Cleanup. Remove copyright year. Reformat.
This commit is contained in:
171
clusterpair/includes/atom.h
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171
clusterpair/includes/atom.h
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/*
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* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
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* All rights reserved. This file is part of MD-Bench.
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* Use of this source code is governed by a LGPL-3.0
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* license that can be found in the LICENSE file.
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*/
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#include <parameter.h>
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#ifndef __ATOM_H_
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#define __ATOM_H_
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#define DELTA 20000
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// Nbnxn layouts (as of GROMACS):
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// Simd4xN: M=4, N=VECTOR_WIDTH
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// Simd2xNN: M=4, N=(VECTOR_WIDTH/2)
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// Cuda: M=8, N=VECTOR_WIDTH
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#ifdef CUDA_TARGET
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# undef VECTOR_WIDTH
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# define VECTOR_WIDTH 8
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# define KERNEL_NAME "CUDA"
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# define CLUSTER_M 8
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# define CLUSTER_N VECTOR_WIDTH
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# define UNROLL_J 1
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# define computeForceLJ computeForceLJ_cuda
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# define initialIntegrate cudaInitialIntegrate
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# define finalIntegrate cudaFinalIntegrate
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# define updatePbc cudaUpdatePbc
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#else
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# define CLUSTER_M 4
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// Simd2xNN (here used for single-precision)
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# if VECTOR_WIDTH > CLUSTER_M * 2
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# define KERNEL_NAME "Simd2xNN"
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# define CLUSTER_N (VECTOR_WIDTH / 2)
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# define UNROLL_I 4
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# define UNROLL_J 2
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# define computeForceLJ computeForceLJ_2xnn
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// Simd4xN
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# else
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# define KERNEL_NAME "Simd4xN"
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# define CLUSTER_N VECTOR_WIDTH
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# define UNROLL_I 4
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# define UNROLL_J 1
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# define computeForceLJ computeForceLJ_4xn
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# endif
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# ifdef USE_REFERENCE_VERSION
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# undef KERNEL_NAME
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# undef computeForceLJ
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# define KERNEL_NAME "Reference"
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# define computeForceLJ computeForceLJ_ref
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# endif
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# define initialIntegrate cpuInitialIntegrate
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# define finalIntegrate cpuFinalIntegrate
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# define updatePbc cpuUpdatePbc
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#endif
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#if CLUSTER_M == CLUSTER_N
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# define CJ0_FROM_CI(a) (a)
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# define CJ1_FROM_CI(a) (a)
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# define CI_BASE_INDEX(a,b) ((a) * CLUSTER_N * (b))
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# define CJ_BASE_INDEX(a,b) ((a) * CLUSTER_N * (b))
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#elif CLUSTER_M == CLUSTER_N * 2 // M > N
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# define CJ0_FROM_CI(a) ((a) << 1)
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# define CJ1_FROM_CI(a) (((a) << 1) | 0x1)
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# define CI_BASE_INDEX(a,b) ((a) * CLUSTER_M * (b))
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# define CJ_BASE_INDEX(a,b) (((a) >> 1) * CLUSTER_M * (b) + ((a) & 0x1) * (CLUSTER_M >> 1))
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#elif CLUSTER_M == CLUSTER_N / 2 // M < N
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# define CJ0_FROM_CI(a) ((a) >> 1)
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# define CJ1_FROM_CI(a) ((a) >> 1)
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# define CI_BASE_INDEX(a,b) (((a) >> 1) * CLUSTER_N * (b) + ((a) & 0x1) * (CLUSTER_N >> 1))
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# define CJ_BASE_INDEX(a,b) ((a) * CLUSTER_N * (b))
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#else
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# error "Invalid cluster configuration!"
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#endif
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#if CLUSTER_N != 2 && CLUSTER_N != 4 && CLUSTER_N != 8
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# error "Cluster N dimension can be only 2, 4 and 8"
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#endif
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#define CI_SCALAR_BASE_INDEX(a) (CI_BASE_INDEX(a, 1))
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#define CI_VECTOR_BASE_INDEX(a) (CI_BASE_INDEX(a, 3))
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#define CJ_SCALAR_BASE_INDEX(a) (CJ_BASE_INDEX(a, 1))
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#define CJ_VECTOR_BASE_INDEX(a) (CJ_BASE_INDEX(a, 3))
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#if CLUSTER_M >= CLUSTER_N
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# define CL_X_OFFSET (0 * CLUSTER_M)
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# define CL_Y_OFFSET (1 * CLUSTER_M)
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# define CL_Z_OFFSET (2 * CLUSTER_M)
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#else
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# define CL_X_OFFSET (0 * CLUSTER_N)
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# define CL_Y_OFFSET (1 * CLUSTER_N)
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# define CL_Z_OFFSET (2 * CLUSTER_N)
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#endif
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typedef struct {
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int natoms;
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MD_FLOAT bbminx, bbmaxx;
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MD_FLOAT bbminy, bbmaxy;
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MD_FLOAT bbminz, bbmaxz;
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} Cluster;
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typedef struct {
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int Natoms, Nlocal, Nghost, Nmax;
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int Nclusters, Nclusters_local, Nclusters_ghost, Nclusters_max;
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MD_FLOAT *x, *y, *z;
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MD_FLOAT *vx, *vy, *vz;
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int *border_map;
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int *type;
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int ntypes;
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MD_FLOAT *epsilon;
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MD_FLOAT *sigma6;
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MD_FLOAT *cutforcesq;
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MD_FLOAT *cutneighsq;
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int *PBCx, *PBCy, *PBCz;
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// Data in cluster format
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MD_FLOAT *cl_x;
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MD_FLOAT *cl_v;
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MD_FLOAT *cl_f;
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int *cl_type;
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Cluster *iclusters, *jclusters;
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int *icluster_bin;
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int dummy_cj;
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MD_UINT *exclusion_filter;
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MD_FLOAT *diagonal_4xn_j_minus_i;
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MD_FLOAT *diagonal_2xnn_j_minus_i;
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unsigned int masks_2xnn_hn[8];
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unsigned int masks_2xnn_fn[8];
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unsigned int masks_4xn_hn[16];
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unsigned int masks_4xn_fn[16];
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} Atom;
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extern void initAtom(Atom*);
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extern void initMasks(Atom*);
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extern void createAtom(Atom*, Parameter*);
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extern int readAtom(Atom*, Parameter*);
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extern int readAtom_pdb(Atom*, Parameter*);
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extern int readAtom_gro(Atom*, Parameter*);
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extern int readAtom_dmp(Atom*, Parameter*);
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extern void growAtom(Atom*);
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extern void growClusters(Atom*);
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#ifdef AOS
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# define POS_DATA_LAYOUT "AoS"
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# define atom_x(i) atom->x[(i) * 3 + 0]
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# define atom_y(i) atom->x[(i) * 3 + 1]
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# define atom_z(i) atom->x[(i) * 3 + 2]
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/*
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# define atom_vx(i) atom->vx[(i) * 3 + 0]
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# define atom_vy(i) atom->vx[(i) * 3 + 1]
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# define atom_vz(i) atom->vx[(i) * 3 + 2]
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# define atom_fx(i) atom->fx[(i) * 3 + 0]
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# define atom_fy(i) atom->fx[(i) * 3 + 1]
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# define atom_fz(i) atom->fx[(i) * 3 + 2]
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*/
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#else
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# define POS_DATA_LAYOUT "SoA"
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# define atom_x(i) atom->x[i]
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# define atom_y(i) atom->y[i]
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# define atom_z(i) atom->z[i]
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#endif
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// TODO: allow to switch velocites and forces to AoS
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# define atom_vx(i) atom->vx[i]
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# define atom_vy(i) atom->vy[i]
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# define atom_vz(i) atom->vz[i]
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# define atom_fx(i) atom->fx[i]
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# define atom_fy(i) atom->fy[i]
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# define atom_fz(i) atom->fz[i]
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#endif
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56
clusterpair/includes/integrate.h
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56
clusterpair/includes/integrate.h
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@@ -0,0 +1,56 @@
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/*
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* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
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* All rights reserved. This file is part of MD-Bench.
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* Use of this source code is governed by a LGPL-3.0
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* license that can be found in the LICENSE file.
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*/
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#include <stdbool.h>
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//---
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#include <atom.h>
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#include <parameter.h>
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#include <util.h>
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void cpuInitialIntegrate(Parameter *param, Atom *atom) {
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DEBUG_MESSAGE("cpuInitialIntegrate start\n");
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for(int ci = 0; ci < atom->Nclusters_local; ci++) {
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int ci_vec_base = CI_VECTOR_BASE_INDEX(ci);
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MD_FLOAT *ci_x = &atom->cl_x[ci_vec_base];
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MD_FLOAT *ci_v = &atom->cl_v[ci_vec_base];
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MD_FLOAT *ci_f = &atom->cl_f[ci_vec_base];
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for(int cii = 0; cii < atom->iclusters[ci].natoms; cii++) {
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ci_v[CL_X_OFFSET + cii] += param->dtforce * ci_f[CL_X_OFFSET + cii];
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ci_v[CL_Y_OFFSET + cii] += param->dtforce * ci_f[CL_Y_OFFSET + cii];
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ci_v[CL_Z_OFFSET + cii] += param->dtforce * ci_f[CL_Z_OFFSET + cii];
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ci_x[CL_X_OFFSET + cii] += param->dt * ci_v[CL_X_OFFSET + cii];
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ci_x[CL_Y_OFFSET + cii] += param->dt * ci_v[CL_Y_OFFSET + cii];
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ci_x[CL_Z_OFFSET + cii] += param->dt * ci_v[CL_Z_OFFSET + cii];
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}
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}
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DEBUG_MESSAGE("cpuInitialIntegrate end\n");
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}
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void cpuFinalIntegrate(Parameter *param, Atom *atom) {
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DEBUG_MESSAGE("cpuFinalIntegrate start\n");
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for(int ci = 0; ci < atom->Nclusters_local; ci++) {
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int ci_vec_base = CI_VECTOR_BASE_INDEX(ci);
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MD_FLOAT *ci_v = &atom->cl_v[ci_vec_base];
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MD_FLOAT *ci_f = &atom->cl_f[ci_vec_base];
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for(int cii = 0; cii < atom->iclusters[ci].natoms; cii++) {
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ci_v[CL_X_OFFSET + cii] += param->dtforce * ci_f[CL_X_OFFSET + cii];
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ci_v[CL_Y_OFFSET + cii] += param->dtforce * ci_f[CL_Y_OFFSET + cii];
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ci_v[CL_Z_OFFSET + cii] += param->dtforce * ci_f[CL_Z_OFFSET + cii];
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}
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}
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DEBUG_MESSAGE("cpuFinalIntegrate end\n");
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}
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#ifdef CUDA_TARGET
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void cudaInitialIntegrate(Parameter*, Atom*);
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void cudaFinalIntegrate(Parameter*, Atom*);
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#endif
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49
clusterpair/includes/neighbor.h
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49
clusterpair/includes/neighbor.h
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@@ -0,0 +1,49 @@
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/*
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* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
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* All rights reserved. This file is part of MD-Bench.
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* Use of this source code is governed by a LGPL-3.0
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* license that can be found in the LICENSE file.
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*/
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#include <atom.h>
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#include <parameter.h>
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#ifndef __NEIGHBOR_H_
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#define __NEIGHBOR_H_
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// Interaction masks from GROMACS, things to remember (maybe these confused just me):
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// 1. These are not "exclusion" masks as the name suggests in GROMACS, but rather
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// interaction masks (1 = interaction, 0 = no interaction)
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// 2. These are inverted (maybe because that is how you use in AVX2/AVX512 masking),
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// so read them from right to left (least significant to most significant bit)
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// All interaction mask is the same for all kernels
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#define NBNXN_INTERACTION_MASK_ALL 0xffffffffU
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// 4x4 kernel diagonal mask
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#define NBNXN_INTERACTION_MASK_DIAG 0x08ceU
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// 4x2 kernel diagonal masks
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#define NBNXN_INTERACTION_MASK_DIAG_J2_0 0x0002U
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#define NBNXN_INTERACTION_MASK_DIAG_J2_1 0x002fU
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// 4x8 kernel diagonal masks
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#define NBNXN_INTERACTION_MASK_DIAG_J8_0 0xf0f8fcfeU
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#define NBNXN_INTERACTION_MASK_DIAG_J8_1 0x0080c0e0U
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typedef struct {
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int every;
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int ncalls;
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int maxneighs;
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int* numneigh;
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int* numneigh_masked;
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int half_neigh;
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int* neighbors;
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unsigned int* neighbors_imask;
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} Neighbor;
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extern void initNeighbor(Neighbor*, Parameter*);
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extern void setupNeighbor(Parameter*, Atom*);
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extern void binatoms(Atom*);
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extern void buildNeighbor(Atom*, Neighbor*);
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extern void pruneNeighbor(Parameter*, Atom*, Neighbor*);
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extern void sortAtom(Atom*);
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extern void buildClusters(Atom*);
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extern void defineJClusters(Atom*);
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extern void binClusters(Atom*);
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extern void updateSingleAtoms(Atom*);
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#endif
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20
clusterpair/includes/pbc.h
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20
clusterpair/includes/pbc.h
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@@ -0,0 +1,20 @@
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/*
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* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
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* All rights reserved. This file is part of MD-Bench.
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* Use of this source code is governed by a LGPL-3.0
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* license that can be found in the LICENSE file.
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*/
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#include <atom.h>
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#include <parameter.h>
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#ifndef __PBC_H_
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#define __PBC_H_
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extern void initPbc();
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extern void cpuUpdatePbc(Atom*, Parameter*, int);
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extern void updateAtomsPbc(Atom*, Parameter*);
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extern void setupPbc(Atom*, Parameter*);
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#ifdef CUDA_TARGET
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extern void cudaUpdatePbc(Atom*, Parameter*, int);
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#endif
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#endif
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35
clusterpair/includes/stats.h
Normal file
35
clusterpair/includes/stats.h
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@@ -0,0 +1,35 @@
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/*
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* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
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* All rights reserved. This file is part of MD-Bench.
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* Use of this source code is governed by a LGPL-3.0
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* license that can be found in the LICENSE file.
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*/
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#include <atom.h>
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#include <parameter.h>
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#ifndef __STATS_H_
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#define __STATS_H_
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typedef struct {
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long long int calculated_forces;
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long long int num_neighs;
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long long int force_iters;
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long long int atoms_within_cutoff;
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long long int atoms_outside_cutoff;
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long long int clusters_within_cutoff;
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long long int clusters_outside_cutoff;
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} Stats;
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void initStats(Stats *s);
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void displayStatistics(Atom *atom, Parameter *param, Stats *stats, double *timer);
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#ifdef COMPUTE_STATS
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# define addStat(stat, value) stat += value;
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# define beginStatTimer() double Si = getTimeStamp();
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# define endStatTimer(stat) stat += getTimeStamp() - Si;
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#else
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# define addStat(stat, value)
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# define beginStatTimer()
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# define endStatTimer(stat)
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#endif
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#endif
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102
clusterpair/includes/tracing.h
Normal file
102
clusterpair/includes/tracing.h
Normal file
@@ -0,0 +1,102 @@
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/*
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* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
|
||||
* All rights reserved. This file is part of MD-Bench.
|
||||
* Use of this source code is governed by a LGPL-3.0
|
||||
* license that can be found in the LICENSE file.
|
||||
*/
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||||
#include <neighbor.h>
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#include <parameter.h>
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#include <atom.h>
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#if defined(MEM_TRACER) || defined(INDEX_TRACER)
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#include <stdio.h>
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#include <stdlib.h>
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#endif
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||||
#ifndef VECTOR_WIDTH
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# define VECTOR_WIDTH 8
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#endif
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||||
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#ifndef TRACER_CONDITION
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# define TRACER_CONDITION (!(timestep % param->every))
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#endif
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#ifdef MEM_TRACER
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# define MEM_TRACER_INIT FILE *mem_tracer_fp; \
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if(TRACER_CONDITION) { \
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char mem_tracer_fn[128]; \
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snprintf(mem_tracer_fn, sizeof mem_tracer_fn, "mem_tracer_%d.out", timestep); \
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mem_tracer_fp = fopen(mem_tracer_fn, "w");
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}
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||||
# define MEM_TRACER_END if(TRACER_CONDITION) { fclose(mem_tracer_fp); }
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# define MEM_TRACE(addr, op) if(TRACER_CONDITION) { fprintf(mem_tracer_fp, "%c: %p\n", op, (void *)(&(addr))); }
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#else
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# define MEM_TRACER_INIT
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# define MEM_TRACER_END
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# define MEM_TRACE(addr, op)
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#endif
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||||
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||||
#ifdef INDEX_TRACER
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# define INDEX_TRACER_INIT FILE *index_tracer_fp; \
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if(TRACER_CONDITION) { \
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char index_tracer_fn[128]; \
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snprintf(index_tracer_fn, sizeof index_tracer_fn, "index_tracer_%d.out", timestep); \
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index_tracer_fp = fopen(index_tracer_fn, "w"); \
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}
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# define INDEX_TRACER_END if(TRACER_CONDITION) { fclose(index_tracer_fp); }
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# define INDEX_TRACE_NATOMS(nl, ng, mn) if(TRACER_CONDITION) { fprintf(index_tracer_fp, "N: %d %d %d\n", nl, ng, mn); }
|
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# define INDEX_TRACE_ATOM(a) if(TRACER_CONDITION) { fprintf(index_tracer_fp, "A: %d\n", a); }
|
||||
# define INDEX_TRACE(l, e) if(TRACER_CONDITION) { \
|
||||
for(int __i = 0; __i < (e); __i += VECTOR_WIDTH) { \
|
||||
int __e = (((e) - __i) < VECTOR_WIDTH) ? ((e) - __i) : VECTOR_WIDTH; \
|
||||
fprintf(index_tracer_fp, "I: "); \
|
||||
for(int __j = 0; __j < __e; ++__j) { \
|
||||
fprintf(index_tracer_fp, "%d ", l[__i + __j]); \
|
||||
} \
|
||||
fprintf(index_tracer_fp, "\n"); \
|
||||
} \
|
||||
}
|
||||
|
||||
# define DIST_TRACE_SORT(l, e) if(TRACER_CONDITION) { \
|
||||
for(int __i = 0; __i < (e); __i += VECTOR_WIDTH) { \
|
||||
int __e = (((e) - __i) < VECTOR_WIDTH) ? ((e) - __i) : VECTOR_WIDTH; \
|
||||
if(__e > 1) { \
|
||||
for(int __j = __i; __j < __i + __e - 1; ++__j) { \
|
||||
for(int __k = __i; __k < __i + __e - (__j - __i) - 1; ++__k) { \
|
||||
if(l[__k] > l[__k + 1]) { \
|
||||
int __t = l[__k]; \
|
||||
l[__k] = l[__k + 1]; \
|
||||
l[__k + 1] = __t; \
|
||||
} \
|
||||
} \
|
||||
} \
|
||||
} \
|
||||
} \
|
||||
}
|
||||
|
||||
# define DIST_TRACE(l, e) if(TRACER_CONDITION) { \
|
||||
for(int __i = 0; __i < (e); __i += VECTOR_WIDTH) { \
|
||||
int __e = (((e) - __i) < VECTOR_WIDTH) ? ((e) - __i) : VECTOR_WIDTH; \
|
||||
if(__e > 1) { \
|
||||
fprintf(index_tracer_fp, "D: "); \
|
||||
for(int __j = 0; __j < __e - 1; ++__j) { \
|
||||
int __dist = abs(l[__i + __j + 1] - l[__i + __j]); \
|
||||
fprintf(index_tracer_fp, "%d ", __dist); \
|
||||
} \
|
||||
fprintf(index_tracer_fp, "\n"); \
|
||||
} \
|
||||
} \
|
||||
}
|
||||
#else
|
||||
# define INDEX_TRACER_INIT
|
||||
# define INDEX_TRACER_END
|
||||
# define INDEX_TRACE_NATOMS(nl, ng, mn)
|
||||
# define INDEX_TRACE_ATOM(a)
|
||||
# define INDEX_TRACE(l, e)
|
||||
# define DIST_TRACE_SORT(l, e)
|
||||
# define DIST_TRACE(l, e)
|
||||
#endif
|
||||
|
||||
extern void traceAddresses(Parameter *param, Atom *atom, Neighbor *neighbor, int timestep);
|
||||
16
clusterpair/includes/vtk.h
Normal file
16
clusterpair/includes/vtk.h
Normal file
@@ -0,0 +1,16 @@
|
||||
/*
|
||||
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
|
||||
* All rights reserved. This file is part of MD-Bench.
|
||||
* Use of this source code is governed by a LGPL-3.0
|
||||
* license that can be found in the LICENSE file.
|
||||
*/
|
||||
#include <atom.h>
|
||||
|
||||
#ifndef __VTK_H_
|
||||
#define __VTK_H_
|
||||
extern void write_data_to_vtk_file(const char *filename, Atom* atom, int timestep);
|
||||
extern int write_local_atoms_to_vtk_file(const char* filename, Atom* atom, int timestep);
|
||||
extern int write_ghost_atoms_to_vtk_file(const char* filename, Atom* atom, int timestep);
|
||||
extern int write_local_cluster_edges_to_vtk_file(const char* filename, Atom* atom, int timestep);
|
||||
extern int write_ghost_cluster_edges_to_vtk_file(const char* filename, Atom* atom, int timestep);
|
||||
#endif
|
||||
21
clusterpair/includes/xtc.h
Normal file
21
clusterpair/includes/xtc.h
Normal file
@@ -0,0 +1,21 @@
|
||||
/*
|
||||
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
|
||||
* All rights reserved. This file is part of MD-Bench.
|
||||
* Use of this source code is governed by a LGPL-3.0
|
||||
* license that can be found in the LICENSE file.
|
||||
*/
|
||||
#include <atom.h>
|
||||
|
||||
#ifndef __XTC_H_
|
||||
#define __XTC_H_
|
||||
|
||||
#ifdef XTC_OUTPUT
|
||||
void xtc_init(const char *, Atom*, int);
|
||||
void xtc_write(Atom*, int, int, int);
|
||||
void xtc_end();
|
||||
#else
|
||||
#define xtc_init(a,b,c)
|
||||
#define xtc_write(a,b,c,d)
|
||||
#define xtc_end()
|
||||
#endif
|
||||
#endif
|
||||
Reference in New Issue
Block a user