forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12042 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
3cfef73208
commit
30361f0dfa
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@ -73,6 +73,7 @@ gpu: use of the GPU package for GPU acceleration
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hugoniostat: Hugoniostat shock dynamics
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indent: spherical indenter into a 2d solid
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kim: use of potentials in Knowledge Base for Interatomic Models (KIM)
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kokkos: use of the KOKKOS package for multi-threading and GPU acceleration
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meam: MEAM test for SiC and shear (same as shear examples)
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melt: rapid melt of 3d LJ system
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micelle: self-assembly of small lipid-like molecules into 2d bilayers
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@ -0,0 +1,35 @@
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These are input scripts designed for use with the GPU package.
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To run them, you must first build LAMMPS with the GPU package
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installed, following the steps explained in Section 2.3 of
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doc/Section_start.html and lib/gpu/README. An overview of building
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and running LAMMPS with the GPU package is given in Section 5.6 of
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doc/Section_accelerate.html. Note that you can choose the precision
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at which computations are performed on the GPU in the build process.
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Note that lines such as this in each of the input scripts:
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package gpu force/neigh 0 1 1
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are set for running on a compute node with 2 GPUs. If you
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have a single GPU, you should comment out the line, since
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the default is 1 GPU per compute node.
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The scripts can be run in the usual manner:
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lmp_g++ < in.gpu.melt.2.5
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lmp_g++ < in.gpu.melt.5.0
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lmp_g++ < in.gpu.phosphate
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lmp_g++ < in.gpu.rhodo
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mpirun -np 4 lmp_g++ < in.gpu.melt.2.5
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mpirun -np 4 lmp_g++ < in.gpu.melt.5.0
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mpirun -np 4 lmp_g++ < in.gpu.phosphate
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mpirun -np 4 lmp_g++ < in.gpu.rhodo
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The first set of commmands will run a single MPI task using a single
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GPU (even if you have 2 GPUs).
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The second set of commands will run 4 MPI tasks, with 2 MPI tasks per
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GPU (if you have 2 GPUs), or 4 MPI tasks per GPU (if you have a single
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GPU).
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@ -0,0 +1,42 @@
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The in.kokkos input script is a copy of the bench/in.lj script,
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but can be run with the KOKKOS package,
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To run it, you must first build LAMMPS with the KOKKOS package
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installed, following the steps explained in Section 2.3.4 of
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doc/Section_start.html. An overview of building and running LAMMPS
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with the KOKKOS package, for different compute-node hardware on your
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machine, is given in Section 5.8 of doc/Section_accelerate.html.
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The example log files included in this directory are for a desktop box
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with dual hex-core CPUs and 2 GPUs.
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Two executables were built in the following manner:
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make yes-kokkos
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make g++ OMP=yes -> lmp_cpu
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make cuda CUDA=yes -> lmp_cuda
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Then the following runs were made. The "->" means that the run
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produced log.lammps which was then copied to the named log file.
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* MPI-only runs
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lmp_cpu -k off < in.kokkos -> log.kokkos.date.mpionly.1
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mpirun -np 4 lmp_cpu -k off < in.kokkos -> log.kokkos.date.mpionly.4
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* OpenMP threaded runs on CPUs only
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lmp_cpu -k on t 1 -sf kk < in.kokkos.half -> log.kokkos.date.cpu.1
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lmp_cpu -k on t 4 -sf kk < in.kokkos -> log.kokkos.date.cpu.4
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Note that in.kokkos.half was use for one of the runs, which uses the
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package command to force the use of half neighbor lists which are
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faster when running on just 1 thread.
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* GPU runs on 1 or 2 GPUs
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lmp_cuda -k on t 6 -sf kk < in.kokkos -> log.kokkos.date.gpu.1
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mpirun -np 2 lmp_cuda -k on t 6 -sf kk < in.kokkos -> log.kokkos.date.gpu.2
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Note that this is a very small problem (32K atoms) to run
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on 1 or 2 GPUs.
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@ -0,0 +1,30 @@
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# 3d Lennard-Jones melt
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variable x index 1
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variable y index 1
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variable z index 1
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variable xx equal 20*$x
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variable yy equal 20*$y
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variable zz equal 20*$z
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units lj
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atom_style atomic
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lattice fcc 0.8442
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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fix 1 all nve
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run 100
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@ -0,0 +1,32 @@
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# 3d Lennard-Jones melt
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variable x index 1
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variable y index 1
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variable z index 1
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variable xx equal 20*$x
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variable yy equal 20*$y
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variable zz equal 20*$z
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package kokkos neigh half
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units lj
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atom_style atomic
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lattice fcc 0.8442
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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fix 1 all nve
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run 100
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@ -0,0 +1,68 @@
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LAMMPS (27 May 2014)
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KOKKOS mode is enabled (../lammps.cpp:468)
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using 1 OpenMP thread(s) per MPI task
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# 3d Lennard-Jones melt
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variable x index 1
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variable y index 1
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variable z index 1
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variable xx equal 20*$x
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variable xx equal 20*1
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variable yy equal 20*$y
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variable yy equal 20*1
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variable zz equal 20*$z
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variable zz equal 20*1
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package kokkos neigh half
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units lj
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atom_style atomic
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lattice fcc 0.8442
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Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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region box block 0 20 0 ${yy} 0 ${zz}
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region box block 0 20 0 20 0 ${zz}
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region box block 0 20 0 20 0 20
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create_box 1 box
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Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 32000 atoms
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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fix 1 all nve
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run 100
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Memory usage per processor = 7.79551 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.44 -6.7733681 0 -4.6134356 -5.0197073
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100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
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Loop time of 2.29105 on 1 procs (1 MPI x 1 OpenMP) for 100 steps with 32000 atoms
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Pair time (%) = 1.82425 (79.6249)
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Neigh time (%) = 0.338632 (14.7806)
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Comm time (%) = 0.0366232 (1.59853)
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Outpt time (%) = 0.000144005 (0.00628553)
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Other time (%) = 0.0914049 (3.98965)
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Nlocal: 32000 ave 32000 max 32000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 19657 ave 19657 max 19657 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 1.20283e+06 ave 1.20283e+06 max 1.20283e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 1202833
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Ave neighs/atom = 37.5885
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Neighbor list builds = 5
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Dangerous builds = 0
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@ -0,0 +1,68 @@
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LAMMPS (27 May 2014)
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KOKKOS mode is enabled (../lammps.cpp:468)
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using 4 OpenMP thread(s) per MPI task
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# 3d Lennard-Jones melt
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variable x index 1
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variable y index 1
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variable z index 1
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variable xx equal 20*$x
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variable xx equal 20*1
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variable yy equal 20*$y
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variable yy equal 20*1
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variable zz equal 20*$z
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variable zz equal 20*1
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units lj
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atom_style atomic
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lattice fcc 0.8442
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Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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region box block 0 20 0 ${yy} 0 ${zz}
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region box block 0 20 0 20 0 ${zz}
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region box block 0 20 0 20 0 20
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create_box 1 box
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Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 32000 atoms
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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fix 1 all nve
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run 100
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Memory usage per processor = 13.2888 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.44 -6.7733681 0 -4.6134356 -5.0197073
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100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
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Loop time of 0.983697 on 4 procs (1 MPI x 4 OpenMP) for 100 steps with 32000 atoms
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Pair time (%) = 0.767155 (77.9869)
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Neigh time (%) = 0.14734 (14.9782)
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Comm time (%) = 0.041466 (4.21532)
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Outpt time (%) = 0.000172138 (0.0174991)
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Other time (%) = 0.0275636 (2.80204)
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Nlocal: 32000 ave 32000 max 32000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 19657 ave 19657 max 19657 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 2.40567e+06 ave 2.40567e+06 max 2.40567e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 2405666
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Ave neighs/atom = 75.1771
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Neighbor list builds = 5
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Dangerous builds = 0
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@ -0,0 +1,68 @@
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LAMMPS (27 May 2014)
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KOKKOS mode is enabled (../lammps.cpp:468)
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using 6 OpenMP thread(s) per MPI task
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# 3d Lennard-Jones melt
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variable x index 1
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variable y index 1
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variable z index 1
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variable xx equal 20*$x
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variable xx equal 20*1
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variable yy equal 20*$y
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variable yy equal 20*1
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variable zz equal 20*$z
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variable zz equal 20*1
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units lj
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atom_style atomic
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lattice fcc 0.8442
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Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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region box block 0 20 0 ${yy} 0 ${zz}
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region box block 0 20 0 20 0 ${zz}
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region box block 0 20 0 20 0 20
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create_box 1 box
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Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 32000 atoms
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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fix 1 all nve
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run 100
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Memory usage per processor = 16.9509 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.44 -6.7733681 0 -4.6134356 -5.0197073
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100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
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Loop time of 0.57192 on 6 procs (1 MPI x 6 OpenMP) for 100 steps with 32000 atoms
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Pair time (%) = 0.205416 (35.917)
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Neigh time (%) = 0.112468 (19.665)
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Comm time (%) = 0.174223 (30.4629)
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Outpt time (%) = 0.000159025 (0.0278055)
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Other time (%) = 0.0796535 (13.9274)
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Nlocal: 32000 ave 32000 max 32000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 19657 ave 19657 max 19657 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 2.40567e+06 ave 2.40567e+06 max 2.40567e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 2405666
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Ave neighs/atom = 75.1771
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Neighbor list builds = 5
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Dangerous builds = 0
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@ -0,0 +1,68 @@
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LAMMPS (27 May 2014)
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KOKKOS mode is enabled (../lammps.cpp:468)
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using 6 OpenMP thread(s) per MPI task
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# 3d Lennard-Jones melt
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variable x index 1
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variable y index 1
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variable z index 1
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variable xx equal 20*$x
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variable xx equal 20*1
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variable yy equal 20*$y
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variable yy equal 20*1
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variable zz equal 20*$z
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variable zz equal 20*1
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units lj
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atom_style atomic
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lattice fcc 0.8442
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Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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region box block 0 20 0 ${yy} 0 ${zz}
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region box block 0 20 0 20 0 ${zz}
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region box block 0 20 0 20 0 20
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create_box 1 box
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Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
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1 by 1 by 2 MPI processor grid
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create_atoms 1 box
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Created 32000 atoms
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mass 1 1.0
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|
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velocity all create 1.44 87287 loop geom
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||||
|
||||
pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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|
||||
neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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fix 1 all nve
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run 100
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Memory usage per processor = 8.95027 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.44 -6.7733681 0 -4.6134356 -5.0197073
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100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
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Loop time of 0.689608 on 12 procs (2 MPI x 6 OpenMP) for 100 steps with 32000 atoms
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Pair time (%) = 0.210953 (30.5903)
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Neigh time (%) = 0.122991 (17.8349)
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Comm time (%) = 0.25264 (36.6353)
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Outpt time (%) = 0.000259042 (0.0375636)
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Other time (%) = 0.102765 (14.9019)
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|
||||
Nlocal: 16000 ave 16001 max 15999 min
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||||
Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 13632.5 ave 13635 max 13630 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 0 ave 0 max 0 min
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||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1.20283e+06 ave 1.20347e+06 max 1.2022e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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|
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Total # of neighbors = 2405666
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Ave neighs/atom = 75.1771
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Neighbor list builds = 5
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Dangerous builds = 0
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|
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@ -0,0 +1,65 @@
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LAMMPS (27 May 2014)
|
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using 1 OpenMP thread(s) per MPI task
|
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# 3d Lennard-Jones melt
|
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|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
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variable xx equal 20*$x
|
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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
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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region box block 0 20 0 ${yy} 0 ${zz}
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region box block 0 20 0 20 0 ${zz}
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region box block 0 20 0 20 0 20
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create_box 1 box
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Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
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1 by 1 by 1 MPI processor grid
|
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create_atoms 1 box
|
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Created 32000 atoms
|
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mass 1 1.0
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|
||||
velocity all create 1.44 87287 loop geom
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||||
|
||||
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
|
||||
|
|
@ -0,0 +1,65 @@
|
|||
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
|
||||
Loading…
Reference in New Issue