3 * This source code is part of
7 * GROningen MAchine for Chemical Simulations
10 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
11 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
12 * Copyright (c) 2001-2004, The GROMACS development team,
13 * check out http://www.gromacs.org for more information.
15 * This program is free software; you can redistribute it and/or
16 * modify it under the terms of the GNU General Public License
17 * as published by the Free Software Foundation; either version 2
18 * of the License, or (at your option) any later version.
20 * If you want to redistribute modifications, please consider that
21 * scientific software is very special. Version control is crucial -
22 * bugs must be traceable. We will be happy to consider code for
23 * inclusion in the official distribution, but derived work must not
24 * be called official GROMACS. Details are found in the README & COPYING
25 * files - if they are missing, get the official version at www.gromacs.org.
27 * To help us fund GROMACS development, we humbly ask that you cite
28 * the papers on the package - you can find them in the top README file.
30 * For more info, check our website at http://www.gromacs.org
33 * GRoups of Organic Molecules in ACtion for Science
42 #include "../thread_mpi/tmpi.h"
43 #include "../thread_mpi/mpi_bindings.h"
45 typedef void* MPI_Comm;
46 typedef void* MPI_Request;
47 typedef void* MPI_Group;
48 #define MPI_COMM_NULL NULL
62 typedef struct gmx_domdec_master *gmx_domdec_master_p_t;
65 int j0; /* j-zone start */
66 int j1; /* j-zone end */
67 int cg1; /* i-charge-group end */
68 int jcg0; /* j-charge-group start */
69 int jcg1; /* j-charge-group end */
70 ivec shift0; /* Minimum shifts to consider */
71 ivec shift1; /* Maximum shifts to consider */
72 } gmx_domdec_ns_ranges_t;
75 rvec x0; /* Zone lower corner in triclinic coordinates */
76 rvec x1; /* Zone upper corner in triclinic coordinates */
77 rvec bb_x0; /* Zone bounding box lower corner in Cartesian coords */
78 rvec bb_x1; /* Zone bounding box upper corner in Cartesian coords */
79 } gmx_domdec_zone_size_t;
82 /* The number of zones including the home zone */
84 /* The shift of the zones with respect to the home zone */
85 ivec shift[DD_MAXZONE];
86 /* The charge group boundaries for the zones */
87 int cg_range[DD_MAXZONE+1];
88 /* The number of neighbor search zones with i-particles */
90 /* The neighbor search charge group ranges for each i-zone */
91 gmx_domdec_ns_ranges_t izone[DD_MAXIZONE];
92 /* Boundaries of the zones */
93 gmx_domdec_zone_size_t size[DD_MAXZONE];
94 /* The cg density of the home zone */
98 typedef struct gmx_ga2la *gmx_ga2la_t;
100 typedef struct gmx_hash *gmx_hash_t;
102 typedef struct gmx_reverse_top *gmx_reverse_top_p_t;
104 typedef struct gmx_domdec_constraints *gmx_domdec_constraints_p_t;
106 typedef struct gmx_domdec_specat_comm *gmx_domdec_specat_comm_p_t;
108 typedef struct gmx_domdec_comm *gmx_domdec_comm_p_t;
110 typedef struct gmx_pme_comm_n_box *gmx_pme_comm_n_box_p_t;
117 /* Tells if the box is skewed for each of the three cartesian directions */
120 /* Orthogonal vectors for triclinic cells, Cartesian index */
122 /* Normal vectors for the cells walls */
128 /* these buffers are used as destination buffers if MPI_IN_PLACE isn't
130 int *ibuf; /* for ints */
133 gmx_large_int_t *libuf;
136 float *fbuf; /* for floats */
139 double *dbuf; /* for doubles */
141 } mpi_in_place_buf_t;
145 /* The DD particle-particle nodes only */
146 /* The communication setup within the communicator all
147 * defined in dd->comm in domdec.c
150 MPI_Comm mpi_comm_all;
151 /* Use MPI_Sendrecv communication instead of non-blocking calls */
153 /* The local DD cell index and rank */
158 /* Communication with the PME only nodes */
160 gmx_bool pme_receive_vir_ener;
161 gmx_pme_comm_n_box_p_t cnb;
163 MPI_Request req_pme[4];
166 /* The communication setup, identical for each cell, cartesian index */
169 ivec dim; /* indexed by 0 to ndim */
172 /* PBC from dim 0 to npbcdim */
178 /* Forward and backward neighboring cells, indexed by 0 to ndim */
179 int neighbor[DIM][2];
181 /* Only available on the master node */
182 gmx_domdec_master_p_t ma;
184 /* Are there inter charge group constraints */
185 gmx_bool bInterCGcons;
186 gmx_bool bInterCGsettles;
188 /* Global atom number to interaction list */
189 gmx_reverse_top_p_t reverse_top;
193 /* The number of inter charge-group exclusions */
197 gmx_hash_t ga2la_vsite;
198 gmx_domdec_specat_comm_p_t vsite_comm;
200 /* Constraint stuff */
201 gmx_domdec_constraints_p_t constraints;
202 gmx_domdec_specat_comm_p_t constraint_comm;
204 /* The local to gobal charge group index and local cg to local atom index */
210 /* Local atom to local cg index, only for special cases */
214 /* The number of home atoms */
216 /* The total number of atoms: home and received zones */
218 /* Index from the local atoms to the global atoms */
222 /* Global atom number to local atom number list */
225 /* Communication stuff */
226 gmx_domdec_comm_p_t comm;
228 /* The partioning count, to keep track of the state */
229 gmx_large_int_t ddp_count;
232 /* gmx_pme_recv_f buffer */
233 int pme_recv_f_alloc;
234 rvec *pme_recv_f_buf;
238 typedef struct gmx_partdec *gmx_partdec_p_t;
243 MPI_Group mpi_group_masters;
244 MPI_Comm mpi_comm_masters;
245 /* these buffers are used as destination buffers if MPI_IN_PLACE isn't
247 mpi_in_place_buf_t *mpb;
250 #define DUTY_PP (1<<0)
251 #define DUTY_PME (1<<1)
262 /* The nodeids in one sim are numbered sequentially from 0.
263 * All communication within some simulation should happen
264 * in mpi_comm_mysim, or its subset mpi_comm_mygroup.
266 int sim_nodeid, nnodes, npmenodes;
268 /* thread numbers: */
269 /* Not used yet: int threadid, nthreads; */
270 /* The nodeid in the PP/PME, PP or PME group */
272 MPI_Comm mpi_comm_mysim;
273 MPI_Comm mpi_comm_mygroup;
275 /* MPI ranks within a physical node for hardware access */
276 int nrank_intranode; /* nr of ranks on this physical node */
277 int rank_intranode; /* our rank on this physical node */
278 int nrank_pp_intranode; /* as nrank_intranode, for particle-particle only */
279 int rank_pp_intranode; /* as rank_intranode, for particle-particle only */
283 /* For domain decomposition */
286 /* For particle decomposition */
289 /* The duties of this node, see the defines above */
294 /* these buffers are used as destination buffers if MPI_IN_PLACE isn't
296 mpi_in_place_buf_t *mpb;
299 #define MASTERNODE(cr) (((cr)->nodeid == 0) || !PAR(cr))
300 /* #define MASTERTHREAD(cr) ((cr)->threadid == 0) */
301 /* #define MASTER(cr) (MASTERNODE(cr) && MASTERTHREAD(cr)) */
302 #define MASTER(cr) MASTERNODE(cr)
303 #define SIMMASTER(cr) ((MASTER(cr) && ((cr)->duty & DUTY_PP)) || !PAR(cr))
304 #define NODEPAR(cr) ((cr)->nnodes > 1)
305 /* #define THREADPAR(cr) ((cr)->nthreads > 1) */
306 /* #define PAR(cr) (NODEPAR(cr) || THREADPAR(cr)) */
307 #define PAR(cr) NODEPAR(cr)
308 #define RANK(cr, nodeid) (nodeid)
309 #define MASTERRANK(cr) (0)
311 #define DOMAINDECOMP(cr) (((cr)->dd != NULL) && PAR(cr))
312 #define DDMASTER(dd) ((dd)->rank == (dd)->masterrank)
314 #define PARTDECOMP(cr) ((cr)->pd != NULL)
316 #define MULTISIM(cr) ((cr)->ms)
317 #define MSRANK(ms, nodeid) (nodeid)
318 #define MASTERSIM(ms) ((ms)->sim == 0)
320 /* The master of all (the node that prints the remaining run time etc.) */
321 #define MULTIMASTER(cr) (SIMMASTER(cr) && (!MULTISIM(cr) || MASTERSIM((cr)->ms)))