forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6406 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
479275be1d
commit
9418bacff7
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# /* ----------------------------------------------------------------------
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# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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# http://lammps.sandia.gov, Sandia National Laboratories
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# Steve Plimpton, sjplimp@sandia.gov
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#
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# Copyright (2003) Sandia Corporation. Under the terms of Contract
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# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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# certain rights in this software. This software is distributed under
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# the GNU General Public License.
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#
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# See the README file in the top-level LAMMPS directory.
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# ------------------------------------------------------------------------- */
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#
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# /* ----------------------------------------------------------------------
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# Contributing authors: Mike Brown (ORNL), brownw@ornl.gov
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# Peng Wang (Nvidia), penwang@nvidia.com
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# Paul Crozier (SNL), pscrozi@sandia.gov
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# ------------------------------------------------------------------------- */
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CUDA_HOME = /usr/local/cuda
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NVCC = nvcc
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CUDA_ARCH = -arch=sm_11
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CUDA_PRECISION = -D_SINGLE_SINGLE
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CUDA_INCLUDE = -I/usr/local/cuda/include
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CUDA_LIB = -L/usr/local/cuda/lib64
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CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math
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#CUDA_OPTS = -DUNIX -g -G
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CUDR_CPP = mpic++ -DMPI_GERYON -DMPICH_IGNORE_CXX_SEEK -fopenmp
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CUDR_OPTS = -g -Wall -O2 -DUCL_NO_EXIT # -xHost -no-prec-div -ansi-alias
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#CUDR_OPTS = -g -Wall -DUCL_SYNC_DEBUG
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BIN_DIR = /home/wb8/bin
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OBJ_DIR = /home/wb8/obj/lammps
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LIB_DIR = /home/wb8/obj/lammps
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AR = ar
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BSH = /bin/sh
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include Nvidia.makefile
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# /* ----------------------------------------------------------------------
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# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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# http://lammps.sandia.gov, Sandia National Laboratories
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# Steve Plimpton, sjplimp@sandia.gov
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#
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# Copyright (2003) Sandia Corporation. Under the terms of Contract
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# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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# certain rights in this software. This software is distributed under
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# the GNU General Public License.
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#
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# See the README file in the top-level LAMMPS directory.
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# ------------------------------------------------------------------------- */
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#
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# /* ----------------------------------------------------------------------
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# Contributing authors: Mike Brown (ORNL), brownw@ornl.gov
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# Peng Wang (Nvidia), penwang@nvidia.com
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# Paul Crozier (SNL), pscrozi@sandia.gov
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# ------------------------------------------------------------------------- */
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OCL_CPP = mpic++ -O3 -DMPI_GERYON -DMPICH_IGNORE_CXX_SEEK -I/usr/local/cuda/include/
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OCL_LINK = -lOpenCL
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OCL_PREC = -D_SINGLE_SINGLE
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BIN_DIR = /home/wb8/bin
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OBJ_DIR = /home/wb8/obj/lammps
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LIB_DIR = /home/wb8/obj/lammps
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AR = ar
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BSH = /bin/sh
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include Opencl.makefile
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/***************************************************************************
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base_ellipsoid.cpp
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-------------------
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W. Michael Brown
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Base class for acceleration of ellipsoid potentials
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__________________________________________________________________________
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This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
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__________________________________________________________________________
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begin : Thu May 5 2011
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email : brownw@ornl.gov
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***************************************************************************/
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#include "base_ellipsoid.h"
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using namespace LAMMPS_AL;
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#ifdef USE_OPENCL
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#include "ellipsoid_nbor_cl.h"
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#else
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#include "ellipsoid_nbor_ptx.h"
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#endif
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#define BaseEllipsoidT BaseEllipsoid<numtyp, acctyp>
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extern PairGPUDevice<PRECISION,ACC_PRECISION> pair_gpu_device;
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template <class numtyp, class acctyp>
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BaseEllipsoidT::BaseEllipsoid() : _compiled(false), _max_bytes(0) {
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device=&pair_gpu_device;
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ans=new PairGPUAns<numtyp,acctyp>();
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nbor=new PairGPUNbor();
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}
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template <class numtyp, class acctyp>
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BaseEllipsoidT::~BaseEllipsoid() {
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delete ans;
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delete nbor;
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}
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template <class numtyp, class acctyp>
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int BaseEllipsoidT::bytes_per_atom(const int max_nbors) const {
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return device->atom.bytes_per_atom()+ans->bytes_per_atom()+
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nbor->bytes_per_atom(max_nbors);
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}
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template <class numtyp, class acctyp>
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int BaseEllipsoidT::init_base(const int nlocal, const int nall,
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const int max_nbors, const int maxspecial,
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const double cell_size, const double gpu_split,
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FILE *_screen, const int ntypes, int **h_form,
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const char *ellipsoid_program,
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const char *lj_program, const bool ellip_sphere) {
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nbor_time_avail=false;
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screen=_screen;
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_ellipsoid_sphere=ellip_sphere;
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bool gpu_nbor=false;
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if (device->gpu_mode()==PairGPUDevice<numtyp,acctyp>::GPU_NEIGH)
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gpu_nbor=true;
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int _gpu_host=0;
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int host_nlocal=hd_balancer.first_host_count(nlocal,gpu_split,gpu_nbor);
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if (host_nlocal>0)
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_gpu_host=1;
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_threads_per_atom=device->threads_per_charge();
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int success=device->init(*ans,false,true,nlocal,host_nlocal,nall,nbor,
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maxspecial,_gpu_host,max_nbors,cell_size,true);
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if (success!=0)
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return success;
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ucl_device=device->gpu;
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atom=&device->atom;
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_block_size=device->pair_block_size();
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compile_kernels(*ucl_device,ellipsoid_program,lj_program,ellip_sphere);
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// Initialize host-device load balancer
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hd_balancer.init(device,gpu_nbor,gpu_split);
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// Initialize timers for the selected GPU
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time_lj.init(*ucl_device);
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time_nbor1.init(*ucl_device);
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time_ellipsoid.init(*ucl_device);
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time_nbor2.init(*ucl_device);
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time_ellipsoid2.init(*ucl_device);
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time_nbor3.init(*ucl_device);
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time_ellipsoid3.init(*ucl_device);
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time_lj.zero();
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time_nbor1.zero();
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time_ellipsoid.zero();
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time_nbor2.zero();
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time_ellipsoid2.zero();
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time_nbor3.zero();
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time_ellipsoid3.zero();
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// See if we want fast GB-sphere or sphere-sphere calculations
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_host_form=h_form;
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_multiple_forms=false;
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for (int i=1; i<ntypes; i++)
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for (int j=i; j<ntypes; j++)
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if (_host_form[i][j]!=ELLIPSE_ELLIPSE)
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_multiple_forms=true;
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if (_multiple_forms && host_nlocal>0) {
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std::cerr << "Cannot use Gayberne with multiple forms and GPU neighbor.\n";
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exit(1);
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}
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if (_multiple_forms)
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ans->dev_ans.zero();
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// Memory for ilist ordered by particle type
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if (host_olist.alloc(nbor->max_atoms(),*ucl_device)==UCL_SUCCESS)
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return 0;
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else return -3;
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_max_an_bytes=ans->gpu_bytes()+nbor->gpu_bytes();
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return 0;
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}
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template <class numtyp, class acctyp>
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void BaseEllipsoidT::estimate_gpu_overhead() {
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device->estimate_gpu_overhead(2,_gpu_overhead,_driver_overhead);
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}
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template <class numtyp, class acctyp>
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void BaseEllipsoidT::clear_base() {
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// Output any timing information
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output_times();
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host_olist.clear();
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if (_compiled) {
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k_nbor_fast.clear();
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k_nbor.clear();
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k_ellipsoid.clear();
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k_ellipsoid_sphere.clear();
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k_sphere_ellipsoid.clear();
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k_lj_fast.clear();
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k_lj.clear();
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delete nbor_program;
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delete ellipsoid_program;
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delete lj_program;
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_compiled=false;
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}
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time_nbor1.clear();
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time_ellipsoid.clear();
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time_nbor2.clear();
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time_ellipsoid2.clear();
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time_nbor3.clear();
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time_ellipsoid3.clear();
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time_lj.clear();
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hd_balancer.clear();
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nbor->clear();
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ans->clear();
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device->clear();
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}
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template <class numtyp, class acctyp>
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void BaseEllipsoidT::output_times() {
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// Output any timing information
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acc_timers();
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double single[9], times[9];
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single[0]=atom->transfer_time()+ans->transfer_time();
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single[1]=nbor->time_nbor.total_seconds();
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single[2]=time_nbor1.total_seconds()+time_nbor2.total_seconds()+
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time_nbor3.total_seconds()+nbor->time_nbor.total_seconds();
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single[3]=time_ellipsoid.total_seconds()+time_ellipsoid2.total_seconds()+
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time_ellipsoid3.total_seconds();
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if (_multiple_forms)
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single[4]=time_lj.total_seconds();
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else
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single[4]=0;
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single[5]=atom->cast_time()+ans->cast_time();
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single[6]=_gpu_overhead;
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single[7]=_driver_overhead;
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single[8]=ans->cpu_idle_time();
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MPI_Reduce(single,times,9,MPI_DOUBLE,MPI_SUM,0,device->replica());
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double avg_split=hd_balancer.all_avg_split();
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_max_bytes+=atom->max_gpu_bytes();
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double mpi_max_bytes;
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MPI_Reduce(&_max_bytes,&mpi_max_bytes,1,MPI_DOUBLE,MPI_MAX,0,
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device->replica());
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double max_mb=mpi_max_bytes/(1024*1024);
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if (device->replica_me()==0)
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if (screen && times[5]>0.0) {
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int replica_size=device->replica_size();
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fprintf(screen,"\n\n-------------------------------------");
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fprintf(screen,"--------------------------------\n");
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fprintf(screen," GPU Time Info (average): ");
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fprintf(screen,"\n-------------------------------------");
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fprintf(screen,"--------------------------------\n");
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if (device->procs_per_gpu()==1) {
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fprintf(screen,"Data Transfer: %.4f s.\n",times[0]/replica_size);
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fprintf(screen,"Data Cast/Pack: %.4f s.\n",times[5]/replica_size);
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fprintf(screen,"Neighbor copy: %.4f s.\n",times[1]/replica_size);
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if (nbor->gpu_nbor())
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fprintf(screen,"Neighbor build: %.4f s.\n",times[2]/replica_size);
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else
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fprintf(screen,"Neighbor unpack: %.4f s.\n",times[2]/replica_size);
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fprintf(screen,"Force calc: %.4f s.\n",times[3]/replica_size);
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fprintf(screen,"LJ calc: %.4f s.\n",times[4]/replica_size);
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}
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fprintf(screen,"GPU Overhead: %.4f s.\n",times[6]/replica_size);
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fprintf(screen,"Average split: %.4f.\n",avg_split);
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fprintf(screen,"Threads / atom: %d.\n",_threads_per_atom);
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fprintf(screen,"Max Mem / Proc: %.2f MB.\n",max_mb);
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fprintf(screen,"CPU Driver_Time: %.4f s.\n",times[7]/replica_size);
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fprintf(screen,"CPU Idle_Time: %.4f s.\n",times[8]/replica_size);
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fprintf(screen,"-------------------------------------");
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fprintf(screen,"--------------------------------\n\n");
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fprintf(screen,"Average split: %.4f.\n",avg_split);
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fprintf(screen,"Max Mem / Proc: %.2f MB.\n",max_mb);
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}
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_max_bytes=0.0;
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}
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// ---------------------------------------------------------------------------
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// Pack neighbors to limit thread divergence for lj-lj and ellipse
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// ---------------------------------------------------------------------------
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template<class numtyp, class acctyp>
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void BaseEllipsoidT::pack_nbors(const int GX, const int BX, const int start,
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const int inum, const int form_low,
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const int form_high, const bool shared_types,
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int ntypes) {
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int stride=nbor->nbor_pitch();
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if (shared_types) {
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k_nbor_fast.set_size(GX,BX);
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k_nbor_fast.run(&atom->dev_x.begin(), &cut_form.begin(),
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&nbor->dev_nbor.begin(), &stride, &start, &inum,
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&nbor->dev_packed.begin(), &form_low, &form_high);
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} else {
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k_nbor.set_size(GX,BX);
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k_nbor.run(&atom->dev_x.begin(), &cut_form.begin(), &ntypes,
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&nbor->dev_nbor.begin(), &stride, &start, &inum,
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&nbor->dev_packed.begin(), &form_low, &form_high);
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}
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}
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// ---------------------------------------------------------------------------
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// Copy neighbor list from host
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// ---------------------------------------------------------------------------
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template <class numtyp, class acctyp>
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void BaseEllipsoidT::reset_nbors(const int nall, const int inum,
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const int osize, int *ilist,
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int *numj, int *type, int **firstneigh,
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bool &success) {
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success=true;
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nbor_time_avail=true;
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int mn=nbor->max_nbor_loop(osize,numj,ilist);
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resize_atom(nall,success);
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resize_local(inum,0,mn,osize,success);
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if (!success)
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return;
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if (_multiple_forms) {
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int p=0;
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for (int i=0; i<osize; i++) {
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int itype=type[ilist[i]];
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if (_host_form[itype][itype]==ELLIPSE_ELLIPSE) {
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host_olist[p]=ilist[i];
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p++;
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}
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}
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_max_last_ellipse=p;
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_last_ellipse=std::min(inum,_max_last_ellipse);
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for (int i=0; i<osize; i++) {
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int itype=type[ilist[i]];
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if (_host_form[itype][itype]!=ELLIPSE_ELLIPSE) {
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host_olist[p]=ilist[i];
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p++;
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}
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}
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nbor->get_host(inum,host_olist.begin(),numj,firstneigh,block_size());
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nbor->copy_unpacked(inum,mn);
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return;
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}
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_last_ellipse=inum;
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_max_last_ellipse=inum;
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nbor->get_host(inum,ilist,numj,firstneigh,block_size());
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nbor->copy_unpacked(inum,mn);
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double bytes=ans->gpu_bytes()+nbor->gpu_bytes();
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if (bytes>_max_an_bytes)
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_max_an_bytes=bytes;
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}
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// ---------------------------------------------------------------------------
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// Build neighbor list on device
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// ---------------------------------------------------------------------------
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template <class numtyp, class acctyp>
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inline void BaseEllipsoidT::build_nbor_list(const int inum, const int host_inum,
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const int nall, double **host_x,
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int *host_type, double *sublo,
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double *subhi, int *tag,
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int **nspecial, int **special,
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bool &success) {
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nbor_time_avail=true;
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success=true;
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resize_atom(nall,success);
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resize_local(inum,host_inum,nbor->max_nbors(),0,success);
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if (!success)
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return;
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atom->cast_copy_x(host_x,host_type);
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int mn;
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nbor->build_nbor_list(inum, host_inum, nall, *atom, sublo, subhi, tag,
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nspecial, special, success, mn);
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nbor->copy_unpacked(inum,mn);
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_last_ellipse=inum;
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_max_last_ellipse=inum;
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double bytes=ans->gpu_bytes()+nbor->gpu_bytes();
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if (bytes>_max_an_bytes)
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_max_an_bytes=bytes;
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}
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// ---------------------------------------------------------------------------
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// Copy nbor list from host if necessary and then calculate forces, virials,..
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// ---------------------------------------------------------------------------
|
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template <class numtyp, class acctyp>
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int* BaseEllipsoidT::compute(const int f_ago, const int inum_full,
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const int nall, double **host_x, int *host_type,
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int *ilist, int *numj, int **firstneigh,
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const bool eflag, const bool vflag,
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const bool eatom, const bool vatom,
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int &host_start, const double cpu_time,
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bool &success, double **host_quat) {
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acc_timers();
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if (inum_full==0) {
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host_start=0;
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zero_timers();
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return NULL;
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}
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int ago=hd_balancer.ago_first(f_ago);
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int inum=hd_balancer.balance(ago,inum_full,cpu_time);
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ans->inum(inum);
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_last_ellipse=std::min(inum,_max_last_ellipse);
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host_start=inum;
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if (ago==0) {
|
||||
reset_nbors(nall, inum, inum_full, ilist, numj, host_type, firstneigh,
|
||||
success);
|
||||
if (!success)
|
||||
return NULL;
|
||||
}
|
||||
int *list;
|
||||
if (_multiple_forms)
|
||||
list=host_olist.begin();
|
||||
else
|
||||
list=ilist;
|
||||
|
||||
atom->cast_x_data(host_x,host_type);
|
||||
atom->cast_quat_data(host_quat[0]);
|
||||
hd_balancer.start_timer();
|
||||
atom->add_x_data(host_x,host_type);
|
||||
atom->add_quat_data();
|
||||
|
||||
loop(eflag,vflag);
|
||||
ans->copy_answers(eflag,vflag,eatom,vatom,list);
|
||||
device->add_ans_object(ans);
|
||||
hd_balancer.stop_timer();
|
||||
return list;
|
||||
}
|
||||
|
||||
// ---------------------------------------------------------------------------
|
||||
// Reneighbor on GPU if necessary and then compute forces, virials, energies
|
||||
// ---------------------------------------------------------------------------
|
||||
template <class numtyp, class acctyp>
|
||||
int** BaseEllipsoidT::compute(const int ago, const int inum_full, const int nall,
|
||||
double **host_x, int *host_type, double *sublo,
|
||||
double *subhi, int *tag, int **nspecial,
|
||||
int **special, const bool eflag, const bool vflag,
|
||||
const bool eatom, const bool vatom,
|
||||
int &host_start, int **ilist, int **jnum,
|
||||
const double cpu_time, bool &success,
|
||||
double **host_quat) {
|
||||
acc_timers();
|
||||
if (inum_full==0) {
|
||||
host_start=0;
|
||||
zero_timers();
|
||||
return NULL;
|
||||
}
|
||||
|
||||
hd_balancer.balance(cpu_time);
|
||||
int inum=hd_balancer.get_gpu_count(ago,inum_full);
|
||||
ans->inum(inum);
|
||||
_last_ellipse=std::min(inum,_max_last_ellipse);
|
||||
host_start=inum;
|
||||
|
||||
// Build neighbor list on GPU if necessary
|
||||
if (ago==0) {
|
||||
build_nbor_list(inum, inum_full-inum, nall, host_x, host_type,
|
||||
sublo, subhi, tag, nspecial, special, success);
|
||||
if (!success)
|
||||
return NULL;
|
||||
atom->cast_quat_data(host_quat[0]);
|
||||
hd_balancer.start_timer();
|
||||
} else {
|
||||
atom->cast_x_data(host_x,host_type);
|
||||
atom->cast_quat_data(host_quat[0]);
|
||||
hd_balancer.start_timer();
|
||||
atom->add_x_data(host_x,host_type);
|
||||
}
|
||||
|
||||
atom->add_quat_data();
|
||||
*ilist=nbor->host_ilist.begin();
|
||||
*jnum=nbor->host_acc.begin();
|
||||
|
||||
loop(eflag,vflag);
|
||||
ans->copy_answers(eflag,vflag,eatom,vatom);
|
||||
device->add_ans_object(ans);
|
||||
hd_balancer.stop_timer();
|
||||
return nbor->host_jlist.begin()-host_start;
|
||||
}
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
double BaseEllipsoidT::host_memory_usage_base() const {
|
||||
return device->atom.host_memory_usage()+nbor->host_memory_usage()+
|
||||
4*sizeof(numtyp)+sizeof(BaseEllipsoid<numtyp,acctyp>);
|
||||
}
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
void BaseEllipsoidT::compile_kernels(UCL_Device &dev,
|
||||
const char *ellipsoid_string,
|
||||
const char *lj_string, const bool e_s) {
|
||||
if (_compiled)
|
||||
return;
|
||||
|
||||
std::string flags="-cl-fast-relaxed-math -cl-mad-enable "+
|
||||
std::string(OCL_PRECISION_COMPILE);
|
||||
|
||||
nbor_program=new UCL_Program(dev);
|
||||
nbor_program->load_string(ellipsoid_nbor,flags.c_str());
|
||||
k_nbor_fast.set_function(*nbor_program,"kernel_nbor_fast");
|
||||
k_nbor.set_function(*nbor_program,"kernel_nbor");
|
||||
|
||||
ellipsoid_program=new UCL_Program(dev);
|
||||
ellipsoid_program->load_string(ellipsoid_string,flags.c_str());
|
||||
k_ellipsoid.set_function(*ellipsoid_program,"kernel_ellipsoid");
|
||||
|
||||
lj_program=new UCL_Program(dev);
|
||||
lj_program->load_string(lj_string,flags.c_str());
|
||||
k_sphere_ellipsoid.set_function(*lj_program,"kernel_sphere_ellipsoid");
|
||||
k_lj_fast.set_function(*lj_program,"kernel_lj_fast");
|
||||
k_lj.set_function(*lj_program,"kernel_lj");
|
||||
if (e_s)
|
||||
k_ellipsoid_sphere.set_function(*lj_program,"kernel_ellipsoid_sphere");
|
||||
|
||||
_compiled=true;
|
||||
}
|
||||
|
||||
template class BaseEllipsoid<PRECISION,ACC_PRECISION>;
|
||||
|
||||
|
|
@ -0,0 +1,255 @@
|
|||
/***************************************************************************
|
||||
base_ellipsoid.h
|
||||
-------------------
|
||||
W. Michael Brown
|
||||
|
||||
Base class for acceleration of ellipsoid potentials
|
||||
|
||||
__________________________________________________________________________
|
||||
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
|
||||
__________________________________________________________________________
|
||||
|
||||
begin : Thu May 5 2011
|
||||
email : brownw@ornl.gov
|
||||
***************************************************************************/
|
||||
|
||||
#ifndef BASE_ELLIPSOID_H
|
||||
#define BASE_ELLIPSOID_H
|
||||
|
||||
#include "pair_gpu_device.h"
|
||||
#include "pair_gpu_balance.h"
|
||||
#include "mpi.h"
|
||||
|
||||
#ifdef USE_OPENCL
|
||||
#include "geryon/ocl_texture.h"
|
||||
#else
|
||||
#include "geryon/nvd_texture.h"
|
||||
#endif
|
||||
|
||||
namespace LAMMPS_AL {
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
class BaseEllipsoid {
|
||||
public:
|
||||
BaseEllipsoid();
|
||||
virtual ~BaseEllipsoid();
|
||||
|
||||
/// Clear any previous data and set up for a new LAMMPS run
|
||||
/** \param max_nbors initial number of rows in the neighbor matrix
|
||||
* \param cell_size cutoff + skin
|
||||
* \param gpu_split fraction of particles handled by device
|
||||
* \param ellipsoid_sphere true if ellipsoid-sphere case handled separately
|
||||
*
|
||||
* Returns:
|
||||
* - 0 if successfull
|
||||
* - -1 if fix gpu not found
|
||||
* - -3 if there is an out of memory error
|
||||
* - -4 if the GPU library was not compiled for GPU
|
||||
* - -5 Double precision is not supported on card **/
|
||||
int init_base(const int nlocal, const int nall, const int max_nbors,
|
||||
const int maxspecial, const double cell_size,
|
||||
const double gpu_split, FILE *screen, const int ntypes,
|
||||
int **h_form, const char *ellipsoid_program,
|
||||
const char *lj_program, const bool ellipsoid_sphere=false);
|
||||
|
||||
/// Estimate the overhead for GPU context changes and CPU driver
|
||||
void estimate_gpu_overhead();
|
||||
|
||||
/// Check if there is enough storage for atom arrays and realloc if not
|
||||
/** \param success set to false if insufficient memory **/
|
||||
inline void resize_atom(const int nall, bool &success) {
|
||||
atom->resize(nall, success);
|
||||
}
|
||||
|
||||
/// Check if there is enough storage for neighbors and realloc if not
|
||||
/** \param nlocal number of particles whose nbors must be stored on device
|
||||
* \param host_inum number of particles whose nbors need to copied to host
|
||||
* \param current maximum number of neighbors
|
||||
* \param olist_size size of list of particles from CPU neighboring
|
||||
* \note host_inum is 0 if the host is performing neighboring
|
||||
* \note if GPU is neighboring nlocal+host_inum=total number local particles
|
||||
* \note if CPU is neighboring olist_size=total number of local particles
|
||||
* \note if GPU is neighboring olist_size=0 **/
|
||||
inline void resize_local(const int nlocal, const int host_inum,
|
||||
const int max_nbors, const int olist_size,
|
||||
bool &success) {
|
||||
ans->resize(nlocal, success);
|
||||
if (_multiple_forms) ans->dev_ans.zero();
|
||||
|
||||
if (olist_size>static_cast<int>(host_olist.numel())) {
|
||||
host_olist.clear();
|
||||
int new_size=static_cast<int>(static_cast<double>(olist_size)*1.10);
|
||||
success=success && (host_olist.alloc(new_size,*ucl_device)==UCL_SUCCESS);
|
||||
}
|
||||
|
||||
nbor->resize(nlocal,host_inum,max_nbors,success);
|
||||
double bytes=ans->gpu_bytes()+nbor->gpu_bytes();
|
||||
if (bytes>_max_bytes)
|
||||
_max_bytes=bytes;
|
||||
}
|
||||
|
||||
/// Clear all host and device data
|
||||
/** \note This is called at the beginning of the init() routine **/
|
||||
void clear_base();
|
||||
|
||||
/// Output any timing information
|
||||
void output_times();
|
||||
|
||||
/// Returns memory usage on device per atom
|
||||
int bytes_per_atom(const int max_nbors) const;
|
||||
|
||||
/// Total host memory used by library for pair style
|
||||
double host_memory_usage_base() const;
|
||||
|
||||
/// Accumulate timers
|
||||
inline void acc_timers() {
|
||||
if (device->time_device()) {
|
||||
if (nbor_time_avail) {
|
||||
nbor->time_nbor.add_to_total();
|
||||
nbor->time_nbor.add_to_total();
|
||||
nbor_time_avail=false;
|
||||
}
|
||||
time_nbor1.add_to_total();
|
||||
time_ellipsoid.add_to_total();
|
||||
if (_multiple_forms) {
|
||||
time_nbor2.add_to_total();
|
||||
time_ellipsoid2.add_to_total();
|
||||
if (_ellipsoid_sphere) {
|
||||
time_nbor3.add_to_total();
|
||||
time_ellipsoid3.add_to_total();
|
||||
}
|
||||
time_lj.add_to_total();
|
||||
}
|
||||
atom->acc_timers();
|
||||
ans->acc_timers();
|
||||
}
|
||||
}
|
||||
|
||||
/// Zero timers
|
||||
inline void zero_timers() {
|
||||
nbor_time_avail=false;
|
||||
time_nbor1.zero();
|
||||
time_ellipsoid.zero();
|
||||
if (_multiple_forms) {
|
||||
time_nbor2.zero();
|
||||
time_ellipsoid2.zero();
|
||||
if (_ellipsoid_sphere) {
|
||||
time_nbor3.zero();
|
||||
time_ellipsoid3.zero();
|
||||
}
|
||||
time_lj.zero();
|
||||
}
|
||||
atom->zero_timers();
|
||||
ans->zero_timers();
|
||||
}
|
||||
|
||||
/// Pack neighbors to limit thread divergence for lj-lj and ellipse
|
||||
void pack_nbors(const int GX, const int BX, const int start, const int inum,
|
||||
const int form_low, const int form_high,
|
||||
const bool shared_types, int ntypes);
|
||||
|
||||
/// Copy neighbor list from host
|
||||
void reset_nbors(const int nall, const int inum, const int osize, int *ilist,
|
||||
int *numj, int *type, int **firstneigh, bool &success);
|
||||
|
||||
/// Build neighbor list on device
|
||||
void build_nbor_list(const int inum, const int host_inum,
|
||||
const int nall, double **host_x, int *host_type,
|
||||
double *sublo, double *subhi, int *tag, int **nspecial,
|
||||
int **special, bool &success);
|
||||
|
||||
/// Pair loop with host neighboring
|
||||
int* compute(const int f_ago, const int inum_full, const int nall,
|
||||
double **host_x, int *host_type, int *ilist, int *numj,
|
||||
int **firstneigh, const bool eflag, const bool vflag,
|
||||
const bool eatom, const bool vatom, int &host_start,
|
||||
const double cpu_time, bool &success, double **quat);
|
||||
|
||||
/// Pair loop with device neighboring
|
||||
int** compute(const int ago, const int inum_full, const int nall,
|
||||
double **host_x, int *host_type, double *sublo,
|
||||
double *subhi, int *tag, int **nspecial,
|
||||
int **special, const bool eflag, const bool vflag,
|
||||
const bool eatom, const bool vatom, int &host_start,
|
||||
int **ilist, int **numj, const double cpu_time, bool &success,
|
||||
double **host_quat);
|
||||
|
||||
/// Build neighbor list on accelerator
|
||||
void build_nbor_list(const int inum, const int host_inum, const int nall,
|
||||
double **host_x, int *host_type, double *sublo,
|
||||
double *subhi, bool &success);
|
||||
|
||||
// -------------------------- DEVICE DATA -------------------------
|
||||
|
||||
/// Device Properties and Atom and Neighbor storage
|
||||
PairGPUDevice<numtyp,acctyp> *device;
|
||||
|
||||
/// Geryon device
|
||||
UCL_Device *ucl_device;
|
||||
|
||||
/// Device Timers
|
||||
UCL_Timer time_nbor1, time_ellipsoid, time_nbor2, time_ellipsoid2, time_lj;
|
||||
UCL_Timer time_nbor3, time_ellipsoid3;
|
||||
|
||||
/// Host device load balancer
|
||||
PairGPUBalance<numtyp,acctyp> hd_balancer;
|
||||
|
||||
/// LAMMPS pointer for screen output
|
||||
FILE *screen;
|
||||
|
||||
// --------------------------- ATOM DATA --------------------------
|
||||
|
||||
/// Atom Data
|
||||
PairGPUAtom<numtyp,acctyp> *atom;
|
||||
|
||||
// --------------------------- TYPE DATA --------------------------
|
||||
|
||||
/// cut_form.x = cutsq, cut_form.y = form
|
||||
UCL_D_Vec<numtyp2> cut_form;
|
||||
|
||||
// ------------------------ FORCE/ENERGY DATA -----------------------
|
||||
|
||||
PairGPUAns<numtyp,acctyp> *ans;
|
||||
|
||||
// --------------------------- NBOR DATA ----------------------------
|
||||
|
||||
/// Neighbor data
|
||||
PairGPUNbor *nbor;
|
||||
/// ilist with particles sorted by type
|
||||
UCL_H_Vec<int> host_olist;
|
||||
/// True if we need to accumulate time for neighboring
|
||||
bool nbor_time_avail;
|
||||
|
||||
// ------------------------- DEVICE KERNELS -------------------------
|
||||
UCL_Program *nbor_program, *ellipsoid_program, *lj_program;
|
||||
UCL_Kernel k_nbor_fast, k_nbor;
|
||||
UCL_Kernel k_ellipsoid, k_ellipsoid_sphere, k_sphere_ellipsoid;
|
||||
UCL_Kernel k_lj_fast, k_lj;
|
||||
inline int block_size() { return _block_size; }
|
||||
|
||||
// --------------------------- TEXTURES -----------------------------
|
||||
UCL_Texture pos_tex;
|
||||
UCL_Texture q_tex;
|
||||
|
||||
protected:
|
||||
bool _compiled, _ellipsoid_sphere;
|
||||
int _block_size, _threads_per_atom;
|
||||
double _max_bytes, _max_an_bytes;
|
||||
double _gpu_overhead, _driver_overhead;
|
||||
UCL_D_Vec<int> *_nbor_data;
|
||||
|
||||
// True if we want to use fast GB-sphere or sphere-sphere calculations
|
||||
bool _multiple_forms;
|
||||
int **_host_form;
|
||||
int _last_ellipse, _max_last_ellipse;
|
||||
|
||||
void compile_kernels(UCL_Device &dev, const char *ellipsoid_string,
|
||||
const char *lj_string, const bool e_s);
|
||||
|
||||
virtual void loop(const bool _eflag, const bool _vflag) = 0;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
|
||||
|
|
@ -0,0 +1,131 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing authors: Mike Brown (ORNL), brownw@ornl.gov
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <iostream>
|
||||
#include <cassert>
|
||||
#include <math.h>
|
||||
|
||||
#include "cmmc_msm_gpu_memory.h"
|
||||
|
||||
using namespace std;
|
||||
|
||||
static CMMM_GPU_Memory<PRECISION,ACC_PRECISION> CMMMMF;
|
||||
|
||||
// ---------------------------------------------------------------------------
|
||||
// Allocate memory on host and device and copy constants to device
|
||||
// ---------------------------------------------------------------------------
|
||||
int cmmm_gpu_init(const int ntypes, double **cutsq, int **cg_type,
|
||||
double **host_lj1, double **host_lj2, double **host_lj3,
|
||||
double **host_lj4, double **offset, double *special_lj,
|
||||
const int inum, const int nall, const int max_nbors,
|
||||
const int maxspecial, const double cell_size, int &gpu_mode,
|
||||
FILE *screen, double **host_cut_ljsq, double host_cut_coulsq,
|
||||
double *host_special_coul, const double qqrd2e,
|
||||
const int smooth) {
|
||||
CMMMMF.clear();
|
||||
gpu_mode=CMMMMF.device->gpu_mode();
|
||||
double gpu_split=CMMMMF.device->particle_split();
|
||||
int first_gpu=CMMMMF.device->first_device();
|
||||
int last_gpu=CMMMMF.device->last_device();
|
||||
int world_me=CMMMMF.device->world_me();
|
||||
int gpu_rank=CMMMMF.device->gpu_rank();
|
||||
int procs_per_gpu=CMMMMF.device->procs_per_gpu();
|
||||
|
||||
CMMMMF.device->init_message(screen,"cg/cmm/coul/msm",first_gpu,last_gpu);
|
||||
|
||||
bool message=false;
|
||||
if (CMMMMF.device->replica_me()==0 && screen)
|
||||
message=true;
|
||||
|
||||
if (message) {
|
||||
fprintf(screen,"Initializing GPU and compiling on process 0...");
|
||||
fflush(screen);
|
||||
}
|
||||
|
||||
int init_ok=0;
|
||||
if (world_me==0)
|
||||
init_ok=CMMMMF.init(ntypes, cutsq, cg_type, host_lj1, host_lj2, host_lj3,
|
||||
host_lj4, offset, special_lj, inum, nall, 300,
|
||||
maxspecial, cell_size, gpu_split, screen, host_cut_ljsq,
|
||||
host_cut_coulsq, host_special_coul, qqrd2e,smooth);
|
||||
|
||||
CMMMMF.device->world_barrier();
|
||||
if (message)
|
||||
fprintf(screen,"Done.\n");
|
||||
|
||||
for (int i=0; i<procs_per_gpu; i++) {
|
||||
if (message) {
|
||||
if (last_gpu-first_gpu==0)
|
||||
fprintf(screen,"Initializing GPU %d on core %d...",first_gpu,i);
|
||||
else
|
||||
fprintf(screen,"Initializing GPUs %d-%d on core %d...",first_gpu,
|
||||
last_gpu,i);
|
||||
fflush(screen);
|
||||
}
|
||||
if (gpu_rank==i && world_me!=0)
|
||||
init_ok=CMMMMF.init(ntypes, cutsq, cg_type, host_lj1, host_lj2, host_lj3,
|
||||
host_lj4, offset, special_lj, inum, nall, 300,
|
||||
maxspecial, cell_size, gpu_split, screen,
|
||||
host_cut_ljsq, host_cut_coulsq, host_special_coul,
|
||||
qqrd2e,smooth);
|
||||
|
||||
CMMMMF.device->gpu_barrier();
|
||||
if (message)
|
||||
fprintf(screen,"Done.\n");
|
||||
}
|
||||
if (message)
|
||||
fprintf(screen,"\n");
|
||||
|
||||
if (init_ok==0)
|
||||
CMMMMF.estimate_gpu_overhead();
|
||||
return init_ok;
|
||||
}
|
||||
|
||||
void cmmm_gpu_clear() {
|
||||
CMMMMF.clear();
|
||||
}
|
||||
|
||||
int** cmmm_gpu_compute_n(const int ago, const int inum_full,
|
||||
const int nall, double **host_x, int *host_type,
|
||||
double *sublo, double *subhi, int *tag, int **nspecial,
|
||||
int **special, const bool eflag, const bool vflag,
|
||||
const bool eatom, const bool vatom, int &host_start,
|
||||
int **ilist, int **jnum, const double cpu_time,
|
||||
bool &success, double *host_q, double *boxlo,
|
||||
double *prd) {
|
||||
return CMMMMF.compute(ago, inum_full, nall, host_x, host_type, sublo,
|
||||
subhi, tag, nspecial, special, eflag, vflag, eatom,
|
||||
vatom, host_start, ilist, jnum, cpu_time, success,
|
||||
host_q, boxlo, prd);
|
||||
}
|
||||
|
||||
void cmmm_gpu_compute(const int ago, const int inum_full, const int nall,
|
||||
double **host_x, int *host_type, int *ilist, int *numj,
|
||||
int **firstneigh, const bool eflag, const bool vflag,
|
||||
const bool eatom, const bool vatom, int &host_start,
|
||||
const double cpu_time, bool &success, double *host_q,
|
||||
const int nlocal, double *boxlo, double *prd) {
|
||||
CMMMMF.compute(ago,inum_full,nall,host_x,host_type,ilist,numj,
|
||||
firstneigh,eflag,vflag,eatom,vatom,host_start,cpu_time,success,
|
||||
host_q,nlocal,boxlo,prd);
|
||||
}
|
||||
|
||||
double cmmm_gpu_bytes() {
|
||||
return CMMMMF.host_memory_usage();
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,169 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing authors: Mike Brown (ORNL), brownw@ornl.gov
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef USE_OPENCL
|
||||
#include "cmmc_msm_gpu_cl.h"
|
||||
#else
|
||||
#include "cmmc_msm_gpu_ptx.h"
|
||||
#endif
|
||||
|
||||
#include "cmmc_msm_gpu_memory.h"
|
||||
#include <cassert>
|
||||
#define CMMM_GPU_MemoryT CMMM_GPU_Memory<numtyp, acctyp>
|
||||
|
||||
extern PairGPUDevice<PRECISION,ACC_PRECISION> pair_gpu_device;
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
CMMM_GPU_MemoryT::CMMM_GPU_Memory() : ChargeGPUMemory<numtyp,acctyp>(),
|
||||
_allocated(false) {
|
||||
}
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
CMMM_GPU_MemoryT::~CMMM_GPU_Memory() {
|
||||
clear();
|
||||
}
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
int CMMM_GPU_MemoryT::bytes_per_atom(const int max_nbors) const {
|
||||
return this->bytes_per_atom_atomic(max_nbors);
|
||||
}
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
int CMMM_GPU_MemoryT::init(const int ntypes, double **host_cutsq,
|
||||
int **host_cg_type, double **host_lj1,
|
||||
double **host_lj2, double **host_lj3,
|
||||
double **host_lj4, double **host_offset,
|
||||
double *host_special_lj, const int nlocal,
|
||||
const int nall, const int max_nbors,
|
||||
const int maxspecial, const double cell_size,
|
||||
const double gpu_split, FILE *_screen,
|
||||
double **host_cut_ljsq,
|
||||
const double host_cut_coulsq,
|
||||
double *host_special_coul, const double qqrd2e,
|
||||
const int smooth) {
|
||||
int success;
|
||||
success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split,
|
||||
_screen,cmmc_msm_gpu_kernel);
|
||||
if (success!=0)
|
||||
return success;
|
||||
|
||||
// If atom type constants fit in shared memory use fast kernel
|
||||
int lj_types=ntypes;
|
||||
shared_types=false;
|
||||
int max_shared_types=this->device->max_shared_types();
|
||||
if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) {
|
||||
lj_types=max_shared_types;
|
||||
shared_types=true;
|
||||
}
|
||||
_lj_types=lj_types;
|
||||
|
||||
// Allocate a host write buffer for data initialization
|
||||
UCL_H_Vec<numtyp> host_write(lj_types*lj_types*32,*(this->ucl_device),
|
||||
UCL_WRITE_OPTIMIZED);
|
||||
|
||||
for (int i=0; i<lj_types*lj_types; i++)
|
||||
host_write[i]=0.0;
|
||||
|
||||
lj1.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
|
||||
this->atom->type_pack4(ntypes,lj_types,lj1,host_write,host_cutsq,
|
||||
host_cut_ljsq,host_lj1,host_lj2);
|
||||
|
||||
lj3.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
|
||||
this->atom->type_pack4(ntypes,lj_types,lj3,host_write,host_cg_type,host_lj3,
|
||||
host_lj4,host_offset);
|
||||
|
||||
sp_lj.alloc(8,*(this->ucl_device),UCL_READ_ONLY);
|
||||
for (int i=0; i<4; i++) {
|
||||
host_write[i]=host_special_lj[i];
|
||||
host_write[i+4]=host_special_coul[i];
|
||||
}
|
||||
ucl_copy(sp_lj,host_write,8,false);
|
||||
|
||||
_cut_coulsq=host_cut_coulsq;
|
||||
_qqrd2e=qqrd2e;
|
||||
_smooth=smooth;
|
||||
|
||||
_allocated=true;
|
||||
this->_max_bytes=lj1.row_bytes()+lj3.row_bytes()+sp_lj.row_bytes();
|
||||
return 0;
|
||||
}
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
void CMMM_GPU_MemoryT::clear() {
|
||||
if (!_allocated)
|
||||
return;
|
||||
_allocated=false;
|
||||
|
||||
lj1.clear();
|
||||
lj3.clear();
|
||||
sp_lj.clear();
|
||||
this->clear_atomic();
|
||||
}
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
double CMMM_GPU_MemoryT::host_memory_usage() const {
|
||||
return this->host_memory_usage_atomic()+sizeof(CMMM_GPU_Memory<numtyp,acctyp>);
|
||||
}
|
||||
|
||||
// ---------------------------------------------------------------------------
|
||||
// Calculate energies, forces, and torques
|
||||
// ---------------------------------------------------------------------------
|
||||
template <class numtyp, class acctyp>
|
||||
void CMMM_GPU_MemoryT::loop(const bool _eflag, const bool _vflag) {
|
||||
// Compute the block size and grid size to keep all cores busy
|
||||
const int BX=this->block_size();
|
||||
int eflag, vflag;
|
||||
if (_eflag)
|
||||
eflag=1;
|
||||
else
|
||||
eflag=0;
|
||||
|
||||
if (_vflag)
|
||||
vflag=1;
|
||||
else
|
||||
vflag=0;
|
||||
|
||||
int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
|
||||
(BX/this->_threads_per_atom)));
|
||||
|
||||
int ainum=this->ans->inum();
|
||||
int nbor_pitch=this->nbor->nbor_pitch();
|
||||
this->time_pair.start();
|
||||
if (shared_types) {
|
||||
this->k_pair_fast.set_size(GX,BX);
|
||||
this->k_pair_fast.run(&this->atom->dev_x.begin(), &lj1.begin(),
|
||||
&lj3.begin(), &sp_lj.begin(),
|
||||
&this->nbor->dev_nbor.begin(),
|
||||
&this->_nbor_data->begin(),
|
||||
&this->ans->dev_ans.begin(),
|
||||
&this->ans->dev_engv.begin(), &eflag, &vflag,
|
||||
&ainum, &nbor_pitch,
|
||||
&this->atom->dev_q.begin(), &_cut_coulsq,
|
||||
&_qqrd2e, &_smooth, &this->_threads_per_atom);
|
||||
} else {
|
||||
this->k_pair.set_size(GX,BX);
|
||||
this->k_pair.run(&this->atom->dev_x.begin(), &lj1.begin(), &lj3.begin(),
|
||||
&_lj_types, &sp_lj.begin(), &this->nbor->dev_nbor.begin(),
|
||||
&this->_nbor_data->begin(), &this->ans->dev_ans.begin(),
|
||||
&this->ans->dev_engv.begin(), &eflag, &vflag, &ainum,
|
||||
&nbor_pitch, &this->atom->dev_q.begin(), &_cut_coulsq,
|
||||
&_qqrd2e, &_smooth, &this->_threads_per_atom);
|
||||
}
|
||||
this->time_pair.stop();
|
||||
}
|
||||
|
||||
template class CMMM_GPU_Memory<PRECISION,ACC_PRECISION>;
|
||||
|
|
@ -0,0 +1,83 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing authors: Mike Brown (ORNL), brownw@ornl.gov
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef CMMM_GPU_MEMORY_H
|
||||
#define CMMM_GPU_MEMORY_H
|
||||
|
||||
#include "charge_gpu_memory.h"
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
class CMMM_GPU_Memory : public ChargeGPUMemory<numtyp, acctyp> {
|
||||
public:
|
||||
CMMM_GPU_Memory();
|
||||
~CMMM_GPU_Memory();
|
||||
|
||||
/// Clear any previous data and set up for a new LAMMPS run
|
||||
/** \param max_nbors initial number of rows in the neighbor matrix
|
||||
* \param cell_size cutoff + skin
|
||||
* \param gpu_split fraction of particles handled by device
|
||||
*
|
||||
* Returns:
|
||||
* - 0 if successfull
|
||||
* - -1 if fix gpu not found
|
||||
* - -3 if there is an out of memory error
|
||||
* - -4 if the GPU library was not compiled for GPU
|
||||
* - -5 Double precision is not supported on card **/
|
||||
int init(const int ntypes, double **host_cutsq, int ** cg_type,
|
||||
double **host_lj1, double **host_lj2, double **host_lj3,
|
||||
double **host_lj4, double **host_offset, double *host_special_lj,
|
||||
const int nlocal, const int nall, const int max_nbors,
|
||||
const int maxspecial, const double cell_size,
|
||||
const double gpu_split, FILE *screen, double **host_cut_ljsq,
|
||||
const double host_cut_coulsq, double *host_special_coul,
|
||||
const double qqrd2e, const int smooth);
|
||||
|
||||
/// Clear all host and device data
|
||||
/** \note This is called at the beginning of the init() routine **/
|
||||
void clear();
|
||||
|
||||
/// Returns memory usage on device per atom
|
||||
int bytes_per_atom(const int max_nbors) const;
|
||||
|
||||
/// Total host memory used by library for pair style
|
||||
double host_memory_usage() const;
|
||||
|
||||
// --------------------------- TYPE DATA --------------------------
|
||||
|
||||
/// lj1.x = cutsq, lj1.y = cutsq_vdw, lj1.z = lj1, lj1.w = lj2,
|
||||
UCL_D_Vec<numtyp4> lj1;
|
||||
/// lj3.x = cg_type, lj3.y = lj3, lj3.z = lj4, lj3.w = offset
|
||||
UCL_D_Vec<numtyp4> lj3;
|
||||
/// Special LJ values [0-3] and Special Coul values [4-7]
|
||||
UCL_D_Vec<numtyp> sp_lj;
|
||||
|
||||
/// If atom type constants fit in shared memory, use fast kernels
|
||||
bool shared_types;
|
||||
|
||||
/// Number of atom types
|
||||
int _lj_types;
|
||||
|
||||
numtyp _cut_coulsq, _qqrd2e;
|
||||
|
||||
private:
|
||||
bool _allocated;
|
||||
int _smooth;
|
||||
void loop(const bool _eflag, const bool _vflag);
|
||||
};
|
||||
|
||||
#endif
|
||||
|
||||
|
|
@ -0,0 +1,424 @@
|
|||
// **************************************************************************
|
||||
// ellipsoid_extra.h
|
||||
// -------------------
|
||||
// W. Michael Brown
|
||||
//
|
||||
// Device code for Ellipsoid math routines
|
||||
//
|
||||
// __________________________________________________________________________
|
||||
// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
|
||||
// __________________________________________________________________________
|
||||
//
|
||||
// begin :
|
||||
// email : brownw@ornl.gov
|
||||
// ***************************************************************************/
|
||||
|
||||
#ifndef ELLIPSOID_EXTRA_H
|
||||
#define ELLIPSOID_EXTRA_H
|
||||
|
||||
enum{SPHERE_SPHERE,SPHERE_ELLIPSE,ELLIPSE_SPHERE,ELLIPSE_ELLIPSE};
|
||||
|
||||
#ifdef _DOUBLE_DOUBLE
|
||||
#define numtyp double
|
||||
#define numtyp2 double2
|
||||
#define numtyp4 double4
|
||||
#define acctyp double
|
||||
#define acctyp4 double4
|
||||
#endif
|
||||
|
||||
#ifdef _SINGLE_DOUBLE
|
||||
#define numtyp float
|
||||
#define numtyp2 float2
|
||||
#define numtyp4 float4
|
||||
#define acctyp double
|
||||
#define acctyp4 double4
|
||||
#endif
|
||||
|
||||
#ifndef numtyp
|
||||
#define numtyp float
|
||||
#define numtyp2 float2
|
||||
#define numtyp4 float4
|
||||
#define acctyp float
|
||||
#define acctyp4 float4
|
||||
#endif
|
||||
|
||||
#ifdef NV_KERNEL
|
||||
|
||||
#include "nv_kernel_def.h"
|
||||
|
||||
#else
|
||||
|
||||
#pragma OPENCL EXTENSION cl_khr_fp64: enable
|
||||
#define GLOBAL_ID_X get_global_id(0)
|
||||
#define THREAD_ID_X get_local_id(0)
|
||||
#define BLOCK_ID_X get_group_id(0)
|
||||
#define BLOCK_SIZE_X get_local_size(0)
|
||||
#define __syncthreads() barrier(CLK_LOCAL_MEM_FENCE)
|
||||
#define __inline inline
|
||||
#define BLOCK_PAIR 64
|
||||
#define MAX_SHARED_TYPES 8
|
||||
|
||||
#endif
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
dot product of 2 vectors
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
__inline numtyp gpu_dot3(const numtyp *v1, const numtyp *v2)
|
||||
{
|
||||
return v1[0]*v2[0]+v1[1]*v2[1]+v1[2]*v2[2];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
cross product of 2 vectors
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
__inline void gpu_cross3(const numtyp *v1, const numtyp *v2, numtyp *ans)
|
||||
{
|
||||
ans[0] = v1[1]*v2[2]-v1[2]*v2[1];
|
||||
ans[1] = v1[2]*v2[0]-v1[0]*v2[2];
|
||||
ans[2] = v1[0]*v2[1]-v1[1]*v2[0];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
determinant of a matrix
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
__inline numtyp gpu_det3(const numtyp m[9])
|
||||
{
|
||||
numtyp ans = m[0]*m[4]*m[8] - m[0]*m[5]*m[7] -
|
||||
m[3]*m[1]*m[8] + m[3]*m[2]*m[7] +
|
||||
m[6]*m[1]*m[5] - m[6]*m[2]*m[4];
|
||||
return ans;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
diagonal matrix times a full matrix
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
__inline void gpu_diag_times3(const numtyp4 shape, const numtyp m[9],
|
||||
numtyp ans[9])
|
||||
{
|
||||
ans[0] = shape.x*m[0];
|
||||
ans[1] = shape.x*m[1];
|
||||
ans[2] = shape.x*m[2];
|
||||
ans[3] = shape.y*m[3];
|
||||
ans[4] = shape.y*m[4];
|
||||
ans[5] = shape.y*m[5];
|
||||
ans[6] = shape.z*m[6];
|
||||
ans[7] = shape.z*m[7];
|
||||
ans[8] = shape.z*m[8];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
add two matrices
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
__inline void gpu_plus3(const numtyp m[9], const numtyp m2[9], numtyp ans[9])
|
||||
{
|
||||
ans[0] = m[0]+m2[0];
|
||||
ans[1] = m[1]+m2[1];
|
||||
ans[2] = m[2]+m2[2];
|
||||
ans[3] = m[3]+m2[3];
|
||||
ans[4] = m[4]+m2[4];
|
||||
ans[5] = m[5]+m2[5];
|
||||
ans[6] = m[6]+m2[6];
|
||||
ans[7] = m[7]+m2[7];
|
||||
ans[8] = m[8]+m2[8];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
multiply the transpose of mat1 times mat2
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
__inline void gpu_transpose_times3(const numtyp m[9], const numtyp m2[9],
|
||||
numtyp ans[9])
|
||||
{
|
||||
ans[0] = m[0]*m2[0]+m[3]*m2[3]+m[6]*m2[6];
|
||||
ans[1] = m[0]*m2[1]+m[3]*m2[4]+m[6]*m2[7];
|
||||
ans[2] = m[0]*m2[2]+m[3]*m2[5]+m[6]*m2[8];
|
||||
ans[3] = m[1]*m2[0]+m[4]*m2[3]+m[7]*m2[6];
|
||||
ans[4] = m[1]*m2[1]+m[4]*m2[4]+m[7]*m2[7];
|
||||
ans[5] = m[1]*m2[2]+m[4]*m2[5]+m[7]*m2[8];
|
||||
ans[6] = m[2]*m2[0]+m[5]*m2[3]+m[8]*m2[6];
|
||||
ans[7] = m[2]*m2[1]+m[5]*m2[4]+m[8]*m2[7];
|
||||
ans[8] = m[2]*m2[2]+m[5]*m2[5]+m[8]*m2[8];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
row vector times matrix
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
__inline void gpu_row_times3(const numtyp *v, const numtyp m[9], numtyp *ans)
|
||||
{
|
||||
ans[0] = m[0]*v[0]+v[1]*m[3]+v[2]*m[6];
|
||||
ans[1] = v[0]*m[1]+m[4]*v[1]+v[2]*m[7];
|
||||
ans[2] = v[0]*m[2]+v[1]*m[5]+m[8]*v[2];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
solve Ax = b or M ans = v
|
||||
use gaussian elimination & partial pivoting on matrix
|
||||
error_flag set to 2 if bad matrix inversion attempted
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
__inline void gpu_mldivide3(const numtyp m[9], const numtyp *v, numtyp *ans,
|
||||
__global int *error_flag)
|
||||
{
|
||||
// create augmented matrix for pivoting
|
||||
|
||||
numtyp aug[12], t;
|
||||
|
||||
aug[3] = v[0];
|
||||
aug[0] = m[0];
|
||||
aug[1] = m[1];
|
||||
aug[2] = m[2];
|
||||
aug[7] = v[1];
|
||||
aug[4] = m[3];
|
||||
aug[5] = m[4];
|
||||
aug[6] = m[5];
|
||||
aug[11] = v[2];
|
||||
aug[8] = m[6];
|
||||
aug[9] = m[7];
|
||||
aug[10] = m[8];
|
||||
|
||||
if (fabs(aug[4]) > fabs(aug[0])) {
|
||||
numtyp swapt;
|
||||
swapt=aug[0]; aug[0]=aug[4]; aug[4]=swapt;
|
||||
swapt=aug[1]; aug[1]=aug[5]; aug[5]=swapt;
|
||||
swapt=aug[2]; aug[2]=aug[6]; aug[6]=swapt;
|
||||
swapt=aug[3]; aug[3]=aug[7]; aug[7]=swapt;
|
||||
}
|
||||
if (fabs(aug[8]) > fabs(aug[0])) {
|
||||
numtyp swapt;
|
||||
swapt=aug[0]; aug[0]=aug[8]; aug[8]=swapt;
|
||||
swapt=aug[1]; aug[1]=aug[9]; aug[9]=swapt;
|
||||
swapt=aug[2]; aug[2]=aug[10]; aug[10]=swapt;
|
||||
swapt=aug[3]; aug[3]=aug[11]; aug[11]=swapt;
|
||||
}
|
||||
|
||||
if (aug[0] != (numtyp)0.0) {
|
||||
if (0!=0) {
|
||||
numtyp swapt;
|
||||
swapt=aug[0]; aug[0]=aug[0]; aug[0]=swapt;
|
||||
swapt=aug[1]; aug[1]=aug[1]; aug[1]=swapt;
|
||||
swapt=aug[2]; aug[2]=aug[2]; aug[2]=swapt;
|
||||
swapt=aug[3]; aug[3]=aug[3]; aug[3]=swapt;
|
||||
}
|
||||
} else if (aug[4] != (numtyp)0.0) {
|
||||
if (1!=0) {
|
||||
numtyp swapt;
|
||||
swapt=aug[0]; aug[0]=aug[4]; aug[4]=swapt;
|
||||
swapt=aug[1]; aug[1]=aug[5]; aug[5]=swapt;
|
||||
swapt=aug[2]; aug[2]=aug[6]; aug[6]=swapt;
|
||||
swapt=aug[3]; aug[3]=aug[7]; aug[7]=swapt;
|
||||
}
|
||||
} else if (aug[8] != (numtyp)0.0) {
|
||||
if (2!=0) {
|
||||
numtyp swapt;
|
||||
swapt=aug[0]; aug[0]=aug[8]; aug[8]=swapt;
|
||||
swapt=aug[1]; aug[1]=aug[9]; aug[9]=swapt;
|
||||
swapt=aug[2]; aug[2]=aug[10]; aug[10]=swapt;
|
||||
swapt=aug[3]; aug[3]=aug[11]; aug[11]=swapt;
|
||||
}
|
||||
} else
|
||||
*error_flag=2;
|
||||
|
||||
t = aug[4]/aug[0];
|
||||
aug[5]-=t*aug[1];
|
||||
aug[6]-=t*aug[2];
|
||||
aug[7]-=t*aug[3];
|
||||
t = aug[8]/aug[0];
|
||||
aug[9]-=t*aug[1];
|
||||
aug[10]-=t*aug[2];
|
||||
aug[11]-=t*aug[3];
|
||||
|
||||
if (fabs(aug[9]) > fabs(aug[5])) {
|
||||
numtyp swapt;
|
||||
swapt=aug[4]; aug[4]=aug[8]; aug[8]=swapt;
|
||||
swapt=aug[5]; aug[5]=aug[9]; aug[9]=swapt;
|
||||
swapt=aug[6]; aug[6]=aug[10]; aug[10]=swapt;
|
||||
swapt=aug[7]; aug[7]=aug[11]; aug[11]=swapt;
|
||||
}
|
||||
|
||||
if (aug[5] != (numtyp)0.0) {
|
||||
if (1!=1) {
|
||||
numtyp swapt;
|
||||
swapt=aug[4]; aug[4]=aug[4]; aug[4]=swapt;
|
||||
swapt=aug[5]; aug[5]=aug[5]; aug[5]=swapt;
|
||||
swapt=aug[6]; aug[6]=aug[6]; aug[6]=swapt;
|
||||
swapt=aug[7]; aug[7]=aug[7]; aug[7]=swapt;
|
||||
}
|
||||
} else if (aug[9] != (numtyp)0.0) {
|
||||
if (2!=1) {
|
||||
numtyp swapt;
|
||||
swapt=aug[4]; aug[4]=aug[8]; aug[8]=swapt;
|
||||
swapt=aug[5]; aug[5]=aug[9]; aug[9]=swapt;
|
||||
swapt=aug[6]; aug[6]=aug[10]; aug[10]=swapt;
|
||||
swapt=aug[7]; aug[7]=aug[11]; aug[11]=swapt;
|
||||
}
|
||||
}
|
||||
|
||||
t = aug[9]/aug[5];
|
||||
aug[10]-=t*aug[6];
|
||||
aug[11]-=t*aug[7];
|
||||
|
||||
if (aug[10] == (numtyp)0.0)
|
||||
*error_flag=2;
|
||||
|
||||
ans[2] = aug[11]/aug[10];
|
||||
t = (numtyp)0.0;
|
||||
t += aug[6]*ans[2];
|
||||
ans[1] = (aug[7]-t) / aug[5];
|
||||
t = (numtyp)0.0;
|
||||
t += aug[1]*ans[1];
|
||||
t += aug[2]*ans[2];
|
||||
ans[0] = (aug[3]-t) / aug[0];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
compute rotation matrix from quaternion conjugate
|
||||
quat = [w i j k]
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
__inline void gpu_quat_to_mat_trans(__global const numtyp4 *qif, const int qi,
|
||||
numtyp mat[9])
|
||||
{
|
||||
numtyp4 q=qif[qi];
|
||||
|
||||
numtyp w2 = q.x*q.x;
|
||||
numtyp i2 = q.y*q.y;
|
||||
numtyp j2 = q.z*q.z;
|
||||
numtyp k2 = q.w*q.w;
|
||||
numtyp twoij = (numtyp)2.0*q.y*q.z;
|
||||
numtyp twoik = (numtyp)2.0*q.y*q.w;
|
||||
numtyp twojk = (numtyp)2.0*q.z*q.w;
|
||||
numtyp twoiw = (numtyp)2.0*q.y*q.x;
|
||||
numtyp twojw = (numtyp)2.0*q.z*q.x;
|
||||
numtyp twokw = (numtyp)2.0*q.w*q.x;
|
||||
|
||||
mat[0] = w2+i2-j2-k2;
|
||||
mat[3] = twoij-twokw;
|
||||
mat[6] = twojw+twoik;
|
||||
|
||||
mat[1] = twoij+twokw;
|
||||
mat[4] = w2-i2+j2-k2;
|
||||
mat[7] = twojk-twoiw;
|
||||
|
||||
mat[2] = twoik-twojw;
|
||||
mat[5] = twojk+twoiw;
|
||||
mat[8] = w2-i2-j2+k2;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
transposed matrix times diagonal matrix
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
__inline void gpu_transpose_times_diag3(const numtyp m[9],
|
||||
const numtyp4 d, numtyp ans[9])
|
||||
{
|
||||
ans[0] = m[0]*d.x;
|
||||
ans[1] = m[3]*d.y;
|
||||
ans[2] = m[6]*d.z;
|
||||
ans[3] = m[1]*d.x;
|
||||
ans[4] = m[4]*d.y;
|
||||
ans[5] = m[7]*d.z;
|
||||
ans[6] = m[2]*d.x;
|
||||
ans[7] = m[5]*d.y;
|
||||
ans[8] = m[8]*d.z;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
multiply mat1 times mat2
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
__inline void gpu_times3(const numtyp m[9], const numtyp m2[9],
|
||||
numtyp ans[9])
|
||||
{
|
||||
ans[0] = m[0]*m2[0] + m[1]*m2[3] + m[2]*m2[6];
|
||||
ans[1] = m[0]*m2[1] + m[1]*m2[4] + m[2]*m2[7];
|
||||
ans[2] = m[0]*m2[2] + m[1]*m2[5] + m[2]*m2[8];
|
||||
ans[3] = m[3]*m2[0] + m[4]*m2[3] + m[5]*m2[6];
|
||||
ans[4] = m[3]*m2[1] + m[4]*m2[4] + m[5]*m2[7];
|
||||
ans[5] = m[3]*m2[2] + m[4]*m2[5] + m[5]*m2[8];
|
||||
ans[6] = m[6]*m2[0] + m[7]*m2[3] + m[8]*m2[6];
|
||||
ans[7] = m[6]*m2[1] + m[7]*m2[4] + m[8]*m2[7];
|
||||
ans[8] = m[6]*m2[2] + m[7]*m2[5] + m[8]*m2[8];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Apply principal rotation generator about x to rotation matrix m
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
__inline void gpu_rotation_generator_x(const numtyp m[9], numtyp ans[9])
|
||||
{
|
||||
ans[0] = 0;
|
||||
ans[1] = -m[2];
|
||||
ans[2] = m[1];
|
||||
ans[3] = 0;
|
||||
ans[4] = -m[5];
|
||||
ans[5] = m[4];
|
||||
ans[6] = 0;
|
||||
ans[7] = -m[8];
|
||||
ans[8] = m[7];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Apply principal rotation generator about y to rotation matrix m
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
__inline void gpu_rotation_generator_y(const numtyp m[9], numtyp ans[9])
|
||||
{
|
||||
ans[0] = m[2];
|
||||
ans[1] = 0;
|
||||
ans[2] = -m[0];
|
||||
ans[3] = m[5];
|
||||
ans[4] = 0;
|
||||
ans[5] = -m[3];
|
||||
ans[6] = m[8];
|
||||
ans[7] = 0;
|
||||
ans[8] = -m[6];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Apply principal rotation generator about z to rotation matrix m
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
__inline void gpu_rotation_generator_z(const numtyp m[9], numtyp ans[9])
|
||||
{
|
||||
ans[0] = -m[1];
|
||||
ans[1] = m[0];
|
||||
ans[2] = 0;
|
||||
ans[3] = -m[4];
|
||||
ans[4] = m[3];
|
||||
ans[5] = 0;
|
||||
ans[6] = -m[7];
|
||||
ans[7] = m[6];
|
||||
ans[8] = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
matrix times vector
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
__inline void gpu_times_column3(const numtyp m[9], const numtyp v[3],
|
||||
numtyp ans[3])
|
||||
{
|
||||
ans[0] = m[0]*v[0] + m[1]*v[1] + m[2]*v[2];
|
||||
ans[1] = m[3]*v[0] + m[4]*v[1] + m[5]*v[2];
|
||||
ans[2] = m[6]*v[0] + m[7]*v[1] + m[8]*v[2];
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
#endif
|
||||
|
|
@ -0,0 +1,307 @@
|
|||
/***************************************************************************
|
||||
gayberne.cpp
|
||||
-------------------
|
||||
W. Michael Brown
|
||||
|
||||
Host code for Gay-Berne potential acceleration
|
||||
|
||||
__________________________________________________________________________
|
||||
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
|
||||
__________________________________________________________________________
|
||||
|
||||
begin :
|
||||
email : brownw@ornl.gov
|
||||
***************************************************************************/
|
||||
|
||||
#ifdef USE_OPENCL
|
||||
#include "gayberne_cl.h"
|
||||
#else
|
||||
#include "gayberne_ptx.h"
|
||||
#endif
|
||||
|
||||
#include "gayberne.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
|
||||
#define GayBerneT GayBerne<numtyp, acctyp>
|
||||
extern PairGPUDevice<PRECISION,ACC_PRECISION> pair_gpu_device;
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
GayBerneT::GayBerne() : BaseEllipsoid<numtyp,acctyp>(),
|
||||
_allocated(false) {
|
||||
}
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
GayBerneT::~GayBerne() {
|
||||
clear();
|
||||
}
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
int GayBerneT::bytes_per_atom(const int max_nbors) const {
|
||||
return this->bytes_per_atom(max_nbors);
|
||||
}
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
int GayBerneT::init(const int ntypes, const double gamma,
|
||||
const double upsilon, const double mu,
|
||||
double **host_shape, double **host_well,
|
||||
double **host_cutsq, double **host_sigma,
|
||||
double **host_epsilon, double *host_lshape,
|
||||
int **h_form, double **host_lj1, double **host_lj2,
|
||||
double **host_lj3, double **host_lj4,
|
||||
double **host_offset, const double *host_special_lj,
|
||||
const int nlocal, const int nall, const int max_nbors,
|
||||
const int maxspecial, const double cell_size,
|
||||
const double gpu_split, FILE *_screen) {
|
||||
int success;
|
||||
success=this->init_base(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split,
|
||||
_screen,ntypes,h_form,gayberne,gayberne_lj);
|
||||
if (success!=0)
|
||||
return success;
|
||||
|
||||
// If atom type constants fit in shared memory use fast kernel
|
||||
int lj_types=ntypes;
|
||||
_shared_types=false;
|
||||
int max_shared_types=this->device->max_shared_types();
|
||||
if (lj_types<=max_shared_types && this->block_size()>=max_shared_types) {
|
||||
lj_types=max_shared_types;
|
||||
_shared_types=true;
|
||||
}
|
||||
_lj_types=lj_types;
|
||||
|
||||
// Allocate a host write buffer for copying type data
|
||||
UCL_H_Vec<numtyp> host_write(lj_types*lj_types*32,*(this->ucl_device),
|
||||
UCL_WRITE_OPTIMIZED);
|
||||
|
||||
for (int i=0; i<lj_types*lj_types; i++)
|
||||
host_write[i]=0.0;
|
||||
|
||||
sigma_epsilon.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
|
||||
this->atom->type_pack2(ntypes,lj_types,sigma_epsilon,host_write,
|
||||
host_sigma,host_epsilon);
|
||||
|
||||
this->cut_form.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
|
||||
this->atom->type_pack2(ntypes,lj_types,this->cut_form,host_write,
|
||||
host_cutsq,h_form);
|
||||
|
||||
lj1.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
|
||||
this->atom->type_pack4(ntypes,lj_types,lj1,host_write,host_lj1,host_lj2,
|
||||
host_cutsq,h_form);
|
||||
|
||||
lj3.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
|
||||
this->atom->type_pack4(ntypes,lj_types,lj3,host_write,host_lj3,host_lj4,
|
||||
host_offset);
|
||||
|
||||
dev_error.alloc(1,*(this->ucl_device));
|
||||
dev_error.zero();
|
||||
|
||||
// Allocate, cast and asynchronous memcpy of constant data
|
||||
// Copy data for bonded interactions
|
||||
gamma_upsilon_mu.alloc(7,*(this->ucl_device),UCL_READ_ONLY);
|
||||
host_write[0]=static_cast<numtyp>(gamma);
|
||||
host_write[1]=static_cast<numtyp>(upsilon);
|
||||
host_write[2]=static_cast<numtyp>(mu);
|
||||
host_write[3]=static_cast<numtyp>(host_special_lj[0]);
|
||||
host_write[4]=static_cast<numtyp>(host_special_lj[1]);
|
||||
host_write[5]=static_cast<numtyp>(host_special_lj[2]);
|
||||
host_write[6]=static_cast<numtyp>(host_special_lj[3]);
|
||||
ucl_copy(gamma_upsilon_mu,host_write,7,false);
|
||||
|
||||
lshape.alloc(ntypes,*(this->ucl_device),UCL_READ_ONLY);
|
||||
UCL_H_Vec<double> d_view;
|
||||
d_view.view(host_lshape,lshape.numel(),*(this->ucl_device));
|
||||
ucl_copy(lshape,d_view,false);
|
||||
|
||||
// Copy shape, well, sigma, epsilon, and cutsq onto GPU
|
||||
// - cast if necessary
|
||||
shape.alloc(ntypes,*(this->ucl_device),UCL_READ_ONLY);
|
||||
for (int i=0; i<ntypes; i++) {
|
||||
host_write[i*4]=host_shape[i][0];
|
||||
host_write[i*4+1]=host_shape[i][1];
|
||||
host_write[i*4+2]=host_shape[i][2];
|
||||
}
|
||||
UCL_H_Vec<numtyp4> view4;
|
||||
view4.view((numtyp4*)host_write.begin(),shape.numel(),*(this->ucl_device));
|
||||
ucl_copy(shape,view4,false);
|
||||
|
||||
well.alloc(ntypes,*(this->ucl_device),UCL_READ_ONLY);
|
||||
for (int i=0; i<ntypes; i++) {
|
||||
host_write[i*4]=host_well[i][0];
|
||||
host_write[i*4+1]=host_well[i][1];
|
||||
host_write[i*4+2]=host_well[i][2];
|
||||
}
|
||||
view4.view((numtyp4*)host_write.begin(),well.numel(),*(this->ucl_device));
|
||||
ucl_copy(well,view4,false);
|
||||
|
||||
_allocated=true;
|
||||
this->_max_bytes=sigma_epsilon.row_bytes()+this->cut_form.row_bytes()+
|
||||
lj1.row_bytes()+lj3.row_bytes()+gamma_upsilon_mu.row_bytes()+
|
||||
lshape.row_bytes()+shape.row_bytes()+well.row_bytes();
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
void GayBerneT::clear() {
|
||||
if (!_allocated)
|
||||
return;
|
||||
|
||||
UCL_H_Vec<int> err_flag(1,*(this->ucl_device));
|
||||
ucl_copy(err_flag,dev_error,false);
|
||||
if (err_flag[0] == 2)
|
||||
std::cerr << "BAD MATRIX INVERSION IN FORCE COMPUTATION.\n";
|
||||
err_flag.clear();
|
||||
|
||||
_allocated=false;
|
||||
|
||||
dev_error.clear();
|
||||
lj1.clear();
|
||||
lj3.clear();
|
||||
sigma_epsilon.clear();
|
||||
this->cut_form.clear();
|
||||
|
||||
shape.clear();
|
||||
well.clear();
|
||||
lshape.clear();
|
||||
gamma_upsilon_mu.clear();
|
||||
|
||||
this->clear_base();
|
||||
}
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
double GayBerneT::host_memory_usage() const {
|
||||
return this->host_memory_usage_base()+sizeof(GayBerneT)+
|
||||
4*sizeof(numtyp);
|
||||
}
|
||||
|
||||
// ---------------------------------------------------------------------------
|
||||
// Calculate energies, forces, and torques
|
||||
// ---------------------------------------------------------------------------
|
||||
template <class numtyp, class acctyp>
|
||||
void GayBerneT::loop(const bool _eflag, const bool _vflag) {
|
||||
const int BX=this->block_size();
|
||||
int eflag, vflag;
|
||||
if (_eflag)
|
||||
eflag=1;
|
||||
else
|
||||
eflag=0;
|
||||
|
||||
if (_vflag)
|
||||
vflag=1;
|
||||
else
|
||||
vflag=0;
|
||||
|
||||
int GX=0, NGX;
|
||||
int stride=this->nbor->nbor_pitch();
|
||||
int ainum=this->ans->inum();
|
||||
|
||||
if (this->_multiple_forms) {
|
||||
this->time_nbor1.start();
|
||||
if (this->_last_ellipse>0) {
|
||||
// ------------ ELLIPSE_ELLIPSE and ELLIPSE_SPHERE ---------------
|
||||
GX=static_cast<int>(ceil(static_cast<double>(this->_last_ellipse)/
|
||||
(BX/this->_threads_per_atom)));
|
||||
NGX=static_cast<int>(ceil(static_cast<double>(this->_last_ellipse)/BX));
|
||||
this->pack_nbors(NGX,BX, 0, this->_last_ellipse,ELLIPSE_SPHERE,
|
||||
ELLIPSE_ELLIPSE,_shared_types,_lj_types);
|
||||
this->time_nbor1.stop();
|
||||
|
||||
this->time_ellipsoid.start();
|
||||
this->k_ellipsoid.set_size(GX,BX);
|
||||
this->k_ellipsoid.run(&this->atom->dev_x.begin(),
|
||||
&this->atom->dev_quat.begin(), &this->shape.begin(), &this->well.begin(),
|
||||
&this->gamma_upsilon_mu.begin(), &this->sigma_epsilon.begin(),
|
||||
&this->_lj_types, &this->lshape.begin(), &this->nbor->dev_nbor.begin(),
|
||||
&stride, &this->ans->dev_ans.begin(),&ainum,&this->ans->dev_engv.begin(),
|
||||
&this->dev_error.begin(), &eflag, &vflag, &this->_last_ellipse,
|
||||
&this->_threads_per_atom);
|
||||
this->time_ellipsoid.stop();
|
||||
|
||||
if (this->_last_ellipse==this->ans->inum()) {
|
||||
this->time_nbor2.start();
|
||||
this->time_nbor2.stop();
|
||||
this->time_ellipsoid2.start();
|
||||
this->time_ellipsoid2.stop();
|
||||
this->time_lj.start();
|
||||
this->time_lj.stop();
|
||||
return;
|
||||
}
|
||||
|
||||
// ------------ SPHERE_ELLIPSE ---------------
|
||||
|
||||
this->time_nbor2.start();
|
||||
GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum()-
|
||||
this->_last_ellipse)/
|
||||
(BX/this->_threads_per_atom)));
|
||||
NGX=static_cast<int>(ceil(static_cast<double>(this->ans->inum()-
|
||||
this->_last_ellipse)/BX));
|
||||
this->pack_nbors(NGX,BX,this->_last_ellipse,this->ans->inum(),
|
||||
SPHERE_ELLIPSE,SPHERE_ELLIPSE,_shared_types,_lj_types);
|
||||
this->time_nbor2.stop();
|
||||
|
||||
this->time_ellipsoid2.start();
|
||||
this->k_sphere_ellipsoid.set_size(GX,BX);
|
||||
this->k_sphere_ellipsoid.run(&this->atom->dev_x.begin(),
|
||||
&this->atom->dev_quat.begin(), &this->shape.begin(),
|
||||
&this->well.begin(), &this->gamma_upsilon_mu.begin(),
|
||||
&this->sigma_epsilon.begin(), &this->_lj_types, &this->lshape.begin(),
|
||||
&this->nbor->dev_nbor.begin(), &stride, &this->ans->dev_ans.begin(),
|
||||
&this->ans->dev_engv.begin(), &this->dev_error.begin(), &eflag,
|
||||
&vflag, &this->_last_ellipse, &ainum, &this->_threads_per_atom);
|
||||
this->time_ellipsoid2.stop();
|
||||
} else {
|
||||
this->ans->dev_ans.zero();
|
||||
this->ans->dev_engv.zero();
|
||||
this->time_nbor1.stop();
|
||||
this->time_ellipsoid.start();
|
||||
this->time_ellipsoid.stop();
|
||||
this->time_nbor2.start();
|
||||
this->time_nbor2.stop();
|
||||
this->time_ellipsoid2.start();
|
||||
this->time_ellipsoid2.stop();
|
||||
}
|
||||
|
||||
// ------------ LJ ---------------
|
||||
this->time_lj.start();
|
||||
if (this->_last_ellipse<this->ans->inum()) {
|
||||
if (this->_shared_types) {
|
||||
this->k_lj_fast.set_size(GX,BX);
|
||||
this->k_lj_fast.run(&this->atom->dev_x.begin(), &this->lj1.begin(),
|
||||
&this->lj3.begin(), &this->gamma_upsilon_mu.begin(), &stride,
|
||||
&this->nbor->dev_packed.begin(), &this->ans->dev_ans.begin(),
|
||||
&this->ans->dev_engv.begin(), &this->dev_error.begin(),
|
||||
&eflag, &vflag, &this->_last_ellipse, &ainum,
|
||||
&this->_threads_per_atom);
|
||||
} else {
|
||||
this->k_lj.set_size(GX,BX);
|
||||
this->k_lj.run(&this->atom->dev_x.begin(), &this->lj1.begin(),
|
||||
&this->lj3.begin(), &this->_lj_types, &this->gamma_upsilon_mu.begin(),
|
||||
&stride, &this->nbor->dev_packed.begin(), &this->ans->dev_ans.begin(),
|
||||
&this->ans->dev_engv.begin(), &this->dev_error.begin(), &eflag,
|
||||
&vflag, &this->_last_ellipse, &ainum, &this->_threads_per_atom);
|
||||
}
|
||||
}
|
||||
this->time_lj.stop();
|
||||
} else {
|
||||
GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
|
||||
(BX/this->_threads_per_atom)));
|
||||
NGX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/BX));
|
||||
this->time_nbor1.start();
|
||||
this->pack_nbors(NGX, BX, 0, this->ans->inum(),SPHERE_SPHERE,
|
||||
ELLIPSE_ELLIPSE,_shared_types,_lj_types);
|
||||
this->time_nbor1.stop();
|
||||
this->time_ellipsoid.start();
|
||||
this->k_ellipsoid.set_size(GX,BX);
|
||||
this->k_ellipsoid.run(&this->atom->dev_x.begin(),
|
||||
&this->atom->dev_quat.begin(), &this->shape.begin(), &this->well.begin(),
|
||||
&this->gamma_upsilon_mu.begin(), &this->sigma_epsilon.begin(),
|
||||
&this->_lj_types, &this->lshape.begin(), &this->nbor->dev_nbor.begin(),
|
||||
&stride, &this->ans->dev_ans.begin(), &ainum,
|
||||
&this->ans->dev_engv.begin(), &this->dev_error.begin(),
|
||||
&eflag, &vflag, &ainum, &this->_threads_per_atom);
|
||||
this->time_ellipsoid.stop();
|
||||
}
|
||||
}
|
||||
|
||||
template class GayBerne<PRECISION,ACC_PRECISION>;
|
||||
|
||||
|
|
@ -0,0 +1,95 @@
|
|||
/***************************************************************************
|
||||
gayberne.h
|
||||
-------------------
|
||||
W. Michael Brown
|
||||
|
||||
Host code for Gay-Berne potential acceleration
|
||||
|
||||
__________________________________________________________________________
|
||||
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
|
||||
__________________________________________________________________________
|
||||
|
||||
begin :
|
||||
email : brownw@ornl.gov
|
||||
***************************************************************************/
|
||||
|
||||
#ifndef GAYBERNE_H
|
||||
#define GAYBERNE_H
|
||||
|
||||
#include "base_ellipsoid.h"
|
||||
#include "mpi.h"
|
||||
|
||||
namespace LAMMPS_AL {
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
class GayBerne : public BaseEllipsoid<numtyp, acctyp> {
|
||||
public:
|
||||
GayBerne();
|
||||
~GayBerne();
|
||||
|
||||
/// Clear any previous data and set up for a new LAMMPS run
|
||||
/** \param gpu_nbor true if neighboring performed on device
|
||||
* \param max_nbors initial number of rows in the neighbor matrix
|
||||
* \param cell_size cutoff + skin
|
||||
* \param gpu_split fraction of particles handled by device
|
||||
* \return false if there is not sufficient memory or device init prob
|
||||
*
|
||||
* Returns:
|
||||
* - 0 if successfull
|
||||
* - -1 if fix gpu not found
|
||||
* - -3 if there is an out of memory error
|
||||
* - -4 if the GPU library was not compiled for GPU
|
||||
* - -5 Double precision is not supported on card **/
|
||||
int init(const int ntypes, const double gamma,
|
||||
const double upsilon, const double mu, double **host_shape,
|
||||
double **host_well, double **host_cutsq, double **host_sigma,
|
||||
double **host_epsilon, double *host_lshape, int **h_form,
|
||||
double **host_lj1, double **host_lj2, double **host_lj3,
|
||||
double **host_lj4, double **host_offset,
|
||||
const double *host_special_lj, const int nlocal, const int nall,
|
||||
const int max_nbors, const int maxspecial, const double cell_size,
|
||||
const double gpu_split, FILE *screen);
|
||||
|
||||
/// Clear all host and device data
|
||||
/** \note This is called at the beginning of the init() routine **/
|
||||
void clear();
|
||||
|
||||
/// Returns memory usage on device per atom
|
||||
int bytes_per_atom(const int max_nbors) const;
|
||||
|
||||
/// Total host memory used by library for pair style
|
||||
double host_memory_usage() const;
|
||||
|
||||
/// Device Error Flag - Set if a bad matrix inversion occurs
|
||||
UCL_D_Vec<int> dev_error;
|
||||
|
||||
// --------------------------- TYPE DATA --------------------------
|
||||
|
||||
/// lj1.x = lj1, lj1.y = lj2, lj1.z = cutsq, lj1.w = form
|
||||
UCL_D_Vec<numtyp4> lj1;
|
||||
/// lj3.x = lj3, lj3.y = lj4, lj3.z = offset
|
||||
UCL_D_Vec<numtyp4> lj3;
|
||||
/// sigma_epsilon.x = sigma, sigma_epsilon.y = epsilon
|
||||
UCL_D_Vec<numtyp2> sigma_epsilon;
|
||||
// 0 - gamma, 1-upsilon, 2-mu, 3-special_lj[0], 4-special_lj[1], ...
|
||||
UCL_D_Vec<numtyp> gamma_upsilon_mu;
|
||||
|
||||
/// If atom type constants fit in shared memory, use fast kernels
|
||||
bool _shared_types;
|
||||
int _lj_types;
|
||||
|
||||
// --------------------------- ATOM DATA --------------------------
|
||||
|
||||
/// Aspherical Const Data for Atoms
|
||||
UCL_D_Vec<numtyp4> shape, well;
|
||||
/// Aspherical Const Data for Atoms
|
||||
UCL_D_Vec<numtyp> lshape;
|
||||
|
||||
private:
|
||||
bool _allocated;
|
||||
void loop(const bool _eflag, const bool _vflag);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
|
|
@ -0,0 +1,141 @@
|
|||
/***************************************************************************
|
||||
gayberne_ext.cpp
|
||||
-------------------
|
||||
W. Michael Brown
|
||||
|
||||
LAMMPS Wrappers for Gay-Berne Acceleration
|
||||
|
||||
__________________________________________________________________________
|
||||
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
|
||||
__________________________________________________________________________
|
||||
|
||||
begin :
|
||||
email : brownw@ornl.gov
|
||||
***************************************************************************/
|
||||
|
||||
#include <iostream>
|
||||
#include <cassert>
|
||||
#include <math.h>
|
||||
|
||||
#include "gayberne.h"
|
||||
|
||||
using namespace std;
|
||||
using namespace LAMMPS_AL;
|
||||
|
||||
static GayBerne<PRECISION,ACC_PRECISION> GBMF;
|
||||
|
||||
// ---------------------------------------------------------------------------
|
||||
// Allocate memory on host and device and copy constants to device
|
||||
// ---------------------------------------------------------------------------
|
||||
int gb_gpu_init(const int ntypes, const double gamma,
|
||||
const double upsilon, const double mu, double **shape,
|
||||
double **well, double **cutsq, double **sigma,
|
||||
double **epsilon, double *host_lshape, int **form,
|
||||
double **host_lj1, double **host_lj2, double **host_lj3,
|
||||
double **host_lj4, double **offset, double *special_lj,
|
||||
const int inum, const int nall, const int max_nbors,
|
||||
const int maxspecial, const double cell_size, int &gpu_mode,
|
||||
FILE *screen) {
|
||||
GBMF.clear();
|
||||
gpu_mode=GBMF.device->gpu_mode();
|
||||
double gpu_split=GBMF.device->particle_split();
|
||||
int first_gpu=GBMF.device->first_device();
|
||||
int last_gpu=GBMF.device->last_device();
|
||||
int world_me=GBMF.device->world_me();
|
||||
int gpu_rank=GBMF.device->gpu_rank();
|
||||
int procs_per_gpu=GBMF.device->procs_per_gpu();
|
||||
|
||||
GBMF.device->init_message(screen,"gayberne",first_gpu,last_gpu);
|
||||
|
||||
bool message=false;
|
||||
if (GBMF.device->replica_me()==0 && screen)
|
||||
message=true;
|
||||
|
||||
if (message) {
|
||||
fprintf(screen,"Initializing GPU and compiling on process 0...");
|
||||
fflush(screen);
|
||||
}
|
||||
|
||||
int init_ok=0;
|
||||
if (world_me==0)
|
||||
init_ok=GBMF.init(ntypes, gamma, upsilon, mu, shape, well, cutsq,
|
||||
sigma, epsilon, host_lshape, form, host_lj1,
|
||||
host_lj2, host_lj3, host_lj4, offset, special_lj,
|
||||
inum, nall, max_nbors, maxspecial, cell_size, gpu_split,
|
||||
screen);
|
||||
|
||||
GBMF.device->world_barrier();
|
||||
if (message)
|
||||
fprintf(screen,"Done.\n");
|
||||
|
||||
for (int i=0; i<procs_per_gpu; i++) {
|
||||
if (message) {
|
||||
if (last_gpu-first_gpu==0)
|
||||
fprintf(screen,"Initializing GPU %d on core %d...",first_gpu,i);
|
||||
else
|
||||
fprintf(screen,"Initializing GPUs %d-%d on core %d...",first_gpu,
|
||||
last_gpu,i);
|
||||
fflush(screen);
|
||||
}
|
||||
if (gpu_rank==i && world_me!=0)
|
||||
init_ok=GBMF.init(ntypes, gamma, upsilon, mu, shape, well, cutsq, sigma,
|
||||
epsilon, host_lshape, form, host_lj1, host_lj2,
|
||||
host_lj3, host_lj4, offset, special_lj, inum, nall,
|
||||
max_nbors, maxspecial, cell_size, gpu_split, screen);
|
||||
|
||||
GBMF.device->gpu_barrier();
|
||||
if (message)
|
||||
fprintf(screen,"Done.\n");
|
||||
}
|
||||
if (message)
|
||||
fprintf(screen,"\n");
|
||||
|
||||
if (init_ok==0)
|
||||
GBMF.estimate_gpu_overhead();
|
||||
return init_ok;
|
||||
}
|
||||
|
||||
// ---------------------------------------------------------------------------
|
||||
// Clear memory on host and device
|
||||
// ---------------------------------------------------------------------------
|
||||
void gb_gpu_clear() {
|
||||
GBMF.clear();
|
||||
}
|
||||
|
||||
int** compute(const int ago, const int inum_full, const int nall,
|
||||
double **host_x, int *host_type, double *sublo,
|
||||
double *subhi, int *tag, int **nspecial,
|
||||
int **special, const bool eflag, const bool vflag,
|
||||
const bool eatom, const bool vatom, int &host_start,
|
||||
int **ilist, int **numj, const double cpu_time, bool &success,
|
||||
double **host_quat);
|
||||
|
||||
int** gb_gpu_compute_n(const int ago, const int inum_full, const int nall,
|
||||
double **host_x, int *host_type, double *sublo,
|
||||
double *subhi, int *tag, int **nspecial, int **special,
|
||||
const bool eflag, const bool vflag, const bool eatom,
|
||||
const bool vatom, int &host_start, int **ilist,
|
||||
int **jnum, const double cpu_time, bool &success,
|
||||
double **host_quat) {
|
||||
return GBMF.compute(ago, inum_full, nall, host_x, host_type, sublo, subhi,
|
||||
tag, nspecial, special, eflag, vflag, eatom, vatom,
|
||||
host_start, ilist, jnum, cpu_time, success, host_quat);
|
||||
}
|
||||
|
||||
int * gb_gpu_compute(const int ago, const int inum_full, const int nall,
|
||||
double **host_x, int *host_type, int *ilist, int *numj,
|
||||
int **firstneigh, const bool eflag, const bool vflag,
|
||||
const bool eatom, const bool vatom, int &host_start,
|
||||
const double cpu_time, bool &success, double **host_quat) {
|
||||
return GBMF.compute(ago, inum_full, nall, host_x, host_type, ilist,
|
||||
numj, firstneigh, eflag, vflag, eatom, vatom, host_start,
|
||||
cpu_time, success, host_quat);
|
||||
}
|
||||
|
||||
// ---------------------------------------------------------------------------
|
||||
// Return memory usage
|
||||
// ---------------------------------------------------------------------------
|
||||
double gb_gpu_bytes() {
|
||||
return GBMF.host_memory_usage();
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,168 @@
|
|||
/***************************************************************************
|
||||
lj_class2_long.cpp
|
||||
-------------------
|
||||
W. Michael Brown
|
||||
|
||||
Host code for COMPASS LJ long potential acceleration
|
||||
|
||||
__________________________________________________________________________
|
||||
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
|
||||
__________________________________________________________________________
|
||||
|
||||
begin : Mon May 16 2011
|
||||
email : brownw@ornl.gov
|
||||
***************************************************************************/
|
||||
|
||||
#ifdef USE_OPENCL
|
||||
#include "lj_class2_long_cl.h"
|
||||
#else
|
||||
#include "lj_class2_long_ptx.h"
|
||||
#endif
|
||||
|
||||
#include "lj_class2_long.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
|
||||
#define LJClass2LongT LJClass2Long<numtyp, acctyp>
|
||||
|
||||
extern PairGPUDevice<PRECISION,ACC_PRECISION> pair_gpu_device;
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
LJClass2LongT::LJClass2Long() : ChargeGPUMemory<numtyp,acctyp>(),
|
||||
_allocated(false) {
|
||||
}
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
LJClass2LongT::~LJClass2Long() {
|
||||
clear();
|
||||
}
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
int LJClass2LongT::bytes_per_atom(const int max_nbors) const {
|
||||
return this->bytes_per_atom_atomic(max_nbors);
|
||||
}
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
int LJClass2LongT::init(const int ntypes, double **host_cutsq,
|
||||
double **host_lj1, double **host_lj2, double **host_lj3,
|
||||
double **host_lj4, double **host_offset,
|
||||
double *host_special_lj, const int nlocal,
|
||||
const int nall, const int max_nbors,
|
||||
const int maxspecial, const double cell_size,
|
||||
const double gpu_split, FILE *_screen,
|
||||
double **host_cut_ljsq, const double host_cut_coulsq,
|
||||
double *host_special_coul, const double qqrd2e,
|
||||
const double g_ewald) {
|
||||
int success;
|
||||
success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split,
|
||||
_screen,lj_class2_long);
|
||||
if (success!=0)
|
||||
return success;
|
||||
|
||||
// If atom type constants fit in shared memory use fast kernel
|
||||
int lj_types=ntypes;
|
||||
shared_types=false;
|
||||
int max_shared_types=this->device->max_shared_types();
|
||||
if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) {
|
||||
lj_types=max_shared_types;
|
||||
shared_types=true;
|
||||
}
|
||||
_lj_types=lj_types;
|
||||
|
||||
// Allocate a host write buffer for data initialization
|
||||
UCL_H_Vec<numtyp> host_write(lj_types*lj_types*32,*(this->ucl_device),
|
||||
UCL_WRITE_OPTIMIZED);
|
||||
|
||||
for (int i=0; i<lj_types*lj_types; i++)
|
||||
host_write[i]=0.0;
|
||||
|
||||
lj1.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
|
||||
this->atom->type_pack4(ntypes,lj_types,lj1,host_write,host_lj1,host_lj2,
|
||||
host_cutsq, host_cut_ljsq);
|
||||
|
||||
lj3.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
|
||||
this->atom->type_pack4(ntypes,lj_types,lj3,host_write,host_lj3,host_lj4,
|
||||
host_offset);
|
||||
|
||||
sp_lj.alloc(8,*(this->ucl_device),UCL_READ_ONLY);
|
||||
for (int i=0; i<4; i++) {
|
||||
host_write[i]=host_special_lj[i];
|
||||
host_write[i+4]=host_special_coul[i];
|
||||
}
|
||||
ucl_copy(sp_lj,host_write,8,false);
|
||||
|
||||
_cut_coulsq=host_cut_coulsq;
|
||||
_qqrd2e=qqrd2e;
|
||||
_g_ewald=g_ewald;
|
||||
|
||||
_allocated=true;
|
||||
this->_max_bytes=lj1.row_bytes()+lj3.row_bytes()+sp_lj.row_bytes();
|
||||
return 0;
|
||||
}
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
void LJClass2LongT::clear() {
|
||||
if (!_allocated)
|
||||
return;
|
||||
_allocated=false;
|
||||
|
||||
lj1.clear();
|
||||
lj3.clear();
|
||||
sp_lj.clear();
|
||||
this->clear_atomic();
|
||||
}
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
double LJClass2LongT::host_memory_usage() const {
|
||||
return this->host_memory_usage_atomic()+sizeof(LJClass2Long<numtyp,acctyp>);
|
||||
}
|
||||
|
||||
// ---------------------------------------------------------------------------
|
||||
// Calculate energies, forces, and torques
|
||||
// ---------------------------------------------------------------------------
|
||||
template <class numtyp, class acctyp>
|
||||
void LJClass2LongT::loop(const bool _eflag, const bool _vflag) {
|
||||
// Compute the block size and grid size to keep all cores busy
|
||||
const int BX=this->block_size();
|
||||
int eflag, vflag;
|
||||
if (_eflag)
|
||||
eflag=1;
|
||||
else
|
||||
eflag=0;
|
||||
|
||||
if (_vflag)
|
||||
vflag=1;
|
||||
else
|
||||
vflag=0;
|
||||
|
||||
int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
|
||||
(BX/this->_threads_per_atom)));
|
||||
|
||||
int ainum=this->ans->inum();
|
||||
int nbor_pitch=this->nbor->nbor_pitch();
|
||||
this->time_pair.start();
|
||||
if (shared_types) {
|
||||
this->k_pair_fast.set_size(GX,BX);
|
||||
this->k_pair_fast.run(&this->atom->dev_x.begin(), &lj1.begin(),
|
||||
&lj3.begin(), &sp_lj.begin(),
|
||||
&this->nbor->dev_nbor.begin(),
|
||||
&this->_nbor_data->begin(),
|
||||
&this->ans->dev_ans.begin(),
|
||||
&this->ans->dev_engv.begin(), &eflag, &vflag,
|
||||
&ainum, &nbor_pitch, &this->atom->dev_q.begin(),
|
||||
&_cut_coulsq, &_qqrd2e, &_g_ewald,
|
||||
&this->_threads_per_atom);
|
||||
} else {
|
||||
this->k_pair.set_size(GX,BX);
|
||||
this->k_pair.run(&this->atom->dev_x.begin(), &lj1.begin(), &lj3.begin(),
|
||||
&_lj_types, &sp_lj.begin(), &this->nbor->dev_nbor.begin(),
|
||||
&this->_nbor_data->begin(), &this->ans->dev_ans.begin(),
|
||||
&this->ans->dev_engv.begin(), &eflag, &vflag, &ainum,
|
||||
&nbor_pitch, &this->atom->dev_q.begin(), &_cut_coulsq,
|
||||
&_qqrd2e, &_g_ewald, &this->_threads_per_atom);
|
||||
}
|
||||
this->time_pair.stop();
|
||||
}
|
||||
|
||||
template class LJClass2Long<PRECISION,ACC_PRECISION>;
|
||||
|
||||
|
|
@ -0,0 +1,84 @@
|
|||
/***************************************************************************
|
||||
lj_class2_long.h
|
||||
-------------------
|
||||
W. Michael Brown
|
||||
|
||||
Host code for COMPASS LJ long potential acceleration
|
||||
|
||||
__________________________________________________________________________
|
||||
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
|
||||
__________________________________________________________________________
|
||||
|
||||
begin : Mon May 16 2011
|
||||
email : brownw@ornl.gov
|
||||
***************************************************************************/
|
||||
|
||||
#ifndef LJ_CLASS2_LONG_H
|
||||
#define LJ_CLASS2_LONG_H
|
||||
|
||||
#include "charge_gpu_memory.h"
|
||||
|
||||
namespace LAMMPS_AL {
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
class LJClass2Long : public ChargeGPUMemory<numtyp, acctyp> {
|
||||
public:
|
||||
LJClass2Long();
|
||||
~LJClass2Long();
|
||||
|
||||
/// Clear any previous data and set up for a new LAMMPS run
|
||||
/** \param max_nbors initial number of rows in the neighbor matrix
|
||||
* \param cell_size cutoff + skin
|
||||
* \param gpu_split fraction of particles handled by device
|
||||
*
|
||||
* Returns:
|
||||
* - 0 if successfull
|
||||
* - -1 if fix gpu not found
|
||||
* - -3 if there is an out of memory error
|
||||
* - -4 if the GPU library was not compiled for GPU
|
||||
* - -5 Double precision is not supported on card **/
|
||||
int init(const int ntypes, double **host_cutsq,
|
||||
double **host_lj1, double **host_lj2, double **host_lj3,
|
||||
double **host_lj4, double **host_offset, double *host_special_lj,
|
||||
const int nlocal, const int nall, const int max_nbors,
|
||||
const int maxspecial, const double cell_size,
|
||||
const double gpu_split, FILE *screen, double **host_cut_ljsq,
|
||||
const double host_cut_coulsq, double *host_special_coul,
|
||||
const double qqrd2e, const double g_ewald);
|
||||
|
||||
/// Clear all host and device data
|
||||
/** \note This is called at the beginning of the init() routine **/
|
||||
void clear();
|
||||
|
||||
/// Returns memory usage on device per atom
|
||||
int bytes_per_atom(const int max_nbors) const;
|
||||
|
||||
/// Total host memory used by library for pair style
|
||||
double host_memory_usage() const;
|
||||
|
||||
// --------------------------- TYPE DATA --------------------------
|
||||
|
||||
/// lj1.x = lj1, lj1.y = lj2, lj1.z = cutsq, lj1.w = cutsq_vdw
|
||||
UCL_D_Vec<numtyp4> lj1;
|
||||
/// lj3.x = lj3, lj3.y = lj4, lj3.z = offset
|
||||
UCL_D_Vec<numtyp4> lj3;
|
||||
/// Special LJ values [0-3] and Special Coul values [4-7]
|
||||
UCL_D_Vec<numtyp> sp_lj;
|
||||
|
||||
/// If atom type constants fit in shared memory, use fast kernels
|
||||
bool shared_types;
|
||||
|
||||
/// Number of atom types
|
||||
int _lj_types;
|
||||
|
||||
numtyp _cut_coulsq, _qqrd2e, _g_ewald;
|
||||
|
||||
private:
|
||||
bool _allocated;
|
||||
void loop(const bool _eflag, const bool _vflag);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
|
||||
|
|
@ -0,0 +1,129 @@
|
|||
/***************************************************************************
|
||||
lj_class2_long_ext.cpp
|
||||
-------------------
|
||||
W. Michael Brown
|
||||
|
||||
LAMMPS Wrappers for COMMPASS LJ long Acceleration
|
||||
|
||||
__________________________________________________________________________
|
||||
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
|
||||
__________________________________________________________________________
|
||||
|
||||
begin : Mon May 16 2011
|
||||
email : brownw@ornl.gov
|
||||
***************************************************************************/
|
||||
|
||||
#include <iostream>
|
||||
#include <cassert>
|
||||
#include <math.h>
|
||||
|
||||
#include "lj_class2_long.h"
|
||||
|
||||
using namespace std;
|
||||
using namespace LAMMPS_AL;
|
||||
|
||||
static LJClass2Long<PRECISION,ACC_PRECISION> C2CLMF;
|
||||
|
||||
// ---------------------------------------------------------------------------
|
||||
// Allocate memory on host and device and copy constants to device
|
||||
// ---------------------------------------------------------------------------
|
||||
int c2cl_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
|
||||
double **host_lj2, double **host_lj3, double **host_lj4,
|
||||
double **offset, double *special_lj, const int inum,
|
||||
const int nall, const int max_nbors, const int maxspecial,
|
||||
const double cell_size, int &gpu_mode, FILE *screen,
|
||||
double **host_cut_ljsq, double host_cut_coulsq,
|
||||
double *host_special_coul, const double qqrd2e,
|
||||
const double g_ewald) {
|
||||
C2CLMF.clear();
|
||||
gpu_mode=C2CLMF.device->gpu_mode();
|
||||
double gpu_split=C2CLMF.device->particle_split();
|
||||
int first_gpu=C2CLMF.device->first_device();
|
||||
int last_gpu=C2CLMF.device->last_device();
|
||||
int world_me=C2CLMF.device->world_me();
|
||||
int gpu_rank=C2CLMF.device->gpu_rank();
|
||||
int procs_per_gpu=C2CLMF.device->procs_per_gpu();
|
||||
|
||||
C2CLMF.device->init_message(screen,"lj/class2/coul/long",first_gpu,last_gpu);
|
||||
|
||||
bool message=false;
|
||||
if (C2CLMF.device->replica_me()==0 && screen)
|
||||
message=true;
|
||||
|
||||
if (message) {
|
||||
fprintf(screen,"Initializing GPU and compiling on process 0...");
|
||||
fflush(screen);
|
||||
}
|
||||
|
||||
int init_ok=0;
|
||||
if (world_me==0)
|
||||
init_ok=C2CLMF.init(ntypes, cutsq, host_lj1, host_lj2, host_lj3, host_lj4,
|
||||
offset, special_lj, inum, nall, 300, maxspecial,
|
||||
cell_size, gpu_split, screen, host_cut_ljsq,
|
||||
host_cut_coulsq, host_special_coul, qqrd2e, g_ewald);
|
||||
|
||||
C2CLMF.device->world_barrier();
|
||||
if (message)
|
||||
fprintf(screen,"Done.\n");
|
||||
|
||||
for (int i=0; i<procs_per_gpu; i++) {
|
||||
if (message) {
|
||||
if (last_gpu-first_gpu==0)
|
||||
fprintf(screen,"Initializing GPU %d on core %d...",first_gpu,i);
|
||||
else
|
||||
fprintf(screen,"Initializing GPUs %d-%d on core %d...",first_gpu,
|
||||
last_gpu,i);
|
||||
fflush(screen);
|
||||
}
|
||||
if (gpu_rank==i && world_me!=0)
|
||||
init_ok=C2CLMF.init(ntypes, cutsq, host_lj1, host_lj2, host_lj3, host_lj4,
|
||||
offset, special_lj, inum, nall, 300, maxspecial,
|
||||
cell_size, gpu_split, screen, host_cut_ljsq,
|
||||
host_cut_coulsq, host_special_coul, qqrd2e, g_ewald);
|
||||
|
||||
C2CLMF.device->gpu_barrier();
|
||||
if (message)
|
||||
fprintf(screen,"Done.\n");
|
||||
}
|
||||
if (message)
|
||||
fprintf(screen,"\n");
|
||||
|
||||
if (init_ok==0)
|
||||
C2CLMF.estimate_gpu_overhead();
|
||||
return init_ok;
|
||||
}
|
||||
|
||||
void c2cl_gpu_clear() {
|
||||
C2CLMF.clear();
|
||||
}
|
||||
|
||||
int** c2cl_gpu_compute_n(const int ago, const int inum_full,
|
||||
const int nall, double **host_x, int *host_type,
|
||||
double *sublo, double *subhi, int *tag, int **nspecial,
|
||||
int **special, const bool eflag, const bool vflag,
|
||||
const bool eatom, const bool vatom, int &host_start,
|
||||
int **ilist, int **jnum, const double cpu_time,
|
||||
bool &success, double *host_q, double *boxlo,
|
||||
double *prd) {
|
||||
return C2CLMF.compute(ago, inum_full, nall, host_x, host_type, sublo,
|
||||
subhi, tag, nspecial, special, eflag, vflag, eatom,
|
||||
vatom, host_start, ilist, jnum, cpu_time, success,
|
||||
host_q, boxlo, prd);
|
||||
}
|
||||
|
||||
void c2cl_gpu_compute(const int ago, const int inum_full, const int nall,
|
||||
double **host_x, int *host_type, int *ilist, int *numj,
|
||||
int **firstneigh, const bool eflag, const bool vflag,
|
||||
const bool eatom, const bool vatom, int &host_start,
|
||||
const double cpu_time, bool &success, double *host_q,
|
||||
const int nlocal, double *boxlo, double *prd) {
|
||||
C2CLMF.compute(ago,inum_full,nall,host_x,host_type,ilist,numj,
|
||||
firstneigh,eflag,vflag,eatom,vatom,host_start,cpu_time,success,
|
||||
host_q,nlocal,boxlo,prd);
|
||||
}
|
||||
|
||||
double c2cl_gpu_bytes() {
|
||||
return C2CLMF.host_memory_usage();
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,308 @@
|
|||
/***************************************************************************
|
||||
re_squared.cpp
|
||||
-------------------
|
||||
W. Michael Brown
|
||||
|
||||
Host code for RE-Squared potential acceleration
|
||||
|
||||
__________________________________________________________________________
|
||||
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
|
||||
__________________________________________________________________________
|
||||
|
||||
begin : Fri May 06 2011
|
||||
email : brownw@ornl.gov
|
||||
***************************************************************************/
|
||||
|
||||
#ifdef USE_OPENCL
|
||||
#include "re_squared_cl.h"
|
||||
#else
|
||||
#include "re_squared_ptx.h"
|
||||
#endif
|
||||
|
||||
#include "re_squared.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
|
||||
#define RESquaredT RESquared<numtyp, acctyp>
|
||||
extern PairGPUDevice<PRECISION,ACC_PRECISION> pair_gpu_device;
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
RESquaredT::RESquared() : BaseEllipsoid<numtyp,acctyp>(),
|
||||
_allocated(false) {
|
||||
}
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
RESquaredT::~RESquared() {
|
||||
clear();
|
||||
}
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
int RESquaredT::bytes_per_atom(const int max_nbors) const {
|
||||
return this->bytes_per_atom(max_nbors);
|
||||
}
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
int RESquaredT::init(const int ntypes, double **host_shape, double **host_well,
|
||||
double **host_cutsq, double **host_sigma,
|
||||
double **host_epsilon, int **h_form, double **host_lj1,
|
||||
double **host_lj2, double **host_lj3, double **host_lj4,
|
||||
double **host_offset, const double *host_special_lj,
|
||||
const int nlocal, const int nall, const int max_nbors,
|
||||
const int maxspecial, const double cell_size,
|
||||
const double gpu_split, FILE *_screen) {
|
||||
int success;
|
||||
success=this->init_base(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split,
|
||||
_screen,ntypes,h_form,re_squared,re_squared_lj,true);
|
||||
if (success!=0)
|
||||
return success;
|
||||
|
||||
// If atom type constants fit in shared memory use fast kernel
|
||||
int lj_types=ntypes;
|
||||
_shared_types=false;
|
||||
int max_shared_types=this->device->max_shared_types();
|
||||
if (lj_types<=max_shared_types && this->block_size()>=max_shared_types) {
|
||||
lj_types=max_shared_types;
|
||||
_shared_types=true;
|
||||
}
|
||||
_lj_types=lj_types;
|
||||
|
||||
// Allocate a host write buffer for copying type data
|
||||
UCL_H_Vec<numtyp> host_write(lj_types*lj_types*32,*(this->ucl_device),
|
||||
UCL_WRITE_OPTIMIZED);
|
||||
|
||||
for (int i=0; i<lj_types*lj_types; i++)
|
||||
host_write[i]=0.0;
|
||||
|
||||
sigma_epsilon.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
|
||||
this->atom->type_pack2(ntypes,lj_types,sigma_epsilon,host_write,
|
||||
host_sigma,host_epsilon);
|
||||
|
||||
this->cut_form.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
|
||||
this->atom->type_pack2(ntypes,lj_types,this->cut_form,host_write,
|
||||
host_cutsq,h_form);
|
||||
|
||||
lj1.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
|
||||
this->atom->type_pack4(ntypes,lj_types,lj1,host_write,host_lj1,host_lj2,
|
||||
host_cutsq,h_form);
|
||||
|
||||
lj3.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
|
||||
this->atom->type_pack4(ntypes,lj_types,lj3,host_write,host_lj3,host_lj4,
|
||||
host_offset);
|
||||
|
||||
dev_error.alloc(1,*(this->ucl_device));
|
||||
dev_error.zero();
|
||||
|
||||
// Allocate, cast and asynchronous memcpy of constant data
|
||||
// Copy data for bonded interactions
|
||||
special_lj.alloc(4,*(this->ucl_device),UCL_READ_ONLY);
|
||||
host_write[0]=static_cast<numtyp>(host_special_lj[0]);
|
||||
host_write[1]=static_cast<numtyp>(host_special_lj[1]);
|
||||
host_write[2]=static_cast<numtyp>(host_special_lj[2]);
|
||||
host_write[3]=static_cast<numtyp>(host_special_lj[3]);
|
||||
ucl_copy(special_lj,host_write,4,false);
|
||||
|
||||
// Copy shape, well, sigma, epsilon, and cutsq onto GPU
|
||||
// - cast if necessary
|
||||
shape.alloc(ntypes,*(this->ucl_device),UCL_READ_ONLY);
|
||||
for (int i=0; i<ntypes; i++) {
|
||||
host_write[i*4]=host_shape[i][0];
|
||||
host_write[i*4+1]=host_shape[i][1];
|
||||
host_write[i*4+2]=host_shape[i][2];
|
||||
}
|
||||
UCL_H_Vec<numtyp4> view4;
|
||||
view4.view((numtyp4*)host_write.begin(),shape.numel(),*(this->ucl_device));
|
||||
ucl_copy(shape,view4,false);
|
||||
|
||||
well.alloc(ntypes,*(this->ucl_device),UCL_READ_ONLY);
|
||||
for (int i=0; i<ntypes; i++) {
|
||||
host_write[i*4]=host_well[i][0];
|
||||
host_write[i*4+1]=host_well[i][1];
|
||||
host_write[i*4+2]=host_well[i][2];
|
||||
}
|
||||
view4.view((numtyp4*)host_write.begin(),well.numel(),*(this->ucl_device));
|
||||
ucl_copy(well,view4,false);
|
||||
|
||||
_allocated=true;
|
||||
this->_max_bytes=sigma_epsilon.row_bytes()+this->cut_form.row_bytes()+
|
||||
lj1.row_bytes()+lj3.row_bytes()+special_lj.row_bytes()+
|
||||
shape.row_bytes()+well.row_bytes();
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
void RESquaredT::clear() {
|
||||
if (!_allocated)
|
||||
return;
|
||||
|
||||
UCL_H_Vec<int> err_flag(1,*(this->ucl_device));
|
||||
ucl_copy(err_flag,dev_error,false);
|
||||
if (err_flag[0] == 2)
|
||||
std::cerr << "BAD MATRIX INVERSION IN FORCE COMPUTATION.\n";
|
||||
err_flag.clear();
|
||||
|
||||
_allocated=false;
|
||||
|
||||
dev_error.clear();
|
||||
lj1.clear();
|
||||
lj3.clear();
|
||||
sigma_epsilon.clear();
|
||||
this->cut_form.clear();
|
||||
|
||||
shape.clear();
|
||||
well.clear();
|
||||
special_lj.clear();
|
||||
|
||||
this->clear_base();
|
||||
}
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
double RESquaredT::host_memory_usage() const {
|
||||
return this->host_memory_usage_base()+sizeof(RESquaredT)+
|
||||
4*sizeof(numtyp);
|
||||
}
|
||||
|
||||
// ---------------------------------------------------------------------------
|
||||
// Calculate energies, forces, and torques
|
||||
// ---------------------------------------------------------------------------
|
||||
template <class numtyp, class acctyp>
|
||||
void RESquaredT::loop(const bool _eflag, const bool _vflag) {
|
||||
const int BX=this->block_size();
|
||||
int eflag, vflag;
|
||||
if (_eflag)
|
||||
eflag=1;
|
||||
else
|
||||
eflag=0;
|
||||
|
||||
if (_vflag)
|
||||
vflag=1;
|
||||
else
|
||||
vflag=0;
|
||||
|
||||
int GX, NGX;
|
||||
int stride=this->nbor->nbor_pitch();
|
||||
int ainum=this->ans->inum();
|
||||
|
||||
if (this->_multiple_forms) {
|
||||
if (this->_last_ellipse>0) {
|
||||
// ------------ ELLIPSE_ELLIPSE ---------------
|
||||
this->time_nbor1.start();
|
||||
GX=static_cast<int>(ceil(static_cast<double>(this->_last_ellipse)/
|
||||
(BX/this->_threads_per_atom)));
|
||||
NGX=static_cast<int>(ceil(static_cast<double>(this->_last_ellipse)/BX));
|
||||
this->pack_nbors(NGX,BX, 0, this->_last_ellipse,ELLIPSE_ELLIPSE,
|
||||
ELLIPSE_ELLIPSE,_shared_types,_lj_types);
|
||||
this->time_nbor1.stop();
|
||||
|
||||
this->time_ellipsoid.start();
|
||||
this->k_ellipsoid.set_size(GX,BX);
|
||||
this->k_ellipsoid.run(&this->atom->dev_x.begin(),
|
||||
&this->atom->dev_quat.begin(), &this->shape.begin(), &this->well.begin(),
|
||||
&this->special_lj.begin(), &this->sigma_epsilon.begin(),
|
||||
&this->_lj_types, &this->nbor->dev_nbor.begin(), &stride,
|
||||
&this->ans->dev_ans.begin(),&ainum,&this->ans->dev_engv.begin(),
|
||||
&this->dev_error.begin(), &eflag, &vflag, &this->_last_ellipse,
|
||||
&this->_threads_per_atom);
|
||||
this->time_ellipsoid.stop();
|
||||
|
||||
// ------------ ELLIPSE_SPHERE ---------------
|
||||
this->time_nbor2.start();
|
||||
this->pack_nbors(NGX,BX, 0, this->_last_ellipse,ELLIPSE_SPHERE,
|
||||
ELLIPSE_SPHERE,_shared_types,_lj_types);
|
||||
this->time_nbor2.stop();
|
||||
|
||||
this->time_ellipsoid2.start();
|
||||
this->k_ellipsoid_sphere.set_size(GX,BX);
|
||||
this->k_ellipsoid_sphere.run(&this->atom->dev_x.begin(),
|
||||
&this->atom->dev_quat.begin(), &this->shape.begin(), &this->well.begin(),
|
||||
&this->special_lj.begin(), &this->sigma_epsilon.begin(),
|
||||
&this->_lj_types, &this->nbor->dev_nbor.begin(), &stride,
|
||||
&this->ans->dev_ans.begin(),&ainum,&this->ans->dev_engv.begin(),
|
||||
&this->dev_error.begin(), &eflag, &vflag, &this->_last_ellipse,
|
||||
&this->_threads_per_atom);
|
||||
this->time_ellipsoid2.stop();
|
||||
|
||||
if (this->_last_ellipse==this->ans->inum()) {
|
||||
this->time_nbor3.zero();
|
||||
this->time_ellipsoid3.zero();
|
||||
this->time_lj.zero();
|
||||
return;
|
||||
}
|
||||
|
||||
// ------------ SPHERE_ELLIPSE ---------------
|
||||
|
||||
this->time_nbor3.start();
|
||||
GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum()-
|
||||
this->_last_ellipse)/
|
||||
(BX/this->_threads_per_atom)));
|
||||
NGX=static_cast<int>(ceil(static_cast<double>(this->ans->inum()-
|
||||
this->_last_ellipse)/BX));
|
||||
this->pack_nbors(NGX,BX,this->_last_ellipse,this->ans->inum(),
|
||||
SPHERE_ELLIPSE,SPHERE_ELLIPSE,_shared_types,_lj_types);
|
||||
this->time_nbor3.stop();
|
||||
|
||||
this->time_ellipsoid3.start();
|
||||
this->k_sphere_ellipsoid.set_size(GX,BX);
|
||||
this->k_sphere_ellipsoid.run(&this->atom->dev_x.begin(),
|
||||
&this->atom->dev_quat.begin(), &this->shape.begin(),
|
||||
&this->well.begin(), &this->special_lj.begin(),
|
||||
&this->sigma_epsilon.begin(), &this->_lj_types,
|
||||
&this->nbor->dev_nbor.begin(), &stride, &this->ans->dev_ans.begin(),
|
||||
&this->ans->dev_engv.begin(), &this->dev_error.begin(), &eflag,
|
||||
&vflag, &this->_last_ellipse, &ainum, &this->_threads_per_atom);
|
||||
this->time_ellipsoid3.stop();
|
||||
} else {
|
||||
this->ans->dev_ans.zero();
|
||||
this->ans->dev_engv.zero();
|
||||
this->time_nbor1.zero();
|
||||
this->time_ellipsoid.zero();
|
||||
this->time_nbor2.zero();
|
||||
this->time_ellipsoid2.zero();
|
||||
this->time_nbor3.zero();
|
||||
this->time_ellipsoid3.zero();
|
||||
}
|
||||
|
||||
// ------------ LJ ---------------
|
||||
this->time_lj.start();
|
||||
if (this->_last_ellipse<this->ans->inum()) {
|
||||
if (this->_shared_types) {
|
||||
this->k_lj_fast.set_size(GX,BX);
|
||||
this->k_lj_fast.run(&this->atom->dev_x.begin(), &this->lj1.begin(),
|
||||
&this->lj3.begin(), &this->special_lj.begin(), &stride,
|
||||
&this->nbor->dev_packed.begin(), &this->ans->dev_ans.begin(),
|
||||
&this->ans->dev_engv.begin(), &this->dev_error.begin(),
|
||||
&eflag, &vflag, &this->_last_ellipse, &ainum,
|
||||
&this->_threads_per_atom);
|
||||
} else {
|
||||
this->k_lj.set_size(GX,BX);
|
||||
this->k_lj.run(&this->atom->dev_x.begin(), &this->lj1.begin(),
|
||||
&this->lj3.begin(), &this->_lj_types, &this->special_lj.begin(),
|
||||
&stride, &this->nbor->dev_packed.begin(), &this->ans->dev_ans.begin(),
|
||||
&this->ans->dev_engv.begin(), &this->dev_error.begin(), &eflag,
|
||||
&vflag, &this->_last_ellipse, &ainum, &this->_threads_per_atom);
|
||||
}
|
||||
}
|
||||
this->time_lj.stop();
|
||||
} else {
|
||||
GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
|
||||
(BX/this->_threads_per_atom)));
|
||||
NGX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/BX));
|
||||
this->time_nbor1.start();
|
||||
this->pack_nbors(NGX, BX, 0, this->ans->inum(),SPHERE_SPHERE,
|
||||
ELLIPSE_ELLIPSE,_shared_types,_lj_types);
|
||||
this->time_nbor1.stop();
|
||||
this->time_ellipsoid.start();
|
||||
this->k_ellipsoid.set_size(GX,BX);
|
||||
this->k_ellipsoid.run(&this->atom->dev_x.begin(),
|
||||
&this->atom->dev_quat.begin(), &this->shape.begin(), &this->well.begin(),
|
||||
&this->special_lj.begin(), &this->sigma_epsilon.begin(),
|
||||
&this->_lj_types, &this->nbor->dev_nbor.begin(), &stride,
|
||||
&this->ans->dev_ans.begin(), &ainum, &this->ans->dev_engv.begin(),
|
||||
&this->dev_error.begin(), &eflag, &vflag, &ainum,
|
||||
&this->_threads_per_atom);
|
||||
this->time_ellipsoid.stop();
|
||||
}
|
||||
}
|
||||
|
||||
template class RESquared<PRECISION,ACC_PRECISION>;
|
||||
|
||||
|
|
@ -0,0 +1,91 @@
|
|||
/***************************************************************************
|
||||
re_squared.h
|
||||
-------------------
|
||||
W. Michael Brown
|
||||
|
||||
Host code for RE-Squared potential acceleration
|
||||
|
||||
__________________________________________________________________________
|
||||
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
|
||||
__________________________________________________________________________
|
||||
|
||||
begin : Fri May 06 2011
|
||||
email : brownw@ornl.gov
|
||||
***************************************************************************/
|
||||
|
||||
#ifndef RE_SQUARED_H
|
||||
#define RE_SQUARED_H
|
||||
|
||||
#include "base_ellipsoid.h"
|
||||
#include "mpi.h"
|
||||
|
||||
namespace LAMMPS_AL {
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
class RESquared : public BaseEllipsoid<numtyp, acctyp> {
|
||||
public:
|
||||
RESquared();
|
||||
~RESquared();
|
||||
|
||||
/// Clear any previous data and set up for a new LAMMPS run
|
||||
/** \param gpu_nbor true if neighboring performed on device
|
||||
* \param max_nbors initial number of rows in the neighbor matrix
|
||||
* \param cell_size cutoff + skin
|
||||
* \param gpu_split fraction of particles handled by device
|
||||
* \return false if there is not sufficient memory or device init prob
|
||||
*
|
||||
* Returns:
|
||||
* - 0 if successfull
|
||||
* - -1 if fix gpu not found
|
||||
* - -3 if there is an out of memory error
|
||||
* - -4 if the GPU library was not compiled for GPU
|
||||
* - -5 Double precision is not supported on card **/
|
||||
int init(const int ntypes, double **host_shape, double **host_well,
|
||||
double **host_cutsq, double **host_sigma, double **host_epsilon,
|
||||
int **h_form, double **host_lj1, double **host_lj2,
|
||||
double **host_lj3, double **host_lj4, double **host_offset,
|
||||
const double *host_special_lj, const int nlocal, const int nall,
|
||||
const int max_nbors, const int maxspecial, const double cell_size,
|
||||
const double gpu_split, FILE *screen);
|
||||
|
||||
/// Clear all host and device data
|
||||
/** \note This is called at the beginning of the init() routine **/
|
||||
void clear();
|
||||
|
||||
/// Returns memory usage on device per atom
|
||||
int bytes_per_atom(const int max_nbors) const;
|
||||
|
||||
/// Total host memory used by library for pair style
|
||||
double host_memory_usage() const;
|
||||
|
||||
/// Device Error Flag - Set if a bad matrix inversion occurs
|
||||
UCL_D_Vec<int> dev_error;
|
||||
|
||||
// --------------------------- TYPE DATA --------------------------
|
||||
|
||||
/// lj1.x = lj1, lj1.y = lj2, lj1.z = cutsq, lj1.w = form
|
||||
UCL_D_Vec<numtyp4> lj1;
|
||||
/// lj3.x = lj3, lj3.y = lj4, lj3.z = offset
|
||||
UCL_D_Vec<numtyp4> lj3;
|
||||
/// sigma_epsilon.x = sigma, sigma_epsilon.y = epsilon
|
||||
UCL_D_Vec<numtyp2> sigma_epsilon;
|
||||
/// special lj 0-4
|
||||
UCL_D_Vec<numtyp> special_lj;
|
||||
|
||||
/// If atom type constants fit in shared memory, use fast kernels
|
||||
bool _shared_types;
|
||||
int _lj_types;
|
||||
|
||||
// --------------------------- ATOM DATA --------------------------
|
||||
|
||||
/// Aspherical Const Data for Atoms
|
||||
UCL_D_Vec<numtyp4> shape, well;
|
||||
|
||||
private:
|
||||
bool _allocated;
|
||||
void loop(const bool _eflag, const bool _vflag);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
|
|
@ -0,0 +1,138 @@
|
|||
/***************************************************************************
|
||||
re_squared_ext.cpp
|
||||
-------------------
|
||||
W. Michael Brown
|
||||
|
||||
LAMMPS Wrappers for RE-Squared Acceleration
|
||||
|
||||
__________________________________________________________________________
|
||||
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
|
||||
__________________________________________________________________________
|
||||
|
||||
begin :
|
||||
email : brownw@ornl.gov
|
||||
***************************************************************************/
|
||||
|
||||
#include <iostream>
|
||||
#include <cassert>
|
||||
#include <math.h>
|
||||
|
||||
#include "re_squared.h"
|
||||
|
||||
using namespace std;
|
||||
using namespace LAMMPS_AL;
|
||||
|
||||
static RESquared<PRECISION,ACC_PRECISION> REMF;
|
||||
|
||||
// ---------------------------------------------------------------------------
|
||||
// Allocate memory on host and device and copy constants to device
|
||||
// ---------------------------------------------------------------------------
|
||||
int re_gpu_init(const int ntypes, double **shape, double **well, double **cutsq,
|
||||
double **sigma, double **epsilon,
|
||||
int **form, double **host_lj1, double **host_lj2,
|
||||
double **host_lj3, double **host_lj4, double **offset,
|
||||
double *special_lj, const int inum, const int nall,
|
||||
const int max_nbors, const int maxspecial,
|
||||
const double cell_size, int &gpu_mode, FILE *screen) {
|
||||
REMF.clear();
|
||||
gpu_mode=REMF.device->gpu_mode();
|
||||
double gpu_split=REMF.device->particle_split();
|
||||
int first_gpu=REMF.device->first_device();
|
||||
int last_gpu=REMF.device->last_device();
|
||||
int world_me=REMF.device->world_me();
|
||||
int gpu_rank=REMF.device->gpu_rank();
|
||||
int procs_per_gpu=REMF.device->procs_per_gpu();
|
||||
|
||||
REMF.device->init_message(screen,"resquared",first_gpu,last_gpu);
|
||||
|
||||
bool message=false;
|
||||
if (REMF.device->replica_me()==0 && screen)
|
||||
message=true;
|
||||
|
||||
if (message) {
|
||||
fprintf(screen,"Initializing GPU and compiling on process 0...");
|
||||
fflush(screen);
|
||||
}
|
||||
|
||||
int init_ok=0;
|
||||
if (world_me==0)
|
||||
init_ok=REMF.init(ntypes, shape, well, cutsq, sigma, epsilon,
|
||||
form, host_lj1, host_lj2, host_lj3, host_lj4, offset,
|
||||
special_lj, inum, nall, max_nbors, maxspecial, cell_size,
|
||||
gpu_split, screen);
|
||||
|
||||
REMF.device->world_barrier();
|
||||
if (message)
|
||||
fprintf(screen,"Done.\n");
|
||||
|
||||
for (int i=0; i<procs_per_gpu; i++) {
|
||||
if (message) {
|
||||
if (last_gpu-first_gpu==0)
|
||||
fprintf(screen,"Initializing GPU %d on core %d...",first_gpu,i);
|
||||
else
|
||||
fprintf(screen,"Initializing GPUs %d-%d on core %d...",first_gpu,
|
||||
last_gpu,i);
|
||||
fflush(screen);
|
||||
}
|
||||
if (gpu_rank==i && world_me!=0)
|
||||
init_ok=REMF.init(ntypes, shape, well, cutsq, sigma, epsilon,
|
||||
form, host_lj1, host_lj2, host_lj3,
|
||||
host_lj4, offset, special_lj, inum, nall,
|
||||
max_nbors, maxspecial, cell_size, gpu_split, screen);
|
||||
|
||||
REMF.device->gpu_barrier();
|
||||
if (message)
|
||||
fprintf(screen,"Done.\n");
|
||||
}
|
||||
if (message)
|
||||
fprintf(screen,"\n");
|
||||
|
||||
if (init_ok==0)
|
||||
REMF.estimate_gpu_overhead();
|
||||
return init_ok;
|
||||
}
|
||||
|
||||
// ---------------------------------------------------------------------------
|
||||
// Clear memory on host and device
|
||||
// ---------------------------------------------------------------------------
|
||||
void re_gpu_clear() {
|
||||
REMF.clear();
|
||||
}
|
||||
|
||||
int** compute(const int ago, const int inum_full, const int nall,
|
||||
double **host_x, int *host_type, double *sublo,
|
||||
double *subhi, int *tag, int **nspecial,
|
||||
int **special, const bool eflag, const bool vflag,
|
||||
const bool eatom, const bool vatom, int &host_start,
|
||||
int **ilist, int **numj, const double cpu_time, bool &success,
|
||||
double **host_quat);
|
||||
|
||||
int** re_gpu_compute_n(const int ago, const int inum_full, const int nall,
|
||||
double **host_x, int *host_type, double *sublo,
|
||||
double *subhi, int *tag, int **nspecial, int **special,
|
||||
const bool eflag, const bool vflag, const bool eatom,
|
||||
const bool vatom, int &host_start, int **ilist,
|
||||
int **jnum, const double cpu_time, bool &success,
|
||||
double **host_quat) {
|
||||
return REMF.compute(ago, inum_full, nall, host_x, host_type, sublo, subhi,
|
||||
tag, nspecial, special, eflag, vflag, eatom, vatom,
|
||||
host_start, ilist, jnum, cpu_time, success, host_quat);
|
||||
}
|
||||
|
||||
int * re_gpu_compute(const int ago, const int inum_full, const int nall,
|
||||
double **host_x, int *host_type, int *ilist, int *numj,
|
||||
int **firstneigh, const bool eflag, const bool vflag,
|
||||
const bool eatom, const bool vatom, int &host_start,
|
||||
const double cpu_time, bool &success, double **host_quat) {
|
||||
return REMF.compute(ago, inum_full, nall, host_x, host_type, ilist,
|
||||
numj, firstneigh, eflag, vflag, eatom, vatom, host_start,
|
||||
cpu_time, success, host_quat);
|
||||
}
|
||||
|
||||
// ---------------------------------------------------------------------------
|
||||
// Return memory usage
|
||||
// ---------------------------------------------------------------------------
|
||||
double re_gpu_bytes() {
|
||||
return REMF.host_memory_usage();
|
||||
}
|
||||
|
||||
Loading…
Reference in New Issue