 56.1923 (69.3786)
|
||||
FFT Gflps 3d (1d only) = 1.25956 2.99555
|
||||
|
||||
Nlocal: 295650 ave 295650 max 295650 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 226982 ave 226982 max 226982 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 0
|
||||
unfix 1
|
||||
74
examples/gpu/log.gpu.phosphate.9Jan12.linux.4
Normal file
74
examples/gpu/log.gpu.phosphate.9Jan12.linux.4
Normal file
@ -0,0 +1,74 @@
|
||||
LAMMPS (10 Jan 2012)
|
||||
# GI-System
|
||||
|
||||
units metal
|
||||
newton off
|
||||
package gpu force/neigh 0 1 1
|
||||
|
||||
atom_style charge
|
||||
read_data data.phosphate
|
||||
orthogonal box = (33.0201 33.0201 33.0201) to (86.9799 86.9799 86.9799)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
10950 atoms
|
||||
10950 velocities
|
||||
|
||||
replicate 3 3 3
|
||||
orthogonal box = (33.0201 33.0201 33.0201) to (194.899 194.899 194.899)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
295650 atoms
|
||||
|
||||
pair_style lj/cut/coul/long/gpu 15.0
|
||||
|
||||
pair_coeff 1 1 0.0 0.29
|
||||
pair_coeff 1 2 0.0 0.29
|
||||
pair_coeff 1 3 0.000668 2.5738064
|
||||
pair_coeff 2 2 0.0 0.29
|
||||
pair_coeff 2 3 0.004251 1.91988674
|
||||
pair_coeff 3 3 0.012185 2.91706967
|
||||
|
||||
kspace_style pppm/gpu 1e-5
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
thermo 100
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all npt temp 400 400 0.01 iso 1000.0 1000.0 1.0
|
||||
run 200
|
||||
PPPM initialization ...
|
||||
G vector = 0.210111
|
||||
grid = 108 108 108
|
||||
stencil order = 5
|
||||
RMS precision = 8.76251e-06
|
||||
using double precision FFTs
|
||||
brick FFT buffer size/proc = 427915 314928 84180
|
||||
Memory usage per processor = 80.0627 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 400.30257 -2381941.5 0 -2366643.7 -449.93522 4242016.4
|
||||
100 411.69683 -2392428.5 0 -2376695.2 7046.7136 4308883.6
|
||||
200 401.28395 -2394152.4 0 -2378817.1 3243.2713 4334284.6
|
||||
Loop time of 62.4573 on 4 procs for 200 steps with 295650 atoms
|
||||
|
||||
Pair time (%) = 5.04743 (8.08141)
|
||||
Kspce time (%) = 35.3904 (56.6633)
|
||||
Neigh time (%) = 0.00620693 (0.00993788)
|
||||
Comm time (%) = 0.473388 (0.757939)
|
||||
Outpt time (%) = 0.000503302 (0.000805833)
|
||||
Other time (%) = 21.5394 (34.4866)
|
||||
|
||||
FFT time (% of Kspce) = 22.1085 (62.4703)
|
||||
FFT Gflps 3d (1d only) = 3.20138 11.8522
|
||||
|
||||
Nlocal: 73912.5 ave 74223 max 73638 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
Nghost: 105257 ave 105797 max 104698 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 0
|
||||
unfix 1
|
||||
121
examples/gpu/log.gpu.rhodo.9Jan12.linux.1
Normal file
121
examples/gpu/log.gpu.rhodo.9Jan12.linux.1
Normal file
@ -0,0 +1,121 @@
|
||||
LAMMPS (10 Jan 2012)
|
||||
# Rhodopsin model
|
||||
|
||||
newton off
|
||||
package gpu force/neigh 0 1 1
|
||||
|
||||
variable x index 2
|
||||
variable y index 2
|
||||
variable z index 2
|
||||
|
||||
units real
|
||||
neigh_modify delay 5 every 1
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
pair_style lj/charmm/coul/long/gpu 8.0 10.0
|
||||
pair_modify mix arithmetic
|
||||
kspace_style pppm/gpu 1e-4
|
||||
|
||||
read_data data.rhodo
|
||||
4 = max bonds/atom
|
||||
18 = max angles/atom
|
||||
40 = max dihedrals/atom
|
||||
4 = max impropers/atom
|
||||
orthogonal box = (-27.5 -38.5 -36.2676) to (27.5 38.5 36.2645)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
32000 atoms
|
||||
32000 velocities
|
||||
27723 bonds
|
||||
40467 angles
|
||||
56829 dihedrals
|
||||
1034 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
12 = max # of 1-3 neighbors
|
||||
24 = max # of 1-4 neighbors
|
||||
26 = max # of special neighbors
|
||||
|
||||
replicate $x $y $z
|
||||
replicate 2 $y $z
|
||||
replicate 2 2 $z
|
||||
replicate 2 2 2
|
||||
orthogonal box = (-27.5 -38.5 -36.2676) to (82.5 115.5 108.797)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
256000 atoms
|
||||
221784 bonds
|
||||
323736 angles
|
||||
454632 dihedrals
|
||||
8272 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
12 = max # of 1-3 neighbors
|
||||
24 = max # of 1-4 neighbors
|
||||
26 = max # of special neighbors
|
||||
|
||||
fix 1 all shake 0.0001 5 0 m 1.0 a 232
|
||||
12936 = # of size 2 clusters
|
||||
29064 = # of size 3 clusters
|
||||
5976 = # of size 4 clusters
|
||||
33864 = # of frozen angles
|
||||
fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
|
||||
|
||||
special_bonds charmm
|
||||
|
||||
thermo 100
|
||||
thermo_style multi
|
||||
timestep 2.0
|
||||
|
||||
run 200
|
||||
PPPM initialization ...
|
||||
G vector = 0.245952
|
||||
grid = 48 64 60
|
||||
stencil order = 5
|
||||
RMS precision = 8.7421e-05
|
||||
using double precision FFTs
|
||||
brick FFT buffer size/proc = 237705 184320 40365
|
||||
Memory usage per processor = 757.714 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = 157025.0401 KinEng = 172792.6155 Temp = 301.1796
|
||||
PotEng = -15767.5754 E_bond = 28164.9917 E_angle = 117224.0742
|
||||
E_dihed = 61174.8491 E_impro = 3752.0273 E_vdwl = 10108.6324
|
||||
E_coul = 1894235.3907 E_long = -2130427.5409 Press = 9562.2425
|
||||
Volume = 2457390.7959
|
||||
---------------- Step 100 ----- CPU = 36.8336 (sec) ----------------
|
||||
TotEng = -233301.4802 KinEng = 123222.6026 Temp = 214.7785
|
||||
PotEng = -356524.0828 E_bond = 13098.4631 E_angle = 56766.9481
|
||||
E_dihed = 45556.8121 E_impro = 1313.9420 E_vdwl = -40863.8988
|
||||
E_coul = 1705023.3608 E_long = -2137419.7102 Press = -1634.3633
|
||||
Volume = 2522232.7977
|
||||
---------------- Step 200 ----- CPU = 72.2618 (sec) ----------------
|
||||
TotEng = -308340.6857 KinEng = 108944.3257 Temp = 189.8913
|
||||
PotEng = -417285.0114 E_bond = 9579.0680 E_angle = 47373.8383
|
||||
E_dihed = 39847.6180 E_impro = 967.6100 E_vdwl = -23634.8218
|
||||
E_coul = 1646565.2623 E_long = -2137983.5863 Press = -1185.9778
|
||||
Volume = 2554683.5150
|
||||
Loop time of 72.2618 on 1 procs for 200 steps with 256000 atoms
|
||||
|
||||
Pair time (%) = 10.1078 (13.9878)
|
||||
Bond time (%) = 29.9182 (41.4025)
|
||||
Kspce time (%) = 7.29844 (10.1)
|
||||
Neigh time (%) = 1.64225 (2.27264)
|
||||
Comm time (%) = 0.614946 (0.850997)
|
||||
Outpt time (%) = 0.00137877 (0.00190803)
|
||||
Other time (%) = 22.6787 (31.3841)
|
||||
|
||||
FFT time (% of Kspce) = 5.23688 (71.7535)
|
||||
FFT Gflps 3d (1d only) = 1.70695 3.00498
|
||||
|
||||
Nlocal: 256000 ave 256000 max 256000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 161678 ave 161678 max 161678 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Ave special neighs/atom = 7.43187
|
||||
Neighbor list builds = 31
|
||||
Dangerous builds = 12
|
||||
121
examples/gpu/log.gpu.rhodo.9Jan12.linux.4
Normal file
121
examples/gpu/log.gpu.rhodo.9Jan12.linux.4
Normal file
@ -0,0 +1,121 @@
|
||||
LAMMPS (10 Jan 2012)
|
||||
# Rhodopsin model
|
||||
|
||||
newton off
|
||||
package gpu force/neigh 0 1 1
|
||||
|
||||
variable x index 2
|
||||
variable y index 2
|
||||
variable z index 2
|
||||
|
||||
units real
|
||||
neigh_modify delay 5 every 1
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
pair_style lj/charmm/coul/long/gpu 8.0 10.0
|
||||
pair_modify mix arithmetic
|
||||
kspace_style pppm/gpu 1e-4
|
||||
|
||||
read_data data.rhodo
|
||||
4 = max bonds/atom
|
||||
18 = max angles/atom
|
||||
40 = max dihedrals/atom
|
||||
4 = max impropers/atom
|
||||
orthogonal box = (-27.5 -38.5 -36.2676) to (27.5 38.5 36.2645)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
32000 atoms
|
||||
32000 velocities
|
||||
27723 bonds
|
||||
40467 angles
|
||||
56829 dihedrals
|
||||
1034 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
12 = max # of 1-3 neighbors
|
||||
24 = max # of 1-4 neighbors
|
||||
26 = max # of special neighbors
|
||||
|
||||
replicate $x $y $z
|
||||
replicate 2 $y $z
|
||||
replicate 2 2 $z
|
||||
replicate 2 2 2
|
||||
orthogonal box = (-27.5 -38.5 -36.2676) to (82.5 115.5 108.797)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
256000 atoms
|
||||
221784 bonds
|
||||
323736 angles
|
||||
454632 dihedrals
|
||||
8272 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
12 = max # of 1-3 neighbors
|
||||
24 = max # of 1-4 neighbors
|
||||
26 = max # of special neighbors
|
||||
|
||||
fix 1 all shake 0.0001 5 0 m 1.0 a 232
|
||||
12936 = # of size 2 clusters
|
||||
29064 = # of size 3 clusters
|
||||
5976 = # of size 4 clusters
|
||||
33864 = # of frozen angles
|
||||
fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
|
||||
|
||||
special_bonds charmm
|
||||
|
||||
thermo 100
|
||||
thermo_style multi
|
||||
timestep 2.0
|
||||
|
||||
run 200
|
||||
PPPM initialization ...
|
||||
G vector = 0.245952
|
||||
grid = 48 64 60
|
||||
stencil order = 5
|
||||
RMS precision = 8.7421e-05
|
||||
using double precision FFTs
|
||||
brick FFT buffer size/proc = 68635 46080 17649
|
||||
Memory usage per processor = 249.821 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = 157025.0390 KinEng = 172792.6155 Temp = 301.1796
|
||||
PotEng = -15767.5765 E_bond = 28164.9917 E_angle = 117224.0742
|
||||
E_dihed = 61174.8491 E_impro = 3752.0273 E_vdwl = 10108.6324
|
||||
E_coul = 1894235.3896 E_long = -2130427.5409 Press = 9562.2425
|
||||
Volume = 2457390.7959
|
||||
---------------- Step 100 ----- CPU = 12.2605 (sec) ----------------
|
||||
TotEng = -233301.4713 KinEng = 123222.6058 Temp = 214.7785
|
||||
PotEng = -356524.0771 E_bond = 13098.4614 E_angle = 56766.9463
|
||||
E_dihed = 45556.8096 E_impro = 1313.9414 E_vdwl = -40863.8548
|
||||
E_coul = 1705023.3285 E_long = -2137419.7095 Press = -1634.3527
|
||||
Volume = 2522232.7976
|
||||
---------------- Step 200 ----- CPU = 23.7724 (sec) ----------------
|
||||
TotEng = -308340.7251 KinEng = 108941.9220 Temp = 189.8871
|
||||
PotEng = -417282.6471 E_bond = 9579.0415 E_angle = 47373.9551
|
||||
E_dihed = 39847.5174 E_impro = 967.5823 E_vdwl = -23636.2292
|
||||
E_coul = 1646568.9776 E_long = -2137983.4917 Press = -1186.1181
|
||||
Volume = 2554683.4248
|
||||
Loop time of 23.7725 on 4 procs for 200 steps with 256000 atoms
|
||||
|
||||
Pair time (%) = 4.55113 (19.1446)
|
||||
Bond time (%) = 7.43137 (31.2604)
|
||||
Kspce time (%) = 3.8699 (16.2789)
|
||||
Neigh time (%) = 0.51208 (2.15409)
|
||||
Comm time (%) = 0.544156 (2.28902)
|
||||
Outpt time (%) = 0.000452995 (0.00190555)
|
||||
Other time (%) = 6.86337 (28.8711)
|
||||
|
||||
FFT time (% of Kspce) = 1.94085 (50.1524)
|
||||
FFT Gflps 3d (1d only) = 4.60577 11.8123
|
||||
|
||||
Nlocal: 64000 ave 64003 max 63997 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Nghost: 70640.8 ave 70645 max 70636 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Ave special neighs/atom = 7.43187
|
||||
Neighbor list builds = 31
|
||||
Dangerous builds = 12
|
||||
Reference in New Issue
Block a user