*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016, 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.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/sim_util.h"
+
+#include "config.h"
#include <assert.h>
#include <math.h>
#include <stdio.h>
#include <string.h>
-#ifdef HAVE_SYS_TIME_H
-#include <sys/time.h>
-#endif
-
-#include "typedefs.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/smalloc.h"
-#include "names.h"
-#include "txtdump.h"
-#include "pbc.h"
-#include "chargegroup.h"
-#include "vec.h"
-#include "nrnb.h"
-#include "mshift.h"
-#include "mdrun.h"
-#include "sim_util.h"
-#include "update.h"
-#include "physics.h"
-#include "main.h"
-#include "mdatoms.h"
-#include "force.h"
-#include "bondf.h"
-#include "pme.h"
-#include "disre.h"
-#include "orires.h"
-#include "network.h"
-#include "calcmu.h"
-#include "constr.h"
-#include "xvgr.h"
-#include "copyrite.h"
-#include "domdec.h"
-#include "genborn.h"
-#include "nbnxn_atomdata.h"
-#include "nbnxn_search.h"
-#include "nbnxn_kernels/nbnxn_kernel_ref.h"
-#include "nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
-#include "nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
-#include "nbnxn_kernels/nbnxn_kernel_gpu_ref.h"
-#include "nonbonded.h"
-#include "../gmxlib/nonbonded/nb_kernel.h"
-#include "../gmxlib/nonbonded/nb_free_energy.h"
-#include "gromacs/timing/wallcycle.h"
-#include "gromacs/timing/walltime_accounting.h"
-#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/domdec/domdec.h"
#include "gromacs/essentialdynamics/edsam.h"
+#include "gromacs/ewald/pme.h"
+#include "gromacs/gmxlib/nonbonded/nb_free_energy.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
+#include "gromacs/imd/imd.h"
+#include "gromacs/legacyheaders/calcmu.h"
+#include "gromacs/legacyheaders/chargegroup.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/disre.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/genborn.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nonbonded.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/orires.h"
+#include "gromacs/legacyheaders/qmmm.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/update.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/listed-forces/bonded.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_atomdata.h"
+#include "gromacs/mdlib/nbnxn_gpu_data_mgmt.h"
+#include "gromacs/mdlib/nbnxn_search.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pulling/pull.h"
#include "gromacs/pulling/pull_rotation.h"
-#include "gromacs/imd/imd.h"
-#include "adress.h"
-#include "qmmm.h"
-
-#include "gmx_omp_nthreads.h"
+#include "gromacs/timing/gpu_timing.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/sysinfo.h"
-#include "nbnxn_cuda_data_mgmt.h"
-#include "nbnxn_cuda/nbnxn_cuda.h"
+#include "adress.h"
+#include "nbnxn_gpu.h"
void print_time(FILE *out,
gmx_walltime_accounting_t walltime_accounting,
* force is kJ mol^-1 nm^-1 = e * kJ mol^-1 nm^-1 / e
*
* Et[] contains the parameters for the time dependent
- * part of the field (not yet used).
+ * part of the field.
* Ex[] contains the parameters for
- * the spatial dependent part of the field. You can have cool periodic
- * fields in principle, but only a constant field is supported
- * now.
+ * the spatial dependent part of the field.
* The function should return the energy due to the electric field
* (if any) but for now returns 0.
*
* For neutral systems with many charged molecules the error is small.
* But for systems with a net charge or a few charged molecules
* the error can be significant when the field is high.
- * Solution: implement a self-consitent electric field into PME.
+ * Solution: implement a self-consistent electric field into PME.
*/
static void calc_f_el(FILE *fp, int start, int homenr,
real charge[], rvec f[],
tensor vir_part, t_graph *graph, matrix box,
t_nrnb *nrnb, const t_forcerec *fr, int ePBC)
{
- int i, j;
- tensor virtest;
+ int i;
/* The short-range virial from surrounding boxes */
clear_mat(vir_part);
}
}
-static void posres_wrapper(FILE *fplog,
- int flags,
- gmx_bool bSepDVDL,
- t_inputrec *ir,
- t_nrnb *nrnb,
- gmx_localtop_t *top,
- matrix box, rvec x[],
- gmx_enerdata_t *enerd,
- real *lambda,
- t_forcerec *fr)
-{
- t_pbc pbc;
- real v, dvdl;
- int i;
-
- /* Position restraints always require full pbc */
- set_pbc(&pbc, ir->ePBC, box);
- dvdl = 0;
- v = posres(top->idef.il[F_POSRES].nr, top->idef.il[F_POSRES].iatoms,
- top->idef.iparams_posres,
- (const rvec*)x, fr->f_novirsum, fr->vir_diag_posres,
- ir->ePBC == epbcNONE ? NULL : &pbc,
- lambda[efptRESTRAINT], &dvdl,
- fr->rc_scaling, fr->ePBC, fr->posres_com, fr->posres_comB);
- if (bSepDVDL)
- {
- gmx_print_sepdvdl(fplog, interaction_function[F_POSRES].longname, v, dvdl);
- }
- enerd->term[F_POSRES] += v;
- /* If just the force constant changes, the FEP term is linear,
- * but if k changes, it is not.
- */
- enerd->dvdl_nonlin[efptRESTRAINT] += dvdl;
- inc_nrnb(nrnb, eNR_POSRES, top->idef.il[F_POSRES].nr/2);
-
- if ((ir->fepvals->n_lambda > 0) && (flags & GMX_FORCE_DHDL))
- {
- for (i = 0; i < enerd->n_lambda; i++)
- {
- real dvdl_dum, lambda_dum;
-
- lambda_dum = (i == 0 ? lambda[efptRESTRAINT] : ir->fepvals->all_lambda[efptRESTRAINT][i-1]);
- v = posres(top->idef.il[F_POSRES].nr, top->idef.il[F_POSRES].iatoms,
- top->idef.iparams_posres,
- (const rvec*)x, NULL, NULL,
- ir->ePBC == epbcNONE ? NULL : &pbc, lambda_dum, &dvdl,
- fr->rc_scaling, fr->ePBC, fr->posres_com, fr->posres_comB);
- enerd->enerpart_lambda[i] += v;
- }
- }
-}
-
-static void fbposres_wrapper(t_inputrec *ir,
- t_nrnb *nrnb,
- gmx_localtop_t *top,
- matrix box, rvec x[],
- gmx_enerdata_t *enerd,
- t_forcerec *fr)
-{
- t_pbc pbc;
- real v;
-
- /* Flat-bottomed position restraints always require full pbc */
- set_pbc(&pbc, ir->ePBC, box);
- v = fbposres(top->idef.il[F_FBPOSRES].nr, top->idef.il[F_FBPOSRES].iatoms,
- top->idef.iparams_fbposres,
- (const rvec*)x, fr->f_novirsum, fr->vir_diag_posres,
- ir->ePBC == epbcNONE ? NULL : &pbc,
- fr->rc_scaling, fr->ePBC, fr->posres_com);
- enerd->term[F_FBPOSRES] += v;
- inc_nrnb(nrnb, eNR_FBPOSRES, top->idef.il[F_FBPOSRES].nr/2);
-}
-
-static void pull_potential_wrapper(FILE *fplog,
- gmx_bool bSepDVDL,
- t_commrec *cr,
+static void pull_potential_wrapper(t_commrec *cr,
t_inputrec *ir,
matrix box, rvec x[],
rvec f[],
set_pbc(&pbc, ir->ePBC, box);
dvdl = 0;
enerd->term[F_COM_PULL] +=
- pull_potential(ir->ePull, ir->pull, mdatoms, &pbc,
+ pull_potential(ir->pull_work, mdatoms, &pbc,
cr, t, lambda[efptRESTRAINT], x, f, vir_force, &dvdl);
- if (bSepDVDL)
- {
- gmx_print_sepdvdl(fplog, "Com pull", enerd->term[F_COM_PULL], dvdl);
- }
enerd->dvdl_lin[efptRESTRAINT] += dvdl;
wallcycle_stop(wcycle, ewcPULLPOT);
}
-static void pme_receive_force_ener(FILE *fplog,
- gmx_bool bSepDVDL,
- t_commrec *cr,
+static void pme_receive_force_ener(t_commrec *cr,
gmx_wallcycle_t wcycle,
gmx_enerdata_t *enerd,
t_forcerec *fr)
{
- real e_q, e_lj, v, dvdl_q, dvdl_lj;
+ real e_q, e_lj, dvdl_q, dvdl_lj;
float cycles_ppdpme, cycles_seppme;
cycles_ppdpme = wallcycle_stop(wcycle, ewcPPDURINGPME);
gmx_pme_receive_f(cr, fr->f_novirsum, fr->vir_el_recip, &e_q,
fr->vir_lj_recip, &e_lj, &dvdl_q, &dvdl_lj,
&cycles_seppme);
- if (bSepDVDL)
- {
- gmx_print_sepdvdl(fplog, "Electrostatic PME mesh", e_q, dvdl_q);
- gmx_print_sepdvdl(fplog, "Lennard-Jones PME mesh", e_lj, dvdl_lj);
- }
enerd->term[F_COUL_RECIP] += e_q;
enerd->term[F_LJ_RECIP] += e_lj;
enerd->dvdl_lin[efptCOUL] += dvdl_q;
t_nrnb *nrnb,
gmx_wallcycle_t wcycle)
{
- int nnbl, kernel_type, enr_nbnxn_kernel_ljc, enr_nbnxn_kernel_lj;
- char *env;
+ int enr_nbnxn_kernel_ljc, enr_nbnxn_kernel_lj;
nonbonded_verlet_group_t *nbvg;
- gmx_bool bCUDA;
+ gmx_bool bUsingGpuKernels;
if (!(flags & GMX_FORCE_NONBONDED))
{
nbvg = &fr->nbv->grp[ilocality];
- /* CUDA kernel launch overhead is already timed separately */
+ /* GPU kernel launch overhead is already timed separately */
if (fr->cutoff_scheme != ecutsVERLET)
{
gmx_incons("Invalid cut-off scheme passed!");
}
- bCUDA = (nbvg->kernel_type == nbnxnk8x8x8_CUDA);
+ bUsingGpuKernels = (nbvg->kernel_type == nbnxnk8x8x8_GPU);
- if (!bCUDA)
+ if (!bUsingGpuKernels)
{
wallcycle_sub_start(wcycle, ewcsNONBONDED);
}
enerd->grpp.ener[egLJSR]);
break;
- case nbnxnk8x8x8_CUDA:
- nbnxn_cuda_launch_kernel(fr->nbv->cu_nbv, nbvg->nbat, flags, ilocality);
+ case nbnxnk8x8x8_GPU:
+ nbnxn_gpu_launch_kernel(fr->nbv->gpu_nbv, nbvg->nbat, flags, ilocality);
break;
case nbnxnk8x8x8_PlainC:
gmx_incons("Invalid nonbonded kernel type passed!");
}
- if (!bCUDA)
+ if (!bUsingGpuKernels)
{
wallcycle_sub_stop(wcycle, ewcsNONBONDED);
}
{
enr_nbnxn_kernel_ljc = eNR_NBNXN_LJ_RF;
}
- else if ((!bCUDA && nbvg->ewald_excl == ewaldexclAnalytical) ||
- (bCUDA && nbnxn_cuda_is_kernel_ewald_analytical(fr->nbv->cu_nbv)))
+ else if ((!bUsingGpuKernels && nbvg->ewald_excl == ewaldexclAnalytical) ||
+ (bUsingGpuKernels && nbnxn_gpu_is_kernel_ewald_analytical(fr->nbv->gpu_nbv)))
{
enr_nbnxn_kernel_ljc = eNR_NBNXN_LJ_EWALD;
}
wallcycle_sub_stop(wcycle, ewcsNONBONDED);
}
+gmx_bool use_GPU(const nonbonded_verlet_t *nbv)
+{
+ return nbv != NULL && nbv->bUseGPU;
+}
+
void do_force_cutsVERLET(FILE *fplog, t_commrec *cr,
t_inputrec *inputrec,
gmx_int64_t step, t_nrnb *nrnb, gmx_wallcycle_t wcycle,
gmx_bool bBornRadii,
int flags)
{
- int cg0, cg1, i, j;
+ int cg1, i, j;
int start, homenr;
- int nb_kernel_type;
double mu[2*DIM];
- gmx_bool bSepDVDL, bStateChanged, bNS, bFillGrid, bCalcCGCM, bBS;
+ gmx_bool bStateChanged, bNS, bFillGrid, bCalcCGCM;
gmx_bool bDoLongRange, bDoForces, bSepLRF, bUseGPU, bUseOrEmulGPU;
gmx_bool bDiffKernels = FALSE;
- matrix boxs;
rvec vzero, box_diag;
- real e, v, dvdl;
float cycles_pme, cycles_force, cycles_wait_gpu;
nonbonded_verlet_t *nbv;
cycles_force = 0;
cycles_wait_gpu = 0;
nbv = fr->nbv;
- nb_kernel_type = fr->nbv->grp[0].kernel_type;
start = 0;
homenr = mdatoms->homenr;
- bSepDVDL = (fr->bSepDVDL && do_per_step(step, inputrec->nstlog));
-
clear_mat(vir_force);
- cg0 = 0;
if (DOMAINDECOMP(cr))
{
cg1 = cr->dd->ncg_tot;
#ifdef GMX_MPI
if (!(cr->duty & DUTY_PME))
{
+ gmx_bool bBS;
+ matrix boxs;
+
/* Send particle coordinates to the pme nodes.
* Since this is only implemented for domain decomposition
* and domain decomposition does not use the graph,
if (bNS)
{
wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU_NB);
- nbnxn_cuda_init_atomdata(nbv->cu_nbv, nbv->grp[eintLocal].nbat);
+ nbnxn_gpu_init_atomdata(nbv->gpu_nbv, nbv->grp[eintLocal].nbat);
wallcycle_stop(wcycle, ewcLAUNCH_GPU_NB);
}
wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU_NB);
- nbnxn_cuda_upload_shiftvec(nbv->cu_nbv, nbv->grp[eintLocal].nbat);
+ nbnxn_gpu_upload_shiftvec(nbv->gpu_nbv, nbv->grp[eintLocal].nbat);
wallcycle_stop(wcycle, ewcLAUNCH_GPU_NB);
}
if (bUseGPU)
{
/* initialize local pair-list on the GPU */
- nbnxn_cuda_init_pairlist(nbv->cu_nbv,
- nbv->grp[eintLocal].nbl_lists.nbl[0],
- eintLocal);
+ nbnxn_gpu_init_pairlist(nbv->gpu_nbv,
+ nbv->grp[eintLocal].nbl_lists.nbl[0],
+ eintLocal);
}
wallcycle_stop(wcycle, ewcNS);
}
wallcycle_sub_stop(wcycle, ewcsNBS_SEARCH_NONLOCAL);
- if (nbv->grp[eintNonlocal].kernel_type == nbnxnk8x8x8_CUDA)
+ if (nbv->grp[eintNonlocal].kernel_type == nbnxnk8x8x8_GPU)
{
/* initialize non-local pair-list on the GPU */
- nbnxn_cuda_init_pairlist(nbv->cu_nbv,
- nbv->grp[eintNonlocal].nbl_lists.nbl[0],
- eintNonlocal);
+ nbnxn_gpu_init_pairlist(nbv->gpu_nbv,
+ nbv->grp[eintNonlocal].nbl_lists.nbl[0],
+ eintNonlocal);
}
wallcycle_stop(wcycle, ewcNS);
}
{
wallcycle_start(wcycle, ewcMOVEX);
dd_move_x(cr->dd, box, x);
-
- /* When we don't need the total dipole we sum it in global_stat */
- if (bStateChanged && NEED_MUTOT(*inputrec))
- {
- gmx_sumd(2*DIM, mu, cr);
- }
wallcycle_stop(wcycle, ewcMOVEX);
wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU_NB);
if (DOMAINDECOMP(cr) && !bDiffKernels)
{
- nbnxn_cuda_launch_cpyback(nbv->cu_nbv, nbv->grp[eintNonlocal].nbat,
- flags, eatNonlocal);
+ nbnxn_gpu_launch_cpyback(nbv->gpu_nbv, nbv->grp[eintNonlocal].nbat,
+ flags, eatNonlocal);
}
- nbnxn_cuda_launch_cpyback(nbv->cu_nbv, nbv->grp[eintLocal].nbat,
- flags, eatLocal);
+ nbnxn_gpu_launch_cpyback(nbv->gpu_nbv, nbv->grp[eintLocal].nbat,
+ flags, eatLocal);
cycles_force += wallcycle_stop(wcycle, ewcLAUNCH_GPU_NB);
}
}
/* Start the force cycle counter.
- * This counter is stopped in do_forcelow_level.
+ * This counter is stopped after do_force_lowlevel.
* No parallel communication should occur while this counter is running,
* since that will interfere with the dynamic load balancing.
*/
clear_rvec(fr->vir_diag_posres);
}
- if (inputrec->ePull == epullCONSTRAINT)
+ if (inputrec->bPull && pull_have_constraint(inputrec->pull_work))
{
- clear_pull_forces(inputrec->pull);
+ clear_pull_forces(inputrec->pull_work);
}
/* We calculate the non-bonded forces, when done on the CPU, here.
- * We do this before calling do_force_lowlevel, as in there bondeds
- * forces are calculated before PME, which does communication.
- * With this order, non-bonded and bonded force calculation imbalance
- * can be balanced out by the domain decomposition load balancing.
+ * We do this before calling do_force_lowlevel, because in that
+ * function, the listed forces are calculated before PME, which
+ * does communication. With this order, non-bonded and listed
+ * force calculation imbalance can be balanced out by the domain
+ * decomposition load balancing.
*/
if (!bUseOrEmulGPU)
}
/* Add all the non-bonded force to the normal force array.
- * This can be split into a local a non-local part when overlapping
+ * This can be split into a local and a non-local part when overlapping
* communication with calculation with domain decomposition.
*/
cycles_force += wallcycle_stop(wcycle, ewcFORCE);
if ((flags & GMX_FORCE_VIRIAL) &&
nbv->grp[aloc].nbl_lists.nnbl > 1)
{
+ /* This is not in a subcounter because it takes a
+ negligible and constant-sized amount of time */
nbnxn_atomdata_add_nbat_fshift_to_fshift(nbv->grp[aloc].nbat,
fr->fshift);
}
update_QMMMrec(cr, fr, x, mdatoms, box, top);
}
- if ((flags & GMX_FORCE_BONDED) && top->idef.il[F_POSRES].nr > 0)
- {
- posres_wrapper(fplog, flags, bSepDVDL, inputrec, nrnb, top, box, x,
- enerd, lambda, fr);
- }
-
- if ((flags & GMX_FORCE_BONDED) && top->idef.il[F_FBPOSRES].nr > 0)
- {
- fbposres_wrapper(inputrec, nrnb, top, box, x, enerd, fr);
- }
-
/* Compute the bonded and non-bonded energies and optionally forces */
- do_force_lowlevel(fplog, step, fr, inputrec, &(top->idef),
+ do_force_lowlevel(fr, inputrec, &(top->idef),
cr, nrnb, wcycle, mdatoms,
x, hist, f, bSepLRF ? fr->f_twin : f, enerd, fcd, top, fr->born,
- &(top->atomtypes), bBornRadii, box,
+ bBornRadii, box,
inputrec->fepvals, lambda, graph, &(top->excls), fr->mu_tot,
flags, &cycles_pme);
float cycles_tmp;
wallcycle_start(wcycle, ewcWAIT_GPU_NB_NL);
- nbnxn_cuda_wait_gpu(nbv->cu_nbv,
- nbv->grp[eintNonlocal].nbat,
- flags, eatNonlocal,
- enerd->grpp.ener[egLJSR], enerd->grpp.ener[egCOULSR],
- fr->fshift);
+ nbnxn_gpu_wait_for_gpu(nbv->gpu_nbv,
+ nbv->grp[eintNonlocal].nbat,
+ flags, eatNonlocal,
+ enerd->grpp.ener[egLJSR], enerd->grpp.ener[egCOULSR],
+ fr->fshift);
cycles_tmp = wallcycle_stop(wcycle, ewcWAIT_GPU_NB_NL);
cycles_wait_gpu += cycles_tmp;
cycles_force += cycles_tmp;
/* wait for local forces (or calculate in emulation mode) */
if (bUseGPU)
{
+#if defined(GMX_GPU) && !defined(GMX_USE_OPENCL)
float cycles_tmp, cycles_wait_est;
const float cuda_api_overhead_margin = 50000.0f; /* cycles */
wallcycle_start(wcycle, ewcWAIT_GPU_NB_L);
- nbnxn_cuda_wait_gpu(nbv->cu_nbv,
- nbv->grp[eintLocal].nbat,
- flags, eatLocal,
- enerd->grpp.ener[egLJSR], enerd->grpp.ener[egCOULSR],
- fr->fshift);
+ nbnxn_gpu_wait_for_gpu(nbv->gpu_nbv,
+ nbv->grp[eintLocal].nbat,
+ flags, eatLocal,
+ enerd->grpp.ener[egLJSR], enerd->grpp.ener[egCOULSR],
+ fr->fshift);
cycles_tmp = wallcycle_stop(wcycle, ewcWAIT_GPU_NB_L);
if (bDoForces && DOMAINDECOMP(cr))
cycles_force += cycles_wait_est;
cycles_wait_gpu += cycles_wait_est;
- /* now clear the GPU outputs while we finish the step on the CPU */
+#elif defined(GMX_GPU) && defined(GMX_USE_OPENCL)
+
+ wallcycle_start(wcycle, ewcWAIT_GPU_NB_L);
+ nbnxn_gpu_wait_for_gpu(nbv->gpu_nbv,
+ nbv->grp[eintLocal].nbat,
+ flags, eatLocal,
+ enerd->grpp.ener[egLJSR], enerd->grpp.ener[egCOULSR],
+ fr->fshift);
+ cycles_wait_gpu += wallcycle_stop(wcycle, ewcWAIT_GPU_NB_L);
+#endif
+ /* now clear the GPU outputs while we finish the step on the CPU */
wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU_NB);
- nbnxn_cuda_clear_outputs(nbv->cu_nbv, flags);
+ nbnxn_gpu_clear_outputs(nbv->gpu_nbv, flags);
wallcycle_stop(wcycle, ewcLAUNCH_GPU_NB);
}
else
}
}
- if (inputrec->ePull == epullUMBRELLA || inputrec->ePull == epullCONST_F)
+ if (inputrec->bPull && pull_have_potential(inputrec->pull_work))
{
/* Since the COM pulling is always done mass-weighted, no forces are
* applied to vsites and this call can be done after vsite spreading.
*/
- pull_potential_wrapper(fplog, bSepDVDL, cr, inputrec, box, x,
+ pull_potential_wrapper(cr, inputrec, box, x,
f, vir_force, mdatoms, enerd, lambda, t,
wcycle);
}
/* In case of node-splitting, the PP nodes receive the long-range
* forces, virial and energy from the PME nodes here.
*/
- pme_receive_force_ener(fplog, bSepDVDL, cr, wcycle, enerd, fr);
+ pme_receive_force_ener(cr, wcycle, enerd, fr);
}
if (bDoForces)
int cg0, cg1, i, j;
int start, homenr;
double mu[2*DIM];
- gmx_bool bSepDVDL, bStateChanged, bNS, bFillGrid, bCalcCGCM, bBS;
- gmx_bool bDoLongRangeNS, bDoForces, bDoPotential, bSepLRF;
+ gmx_bool bStateChanged, bNS, bFillGrid, bCalcCGCM;
+ gmx_bool bDoLongRangeNS, bDoForces, bSepLRF;
gmx_bool bDoAdressWF;
- matrix boxs;
- rvec vzero, box_diag;
- real e, v, dvdlambda[efptNR];
t_pbc pbc;
float cycles_pme, cycles_force;
start = 0;
homenr = mdatoms->homenr;
- bSepDVDL = (fr->bSepDVDL && do_per_step(step, inputrec->nstlog));
-
clear_mat(vir_force);
cg0 = 0;
bFillGrid = (bNS && bStateChanged);
bCalcCGCM = (bFillGrid && !DOMAINDECOMP(cr));
bDoForces = (flags & GMX_FORCE_FORCES);
- bDoPotential = (flags & GMX_FORCE_ENERGY);
bSepLRF = ((inputrec->nstcalclr > 1) && bDoForces &&
(flags & GMX_FORCE_SEPLRF) && (flags & GMX_FORCE_DO_LR));
#ifdef GMX_MPI
if (!(cr->duty & DUTY_PME))
{
+ gmx_bool bBS;
+ matrix boxs;
+
/* Send particle coordinates to the pme nodes.
* Since this is only implemented for domain decomposition
* and domain decomposition does not use the graph,
}
/* Start the force cycle counter.
- * This counter is stopped in do_forcelow_level.
+ * This counter is stopped after do_force_lowlevel.
* No parallel communication should occur while this counter is running,
* since that will interfere with the dynamic load balancing.
*/
clear_rvec(fr->vir_diag_posres);
}
- if (inputrec->ePull == epullCONSTRAINT)
+ if (inputrec->bPull && pull_have_constraint(inputrec->pull_work))
{
- clear_pull_forces(inputrec->pull);
+ clear_pull_forces(inputrec->pull_work);
}
/* update QMMMrec, if necessary */
update_QMMMrec(cr, fr, x, mdatoms, box, top);
}
- if ((flags & GMX_FORCE_BONDED) && top->idef.il[F_POSRES].nr > 0)
- {
- posres_wrapper(fplog, flags, bSepDVDL, inputrec, nrnb, top, box, x,
- enerd, lambda, fr);
- }
-
- if ((flags & GMX_FORCE_BONDED) && top->idef.il[F_FBPOSRES].nr > 0)
- {
- fbposres_wrapper(inputrec, nrnb, top, box, x, enerd, fr);
- }
-
/* Compute the bonded and non-bonded energies and optionally forces */
- do_force_lowlevel(fplog, step, fr, inputrec, &(top->idef),
+ do_force_lowlevel(fr, inputrec, &(top->idef),
cr, nrnb, wcycle, mdatoms,
x, hist, f, bSepLRF ? fr->f_twin : f, enerd, fcd, top, fr->born,
- &(top->atomtypes), bBornRadii, box,
+ bBornRadii, box,
inputrec->fepvals, lambda,
graph, &(top->excls), fr->mu_tot,
flags,
}
}
- if (inputrec->ePull == epullUMBRELLA || inputrec->ePull == epullCONST_F)
+ if (inputrec->bPull && pull_have_potential(inputrec->pull_work))
{
- pull_potential_wrapper(fplog, bSepDVDL, cr, inputrec, box, x,
+ pull_potential_wrapper(cr, inputrec, box, x,
f, vir_force, mdatoms, enerd, lambda, t,
wcycle);
}
/* In case of node-splitting, the PP nodes receive the long-range
* forces, virial and energy from the PME nodes here.
*/
- pme_receive_force_ener(fplog, bSepDVDL, cr, wcycle, enerd, fr);
+ pme_receive_force_ener(cr, wcycle, enerd, fr);
}
if (bDoForces)
/* constrain the current position */
constrain(NULL, TRUE, FALSE, constr, &(top->idef),
- ir, NULL, cr, step, 0, 1.0, md,
+ ir, cr, step, 0, 1.0, md,
state->x, state->x, NULL,
fr->bMolPBC, state->box,
state->lambda[efptBONDED], &dvdl_dum,
- NULL, NULL, nrnb, econqCoord,
- ir->epc == epcMTTK, state->veta, state->veta);
+ NULL, NULL, nrnb, econqCoord);
if (EI_VV(ir->eI))
{
/* constrain the inital velocity, and save it */
/* also may be useful if we need the ekin from the halfstep for velocity verlet */
- /* might not yet treat veta correctly */
constrain(NULL, TRUE, FALSE, constr, &(top->idef),
- ir, NULL, cr, step, 0, 1.0, md,
+ ir, cr, step, 0, 1.0, md,
state->x, state->v, state->v,
fr->bMolPBC, state->box,
state->lambda[efptBONDED], &dvdl_dum,
- NULL, NULL, nrnb, econqVeloc,
- ir->epc == epcMTTK, state->veta, state->veta);
+ NULL, NULL, nrnb, econqVeloc);
}
/* constrain the inital velocities at t-dt/2 */
if (EI_STATE_VELOCITY(ir->eI) && ir->eI != eiVV)
}
dvdl_dum = 0;
constrain(NULL, TRUE, FALSE, constr, &(top->idef),
- ir, NULL, cr, step, -1, 1.0, md,
+ ir, cr, step, -1, 1.0, md,
state->x, savex, NULL,
fr->bMolPBC, state->box,
state->lambda[efptBONDED], &dvdl_dum,
- state->v, NULL, nrnb, econqCoord,
- ir->epc == epcMTTK, state->veta, state->veta);
+ state->v, NULL, nrnb, econqCoord);
for (i = start; i < end; i++)
{
double invscale, invscale2, invscale3;
double r, ea, eb, ec, pa, pb, pc, pd;
double y0, f, g, h;
- int ri, offset, tabfactor;
+ int ri, offset;
+ double tabfactor;
invscale = 1.0/scale;
invscale2 = invscale*invscale;
void calc_enervirdiff(FILE *fplog, int eDispCorr, t_forcerec *fr)
{
- double eners[2], virs[2], enersum, virsum, y0, f, g, h;
- double r0, r1, r, rc3, rc9, ea, eb, ec, pa, pb, pc, pd;
- double invscale, invscale2, invscale3;
- int ri0, ri1, ri, i, offstart, offset;
- real scale, *vdwtab, tabfactor, tmp;
+ double eners[2], virs[2], enersum, virsum;
+ double r0, rc3, rc9;
+ int ri0, ri1, i;
+ real scale, *vdwtab;
fr->enershiftsix = 0;
fr->enershifttwelve = 0;
vdwtab = fr->nblists[0].table_vdw.data;
/* Round the cut-offs to exact table values for precision */
- ri0 = floor(fr->rvdw_switch*scale);
- ri1 = ceil(fr->rvdw*scale);
+ ri0 = static_cast<int>(floor(fr->rvdw_switch*scale));
+ ri1 = static_cast<int>(ceil(fr->rvdw*scale));
/* The code below has some support for handling force-switching, i.e.
* when the force (instead of potential) is switched over a limited
ri0 = (fr->vdw_modifier == eintmodPOTSHIFT) ? ri1 : ri0;
r0 = ri0/scale;
- r1 = ri1/scale;
rc3 = r0*r0*r0;
rc9 = rc3*rc3*rc3;
}
}
-void calc_dispcorr(FILE *fplog, t_inputrec *ir, t_forcerec *fr,
- gmx_int64_t step, int natoms,
+void calc_dispcorr(t_inputrec *ir, t_forcerec *fr,
+ int natoms,
matrix box, real lambda, tensor pres, tensor virial,
real *prescorr, real *enercorr, real *dvdlcorr)
{
}
}
- if (fr->bSepDVDL && do_per_step(step, ir->nstlog))
- {
- gmx_print_sepdvdl(fplog, "Dispersion correction", *enercorr, dvdlambda);
- }
if (fr->efep != efepNO)
{
*dvdlcorr += dvdlambda;
t_inputrec *inputrec,
t_nrnb nrnb[], gmx_wallcycle_t wcycle,
gmx_walltime_accounting_t walltime_accounting,
- wallclock_gpu_t *gputimes,
+ nonbonded_verlet_t *nbv,
gmx_bool bWriteStat)
{
- int i, j;
t_nrnb *nrnb_tot = NULL;
- real delta_t;
- double nbfs, mflop;
+ double delta_t = 0;
+ double nbfs = 0, mflop = 0;
double elapsed_time,
elapsed_time_over_all_ranks,
elapsed_time_over_all_threads,
if (SIMMASTER(cr))
{
+ struct gmx_wallclock_gpu_t* gputimes = use_GPU(nbv) ? nbnxn_gpu_get_timings(nbv->gpu_nbv) : NULL;
+
wallcycle_print(fplog, cr->nnodes, cr->npmenodes,
elapsed_time_over_all_ranks,
wcycle, gputimes);
{
delta_t = inputrec->delta_t;
}
- else
- {
- delta_t = 0;
- }
if (fplog)
{
gmx_bool *bSimAnn, t_vcm **vcm, unsigned long Flags,
gmx_wallcycle_t wcycle)
{
- int i, j, n;
- real tmpt, mod;
+ int i;
/* Initial values */
*t = *t0 = ir->init_t;
please_cite(fplog, "Goga2012");
}
}
-
+ if ((ir->et[XX].n > 0) || (ir->et[YY].n > 0) || (ir->et[ZZ].n > 0))
+ {
+ please_cite(fplog, "Caleman2008a");
+ }
init_nrnb(nrnb);
if (nfile != -1)
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff