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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12600 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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examples/kokkos/README
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The in.kokkos input script is a copy of the bench/in.lj script,
but can be run with the KOKKOS package,
To run it, you must first build LAMMPS with the KOKKOS package
installed, following the steps explained in Section 2.3.4 of
doc/Section_start.html. An overview of building and running LAMMPS
with the KOKKOS package, for different compute-node hardware on your
machine, is given in Section 5.8 of doc/Section_accelerate.html.
The example log files included in this directory are for a desktop box
with dual hex-core CPUs and 2 GPUs.
Two executables were built in the following manner:
make yes-kokkos
make g++ OMP=yes -> lmp_cpu
make cuda CUDA=yes -> lmp_cuda
Then the following runs were made. The "->" means that the run
produced log.lammps which was then copied to the named log file.
* MPI-only (non-KOKKOS) runs
lmp_cpu < in.kokkos -> log.kokkos.date.mpionly.1
mpirun -np 4 lmp_cpu < in.kokkos -> log.kokkos.date.mpionly.4
* OpenMP threaded runs on CPUs only
lmp_cpu -k on t 1 -sf kk < in.kokkos.half -> log.kokkos.date.cpu.1
lmp_cpu -k on t 4 -sf kk < in.kokkos -> log.kokkos.date.cpu.4
Note that in.kokkos.half was use for one of the runs, which uses the
package command to force the use of half neighbor lists which are
faster when running on just 1 thread.
* GPU runs on 1 or 2 GPUs
lmp_cuda -k on t 6 -sf kk < in.kokkos -> log.kokkos.date.gpu.1
mpirun -np 2 lmp_cuda -k on t 6 -sf kk < in.kokkos -> log.kokkos.date.gpu.2
Note that this is a very small problem (32K atoms) to run
on 1 or 2 GPUs.

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examples/kokkos/in.kokkos
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# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 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
run 100

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examples/kokkos/in.kokkos.half
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# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
package kokkos neigh half
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 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
run 100

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examples/kokkos/log.kokkos.1Feb14.cpu.1
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LAMMPS (27 May 2014)
KOKKOS mode is enabled (../lammps.cpp:468)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
package kokkos neigh half
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 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 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
run 100
Memory usage per processor = 7.79551 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
Loop time of 2.29105 on 1 procs (1 MPI x 1 OpenMP) for 100 steps with 32000 atoms
Pair time (%) = 1.82425 (79.6249)
Neigh time (%) = 0.338632 (14.7806)
Comm time (%) = 0.0366232 (1.59853)
Outpt time (%) = 0.000144005 (0.00628553)
Other time (%) = 0.0914049 (3.98965)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19657 ave 19657 max 19657 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.20283e+06 ave 1.20283e+06 max 1.20283e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1202833
Ave neighs/atom = 37.5885
Neighbor list builds = 5
Dangerous builds = 0

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examples/kokkos/log.kokkos.1Feb14.cpu.4
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LAMMPS (27 May 2014)
KOKKOS mode is enabled (../lammps.cpp:468)
using 4 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
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 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 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
run 100
Memory usage per processor = 13.2888 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
Loop time of 0.983697 on 4 procs (1 MPI x 4 OpenMP) for 100 steps with 32000 atoms
Pair time (%) = 0.767155 (77.9869)
Neigh time (%) = 0.14734 (14.9782)
Comm time (%) = 0.041466 (4.21532)
Outpt time (%) = 0.000172138 (0.0174991)
Other time (%) = 0.0275636 (2.80204)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19657 ave 19657 max 19657 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
FullNghs: 2.40567e+06 ave 2.40567e+06 max 2.40567e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2405666
Ave neighs/atom = 75.1771
Neighbor list builds = 5
Dangerous builds = 0

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examples/kokkos/log.kokkos.1Feb14.gpu.1
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LAMMPS (27 May 2014)
KOKKOS mode is enabled (../lammps.cpp:468)
using 6 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
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 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 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
run 100
Memory usage per processor = 16.9509 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
Loop time of 0.57192 on 6 procs (1 MPI x 6 OpenMP) for 100 steps with 32000 atoms
Pair time (%) = 0.205416 (35.917)
Neigh time (%) = 0.112468 (19.665)
Comm time (%) = 0.174223 (30.4629)
Outpt time (%) = 0.000159025 (0.0278055)
Other time (%) = 0.0796535 (13.9274)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19657 ave 19657 max 19657 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
FullNghs: 2.40567e+06 ave 2.40567e+06 max 2.40567e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2405666
Ave neighs/atom = 75.1771
Neighbor list builds = 5
Dangerous builds = 0

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examples/kokkos/log.kokkos.1Feb14.gpu.2
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LAMMPS (27 May 2014)
KOKKOS mode is enabled (../lammps.cpp:468)
using 6 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
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 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
1 by 1 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 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
run 100
Memory usage per processor = 8.95027 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
Loop time of 0.689608 on 12 procs (2 MPI x 6 OpenMP) for 100 steps with 32000 atoms
Pair time (%) = 0.210953 (30.5903)
Neigh time (%) = 0.122991 (17.8349)
Comm time (%) = 0.25264 (36.6353)
Outpt time (%) = 0.000259042 (0.0375636)
Other time (%) = 0.102765 (14.9019)
Nlocal: 16000 ave 16001 max 15999 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 13632.5 ave 13635 max 13630 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 0
FullNghs: 1.20283e+06 ave 1.20347e+06 max 1.2022e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 2405666
Ave neighs/atom = 75.1771
Neighbor list builds = 5
Dangerous builds = 0

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examples/kokkos/log.kokkos.1Feb14.mpionly.1
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LAMMPS (27 May 2014)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
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 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 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
run 100
Memory usage per processor = 8.21387 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
Loop time of 2.57975 on 1 procs (1 MPI x 1 OpenMP) for 100 steps with 32000 atoms
Pair time (%) = 2.20959 (85.6512)
Neigh time (%) = 0.269136 (10.4326)
Comm time (%) = 0.0252256 (0.977833)
Outpt time (%) = 0.000126123 (0.00488898)
Other time (%) = 0.0756752 (2.93343)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19657 ave 19657 max 19657 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.20283e+06 ave 1.20283e+06 max 1.20283e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1202833
Ave neighs/atom = 37.5885
Neighbor list builds = 5
Dangerous builds = 0

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examples/kokkos/log.kokkos.1Feb14.mpionly.4
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LAMMPS (27 May 2014)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
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 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 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
run 100
Memory usage per processor = 4.09506 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
Loop time of 0.709072 on 4 procs (4 MPI x 1 OpenMP) for 100 steps with 32000 atoms
Pair time (%) = 0.574495 (81.0206)
Neigh time (%) = 0.0709588 (10.0073)
Comm time (%) = 0.0474771 (6.69567)
Outpt time (%) = 6.62804e-05 (0.00934748)
Other time (%) = 0.0160753 (2.26708)
Nlocal: 8000 ave 8037 max 7964 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 9007.5 ave 9050 max 8968 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 300708 ave 305113 max 297203 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Total # of neighbors = 1202833
Ave neighs/atom = 37.5885
Neighbor list builds = 5
Dangerous builds = 0