/*
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * This file is part of the GROMACS molecular simulation package.
+ *
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
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- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
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* of the License, or (at your option) any later version.
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*/
#ifndef _commrec_h
#define _commrec_h
-#ifdef GMX_LIB_MPI
-#include <mpi.h>
-#else
-#ifdef GMX_THREAD_MPI
-#include "../tmpi.h"
-#else
-typedef void* MPI_Comm;
-typedef void* MPI_Request;
-typedef void* MPI_Group;
-#endif
-#endif
-
-#include "idef.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/gmxmpi.h"
#ifdef __cplusplus
extern "C" {
typedef struct gmx_domdec_master *gmx_domdec_master_p_t;
typedef struct {
- int j0; /* j-cell start */
- int j1; /* j-cell end */
- int cg1; /* i-charge-group end */
- int jcg0; /* j-charge-group start */
- int jcg1; /* j-charge-group end */
- ivec shift0; /* Minimum shifts to consider */
- ivec shift1; /* Maximum shifts to consider */
+ int j0; /* j-zone start */
+ int j1; /* j-zone end */
+ int cg1; /* i-charge-group end */
+ int jcg0; /* j-charge-group start */
+ int jcg1; /* j-charge-group end */
+ ivec shift0; /* Minimum shifts to consider */
+ ivec shift1; /* Maximum shifts to consider */
} gmx_domdec_ns_ranges_t;
typedef struct {
- /* The number of zones including the home zone */
- int n;
- /* The shift of the zones with respect to the home zone */
- ivec shift[DD_MAXZONE];
- /* The charge group boundaries for the zones */
- int cg_range[DD_MAXZONE+1];
- /* The number of neighbor search zones with i-particles */
- int nizone;
- /* The neighbor search charge group ranges for each i-zone */
- gmx_domdec_ns_ranges_t izone[DD_MAXIZONE];
-} gmx_domdec_zones_t;
+ rvec x0; /* Zone lower corner in triclinic coordinates */
+ rvec x1; /* Zone upper corner in triclinic coordinates */
+ rvec bb_x0; /* Zone bounding box lower corner in Cartesian coords */
+ rvec bb_x1; /* Zone bounding box upper corner in Cartesian coords */
+} gmx_domdec_zone_size_t;
+
+struct gmx_domdec_zones_t {
+ /* The number of zones including the home zone */
+ int n;
+ /* The shift of the zones with respect to the home zone */
+ ivec shift[DD_MAXZONE];
+ /* The charge group boundaries for the zones */
+ int cg_range[DD_MAXZONE+1];
+ /* The number of neighbor search zones with i-particles */
+ int nizone;
+ /* The neighbor search charge group ranges for each i-zone */
+ gmx_domdec_ns_ranges_t izone[DD_MAXIZONE];
+ /* Boundaries of the zones */
+ gmx_domdec_zone_size_t size[DD_MAXZONE];
+ /* The cg density of the home zone */
+ real dens_zone0;
+};
typedef struct gmx_ga2la *gmx_ga2la_t;
+typedef struct gmx_hash *gmx_hash_t;
+
typedef struct gmx_reverse_top *gmx_reverse_top_p_t;
typedef struct gmx_domdec_constraints *gmx_domdec_constraints_p_t;
typedef struct gmx_pme_comm_n_box *gmx_pme_comm_n_box_p_t;
-typedef struct {
- int npbcdim;
- int nboundeddim;
- rvec box0;
- rvec box_size;
- /* Tells if the box is skewed for each of the three cartesian directions */
- ivec tric_dir;
- rvec skew_fac;
- /* Orthogonal vectors for triclinic cells, Cartesian index */
- rvec v[DIM][DIM];
- /* Normal vectors for the cells walls */
- rvec normal[DIM];
-} gmx_ddbox_t;
+struct gmx_ddbox_t {
+ int npbcdim;
+ int nboundeddim;
+ rvec box0;
+ rvec box_size;
+ /* Tells if the box is skewed for each of the three cartesian directions */
+ ivec tric_dir;
+ rvec skew_fac;
+ /* Orthogonal vectors for triclinic cells, Cartesian index */
+ rvec v[DIM][DIM];
+ /* Normal vectors for the cells walls */
+ rvec normal[DIM];
+};
typedef struct {
- /* these buffers are used as destination buffers if MPI_IN_PLACE isn't
- supported.*/
- int *ibuf; /* for ints */
- int ibuf_alloc;
+ /* these buffers are used as destination buffers if MPI_IN_PLACE isn't
+ supported.*/
+ int *ibuf; /* for ints */
+ int ibuf_alloc;
- gmx_large_int_t *libuf;
- int libuf_alloc;
+ gmx_int64_t *libuf;
+ int libuf_alloc;
- float *fbuf; /* for floats */
- int fbuf_alloc;
+ float *fbuf; /* for floats */
+ int fbuf_alloc;
- double *dbuf; /* for doubles */
- int dbuf_alloc;
+ double *dbuf; /* for doubles */
+ int dbuf_alloc;
} mpi_in_place_buf_t;
-typedef struct {
- /* The DD particle-particle nodes only */
- /* The communication setup within the communicator all
- * defined in dd->comm in domdec.c
- */
- int nnodes;
- MPI_Comm mpi_comm_all;
- /* Use MPI_Sendrecv communication instead of non-blocking calls */
- gmx_bool bSendRecv2;
- /* The local DD cell index and rank */
- ivec ci;
- int rank;
- ivec master_ci;
- int masterrank;
- /* Communication with the PME only nodes */
- int pme_nodeid;
- gmx_bool pme_receive_vir_ener;
- gmx_pme_comm_n_box_p_t cnb;
- int nreq_pme;
- MPI_Request req_pme[4];
-
-
- /* The communication setup, identical for each cell, cartesian index */
- ivec nc;
- int ndim;
- ivec dim; /* indexed by 0 to ndim */
- gmx_bool bGridJump;
-
- /* PBC from dim 0 to npbcdim */
- int npbcdim;
-
- /* Screw PBC? */
- gmx_bool bScrewPBC;
-
- /* Forward and backward neighboring cells, indexed by 0 to ndim */
- int neighbor[DIM][2];
-
- /* Only available on the master node */
- gmx_domdec_master_p_t ma;
-
- /* Are there inter charge group constraints */
- gmx_bool bInterCGcons;
-
- /* Global atom number to interaction list */
- gmx_reverse_top_p_t reverse_top;
- int nbonded_global;
- int nbonded_local;
-
- /* The number of inter charge-group exclusions */
- int n_intercg_excl;
-
- /* Vsite stuff */
- int *ga2la_vsite;
- gmx_domdec_specat_comm_p_t vsite_comm;
-
- /* Constraint stuff */
- gmx_domdec_constraints_p_t constraints;
- gmx_domdec_specat_comm_p_t constraint_comm;
-
- /* The local to gobal charge group index and local cg to local atom index */
- int ncg_home;
- int ncg_tot;
- int *index_gl;
- int *cgindex;
- int cg_nalloc;
- /* Local atom to local cg index, only for special cases */
- int *la2lc;
- int la2lc_nalloc;
-
- /* The number of home atoms */
- int nat_home;
- /* The total number of atoms: home and received zones */
- int nat_tot;
- /* Index from the local atoms to the global atoms */
- int *gatindex;
- int gatindex_nalloc;
-
- /* Global atom number to local atom number list */
- gmx_ga2la_t ga2la;
-
- /* Communication stuff */
- gmx_domdec_comm_p_t comm;
-
- /* The partioning count, to keep track of the state */
- gmx_large_int_t ddp_count;
-
-
- /* gmx_pme_recv_f buffer */
- int pme_recv_f_alloc;
- rvec *pme_recv_f_buf;
-
-} gmx_domdec_t;
-
-typedef struct gmx_partdec *gmx_partdec_p_t;
-
-typedef struct {
- int nsim;
- int sim;
- MPI_Group mpi_group_masters;
- MPI_Comm mpi_comm_masters;
- /* these buffers are used as destination buffers if MPI_IN_PLACE isn't
- supported.*/
- mpi_in_place_buf_t *mpb;
-} gmx_multisim_t;
+struct gmx_domdec_t {
+ /* The DD particle-particle nodes only */
+ /* The communication setup within the communicator all
+ * defined in dd->comm in domdec.c
+ */
+ int nnodes;
+ MPI_Comm mpi_comm_all;
+ /* Use MPI_Sendrecv communication instead of non-blocking calls */
+ gmx_bool bSendRecv2;
+ /* The local DD cell index and rank */
+ ivec ci;
+ int rank;
+ ivec master_ci;
+ int masterrank;
+ /* Communication with the PME only nodes */
+ int pme_nodeid;
+ gmx_bool pme_receive_vir_ener;
+ gmx_pme_comm_n_box_p_t cnb;
+ int nreq_pme;
+ MPI_Request req_pme[8];
+
+
+ /* The communication setup, identical for each cell, cartesian index */
+ ivec nc;
+ int ndim;
+ ivec dim; /* indexed by 0 to ndim */
+ gmx_bool bGridJump;
+
+ /* PBC from dim 0 to npbcdim */
+ int npbcdim;
+
+ /* Screw PBC? */
+ gmx_bool bScrewPBC;
+
+ /* Forward and backward neighboring cells, indexed by 0 to ndim */
+ int neighbor[DIM][2];
+
+ /* Only available on the master node */
+ gmx_domdec_master_p_t ma;
+
+ /* Are there inter charge group constraints */
+ gmx_bool bInterCGcons;
+ gmx_bool bInterCGsettles;
+
+ /* Global atom number to interaction list */
+ gmx_reverse_top_p_t reverse_top;
+ int nbonded_global;
+ int nbonded_local;
+
+ /* The number of inter charge-group exclusions */
+ int n_intercg_excl;
+
+ /* Vsite stuff */
+ gmx_hash_t ga2la_vsite;
+ gmx_domdec_specat_comm_p_t vsite_comm;
+
+ /* Constraint stuff */
+ gmx_domdec_constraints_p_t constraints;
+ gmx_domdec_specat_comm_p_t constraint_comm;
+
+ /* The local to gobal charge group index and local cg to local atom index */
+ int ncg_home;
+ int ncg_tot;
+ int *index_gl;
+ int *cgindex;
+ int cg_nalloc;
+ /* Local atom to local cg index, only for special cases */
+ int *la2lc;
+ int la2lc_nalloc;
+
+ /* The number of home atoms */
+ int nat_home;
+ /* The total number of atoms: home and received zones */
+ int nat_tot;
+ /* Index from the local atoms to the global atoms */
+ int *gatindex;
+ int gatindex_nalloc;
+
+ /* Global atom number to local atom number list */
+ gmx_ga2la_t ga2la;
+
+ /* Communication stuff */
+ gmx_domdec_comm_p_t comm;
+
+ /* The partioning count, to keep track of the state */
+ gmx_int64_t ddp_count;
+
+
+ /* gmx_pme_recv_f buffer */
+ int pme_recv_f_alloc;
+ rvec *pme_recv_f_buf;
+
+};
+
+struct gmx_multisim_t {
+ int nsim;
+ int sim;
+ MPI_Group mpi_group_masters;
+ MPI_Comm mpi_comm_masters;
+ /* these buffers are used as destination buffers if MPI_IN_PLACE isn't
+ supported.*/
+ mpi_in_place_buf_t *mpb;
+};
#define DUTY_PP (1<<0)
#define DUTY_PME (1<<1)
typedef struct {
- int bUse;
- MPI_Comm comm_intra;
- int rank_intra;
- MPI_Comm comm_inter;
-
+ int bUse;
+ MPI_Comm comm_intra;
+ int rank_intra;
+ MPI_Comm comm_inter;
+
} gmx_nodecomm_t;
-typedef struct {
- int dummy;
-} gmx_commrec_thread_t;
+struct t_commrec {
+ /* The nodeids in one sim are numbered sequentially from 0.
+ * All communication within some simulation should happen
+ * in mpi_comm_mysim, or its subset mpi_comm_mygroup.
+ */
+ int sim_nodeid, nnodes, npmenodes;
-typedef struct {
- /* The nodeids in one sim are numbered sequentially from 0.
- * All communication within some simulation should happen
- * in mpi_comm_mysim, or its subset mpi_comm_mygroup.
- */
- int sim_nodeid,nnodes,npmenodes;
-
- /* thread numbers: */
- /* Not used yet: int threadid, nthreads; */
- /* The nodeid in the PP/PME, PP or PME group */
- int nodeid;
- MPI_Comm mpi_comm_mysim;
- MPI_Comm mpi_comm_mygroup;
-
-#ifdef GMX_THREAD_SHM_FDECOMP
- gmx_commrec_thread_t thread;
-#endif
+ /* thread numbers: */
+ /* Not used yet: int threadid, nthreads; */
+ /* The nodeid in the PP/PME, PP or PME group */
+ int nodeid;
+ MPI_Comm mpi_comm_mysim;
+ MPI_Comm mpi_comm_mygroup;
+
+ /* MPI ranks within a physical node for hardware access */
+ int nrank_intranode; /* nr of ranks on this physical node */
+ int rank_intranode; /* our rank on this physical node */
+ int nrank_pp_intranode; /* as nrank_intranode, for particle-particle only */
+ int rank_pp_intranode; /* as rank_intranode, for particle-particle only */
- gmx_nodecomm_t nc;
-
- /* For domain decomposition */
- gmx_domdec_t *dd;
+ gmx_nodecomm_t nc;
- /* For particle decomposition */
- gmx_partdec_p_t pd;
+ /* For domain decomposition */
+ gmx_domdec_t *dd;
- /* The duties of this node, see the defines above */
- int duty;
+ /* The duties of this node, see the defines above */
+ int duty;
- gmx_multisim_t *ms;
+ gmx_multisim_t *ms;
- /* these buffers are used as destination buffers if MPI_IN_PLACE isn't
- supported.*/
- mpi_in_place_buf_t *mpb;
-} t_commrec;
+ /* these buffers are used as destination buffers if MPI_IN_PLACE isn't
+ supported.*/
+ mpi_in_place_buf_t *mpb;
+};
#define MASTERNODE(cr) (((cr)->nodeid == 0) || !PAR(cr))
- /* #define MASTERTHREAD(cr) ((cr)->threadid == 0) */
- /* #define MASTER(cr) (MASTERNODE(cr) && MASTERTHREAD(cr)) */
+/* #define MASTERTHREAD(cr) ((cr)->threadid == 0) */
+/* #define MASTER(cr) (MASTERNODE(cr) && MASTERTHREAD(cr)) */
#define MASTER(cr) MASTERNODE(cr)
-#define SIMMASTER(cr) (MASTER(cr) && ((cr)->duty & DUTY_PP))
+#define SIMMASTER(cr) ((MASTER(cr) && ((cr)->duty & DUTY_PP)) || !PAR(cr))
#define NODEPAR(cr) ((cr)->nnodes > 1)
- /* #define THREADPAR(cr) ((cr)->nthreads > 1) */
- /* #define PAR(cr) (NODEPAR(cr) || THREADPAR(cr)) */
+/* #define THREADPAR(cr) ((cr)->nthreads > 1) */
+/* #define PAR(cr) (NODEPAR(cr) || THREADPAR(cr)) */
#define PAR(cr) NODEPAR(cr)
-#define RANK(cr,nodeid) (nodeid)
+#define RANK(cr, nodeid) (nodeid)
#define MASTERRANK(cr) (0)
+/* Note that even with particle decomposition removed, the use of
+ * non-DD parallelization in TPI, NM and multi-simulations means that
+ * PAR(cr) and DOMAINDECOMP(cr) are not universally synonymous. In
+ * particular, DOMAINDECOMP(cr) == true indicates that there is more
+ * than one domain, not just that the dd algorithm is active. */
#define DOMAINDECOMP(cr) (((cr)->dd != NULL) && PAR(cr))
#define DDMASTER(dd) ((dd)->rank == (dd)->masterrank)
-#define PARTDECOMP(cr) ((cr)->pd != NULL)
-
#define MULTISIM(cr) ((cr)->ms)
-#define MSRANK(ms,nodeid) (nodeid)
+#define MSRANK(ms, nodeid) (nodeid)
#define MASTERSIM(ms) ((ms)->sim == 0)
/* The master of all (the node that prints the remaining run time etc.) */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff