-/* -*- 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 source code is part of
- *
- * G R O M A C S
- *
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- *
- * VERSION 3.2.0
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* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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+ * 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.
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+#include "config.h"
+#include <math.h>
#include <stdio.h>
#include <string.h>
-#include <math.h>
-#include "typedefs.h"
-#include "smalloc.h"
-#include "gmx_fatal.h"
-#include "vec.h"
-#include "pme.h"
-#include "network.h"
-#include "domdec.h"
-#include "sighandler.h"
-
-#ifdef GMX_LIB_MPI
-#include <mpi.h>
-#endif
-#ifdef GMX_THREAD_MPI
-#include "tmpi.h"
-#endif
-#define PP_PME_CHARGE (1<<0)
-#define PP_PME_CHARGEB (1<<1)
-#define PP_PME_COORD (1<<2)
-#define PP_PME_FEP (1<<3)
-#define PP_PME_ENER_VIR (1<<4)
-#define PP_PME_FINISH (1<<5)
-#define PP_PME_SWITCH (1<<6)
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/pme.h"
+#include "gromacs/legacyheaders/sighandler.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
+
+enum {
+ eCommType_ChargeA, eCommType_ChargeB, eCommType_SQRTC6A, eCommType_SQRTC6B,
+ eCommType_SigmaA, eCommType_SigmaB, eCommType_NR, eCommType_COORD,
+ eCommType_CNB
+};
+
+/* Some parts of the code(gmx_pme_send_q, gmx_pme_recv_q_x) assume
+ * that the six first flags are exactly in this order.
+ * If more PP_PME_...-flags are to be introduced be aware of some of
+ * the PME-specific flags in pme.h. Currently, they are also passed
+ * through here.
+ */
-#define PME_PP_SIGSTOP (1<<0)
+#define PP_PME_CHARGE (1<<0)
+#define PP_PME_CHARGEB (1<<1)
+#define PP_PME_SQRTC6 (1<<2)
+#define PP_PME_SQRTC6B (1<<3)
+#define PP_PME_SIGMA (1<<4)
+#define PP_PME_SIGMAB (1<<5)
+#define PP_PME_COORD (1<<6)
+#define PP_PME_FEP_Q (1<<7)
+#define PP_PME_FEP_LJ (1<<8)
+#define PP_PME_ENER_VIR (1<<9)
+#define PP_PME_FINISH (1<<10)
+#define PP_PME_SWITCHGRID (1<<11)
+#define PP_PME_RESETCOUNTERS (1<<12)
+
+#define PME_PP_SIGSTOP (1<<0)
#define PME_PP_SIGSTOPNSS (1<<1)
typedef struct gmx_pme_pp {
#ifdef GMX_MPI
- MPI_Comm mpi_comm_mysim;
+ MPI_Comm mpi_comm_mysim;
#endif
- int nnode; /* The number of PP node to communicate with */
- int *node; /* The PP node ranks */
- int node_peer; /* The peer PP node rank */
- int *nat; /* The number of atom for each PP node */
- int flags_charge; /* The flags sent along with the last charges */
- real *chargeA;
- real *chargeB;
- rvec *x;
- rvec *f;
- int nalloc;
+ int nnode; /* The number of PP node to communicate with */
+ int *node; /* The PP node ranks */
+ int node_peer; /* The peer PP node rank */
+ int *nat; /* The number of atom for each PP node */
+ int flags_charge; /* The flags sent along with the last charges */
+ real *chargeA;
+ real *chargeB;
+ real *sqrt_c6A;
+ real *sqrt_c6B;
+ real *sigmaA;
+ real *sigmaB;
+ rvec *x;
+ rvec *f;
+ int nalloc;
#ifdef GMX_MPI
- MPI_Request *req;
- MPI_Status *stat;
+ MPI_Request *req;
+ MPI_Status *stat;
#endif
} t_gmx_pme_pp;
typedef struct gmx_pme_comm_n_box {
- int natoms;
- matrix box;
- int maxshift_x;
- int maxshift_y;
- real lambda;
- int flags;
- gmx_large_int_t step;
- ivec grid_size; /* For PME grid tuning */
- real ewaldcoeff; /* For PME grid tuning */
+ int natoms;
+ matrix box;
+ int maxshift_x;
+ int maxshift_y;
+ real lambda_q;
+ real lambda_lj;
+ int flags;
+ gmx_int64_t step;
+ ivec grid_size; /* For PME grid tuning */
+ real ewaldcoeff_q; /* For PME grid tuning */
+ real ewaldcoeff_lj;
} gmx_pme_comm_n_box_t;
typedef struct {
- matrix vir;
- real energy;
- real dvdlambda;
- float cycles;
- gmx_stop_cond_t stop_cond;
+ matrix vir_q;
+ matrix vir_lj;
+ real energy_q;
+ real energy_lj;
+ real dvdlambda_q;
+ real dvdlambda_lj;
+ float cycles;
+ gmx_stop_cond_t stop_cond;
} gmx_pme_comm_vir_ene_t;
-gmx_pme_pp_t gmx_pme_pp_init(t_commrec *cr)
+gmx_pme_pp_t gmx_pme_pp_init(t_commrec gmx_unused *cr)
{
- struct gmx_pme_pp *pme_pp;
- int rank;
+ struct gmx_pme_pp *pme_pp;
+ int rank;
- snew(pme_pp,1);
+ snew(pme_pp, 1);
#ifdef GMX_MPI
- pme_pp->mpi_comm_mysim = cr->mpi_comm_mysim;
- MPI_Comm_rank(cr->mpi_comm_mygroup,&rank);
- get_pme_ddnodes(cr,rank,&pme_pp->nnode,&pme_pp->node,&pme_pp->node_peer);
- snew(pme_pp->nat,pme_pp->nnode);
- snew(pme_pp->req,2*pme_pp->nnode);
- snew(pme_pp->stat,2*pme_pp->nnode);
- pme_pp->nalloc = 0;
- pme_pp->flags_charge = 0;
+ pme_pp->mpi_comm_mysim = cr->mpi_comm_mysim;
+ MPI_Comm_rank(cr->mpi_comm_mygroup, &rank);
+ get_pme_ddnodes(cr, rank, &pme_pp->nnode, &pme_pp->node, &pme_pp->node_peer);
+ snew(pme_pp->nat, pme_pp->nnode);
+ snew(pme_pp->req, eCommType_NR*pme_pp->nnode);
+ snew(pme_pp->stat, eCommType_NR*pme_pp->nnode);
+ pme_pp->nalloc = 0;
+ pme_pp->flags_charge = 0;
#endif
- return pme_pp;
+ return pme_pp;
}
/* This should be faster with a real non-blocking MPI implementation */
/* #define GMX_PME_DELAYED_WAIT */
-static void gmx_pme_send_q_x_wait(gmx_domdec_t *dd)
+static void gmx_pme_send_coeffs_coords_wait(gmx_domdec_t gmx_unused *dd)
{
#ifdef GMX_MPI
- if (dd->nreq_pme) {
- MPI_Waitall(dd->nreq_pme,dd->req_pme,MPI_STATUSES_IGNORE);
- dd->nreq_pme = 0;
- }
+ if (dd->nreq_pme)
+ {
+ MPI_Waitall(dd->nreq_pme, dd->req_pme, MPI_STATUSES_IGNORE);
+ dd->nreq_pme = 0;
+ }
#endif
}
-static void gmx_pme_send_q_x(t_commrec *cr, int flags,
- real *chargeA, real *chargeB,
- matrix box, rvec *x,
- real lambda,
- int maxshift_x, int maxshift_y,
- gmx_large_int_t step)
+static void gmx_pme_send_coeffs_coords(t_commrec *cr, int flags,
+ real gmx_unused *chargeA, real gmx_unused *chargeB,
+ real gmx_unused *c6A, real gmx_unused *c6B,
+ real gmx_unused *sigmaA, real gmx_unused *sigmaB,
+ matrix box, rvec gmx_unused *x,
+ real lambda_q, real lambda_lj,
+ int maxshift_x, int maxshift_y,
+ gmx_int64_t step)
{
- gmx_domdec_t *dd;
- gmx_pme_comm_n_box_t *cnb;
- int n;
+ gmx_domdec_t *dd;
+ gmx_pme_comm_n_box_t *cnb;
+ int n;
- dd = cr->dd;
- n = dd->nat_home;
+ dd = cr->dd;
+ n = dd->nat_home;
- if (debug)
- fprintf(debug,"PP node %d sending to PME node %d: %d%s%s\n",
- cr->sim_nodeid,dd->pme_nodeid,n,
- flags & PP_PME_CHARGE ? " charges" : "",
- flags & PP_PME_COORD ? " coordinates" : "");
+ if (debug)
+ {
+ fprintf(debug, "PP rank %d sending to PME rank %d: %d%s%s%s%s\n",
+ cr->sim_nodeid, dd->pme_nodeid, n,
+ flags & PP_PME_CHARGE ? " charges" : "",
+ flags & PP_PME_SQRTC6 ? " sqrtC6" : "",
+ flags & PP_PME_SIGMA ? " sigma" : "",
+ flags & PP_PME_COORD ? " coordinates" : "");
+ }
#ifdef GMX_PME_DELAYED_WAIT
- /* When can not use cnb until pending communication has finished */
- gmx_pme_send_x_q_wait(dd);
+ /* When can not use cnb until pending communication has finished */
+ gmx_pme_send_coeffs_coords_wait(dd);
#endif
- if (dd->pme_receive_vir_ener) {
- /* Peer PP node: communicate all data */
- if (dd->cnb == NULL)
- snew(dd->cnb,1);
- cnb = dd->cnb;
-
- cnb->flags = flags;
- cnb->natoms = n;
- cnb->maxshift_x = maxshift_x;
- cnb->maxshift_y = maxshift_y;
- cnb->lambda = lambda;
- cnb->step = step;
- if (flags & PP_PME_COORD)
- copy_mat(box,cnb->box);
+ if (dd->pme_receive_vir_ener)
+ {
+ /* Peer PP node: communicate all data */
+ if (dd->cnb == NULL)
+ {
+ snew(dd->cnb, 1);
+ }
+ cnb = dd->cnb;
+
+ cnb->flags = flags;
+ cnb->natoms = n;
+ cnb->maxshift_x = maxshift_x;
+ cnb->maxshift_y = maxshift_y;
+ cnb->lambda_q = lambda_q;
+ cnb->lambda_lj = lambda_lj;
+ cnb->step = step;
+ if (flags & PP_PME_COORD)
+ {
+ copy_mat(box, cnb->box);
+ }
#ifdef GMX_MPI
- MPI_Isend(cnb,sizeof(*cnb),MPI_BYTE,
- dd->pme_nodeid,0,cr->mpi_comm_mysim,
- &dd->req_pme[dd->nreq_pme++]);
+ MPI_Isend(cnb, sizeof(*cnb), MPI_BYTE,
+ dd->pme_nodeid, eCommType_CNB, cr->mpi_comm_mysim,
+ &dd->req_pme[dd->nreq_pme++]);
#endif
- } else if (flags & PP_PME_CHARGE) {
+ }
+ else if (flags & (PP_PME_CHARGE | PP_PME_SQRTC6 | PP_PME_SIGMA))
+ {
#ifdef GMX_MPI
- /* Communicate only the number of atoms */
- MPI_Isend(&n,sizeof(n),MPI_BYTE,
- dd->pme_nodeid,0,cr->mpi_comm_mysim,
- &dd->req_pme[dd->nreq_pme++]);
+ /* Communicate only the number of atoms */
+ MPI_Isend(&n, sizeof(n), MPI_BYTE,
+ dd->pme_nodeid, eCommType_CNB, cr->mpi_comm_mysim,
+ &dd->req_pme[dd->nreq_pme++]);
#endif
- }
+ }
#ifdef GMX_MPI
- if (n > 0) {
- if (flags & PP_PME_CHARGE) {
- MPI_Isend(chargeA,n*sizeof(real),MPI_BYTE,
- dd->pme_nodeid,1,cr->mpi_comm_mysim,
- &dd->req_pme[dd->nreq_pme++]);
- }
- if (flags & PP_PME_CHARGEB) {
- MPI_Isend(chargeB,n*sizeof(real),MPI_BYTE,
- dd->pme_nodeid,2,cr->mpi_comm_mysim,
- &dd->req_pme[dd->nreq_pme++]);
- }
- if (flags & PP_PME_COORD) {
- MPI_Isend(x[0],n*sizeof(rvec),MPI_BYTE,
- dd->pme_nodeid,3,cr->mpi_comm_mysim,
- &dd->req_pme[dd->nreq_pme++]);
+ if (n > 0)
+ {
+ if (flags & PP_PME_CHARGE)
+ {
+ MPI_Isend(chargeA, n*sizeof(real), MPI_BYTE,
+ dd->pme_nodeid, eCommType_ChargeA, cr->mpi_comm_mysim,
+ &dd->req_pme[dd->nreq_pme++]);
+ }
+ if (flags & PP_PME_CHARGEB)
+ {
+ MPI_Isend(chargeB, n*sizeof(real), MPI_BYTE,
+ dd->pme_nodeid, eCommType_ChargeB, cr->mpi_comm_mysim,
+ &dd->req_pme[dd->nreq_pme++]);
+ }
+ if (flags & PP_PME_SQRTC6)
+ {
+ MPI_Isend(c6A, n*sizeof(real), MPI_BYTE,
+ dd->pme_nodeid, eCommType_SQRTC6A, cr->mpi_comm_mysim,
+ &dd->req_pme[dd->nreq_pme++]);
+ }
+ if (flags & PP_PME_SQRTC6B)
+ {
+ MPI_Isend(c6B, n*sizeof(real), MPI_BYTE,
+ dd->pme_nodeid, eCommType_SQRTC6B, cr->mpi_comm_mysim,
+ &dd->req_pme[dd->nreq_pme++]);
+ }
+ if (flags & PP_PME_SIGMA)
+ {
+ MPI_Isend(sigmaA, n*sizeof(real), MPI_BYTE,
+ dd->pme_nodeid, eCommType_SigmaA, cr->mpi_comm_mysim,
+ &dd->req_pme[dd->nreq_pme++]);
+ }
+ if (flags & PP_PME_SIGMAB)
+ {
+ MPI_Isend(sigmaB, n*sizeof(real), MPI_BYTE,
+ dd->pme_nodeid, eCommType_SigmaB, cr->mpi_comm_mysim,
+ &dd->req_pme[dd->nreq_pme++]);
+ }
+ if (flags & PP_PME_COORD)
+ {
+ MPI_Isend(x[0], n*sizeof(rvec), MPI_BYTE,
+ dd->pme_nodeid, eCommType_COORD, cr->mpi_comm_mysim,
+ &dd->req_pme[dd->nreq_pme++]);
+ }
}
- }
#ifndef GMX_PME_DELAYED_WAIT
- /* Wait for the data to arrive */
- /* We can skip this wait as we are sure x and q will not be modified
- * before the next call to gmx_pme_send_x_q or gmx_pme_receive_f.
- */
- gmx_pme_send_q_x_wait(dd);
+ /* Wait for the data to arrive */
+ /* We can skip this wait as we are sure x and q will not be modified
+ * before the next call to gmx_pme_send_x_q or gmx_pme_receive_f.
+ */
+ gmx_pme_send_coeffs_coords_wait(dd);
#endif
#endif
}
-void gmx_pme_send_q(t_commrec *cr,
- gmx_bool bFreeEnergy, real *chargeA, real *chargeB,
- int maxshift_x, int maxshift_y)
+void gmx_pme_send_parameters(t_commrec *cr,
+ const interaction_const_t *ic,
+ gmx_bool bFreeEnergy_q, gmx_bool bFreeEnergy_lj,
+ real *chargeA, real *chargeB,
+ real *sqrt_c6A, real *sqrt_c6B,
+ real *sigmaA, real *sigmaB,
+ int maxshift_x, int maxshift_y)
{
- int flags;
+ int flags;
- flags = PP_PME_CHARGE;
- if (bFreeEnergy)
- flags |= PP_PME_CHARGEB;
+ flags = 0;
+ if (EEL_PME(ic->eeltype))
+ {
+ flags |= PP_PME_CHARGE;
+ }
+ if (EVDW_PME(ic->vdwtype))
+ {
+ flags |= (PP_PME_SQRTC6 | PP_PME_SIGMA);
+ }
+ if (bFreeEnergy_q || bFreeEnergy_lj)
+ {
+ /* Assumes that the B state flags are in the bits just above
+ * the ones for the A state. */
+ flags |= (flags << 1);
+ }
- gmx_pme_send_q_x(cr,flags,
- chargeA,chargeB,NULL,NULL,0,maxshift_x,maxshift_y,-1);
+ gmx_pme_send_coeffs_coords(cr, flags,
+ chargeA, chargeB,
+ sqrt_c6A, sqrt_c6B, sigmaA, sigmaB,
+ NULL, NULL, 0, 0, maxshift_x, maxshift_y, -1);
}
-void gmx_pme_send_x(t_commrec *cr, matrix box, rvec *x,
- gmx_bool bFreeEnergy, real lambda,
- gmx_bool bEnerVir,
- gmx_large_int_t step)
+void gmx_pme_send_coordinates(t_commrec *cr, matrix box, rvec *x,
+ gmx_bool bFreeEnergy_q, gmx_bool bFreeEnergy_lj,
+ real lambda_q, real lambda_lj,
+ gmx_bool bEnerVir, int pme_flags,
+ gmx_int64_t step)
{
- int flags;
-
- flags = PP_PME_COORD;
- if (bFreeEnergy)
- flags |= PP_PME_FEP;
- if (bEnerVir)
- flags |= PP_PME_ENER_VIR;
-
- gmx_pme_send_q_x(cr,flags,NULL,NULL,box,x,lambda,0,0,step);
+ int flags;
+
+ flags = pme_flags | PP_PME_COORD;
+ if (bFreeEnergy_q)
+ {
+ flags |= PP_PME_FEP_Q;
+ }
+ if (bFreeEnergy_lj)
+ {
+ flags |= PP_PME_FEP_LJ;
+ }
+ if (bEnerVir)
+ {
+ flags |= PP_PME_ENER_VIR;
+ }
+ gmx_pme_send_coeffs_coords(cr, flags, NULL, NULL, NULL, NULL, NULL, NULL,
+ box, x, lambda_q, lambda_lj, 0, 0, step);
}
void gmx_pme_send_finish(t_commrec *cr)
{
- int flags;
+ int flags;
- flags = PP_PME_FINISH;
+ flags = PP_PME_FINISH;
- gmx_pme_send_q_x(cr,flags,NULL,NULL,NULL,NULL,0,0,0,-1);
+ gmx_pme_send_coeffs_coords(cr, flags, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, 0, -1);
}
-void gmx_pme_send_switch(t_commrec *cr, ivec grid_size, real ewaldcoeff)
+void gmx_pme_send_switchgrid(t_commrec gmx_unused *cr,
+ ivec gmx_unused grid_size,
+ real gmx_unused ewaldcoeff_q,
+ real gmx_unused ewaldcoeff_lj)
{
#ifdef GMX_MPI
gmx_pme_comm_n_box_t cnb;
+ /* Only let one PP node signal each PME node */
if (cr->dd->pme_receive_vir_ener)
{
- cnb.flags = PP_PME_SWITCH;
- copy_ivec(grid_size,cnb.grid_size);
- cnb.ewaldcoeff = ewaldcoeff;
+ cnb.flags = PP_PME_SWITCHGRID;
+ copy_ivec(grid_size, cnb.grid_size);
+ cnb.ewaldcoeff_q = ewaldcoeff_q;
+ cnb.ewaldcoeff_lj = ewaldcoeff_lj;
/* We send this, uncommon, message blocking to simplify the code */
- MPI_Send(&cnb,sizeof(cnb),MPI_BYTE,
- cr->dd->pme_nodeid,0,cr->mpi_comm_mysim);
+ MPI_Send(&cnb, sizeof(cnb), MPI_BYTE,
+ cr->dd->pme_nodeid, eCommType_CNB, cr->mpi_comm_mysim);
}
#endif
}
-int gmx_pme_recv_q_x(struct gmx_pme_pp *pme_pp,
- real **chargeA, real **chargeB,
- matrix box, rvec **x,rvec **f,
- int *maxshift_x, int *maxshift_y,
- gmx_bool *bFreeEnergy,real *lambda,
- gmx_bool *bEnerVir,
- gmx_large_int_t *step,
- ivec grid_size, real *ewaldcoeff)
+void gmx_pme_send_resetcounters(t_commrec gmx_unused *cr, gmx_int64_t gmx_unused step)
{
+#ifdef GMX_MPI
gmx_pme_comm_n_box_t cnb;
- int nat=0,q,messages,sender;
- real *charge_pp;
+
+ /* Only let one PP node signal each PME node */
+ if (cr->dd->pme_receive_vir_ener)
+ {
+ cnb.flags = PP_PME_RESETCOUNTERS;
+ cnb.step = step;
+
+ /* We send this, uncommon, message blocking to simplify the code */
+ MPI_Send(&cnb, sizeof(cnb), MPI_BYTE,
+ cr->dd->pme_nodeid, eCommType_CNB, cr->mpi_comm_mysim);
+ }
+#endif
+}
+
+int gmx_pme_recv_coeffs_coords(struct gmx_pme_pp *pme_pp,
+ int *natoms,
+ real **chargeA,
+ real **chargeB,
+ real **sqrt_c6A,
+ real **sqrt_c6B,
+ real **sigmaA,
+ real **sigmaB,
+ matrix gmx_unused box,
+ rvec **x,
+ rvec **f,
+ int gmx_unused *maxshift_x,
+ int gmx_unused *maxshift_y,
+ gmx_bool gmx_unused *bFreeEnergy_q,
+ gmx_bool gmx_unused *bFreeEnergy_lj,
+ real gmx_unused *lambda_q,
+ real gmx_unused *lambda_lj,
+ gmx_bool gmx_unused *bEnerVir,
+ int *pme_flags,
+ gmx_int64_t gmx_unused *step,
+ ivec gmx_unused grid_size,
+ real gmx_unused *ewaldcoeff_q,
+ real gmx_unused *ewaldcoeff_lj)
+{
+ gmx_pme_comm_n_box_t cnb;
+ int nat = 0, q, messages, sender;
+ real *charge_pp;
messages = 0;
/* avoid compiler warning about unused variable without MPI support */
- cnb.flags = 0;
+ cnb.flags = 0;
+ *pme_flags = 0;
#ifdef GMX_MPI
- do {
+ do
+ {
/* Receive the send count, box and time step from the peer PP node */
- MPI_Recv(&cnb,sizeof(cnb),MPI_BYTE,
- pme_pp->node_peer,0,
- pme_pp->mpi_comm_mysim,MPI_STATUS_IGNORE);
+ MPI_Recv(&cnb, sizeof(cnb), MPI_BYTE,
+ pme_pp->node_peer, eCommType_CNB,
+ pme_pp->mpi_comm_mysim, MPI_STATUS_IGNORE);
if (debug)
{
- fprintf(debug,"PME only node receiving:%s%s%s%s\n",
- (cnb.flags & PP_PME_CHARGE) ? " charges" : "",
- (cnb.flags & PP_PME_COORD ) ? " coordinates" : "",
- (cnb.flags & PP_PME_FINISH) ? " finish" : "",
- (cnb.flags & PP_PME_SWITCH) ? " switch" : "");
+ fprintf(debug, "PME only rank receiving:%s%s%s%s%s\n",
+ (cnb.flags & PP_PME_CHARGE) ? " charges" : "",
+ (cnb.flags & PP_PME_COORD ) ? " coordinates" : "",
+ (cnb.flags & PP_PME_FINISH) ? " finish" : "",
+ (cnb.flags & PP_PME_SWITCHGRID) ? " switch grid" : "",
+ (cnb.flags & PP_PME_RESETCOUNTERS) ? " reset counters" : "");
}
- if (cnb.flags & PP_PME_SWITCH)
+ if (cnb.flags & PP_PME_SWITCHGRID)
{
/* Special case, receive the new parameters and return */
- copy_ivec(cnb.grid_size,grid_size);
- *ewaldcoeff = cnb.ewaldcoeff;
+ copy_ivec(cnb.grid_size, grid_size);
+ *ewaldcoeff_q = cnb.ewaldcoeff_q;
+ *ewaldcoeff_lj = cnb.ewaldcoeff_lj;
+ return pmerecvqxSWITCHGRID;
+ }
+
+ if (cnb.flags & PP_PME_RESETCOUNTERS)
+ {
+ /* Special case, receive the step and return */
+ *step = cnb.step;
- return -2;
+ return pmerecvqxRESETCOUNTERS;
}
- if (cnb.flags & PP_PME_CHARGE) {
+ if (cnb.flags & (PP_PME_CHARGE | PP_PME_SQRTC6 | PP_PME_SIGMA))
+ {
/* Receive the send counts from the other PP nodes */
- for(sender=0; sender<pme_pp->nnode; sender++) {
- if (pme_pp->node[sender] == pme_pp->node_peer) {
+ for (sender = 0; sender < pme_pp->nnode; sender++)
+ {
+ if (pme_pp->node[sender] == pme_pp->node_peer)
+ {
pme_pp->nat[sender] = cnb.natoms;
- } else {
- MPI_Irecv(&(pme_pp->nat[sender]),sizeof(pme_pp->nat[0]),
+ }
+ else
+ {
+ MPI_Irecv(&(pme_pp->nat[sender]), sizeof(pme_pp->nat[0]),
MPI_BYTE,
- pme_pp->node[sender],0,
- pme_pp->mpi_comm_mysim,&pme_pp->req[messages++]);
+ pme_pp->node[sender], eCommType_CNB,
+ pme_pp->mpi_comm_mysim, &pme_pp->req[messages++]);
}
}
MPI_Waitall(messages, pme_pp->req, pme_pp->stat);
messages = 0;
nat = 0;
- for(sender=0; sender<pme_pp->nnode; sender++)
+ for (sender = 0; sender < pme_pp->nnode; sender++)
+ {
nat += pme_pp->nat[sender];
+ }
- if (nat > pme_pp->nalloc) {
+ if (nat > pme_pp->nalloc)
+ {
pme_pp->nalloc = over_alloc_dd(nat);
- srenew(pme_pp->chargeA,pme_pp->nalloc);
+ if (cnb.flags & PP_PME_CHARGE)
+ {
+ srenew(pme_pp->chargeA, pme_pp->nalloc);
+ }
if (cnb.flags & PP_PME_CHARGEB)
- srenew(pme_pp->chargeB,pme_pp->nalloc);
- srenew(pme_pp->x,pme_pp->nalloc);
- srenew(pme_pp->f,pme_pp->nalloc);
+ {
+ srenew(pme_pp->chargeB, pme_pp->nalloc);
+ }
+ if (cnb.flags & PP_PME_SQRTC6)
+ {
+ srenew(pme_pp->sqrt_c6A, pme_pp->nalloc);
+ }
+ if (cnb.flags & PP_PME_SQRTC6B)
+ {
+ srenew(pme_pp->sqrt_c6B, pme_pp->nalloc);
+ }
+ if (cnb.flags & PP_PME_SIGMA)
+ {
+ srenew(pme_pp->sigmaA, pme_pp->nalloc);
+ }
+ if (cnb.flags & PP_PME_SIGMAB)
+ {
+ srenew(pme_pp->sigmaB, pme_pp->nalloc);
+ }
+ srenew(pme_pp->x, pme_pp->nalloc);
+ srenew(pme_pp->f, pme_pp->nalloc);
}
/* maxshift is sent when the charges are sent */
*maxshift_y = cnb.maxshift_y;
/* Receive the charges in place */
- for(q=0; q<((cnb.flags & PP_PME_CHARGEB) ? 2 : 1); q++) {
- if (q == 0)
- charge_pp = pme_pp->chargeA;
- else
- charge_pp = pme_pp->chargeB;
+ for (q = 0; q < eCommType_NR; q++)
+ {
+ if (!(cnb.flags & (PP_PME_CHARGE<<q)))
+ {
+ continue;
+ }
+ switch (q)
+ {
+ case eCommType_ChargeA: charge_pp = pme_pp->chargeA; break;
+ case eCommType_ChargeB: charge_pp = pme_pp->chargeB; break;
+ case eCommType_SQRTC6A: charge_pp = pme_pp->sqrt_c6A; break;
+ case eCommType_SQRTC6B: charge_pp = pme_pp->sqrt_c6B; break;
+ case eCommType_SigmaA: charge_pp = pme_pp->sigmaA; break;
+ case eCommType_SigmaB: charge_pp = pme_pp->sigmaB; break;
+ default: gmx_incons("Wrong eCommType");
+ }
nat = 0;
- for(sender=0; sender<pme_pp->nnode; sender++) {
- if (pme_pp->nat[sender] > 0) {
+ for (sender = 0; sender < pme_pp->nnode; sender++)
+ {
+ if (pme_pp->nat[sender] > 0)
+ {
MPI_Irecv(charge_pp+nat,
pme_pp->nat[sender]*sizeof(real),
MPI_BYTE,
- pme_pp->node[sender],1+q,
+ pme_pp->node[sender], q,
pme_pp->mpi_comm_mysim,
&pme_pp->req[messages++]);
nat += pme_pp->nat[sender];
if (debug)
- fprintf(debug,"Received from PP node %d: %d "
- "charges\n",
- pme_pp->node[sender],pme_pp->nat[sender]);
+ {
+ fprintf(debug, "Received from PP rank %d: %d %s\n",
+ pme_pp->node[sender], pme_pp->nat[sender],
+ (q == eCommType_ChargeA ||
+ q == eCommType_ChargeB) ? "charges" : "params");
+ }
}
}
}
pme_pp->flags_charge = cnb.flags;
}
- if (cnb.flags & PP_PME_COORD) {
- if (!(pme_pp->flags_charge & PP_PME_CHARGE))
- gmx_incons("PME-only node received coordinates before charges"
- );
+ if (cnb.flags & PP_PME_COORD)
+ {
+ if (!(pme_pp->flags_charge & (PP_PME_CHARGE | PP_PME_SQRTC6)))
+ {
+ gmx_incons("PME-only rank received coordinates before charges and/or C6-values"
+ );
+ }
/* The box, FE flag and lambda are sent along with the coordinates
* */
- copy_mat(cnb.box,box);
- *bFreeEnergy = (cnb.flags & PP_PME_FEP);
- *lambda = cnb.lambda;
- *bEnerVir = (cnb.flags & PP_PME_ENER_VIR);
+ copy_mat(cnb.box, box);
+ *bFreeEnergy_q = ((cnb.flags & GMX_PME_DO_COULOMB) &&
+ (cnb.flags & PP_PME_FEP_Q));
+ *bFreeEnergy_lj = ((cnb.flags & GMX_PME_DO_LJ) &&
+ (cnb.flags & PP_PME_FEP_LJ));
+ *lambda_q = cnb.lambda_q;
+ *lambda_lj = cnb.lambda_lj;
+ *bEnerVir = (cnb.flags & PP_PME_ENER_VIR);
+ *pme_flags = cnb.flags;
+
+ if (*bFreeEnergy_q && !(pme_pp->flags_charge & PP_PME_CHARGEB))
+ {
+ gmx_incons("PME-only rank received free energy request, but "
+ "did not receive B-state charges");
+ }
- if (*bFreeEnergy && !(pme_pp->flags_charge & PP_PME_CHARGEB))
- gmx_incons("PME-only node received free energy request, but "
- "did not receive B-state charges");
+ if (*bFreeEnergy_lj && !(pme_pp->flags_charge & PP_PME_SQRTC6B))
+ {
+ gmx_incons("PME-only rank received free energy request, but "
+ "did not receive B-state C6-values");
+ }
/* Receive the coordinates in place */
nat = 0;
- for(sender=0; sender<pme_pp->nnode; sender++) {
- if (pme_pp->nat[sender] > 0) {
- MPI_Irecv(pme_pp->x[nat],pme_pp->nat[sender]*sizeof(rvec),
+ for (sender = 0; sender < pme_pp->nnode; sender++)
+ {
+ if (pme_pp->nat[sender] > 0)
+ {
+ MPI_Irecv(pme_pp->x[nat], pme_pp->nat[sender]*sizeof(rvec),
MPI_BYTE,
- pme_pp->node[sender],3,
- pme_pp->mpi_comm_mysim,&pme_pp->req[messages++]);
+ pme_pp->node[sender], eCommType_COORD,
+ pme_pp->mpi_comm_mysim, &pme_pp->req[messages++]);
nat += pme_pp->nat[sender];
if (debug)
- fprintf(debug,"Received from PP node %d: %d "
- "coordinates\n",
- pme_pp->node[sender],pme_pp->nat[sender]);
+ {
+ fprintf(debug, "Received from PP rank %d: %d "
+ "coordinates\n",
+ pme_pp->node[sender], pme_pp->nat[sender]);
+ }
}
}
}
/* Wait for the coordinates and/or charges to arrive */
MPI_Waitall(messages, pme_pp->req, pme_pp->stat);
messages = 0;
- } while (!(cnb.flags & (PP_PME_COORD | PP_PME_FINISH)));
+ }
+ while (!(cnb.flags & (PP_PME_COORD | PP_PME_FINISH)));
*step = cnb.step;
#endif
- *chargeA = pme_pp->chargeA;
- *chargeB = pme_pp->chargeB;
- *x = pme_pp->x;
- *f = pme_pp->f;
-
-
- return ((cnb.flags & PP_PME_FINISH) ? -1 : nat);
+ *natoms = nat;
+ *chargeA = pme_pp->chargeA;
+ *chargeB = pme_pp->chargeB;
+ *sqrt_c6A = pme_pp->sqrt_c6A;
+ *sqrt_c6B = pme_pp->sqrt_c6B;
+ *sigmaA = pme_pp->sigmaA;
+ *sigmaB = pme_pp->sigmaB;
+ *x = pme_pp->x;
+ *f = pme_pp->f;
+
+ return ((cnb.flags & PP_PME_FINISH) ? pmerecvqxFINISH : pmerecvqxX);
}
static void receive_virial_energy(t_commrec *cr,
- matrix vir,real *energy,real *dvdlambda,
- float *pme_cycles)
+ matrix vir_q, real *energy_q,
+ matrix vir_lj, real *energy_lj,
+ real *dvdlambda_q, real *dvdlambda_lj,
+ float *pme_cycles)
{
- gmx_pme_comm_vir_ene_t cve;
+ gmx_pme_comm_vir_ene_t cve;
- if (cr->dd->pme_receive_vir_ener) {
- if (debug)
- fprintf(debug,
- "PP node %d receiving from PME node %d: virial and energy\n",
- cr->sim_nodeid,cr->dd->pme_nodeid);
+ if (cr->dd->pme_receive_vir_ener)
+ {
+ if (debug)
+ {
+ fprintf(debug,
+ "PP rank %d receiving from PME rank %d: virial and energy\n",
+ cr->sim_nodeid, cr->dd->pme_nodeid);
+ }
#ifdef GMX_MPI
- MPI_Recv(&cve,sizeof(cve),MPI_BYTE,cr->dd->pme_nodeid,1,cr->mpi_comm_mysim,
- MPI_STATUS_IGNORE);
+ MPI_Recv(&cve, sizeof(cve), MPI_BYTE, cr->dd->pme_nodeid, 1, cr->mpi_comm_mysim,
+ MPI_STATUS_IGNORE);
#else
- memset(&cve,0,sizeof(cve));
+ memset(&cve, 0, sizeof(cve));
#endif
-
- m_add(vir,cve.vir,vir);
- *energy = cve.energy;
- *dvdlambda += cve.dvdlambda;
- *pme_cycles = cve.cycles;
- if ( cve.stop_cond != gmx_stop_cond_none )
+ m_add(vir_q, cve.vir_q, vir_q);
+ m_add(vir_lj, cve.vir_lj, vir_lj);
+ *energy_q = cve.energy_q;
+ *energy_lj = cve.energy_lj;
+ *dvdlambda_q += cve.dvdlambda_q;
+ *dvdlambda_lj += cve.dvdlambda_lj;
+ *pme_cycles = cve.cycles;
+
+ if (cve.stop_cond != gmx_stop_cond_none)
+ {
+ gmx_set_stop_condition(cve.stop_cond);
+ }
+ }
+ else
{
- gmx_set_stop_condition(cve.stop_cond);
+ *energy_q = 0;
+ *energy_lj = 0;
+ *pme_cycles = 0;
}
- } else {
- *energy = 0;
- *pme_cycles = 0;
- }
}
void gmx_pme_receive_f(t_commrec *cr,
- rvec f[], matrix vir,
- real *energy, real *dvdlambda,
- float *pme_cycles)
+ rvec f[], matrix vir_q, real *energy_q,
+ matrix vir_lj, real *energy_lj,
+ real *dvdlambda_q, real *dvdlambda_lj,
+ float *pme_cycles)
{
- int natoms,i;
+ int natoms, i;
#ifdef GMX_PME_DELAYED_WAIT
- /* Wait for the x request to finish */
- gmx_pme_send_q_x_wait(cr->dd);
+ /* Wait for the x request to finish */
+ gmx_pme_send_coeffs_coords_wait(cr->dd);
#endif
- natoms = cr->dd->nat_home;
+ natoms = cr->dd->nat_home;
- if (natoms > cr->dd->pme_recv_f_alloc)
- {
- cr->dd->pme_recv_f_alloc = over_alloc_dd(natoms);
- srenew(cr->dd->pme_recv_f_buf, cr->dd->pme_recv_f_alloc);
- }
+ if (natoms > cr->dd->pme_recv_f_alloc)
+ {
+ cr->dd->pme_recv_f_alloc = over_alloc_dd(natoms);
+ srenew(cr->dd->pme_recv_f_buf, cr->dd->pme_recv_f_alloc);
+ }
-#ifdef GMX_MPI
- MPI_Recv(cr->dd->pme_recv_f_buf[0],
- natoms*sizeof(rvec),MPI_BYTE,
- cr->dd->pme_nodeid,0,cr->mpi_comm_mysim,
- MPI_STATUS_IGNORE);
+#ifdef GMX_MPI
+ MPI_Recv(cr->dd->pme_recv_f_buf[0],
+ natoms*sizeof(rvec), MPI_BYTE,
+ cr->dd->pme_nodeid, 0, cr->mpi_comm_mysim,
+ MPI_STATUS_IGNORE);
#endif
- for(i=0; i<natoms; i++)
- rvec_inc(f[i],cr->dd->pme_recv_f_buf[i]);
+ for (i = 0; i < natoms; i++)
+ {
+ rvec_inc(f[i], cr->dd->pme_recv_f_buf[i]);
+ }
-
- receive_virial_energy(cr,vir,energy,dvdlambda,pme_cycles);
+
+ receive_virial_energy(cr, vir_q, energy_q, vir_lj, energy_lj, dvdlambda_q, dvdlambda_lj, pme_cycles);
}
void gmx_pme_send_force_vir_ener(struct gmx_pme_pp *pme_pp,
- rvec *f, matrix vir,
- real energy, real dvdlambda,
- float cycles)
+ rvec gmx_unused *f,
+ matrix vir_q, real energy_q,
+ matrix vir_lj, real energy_lj,
+ real dvdlambda_q, real dvdlambda_lj,
+ float cycles)
{
- gmx_pme_comm_vir_ene_t cve;
- int messages,ind_start,ind_end,receiver;
+ gmx_pme_comm_vir_ene_t cve;
+ int messages, ind_start, ind_end, receiver;
- cve.cycles = cycles;
+ cve.cycles = cycles;
- /* Now the evaluated forces have to be transferred to the PP nodes */
- messages = 0;
- ind_end = 0;
- for (receiver=0; receiver<pme_pp->nnode; receiver++) {
- ind_start = ind_end;
- ind_end = ind_start + pme_pp->nat[receiver];
+ /* Now the evaluated forces have to be transferred to the PP nodes */
+ messages = 0;
+ ind_end = 0;
+ for (receiver = 0; receiver < pme_pp->nnode; receiver++)
+ {
+ ind_start = ind_end;
+ ind_end = ind_start + pme_pp->nat[receiver];
#ifdef GMX_MPI
- if (MPI_Isend(f[ind_start],(ind_end-ind_start)*sizeof(rvec),MPI_BYTE,
- pme_pp->node[receiver],0,
- pme_pp->mpi_comm_mysim,&pme_pp->req[messages++]) != 0)
- gmx_comm("MPI_Isend failed in do_pmeonly");
+ if (MPI_Isend(f[ind_start], (ind_end-ind_start)*sizeof(rvec), MPI_BYTE,
+ pme_pp->node[receiver], 0,
+ pme_pp->mpi_comm_mysim, &pme_pp->req[messages++]) != 0)
+ {
+ gmx_comm("MPI_Isend failed in do_pmeonly");
+ }
#endif
}
-
- /* send virial and energy to our last PP node */
- copy_mat(vir,cve.vir);
- cve.energy = energy;
- cve.dvdlambda = dvdlambda;
- /* check for the signals to send back to a PP node */
- cve.stop_cond = gmx_get_stop_condition();
-
- cve.cycles = cycles;
-
- if (debug)
- fprintf(debug,"PME node sending to PP node %d: virial and energy\n",
- pme_pp->node_peer);
+
+ /* send virial and energy to our last PP node */
+ copy_mat(vir_q, cve.vir_q);
+ copy_mat(vir_lj, cve.vir_lj);
+ cve.energy_q = energy_q;
+ cve.energy_lj = energy_lj;
+ cve.dvdlambda_q = dvdlambda_q;
+ cve.dvdlambda_lj = dvdlambda_lj;
+ /* check for the signals to send back to a PP node */
+ cve.stop_cond = gmx_get_stop_condition();
+
+ cve.cycles = cycles;
+
+ if (debug)
+ {
+ fprintf(debug, "PME rank sending to PP rank %d: virial and energy\n",
+ pme_pp->node_peer);
+ }
#ifdef GMX_MPI
- MPI_Isend(&cve,sizeof(cve),MPI_BYTE,
- pme_pp->node_peer,1,
- pme_pp->mpi_comm_mysim,&pme_pp->req[messages++]);
-
- /* Wait for the forces to arrive */
- MPI_Waitall(messages, pme_pp->req, pme_pp->stat);
+ MPI_Isend(&cve, sizeof(cve), MPI_BYTE,
+ pme_pp->node_peer, 1,
+ pme_pp->mpi_comm_mysim, &pme_pp->req[messages++]);
+
+ /* Wait for the forces to arrive */
+ MPI_Waitall(messages, pme_pp->req, pme_pp->stat);
#endif
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff