/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 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.
* 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 "smalloc.h"
-#include "network.h"
-#include "calcgrid.h"
-#include "pme.h"
-#include "vec.h"
-#include "domdec.h"
-#include "nbnxn_cuda_data_mgmt.h"
-#include "force.h"
-#include "macros.h"
-#include "md_logging.h"
+#include "gmxpre.h"
+
#include "pme_loadbal.h"
+#include "config.h"
+
+#include "gromacs/legacyheaders/calcgrid.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/md_logging.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/pme.h"
+#include "gromacs/legacyheaders/sim_util.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/smalloc.h"
+
/* Parameters and setting for one PP-PME setup */
typedef struct {
real rcut_coulomb; /* Coulomb cut-off */
while (sp <= 1.001*pme_lb->setup[pme_lb->cur].spacing || !grid_ok);
set->rcut_coulomb = pme_lb->cut_spacing*sp;
+ if (set->rcut_coulomb < pme_lb->rcut_coulomb_start)
+ {
+ /* This is unlikely, but can happen when e.g. continuing from
+ * a checkpoint after equilibration where the box shrank a lot.
+ * We want to avoid rcoulomb getting smaller than rvdw
+ * and there might be more issues with decreasing rcoulomb.
+ */
+ set->rcut_coulomb = pme_lb->rcut_coulomb_start;
+ }
if (pme_lb->cutoff_scheme == ecutsVERLET)
{
/* The Ewald coefficient is inversly proportional to the cut-off */
set->ewaldcoeff_q =
pme_lb->setup[0].ewaldcoeff_q*pme_lb->setup[0].rcut_coulomb/set->rcut_coulomb;
+ /* We set ewaldcoeff_lj in set, even when LJ-PME is not used */
+ set->ewaldcoeff_lj =
+ pme_lb->setup[0].ewaldcoeff_lj*pme_lb->setup[0].rcut_coulomb/set->rcut_coulomb;
set->count = 0;
set->cycles = 0;
pme_lb->cur = pme_lb->start - 1;
}
-gmx_bool pme_load_balance(pme_load_balancing_t pme_lb,
- t_commrec *cr,
- FILE *fp_err,
- FILE *fp_log,
- t_inputrec *ir,
- t_state *state,
- double cycles,
- interaction_const_t *ic,
- nonbonded_verlet_t *nbv,
- gmx_pme_t *pmedata,
- gmx_int64_t step)
+gmx_bool pme_load_balance(pme_load_balancing_t pme_lb,
+ t_commrec *cr,
+ FILE *fp_err,
+ FILE *fp_log,
+ t_inputrec *ir,
+ t_state *state,
+ double cycles,
+ interaction_const_t *ic,
+ struct nonbonded_verlet_t *nbv,
+ gmx_pme_t *pmedata,
+ gmx_int64_t step)
{
gmx_bool OK;
pme_setup_t *set;
ic->rlistlong = set->rlistlong;
ir->nstcalclr = set->nstcalclr;
ic->ewaldcoeff_q = set->ewaldcoeff_q;
-
- bUsesSimpleTables = uses_simple_tables(ir->cutoff_scheme, nbv, 0);
- if (pme_lb->cutoff_scheme == ecutsVERLET &&
- nbv->grp[0].kernel_type == nbnxnk8x8x8_CUDA)
- {
- nbnxn_cuda_pme_loadbal_update_param(nbv->cu_nbv, ic);
-
- /* With tMPI + GPUs some ranks may be sharing GPU(s) and therefore
- * also sharing texture references. To keep the code simple, we don't
- * treat texture references as shared resources, but this means that
- * the coulomb_tab texture ref will get updated by multiple threads.
- * Hence, to ensure that the non-bonded kernels don't start before all
- * texture binding operations are finished, we need to wait for all ranks
- * to arrive here before continuing.
- *
- * Note that we could omit this barrier if GPUs are not shared (or
- * texture objects are used), but as this is initialization code, there
- * is not point in complicating things.
- */
-#ifdef GMX_THREAD_MPI
- if (PAR(cr))
- {
- gmx_barrier(cr);
- }
-#endif /* GMX_THREAD_MPI */
+ /* TODO: centralize the code that sets the potentials shifts */
+ if (ic->coulomb_modifier == eintmodPOTSHIFT)
+ {
+ ic->sh_ewald = gmx_erfc(ic->ewaldcoeff_q*ic->rcoulomb);
}
- else
+ if (EVDW_PME(ic->vdwtype))
{
- init_interaction_const_tables(NULL, ic, bUsesSimpleTables,
- rtab);
+ /* We have PME for both Coulomb and VdW, set rvdw equal to rcoulomb */
+ ic->rvdw = set->rcut_coulomb;
+ ic->ewaldcoeff_lj = set->ewaldcoeff_lj;
+ if (ic->vdw_modifier == eintmodPOTSHIFT)
+ {
+ real crc2;
+
+ ic->dispersion_shift.cpot = -pow(ic->rvdw, -6.0);
+ ic->repulsion_shift.cpot = -pow(ic->rvdw, -12.0);
+ ic->sh_invrc6 = -ic->dispersion_shift.cpot;
+ crc2 = sqr(ic->ewaldcoeff_lj*ic->rvdw);
+ ic->sh_lj_ewald = (exp(-crc2)*(1 + crc2 + 0.5*crc2*crc2) - 1)*pow(ic->rvdw, -6.0);
+ }
}
- if (pme_lb->cutoff_scheme == ecutsVERLET && nbv->ngrp > 1)
+ bUsesSimpleTables = uses_simple_tables(ir->cutoff_scheme, nbv, 0);
+ nbnxn_cuda_pme_loadbal_update_param(nbv, ic);
+
+ /* With tMPI + GPUs some ranks may be sharing GPU(s) and therefore
+ * also sharing texture references. To keep the code simple, we don't
+ * treat texture references as shared resources, but this means that
+ * the coulomb_tab texture ref will get updated by multiple threads.
+ * Hence, to ensure that the non-bonded kernels don't start before all
+ * texture binding operations are finished, we need to wait for all ranks
+ * to arrive here before continuing.
+ *
+ * Note that we could omit this barrier if GPUs are not shared (or
+ * texture objects are used), but as this is initialization code, there
+ * is not point in complicating things.
+ */
+#ifdef GMX_THREAD_MPI
+ if (PAR(cr) && use_GPU(nbv))
{
- init_interaction_const_tables(NULL, ic, bUsesSimpleTables,
- rtab);
+ gmx_barrier(cr);
}
+#endif /* GMX_THREAD_MPI */
+
+ /* Usually we won't need the simple tables with GPUs.
+ * But we do with hybrid acceleration and with free energy.
+ * To avoid bugs, we always re-initialize the simple tables here.
+ */
+ init_interaction_const_tables(NULL, ic, bUsesSimpleTables, rtab);
if (cr->duty & DUTY_PME)
{
{
md_print_warn(cr, fplog,
"NOTE: PME load balancing increased the non-bonded workload by more than 50%%.\n"
- " For better performance use (more) PME nodes (mdrun -npme),\n"
- " or in case you are beyond the scaling limit, use less nodes in total.\n");
+ " For better performance, use (more) PME ranks (mdrun -npme),\n"
+ " or if you are beyond the scaling limit, use fewer total ranks (or nodes).\n");
}
else
{
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff