-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
- *
- * This file is part of Gromacs Copyright (c) 1991-2008
- * David van der Spoel, Erik Lindahl, Berk Hess, University of Groningen.
+ * Copyright (c) 2005,2006,2007,2008,2009,2010,2012,2013,2014, 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.
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
* To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org
- *
- * And Hey:
- * Gnomes, ROck Monsters And Chili Sauce
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
#ifndef _domdec_h
#define _domdec_h
-#include "typedefs.h"
-#include "types/commrec.h"
-#include "vsite.h"
-#include "genborn.h"
+#include "gromacs/legacyheaders/genborn.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/vsite.h"
+#include "gromacs/timing/wallcycle.h"
#ifdef __cplusplus
extern "C" {
#endif
-int ddglatnr(gmx_domdec_t *dd,int i);
+int ddglatnr(gmx_domdec_t *dd, int i);
/* Returns the global topology atom number belonging to local atom index i.
* This function is intended for writing ascii output
* and returns atom numbers starting at 1.
gmx_bool dd_filled_nsgrid_home(gmx_domdec_t *dd);
/* Is the ns grid already filled with the home particles? */
-void dd_store_state(gmx_domdec_t *dd,t_state *state);
+void dd_store_state(gmx_domdec_t *dd, t_state *state);
/* Store the global cg indices of the home cgs in state,
* so it can be reset, even after a new DD partitioning.
*/
gmx_domdec_zones_t *domdec_zones(gmx_domdec_t *dd);
-void dd_get_ns_ranges(gmx_domdec_t *dd,int icg,
- int *jcg0,int *jcg1,ivec shift0,ivec shift1);
+void dd_get_ns_ranges(gmx_domdec_t *dd, int icg,
+ int *jcg0, int *jcg1, ivec shift0, ivec shift1);
int dd_natoms_vsite(gmx_domdec_t *dd);
void dd_get_constraint_range(gmx_domdec_t *dd,
- int *at_start,int *at_end);
+ int *at_start, int *at_end);
real dd_cutoff_mbody(gmx_domdec_t *dd);
real dd_cutoff_twobody(gmx_domdec_t *dd);
-gmx_bool gmx_pmeonlynode(t_commrec *cr,int nodeid);
+void get_pme_nnodes(const gmx_domdec_t *dd,
+ int *npmenodes_x, int *npmenodes_y);
+/* Get the number of PME nodes along x and y, can be called with dd=NULL */
+
+gmx_bool gmx_pmeonlynode(t_commrec *cr, int nodeid);
/* Return if nodeid in cr->mpi_comm_mysim is a PME-only node */
-void get_pme_ddnodes(t_commrec *cr,int pmenodeid,
- int *nmy_ddnodes,int **my_ddnodes,int *node_peer);
+void get_pme_ddnodes(t_commrec *cr, int pmenodeid,
+ int *nmy_ddnodes, int **my_ddnodes, int *node_peer);
/* Returns the set of DD nodes that communicate with pme node cr->nodeid */
int dd_pme_maxshift_x(gmx_domdec_t *dd);
int dd_pme_maxshift_y(gmx_domdec_t *dd);
/* Returns the maximum shift for coordinate communication in PME, dim y */
-void make_dd_communicators(FILE *fplog,t_commrec *cr,int dd_node_order);
+void make_dd_communicators(FILE *fplog, t_commrec *cr, int dd_node_order);
gmx_domdec_t *
init_domain_decomposition(FILE *fplog,
t_commrec *cr,
unsigned long Flags,
ivec nc,
- real comm_distance_min,real rconstr,
- const char *dlb_opt,real dlb_scale,
- const char *sizex,const char *sizey,const char *sizez,
- gmx_mtop_t *mtop,t_inputrec *ir,
- matrix box,rvec *x,
+ real comm_distance_min, real rconstr,
+ const char *dlb_opt, real dlb_scale,
+ const char *sizex, const char *sizey, const char *sizez,
+ gmx_mtop_t *mtop, t_inputrec *ir,
+ matrix box, rvec *x,
gmx_ddbox_t *ddbox,
int *npme_x, int *npme_y);
void dd_init_bondeds(FILE *fplog,
- gmx_domdec_t *dd,gmx_mtop_t *mtop,
- gmx_vsite_t *vsite,gmx_constr_t constr,
- t_inputrec *ir,gmx_bool bBCheck,cginfo_mb_t *cginfo_mb);
+ gmx_domdec_t *dd, gmx_mtop_t *mtop,
+ gmx_vsite_t *vsite,
+ t_inputrec *ir, gmx_bool bBCheck, cginfo_mb_t *cginfo_mb);
/* Initialize data structures for bonded interactions */
-gmx_bool dd_bonded_molpbc(gmx_domdec_t *dd,int ePBC);
+gmx_bool dd_bonded_molpbc(gmx_domdec_t *dd, int ePBC);
/* Returns if we need to do pbc for calculating bonded interactions */
-void set_dd_parameters(FILE *fplog,gmx_domdec_t *dd,real dlb_scale,
- t_inputrec *ir,t_forcerec *fr,
- gmx_ddbox_t *ddbox);
+void set_dd_parameters(FILE *fplog, gmx_domdec_t *dd, real dlb_scale,
+ t_inputrec *ir,
+ gmx_ddbox_t *ddbox);
/* Set DD grid dimensions and limits,
* should be called after calling dd_init_bondeds.
*/
-gmx_bool change_dd_cutoff(t_commrec *cr,t_state *state,t_inputrec *ir,
+gmx_bool change_dd_cutoff(t_commrec *cr, t_state *state, t_inputrec *ir,
real cutoff_req );
/* Change the DD non-bonded communication cut-off.
* This could fail when trying to increase the cut-off,
* then FALSE will be returned and the cut-off is not modified.
*/
-void setup_dd_grid(FILE *fplog,gmx_domdec_t *dd);
+void change_dd_dlb_cutoff_limit(t_commrec *cr);
+/* Domain boundary changes due to the DD dynamic load balancing can limit
+ * the cut-off distance that can be set in change_dd_cutoff. This function
+ * limits the DLB such that using the currently set cut-off should still be
+ * possible after subsequently setting a shorter cut-off with change_dd_cutoff.
+ */
+
+gmx_bool dd_dlb_is_locked(const gmx_domdec_t *dd);
+/* Return if the DLB lock is set */
+
+void dd_dlb_set_lock(gmx_domdec_t *dd, gmx_bool bValue);
+/* Set a lock such that with DLB=auto DLB can (not) get turned on */
+
+void dd_setup_dlb_resource_sharing(t_commrec *cr,
+ const gmx_hw_info_t *hwinfo,
+ const gmx_hw_opt_t *hw_opt);
+/* When domains (PP MPI ranks) share a GPU, the individual GPU wait times
+ * are meaningless, as it depends on the order in which tasks on the same
+ * GPU finish. Therefore there wait times need to be averaged over the ranks
+ * sharing the same GPU. This function sets up the communication for that.
+ */
+
+void setup_dd_grid(FILE *fplog, gmx_domdec_t *dd);
void dd_collect_vec(gmx_domdec_t *dd,
- t_state *state_local,rvec *lv,rvec *v);
+ t_state *state_local, rvec *lv, rvec *v);
void dd_collect_state(gmx_domdec_t *dd,
- t_state *state_local,t_state *state);
+ t_state *state_local, t_state *state);
-enum { ddCyclStep, ddCyclPPduringPME, ddCyclF, ddCyclPME, ddCyclNr };
+enum {
+ ddCyclStep, ddCyclPPduringPME, ddCyclF, ddCyclWaitGPU, ddCyclPME, ddCyclNr
+};
-void dd_cycles_add(gmx_domdec_t *dd,float cycles,int ddCycl);
+void dd_cycles_add(gmx_domdec_t *dd, float cycles, int ddCycl);
/* Add the wallcycle count to the DD counter */
-void dd_force_flop_start(gmx_domdec_t *dd,t_nrnb *nrnb);
+void dd_force_flop_start(gmx_domdec_t *dd, t_nrnb *nrnb);
/* Start the force flop count */
-void dd_force_flop_stop(gmx_domdec_t *dd,t_nrnb *nrnb);
+void dd_force_flop_stop(gmx_domdec_t *dd, t_nrnb *nrnb);
/* Stop the force flop count */
float dd_pme_f_ratio(gmx_domdec_t *dd);
* Should only be called on the DD master node.
*/
-void dd_move_x(gmx_domdec_t *dd,matrix box,rvec x[]);
+void dd_move_x(gmx_domdec_t *dd, matrix box, rvec x[]);
/* Communicate the coordinates to the neighboring cells and do pbc. */
-void dd_move_f(gmx_domdec_t *dd,rvec f[],rvec *fshift);
+void dd_move_f(gmx_domdec_t *dd, rvec f[], rvec *fshift);
/* Sum the forces over the neighboring cells.
* When fshift!=NULL the shift forces are updated to obtain
* the correct virial from the single sum including f.
*/
-void dd_atom_spread_real(gmx_domdec_t *dd,real v[]);
+void dd_atom_spread_real(gmx_domdec_t *dd, real v[]);
/* Communicate a real for each atom to the neighboring cells. */
-void dd_atom_sum_real(gmx_domdec_t *dd,real v[]);
+void dd_atom_sum_real(gmx_domdec_t *dd, real v[]);
/* Sum the contributions to a real for each atom over the neighboring cells. */
-void dd_partition_system(FILE *fplog,
- gmx_large_int_t step,
- t_commrec *cr,
- gmx_bool bMasterState,
- int nstglobalcomm,
- t_state *state_global,
- gmx_mtop_t *top_global,
- t_inputrec *ir,
- t_state *state_local,
- rvec **f,
- t_mdatoms *mdatoms,
- gmx_localtop_t *top_local,
- t_forcerec *fr,
- gmx_vsite_t *vsite,
- gmx_shellfc_t shellfc,
- gmx_constr_t constr,
- t_nrnb *nrnb,
- gmx_wallcycle_t wcycle,
- gmx_bool bVerbose);
+void dd_partition_system(FILE *fplog,
+ gmx_int64_t step,
+ t_commrec *cr,
+ gmx_bool bMasterState,
+ int nstglobalcomm,
+ t_state *state_global,
+ gmx_mtop_t *top_global,
+ t_inputrec *ir,
+ t_state *state_local,
+ rvec **f,
+ t_mdatoms *mdatoms,
+ gmx_localtop_t *top_local,
+ t_forcerec *fr,
+ gmx_vsite_t *vsite,
+ gmx_shellfc_t shellfc,
+ gmx_constr_t constr,
+ t_nrnb *nrnb,
+ gmx_wallcycle_t wcycle,
+ gmx_bool bVerbose);
/* Partition the system over the nodes.
* step is only used for printing error messages.
* If bMasterState==TRUE then state_global from the master node is used,
void reset_dd_statistics_counters(gmx_domdec_t *dd);
/* Reset all the statistics and counters for total run counting */
-void print_dd_statistics(t_commrec *cr,t_inputrec *ir,FILE *fplog);
+void print_dd_statistics(t_commrec *cr, t_inputrec *ir, FILE *fplog);
/* In domdec_con.c */
-void dd_move_f_vsites(gmx_domdec_t *dd,rvec *f,rvec *fshift);
+void dd_move_f_vsites(gmx_domdec_t *dd, rvec *f, rvec *fshift);
-void dd_clear_f_vsites(gmx_domdec_t *dd,rvec *f);
+void dd_clear_f_vsites(gmx_domdec_t *dd, rvec *f);
-void dd_move_x_constraints(gmx_domdec_t *dd,matrix box,
- rvec *x0,rvec *x1);
-/* Move x0 and also x1 if x1!=NULL */
+void dd_move_x_constraints(gmx_domdec_t *dd, matrix box,
+ rvec *x0, rvec *x1, gmx_bool bX1IsCoord);
+/* Move x0 and also x1 if x1!=NULL. bX1IsCoord tells if to do PBC on x1 */
-void dd_move_x_vsites(gmx_domdec_t *dd,matrix box,rvec *x);
+void dd_move_x_vsites(gmx_domdec_t *dd, matrix box, rvec *x);
int *dd_constraints_nlocalatoms(gmx_domdec_t *dd);
void dd_clear_local_vsite_indices(gmx_domdec_t *dd);
-int dd_make_local_vsites(gmx_domdec_t *dd,int at_start,t_ilist *lil);
+int dd_make_local_vsites(gmx_domdec_t *dd, int at_start, t_ilist *lil);
-int dd_make_local_constraints(gmx_domdec_t *dd,int at_start,
+int dd_make_local_constraints(gmx_domdec_t *dd, int at_start,
const gmx_mtop_t *mtop,
const int *cginfo,
- gmx_constr_t constr,int nrec,
+ gmx_constr_t constr, int nrec,
t_ilist *il_local);
void init_domdec_constraints(gmx_domdec_t *dd,
- gmx_mtop_t *mtop,
- gmx_constr_t constr);
+ gmx_mtop_t *mtop);
-void init_domdec_vsites(gmx_domdec_t *dd,int n_intercg_vsite);
+void init_domdec_vsites(gmx_domdec_t *dd, int n_intercg_vsite);
/* In domdec_top.c */
-void dd_print_missing_interactions(FILE *fplog,t_commrec *cr,
- int local_count, gmx_mtop_t *top_global, t_state *state_local);
+void dd_print_missing_interactions(FILE *fplog, t_commrec *cr,
+ int local_count, gmx_mtop_t *top_global, t_state *state_local);
void dd_make_reverse_top(FILE *fplog,
- gmx_domdec_t *dd,gmx_mtop_t *mtop,
- gmx_vsite_t *vsite,gmx_constr_t constr,
- t_inputrec *ir,gmx_bool bBCheck);
+ gmx_domdec_t *dd, gmx_mtop_t *mtop,
+ gmx_vsite_t *vsite,
+ t_inputrec *ir, gmx_bool bBCheck);
-void dd_make_local_cgs(gmx_domdec_t *dd,t_block *lcgs);
+void dd_make_local_cgs(gmx_domdec_t *dd, t_block *lcgs);
-void dd_make_local_top(FILE *fplog,
- gmx_domdec_t *dd,gmx_domdec_zones_t *zones,
- int npbcdim,matrix box,
- rvec cellsize_min,ivec npulse,
+void dd_make_local_top(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
+ int npbcdim, matrix box,
+ rvec cellsize_min, ivec npulse,
t_forcerec *fr,
rvec *cgcm_or_x,
gmx_vsite_t *vsite,
- gmx_mtop_t *top,gmx_localtop_t *ltop);
+ gmx_mtop_t *top, gmx_localtop_t *ltop);
-void dd_sort_local_top(gmx_domdec_t *dd,t_mdatoms *mdatoms,
- gmx_localtop_t *ltop);
+void dd_sort_local_top(gmx_domdec_t *dd, t_mdatoms *mdatoms,
+ gmx_localtop_t *ltop);
/* Sort ltop->ilist when we are doing free energy. */
gmx_localtop_t *dd_init_local_top(gmx_mtop_t *top_global);
void dd_init_local_state(gmx_domdec_t *dd,
- t_state *state_global,t_state *local_state);
+ t_state *state_global, t_state *local_state);
-t_blocka *make_charge_group_links(gmx_mtop_t *mtop,gmx_domdec_t *dd,
- cginfo_mb_t *cginfo_mb);
+t_blocka *make_charge_group_links(gmx_mtop_t *mtop, gmx_domdec_t *dd,
+ cginfo_mb_t *cginfo_mb);
-void dd_bonded_cg_distance(FILE *fplog,
- gmx_domdec_t *dd,gmx_mtop_t *mtop,
- t_inputrec *ir,rvec *x,matrix box,
- gmx_bool bBCheck,
- real *r_2b,real *r_mb);
+void dd_bonded_cg_distance(FILE *fplog, gmx_mtop_t *mtop,
+ t_inputrec *ir, rvec *x, matrix box,
+ gmx_bool bBCheck,
+ real *r_2b, real *r_mb);
-void write_dd_pdb(const char *fn,gmx_large_int_t step,const char *title,
- gmx_mtop_t *mtop,
- t_commrec *cr,
- int natoms,rvec x[],matrix box);
+void write_dd_pdb(const char *fn, gmx_int64_t step, const char *title,
+ gmx_mtop_t *mtop,
+ t_commrec *cr,
+ int natoms, rvec x[], matrix box);
/* Dump a pdb file with the current DD home + communicated atoms.
* When natoms=-1, dump all known atoms.
*/
/* In domdec_setup.c */
-real comm_box_frac(ivec dd_nc,real cutoff,gmx_ddbox_t *ddbox);
+real comm_box_frac(ivec dd_nc, real cutoff, gmx_ddbox_t *ddbox);
/* Returns the volume fraction of the system that is communicated */
real dd_choose_grid(FILE *fplog,
- t_commrec *cr,gmx_domdec_t *dd,t_inputrec *ir,
- gmx_mtop_t *mtop,matrix box,gmx_ddbox_t *ddbox,
- gmx_bool bDynLoadBal,real dlb_scale,
- real cellsize_limit,real cutoff_dd,
- gmx_bool bInterCGBondeds,gmx_bool bInterCGMultiBody);
+ t_commrec *cr, gmx_domdec_t *dd, t_inputrec *ir,
+ gmx_mtop_t *mtop, matrix box, gmx_ddbox_t *ddbox,
+ gmx_bool bDynLoadBal, real dlb_scale,
+ real cellsize_limit, real cutoff_dd,
+ gmx_bool bInterCGBondeds);
/* Determines the optimal DD cell setup dd->nc and possibly npmenodes
* for the system.
* On the master node returns the actual cellsize limit used.
/* In domdec_box.c */
-void set_ddbox(gmx_domdec_t *dd,gmx_bool bMasterState,t_commrec *cr_sum,
- t_inputrec *ir,matrix box,
- gmx_bool bCalcUnboundedSize,t_block *cgs,rvec *x,
- gmx_ddbox_t *ddbox);
+void set_ddbox(gmx_domdec_t *dd, gmx_bool bMasterState, t_commrec *cr_sum,
+ t_inputrec *ir, matrix box,
+ gmx_bool bCalcUnboundedSize, t_block *cgs, rvec *x,
+ gmx_ddbox_t *ddbox);
-void set_ddbox_cr(t_commrec *cr,ivec *dd_nc,
- t_inputrec *ir,matrix box,t_block *cgs,rvec *x,
- gmx_ddbox_t *ddbox);
+void set_ddbox_cr(t_commrec *cr, ivec *dd_nc,
+ t_inputrec *ir, matrix box, t_block *cgs, rvec *x,
+ gmx_ddbox_t *ddbox);
#ifdef __cplusplus
}
#endif
-#endif /* _domdec_h */
+#endif /* _domdec_h */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff