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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12678 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
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52408b16d2
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@ -12,10 +12,11 @@ libfwrapper.c is the Fortran-to-C wrapper
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The 3 codes do the same thing, so you can compare them to see how to
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drive LAMMPS in this manner. The C driver is similar in spirit to what
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one could use to write a scripting language interface. The Fortran
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driver in addition requires a wrapper library that interfaces the C
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interface of the LAMMPS library to Fortran and also translates the MPI
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communicator from Fortran to C.
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one could use to write a scripting language interface. See
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python/examples/simple.py for an example of using Python as a wrapper
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in that way. The Fortran driver in addition requires a wrapper
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library that interfaces the C interface of the LAMMPS library to
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Fortran and also translates the MPI communicator from Fortran to C.
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First, you must build LAMMPS as a library, either static or shared.
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See http://lammps.sandia.gov/doc/Section_start.html#start_5 for
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@ -206,13 +206,13 @@ void PPPMGPU::compute(int eflag, int vflag)
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else evflag = evflag_atom = eflag_global = vflag_global =
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eflag_atom = vflag_atom = 0;
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// If need per-atom energies/virials, also do particle map on host
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// concurrently with GPU calculations
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// If need per-atom energies/virials, allocate per-atom arrays here
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// so that particle map on host can be done concurrently with GPU calculations
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if (evflag_atom && !peratom_allocate_flag) {
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allocate_peratom();
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cg_peratom->ghost_notify();
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cg_peratom->setup();
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peratom_allocate_flag = 1;
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}
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bool success = true;
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@ -233,12 +233,19 @@ void PPPMGPU::compute(int eflag, int vflag)
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domain->x2lamda(atom->nlocal);
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}
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// extend size of per-atom arrays if necessary
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// If need per-atom energies/virials, also do particle map on host
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// concurrently with GPU calculations
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if (evflag_atom) {
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// extend size of per-atom arrays if necessary
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if (atom->nlocal > nmax) {
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memory->destroy(part2grid);
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nmax = atom->nmax;
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memory->create(part2grid,nmax,3,"pppm:part2grid");
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}
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if (evflag_atom && atom->nlocal > nmax) {
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memory->destroy(part2grid);
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nmax = atom->nmax;
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memory->create(part2grid,nmax,3,"pppm:part2grid");
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particle_map();
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}
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@ -0,0 +1,67 @@
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If you run in another directory, please edit the read_data line to point to
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the data.rhodo file. This is included in the LAMMPS distribution in the
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'bench' directory.
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++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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Expected times are the expected LOOP times based on runs using dual-socket
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Intel Xeon processor E5-2697 V2 with Intel Xeon Phi coprocessor 7120P.
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++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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TO RUN WITHOUT A PACKAGE:
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-----------------------------------------------------------------------------
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mpirun -np 48 ../../../src/lmp_YOUR_MACHINE -in in.intel.rhodo -log none -v b 0 -v s off
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mpirun -np 48 ../../../src/lmp_YOUR_MACHINE -in in.intel.lc -log none -v b 0 -v s off
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TO RUN WITH OMP PACKAGE
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-----------------------------------------------------------------------------
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env OMP_NUM_THREADS=2 mpirun -np 24 ../../../src/lmp_YOUR_MACHINE -in in.intel.rhodo -log none -v b 0 -v s omp
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+++++++++++++++++++++++
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+ EXPECTED TIME: 20.33s
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+++++++++++++++++++++++
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env OMP_NUM_THREADS=1 mpirun -np 48 ../../../src/lmp_YOUR_MACHINE -in in.intel.lc -log none -v b 0 -v s omp
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+++++++++++++++++++++++
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+ EXPECTED TIME: 19.92s
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+++++++++++++++++++++++
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TO RUN WITH INTEL+OMP PACKAGE WITHOUT OFFLOAD:
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-----------------------------------------------------------------------------
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env OMP_NUM_THREADS=2 mpirun -np 24 ../../../src/lmp_YOUR_MACHINE -in in.intel.rhodo -log none -v b 0 -v s intel
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+++++++++++++++++++++++
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+ EXPECTED TIME: 16.94s
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+++++++++++++++++++++++
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env OMP_NUM_THREADS=2 mpirun -np 24 ../../../src/lmp_YOUR_MACHINE -in in.intel.lc -log none -v b 0 -v s intel
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+++++++++++++++++++++++
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+ EXPECTED TIME: 5.80s
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+++++++++++++++++++++++
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TO RUN WITH INTEL+OMP PACKAGE WITH OFFLOAD TO XEON PHI (AUTO-BALANCED):
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-----------------------------------------------------------------------------
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env OMP_NUM_THREADS=1 mpirun -np 24 ../../../src/lmp_YOUR_MACHINE -in in.intel.rhodo -log none -v b -1 -v s intel
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+++++++++++++++++++++++
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+ EXPECTED TIME: 12.31s
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+++++++++++++++++++++++
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env OMP_NUM_THREADS=1 mpirun -np 24 ../../../src/lmp_YOUR_MACHINE -in in.intel.lc -log none -v b -1 -v s intel
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+++++++++++++++++++++++
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+ EXPECTED TIME: 4.00s
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+++++++++++++++++++++++
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TO RUN WITH INTEL+OMP PACKAGE WITH OFFLOAD TO XEON PHI (FIXED BALANCE):
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-----------------------------------------------------------------------------
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env OMP_NUM_THREADS=1 mpirun -np 24 ../../../src/lmp_YOUR_MACHINE -in in.intel.rhodo -log none -v b 0.68 -v s intel
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+++++++++++++++++++++++
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+ EXPECTED TIME: 11.40s
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+++++++++++++++++++++++
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env OMP_NUM_THREADS=1 mpirun -np 24 ../../../src/lmp_YOUR_MACHINE -in in.intel.lc -log none -v b 0.53 -v s intel
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+++++++++++++++++++++++
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+ EXPECTED TIME: 3.93s
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+++++++++++++++++++++++
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@ -0,0 +1,61 @@
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# Gay-Berne benchmark
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# biaxial ellipsoid mesogens in isotropic phase
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# shape: 2 1.5 1
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# cutoff 4.0 with skin 0.8
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# NPT, T=2.4, P=8.0
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package intel 1 mode mixed balance $b
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package omp 0
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suffix $s
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processors * * * grid numa
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variable x index 4
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variable y index 2
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variable z index 2
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variable i equal $x*32
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variable j equal $y*32
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variable k equal $z*32
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units lj
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atom_style ellipsoid
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# creation
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lattice sc 0.22
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region box block 0 $i 0 $j 0 $k
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create_box 1 box
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create_atoms 1 box
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# read_data data.gb
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set type 1 mass 1.5
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set type 1 shape 1 1.5 2
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set group all quat/random 982381
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compute rot all temp/asphere
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group spheroid type 1
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variable dof equal count(spheroid)+3
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compute_modify rot extra ${dof}
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velocity all create 2.4 41787 loop geom
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pair_style gayberne 1.0 3.0 1.0 4.0
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pair_coeff 1 1 1.0 1.0 1.0 0.5 0.2 1.0 0.5 0.2
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neighbor 0.8 bin
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timestep 0.002
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thermo 300
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# equilibration run
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fix 1 all npt/asphere temp 2.4 2.4 0.1 iso 5.0 8.0 0.1
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compute_modify 1_temp extra ${dof}
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run 210
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thermo 100
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reset_timestep 0
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unfix 1
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fix 1 all nve/asphere
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run 10
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run 50
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@ -0,0 +1,39 @@
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# Rhodopsin model
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package intel 1 mode mixed balance $b
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package omp 0
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suffix $s
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variable x index 4
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variable y index 2
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variable z index 2
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units real
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neigh_modify delay 5 every 1
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atom_style full
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atom_modify map hash
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bond_style harmonic
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angle_style charmm
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dihedral_style charmm
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improper_style harmonic
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pair_style lj/charmm/coul/long 8.0 10.0
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pair_modify mix arithmetic
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kspace_style pppm 1e-4
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read_data ../../../bench/data.rhodo
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replicate $x $y $z
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fix 1 all shake 0.0001 5 0 m 1.0 a 232
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fix 2 all npt temp 300.0 300.0 100.0 &
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z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
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special_bonds charmm
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thermo 50
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thermo_style multi
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timestep 2.0
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run 10
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run 100
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