*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017 The GROMACS development team.
+ * Copyright (c) 2018,2019,2020,2021, 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.
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/simulation_workload.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/timing/cyclecounter.h"
#include "gromacs/timing/wallcycle.h"
{
errorReasons.emplace_back("a double-precision build");
}
- if (GMX_GPU == GMX_GPU_NONE)
+ if (!GMX_GPU)
{
errorReasons.emplace_back("a non-GPU build");
}
+ if (GMX_GPU_SYCL)
+ {
+ errorReasons.emplace_back("SYCL build"); // SYCL-TODO
+ }
return addMessageIfNotSupported(errorReasons, error);
}
{
std::list<std::string> errorReasons;
- if (GMX_GPU == GMX_GPU_OPENCL)
+ if (GMX_GPU_OPENCL)
{
#ifdef __APPLE__
errorReasons.emplace_back("Apple OS X operating system");
return addMessageIfNotSupported(errorReasons, error);
}
-bool pme_gpu_supports_input(const t_inputrec& ir, const gmx_mtop_t& mtop, std::string* error)
+bool pme_gpu_supports_input(const t_inputrec& ir, std::string* error)
{
std::list<std::string> errorReasons;
if (!EEL_PME(ir.coulombtype))
{
errorReasons.emplace_back("interpolation orders other than 4");
}
- if (ir.efep != efepNO)
- {
- if (gmx_mtop_has_perturbed_charges(mtop))
- {
- errorReasons.emplace_back(
- "free energy calculations with perturbed charges (multiple grids)");
- }
- }
if (EVDW_PME(ir.vdwtype))
{
errorReasons.emplace_back("Lennard-Jones PME");
}
if (!EI_DYNAMICS(ir.eI))
{
- errorReasons.emplace_back("not a dynamical integrator");
+ errorReasons.emplace_back(
+ "Cannot compute PME interactions on a GPU, because PME GPU requires a dynamical "
+ "integrator (md, sd, etc).");
+ }
+ return addMessageIfNotSupported(errorReasons, error);
+}
+
+bool pme_gpu_mixed_mode_supports_input(const t_inputrec& ir, std::string* error)
+{
+ std::list<std::string> errorReasons;
+ if (ir.efep != efepNO)
+ {
+ errorReasons.emplace_back("Free Energy Perturbation (in PME GPU mixed mode)");
}
return addMessageIfNotSupported(errorReasons, error);
}
{
errorReasons.emplace_back("interpolation orders other than 4");
}
- if (pme->bFEP)
- {
- errorReasons.emplace_back("free energy calculations (multiple grids)");
- }
if (pme->doLJ)
{
errorReasons.emplace_back("Lennard-Jones PME");
{
errorReasons.emplace_back("double precision");
}
- if (GMX_GPU == GMX_GPU_NONE)
+ if (!GMX_GPU)
{
errorReasons.emplace_back("non-GPU build of GROMACS");
}
-
+ if (GMX_GPU_SYCL)
+ {
+ errorReasons.emplace_back("SYCL build of GROMACS"); // SYCL-TODO
+ }
return addMessageIfNotSupported(errorReasons, error);
}
return (enumerator + denominator - 1) / denominator;
}
-gmx_pme_t* gmx_pme_init(const t_commrec* cr,
- const NumPmeDomains& numPmeDomains,
- const t_inputrec* ir,
- gmx_bool bFreeEnergy_q,
- gmx_bool bFreeEnergy_lj,
- gmx_bool bReproducible,
- real ewaldcoeff_q,
- real ewaldcoeff_lj,
- int nthread,
- PmeRunMode runMode,
- PmeGpu* pmeGpu,
- const gmx_device_info_t* gpuInfo,
- const PmeGpuProgram* pmeGpuProgram,
- const gmx::MDLogger& /*mdlog*/)
+gmx_pme_t* gmx_pme_init(const t_commrec* cr,
+ const NumPmeDomains& numPmeDomains,
+ const t_inputrec* ir,
+ gmx_bool bFreeEnergy_q,
+ gmx_bool bFreeEnergy_lj,
+ gmx_bool bReproducible,
+ real ewaldcoeff_q,
+ real ewaldcoeff_lj,
+ int nthread,
+ PmeRunMode runMode,
+ PmeGpu* pmeGpu,
+ const DeviceContext* deviceContext,
+ const DeviceStream* deviceStream,
+ const PmeGpuProgram* pmeGpuProgram,
+ const gmx::MDLogger& mdlog)
{
int use_threads, sum_use_threads, i;
ivec ndata;
imbal = estimate_pme_load_imbalance(pme.get());
if (imbal >= 1.2 && pme->nodeid_major == 0 && pme->nodeid_minor == 0)
{
- fprintf(stderr,
- "\n"
- "NOTE: The load imbalance in PME FFT and solve is %d%%.\n"
- " For optimal PME load balancing\n"
- " PME grid_x (%d) and grid_y (%d) should be divisible by #PME_ranks_x "
- "(%d)\n"
- " and PME grid_y (%d) and grid_z (%d) should be divisible by #PME_ranks_y "
- "(%d)\n"
- "\n",
- gmx::roundToInt((imbal - 1) * 100), pme->nkx, pme->nky, pme->nnodes_major,
- pme->nky, pme->nkz, pme->nnodes_minor);
+ GMX_LOG(mdlog.warning)
+ .asParagraph()
+ .appendTextFormatted(
+ "NOTE: The load imbalance in PME FFT and solve is %d%%.\n"
+ " For optimal PME load balancing\n"
+ " PME grid_x (%d) and grid_y (%d) should be divisible by "
+ "#PME_ranks_x "
+ "(%d)\n"
+ " and PME grid_y (%d) and grid_z (%d) should be divisible by "
+ "#PME_ranks_y "
+ "(%d)",
+ gmx::roundToInt((imbal - 1) * 100), pme->nkx, pme->nky,
+ pme->nnodes_major, pme->nky, pme->nkz, pme->nnodes_minor);
}
}
{
GMX_THROW(gmx::NotImplementedError(errorString));
}
+ pme_gpu_reinit(pme.get(), deviceContext, deviceStream, pmeGpuProgram);
+ }
+ else
+ {
+ GMX_ASSERT(pme->gpu == nullptr, "Should not have PME GPU object when PME is on a CPU.");
}
- pme_gpu_reinit(pme.get(), gpuInfo, pmeGpuProgram);
+
pme_init_all_work(&pme->solve_work, pme->nthread, pme->nkx);
try
{
+ // This is reinit. Any logging should have been done at first init.
+ // Here we should avoid writing notes for settings the user did not
+ // set directly.
const gmx::MDLogger dummyLogger;
- // This is reinit which is currently only changing grid size/coefficients,
- // so we don't expect the actual logging.
- // TODO: when PME is an object, it should take reference to mdlog on construction and save it.
GMX_ASSERT(pmedata, "Invalid PME pointer");
NumPmeDomains numPmeDomains = { pme_src->nnodes_major, pme_src->nnodes_minor };
*pmedata = gmx_pme_init(cr, numPmeDomains, &irc, pme_src->bFEP_q, pme_src->bFEP_lj, FALSE,
ewaldcoeff_q, ewaldcoeff_lj, pme_src->nthread, pme_src->runMode,
- pme_src->gpu, nullptr, nullptr, dummyLogger);
+ pme_src->gpu, nullptr, nullptr, nullptr, dummyLogger);
/* When running PME on the CPU not using domain decomposition,
* the atom data is allocated once only in gmx_pme_(re)init().
*/
if (!pme_src->gpu && pme_src->nnodes == 1)
{
- gmx_pme_reinit_atoms(*pmedata, pme_src->atc[0].numAtoms(), nullptr);
+ gmx_pme_reinit_atoms(*pmedata, pme_src->atc[0].numAtoms(), nullptr, nullptr);
}
// TODO this is mostly passing around current values
}
real lambda_lj,
real* dvdlambda_q,
real* dvdlambda_lj,
- int flags)
+ const gmx::StepWorkload& stepWork)
{
GMX_ASSERT(pme->runMode == PmeRunMode::CPU,
"gmx_pme_do should not be called on the GPU PME run.");
gmx_bool bFirst, bDoSplines;
int fep_state;
int fep_states_lj = pme->bFEP_lj ? 2 : 1;
- const gmx_bool bCalcEnerVir = (flags & GMX_PME_CALC_ENER_VIR) != 0;
- const gmx_bool bBackFFT = (flags & (GMX_PME_CALC_F | GMX_PME_CALC_POT)) != 0;
- const gmx_bool bCalcF = (flags & GMX_PME_CALC_F) != 0;
+ // There's no support for computing energy without virial, or vice versa
+ const bool computeEnergyAndVirial = (stepWork.computeEnergy || stepWork.computeVirial);
- /* We could be passing lambda!=1 while no q or LJ is actually perturbed */
+ /* We could be passing lambda!=0 while no q or LJ is actually perturbed */
if (!pme->bFEP_q)
{
- lambda_q = 1;
+ lambda_q = 0;
}
if (!pme->bFEP_lj)
{
- lambda_lj = 1;
+ lambda_lj = 0;
}
assert(pme->nnodes > 0);
fprintf(debug, "Rank= %6d, pme local particles=%6d\n", cr->nodeid, atc.numAtoms());
}
- if (flags & GMX_PME_SPREAD)
+ wallcycle_start(wcycle, ewcPME_SPREAD);
+
+ /* Spread the coefficients on a grid */
+ spread_on_grid(pme, &atc, pmegrid, bFirst, TRUE, fftgrid, bDoSplines, grid_index);
+
+ if (bFirst)
{
- wallcycle_start(wcycle, ewcPME_SPREAD);
+ inc_nrnb(nrnb, eNR_WEIGHTS, DIM * atc.numAtoms());
+ }
+ inc_nrnb(nrnb, eNR_SPREADBSP, pme->pme_order * pme->pme_order * pme->pme_order * atc.numAtoms());
- /* Spread the coefficients on a grid */
- spread_on_grid(pme, &atc, pmegrid, bFirst, TRUE, fftgrid, bDoSplines, grid_index);
+ if (!pme->bUseThreads)
+ {
+ wrap_periodic_pmegrid(pme, grid);
- if (bFirst)
+ /* sum contributions to local grid from other nodes */
+ if (pme->nnodes > 1)
{
- inc_nrnb(nrnb, eNR_WEIGHTS, DIM * atc.numAtoms());
+ gmx_sum_qgrid_dd(pme, grid, GMX_SUM_GRID_FORWARD);
}
- inc_nrnb(nrnb, eNR_SPREADBSP,
- pme->pme_order * pme->pme_order * pme->pme_order * atc.numAtoms());
-
- if (!pme->bUseThreads)
- {
- wrap_periodic_pmegrid(pme, grid);
- /* sum contributions to local grid from other nodes */
- if (pme->nnodes > 1)
- {
- gmx_sum_qgrid_dd(pme, grid, GMX_SUM_GRID_FORWARD);
- }
-
- copy_pmegrid_to_fftgrid(pme, grid, fftgrid, grid_index);
- }
+ copy_pmegrid_to_fftgrid(pme, grid, fftgrid, grid_index);
+ }
- wallcycle_stop(wcycle, ewcPME_SPREAD);
+ wallcycle_stop(wcycle, ewcPME_SPREAD);
- /* TODO If the OpenMP and single-threaded implementations
- converge, then spread_on_grid() and
- copy_pmegrid_to_fftgrid() will perhaps live in the same
- source file.
- */
- }
+ /* TODO If the OpenMP and single-threaded implementations
+ converge, then spread_on_grid() and
+ copy_pmegrid_to_fftgrid() will perhaps live in the same
+ source file.
+ */
/* Here we start a large thread parallel region */
#pragma omp parallel num_threads(pme->nthread) private(thread)
try
{
thread = gmx_omp_get_thread_num();
- if (flags & GMX_PME_SOLVE)
- {
- int loop_count;
+ int loop_count;
- /* do 3d-fft */
- if (thread == 0)
- {
- wallcycle_start(wcycle, ewcPME_FFT);
- }
- gmx_parallel_3dfft_execute(pfft_setup, GMX_FFT_REAL_TO_COMPLEX, thread, wcycle);
- if (thread == 0)
- {
- wallcycle_stop(wcycle, ewcPME_FFT);
- }
-
- /* solve in k-space for our local cells */
- if (thread == 0)
- {
- wallcycle_start(wcycle, (grid_index < DO_Q ? ewcPME_SOLVE : ewcLJPME));
- }
- if (grid_index < DO_Q)
- {
- loop_count = solve_pme_yzx(
- pme, cfftgrid, scaledBox[XX][XX] * scaledBox[YY][YY] * scaledBox[ZZ][ZZ],
- bCalcEnerVir, pme->nthread, thread);
- }
- else
- {
- loop_count = solve_pme_lj_yzx(
- pme, &cfftgrid, FALSE,
- scaledBox[XX][XX] * scaledBox[YY][YY] * scaledBox[ZZ][ZZ],
- bCalcEnerVir, pme->nthread, thread);
- }
+ /* do 3d-fft */
+ if (thread == 0)
+ {
+ wallcycle_start(wcycle, ewcPME_FFT);
+ }
+ gmx_parallel_3dfft_execute(pfft_setup, GMX_FFT_REAL_TO_COMPLEX, thread, wcycle);
+ if (thread == 0)
+ {
+ wallcycle_stop(wcycle, ewcPME_FFT);
+ }
- if (thread == 0)
- {
- wallcycle_stop(wcycle, (grid_index < DO_Q ? ewcPME_SOLVE : ewcLJPME));
- inc_nrnb(nrnb, eNR_SOLVEPME, loop_count);
- }
+ /* solve in k-space for our local cells */
+ if (thread == 0)
+ {
+ wallcycle_start(wcycle, (grid_index < DO_Q ? ewcPME_SOLVE : ewcLJPME));
+ }
+ if (grid_index < DO_Q)
+ {
+ loop_count = solve_pme_yzx(
+ pme, cfftgrid, scaledBox[XX][XX] * scaledBox[YY][YY] * scaledBox[ZZ][ZZ],
+ computeEnergyAndVirial, pme->nthread, thread);
+ }
+ else
+ {
+ loop_count =
+ solve_pme_lj_yzx(pme, &cfftgrid, FALSE,
+ scaledBox[XX][XX] * scaledBox[YY][YY] * scaledBox[ZZ][ZZ],
+ computeEnergyAndVirial, pme->nthread, thread);
}
- if (bBackFFT)
+ if (thread == 0)
{
- /* do 3d-invfft */
- if (thread == 0)
- {
- wallcycle_start(wcycle, ewcPME_FFT);
- }
- gmx_parallel_3dfft_execute(pfft_setup, GMX_FFT_COMPLEX_TO_REAL, thread, wcycle);
- if (thread == 0)
- {
- wallcycle_stop(wcycle, ewcPME_FFT);
+ wallcycle_stop(wcycle, (grid_index < DO_Q ? ewcPME_SOLVE : ewcLJPME));
+ inc_nrnb(nrnb, eNR_SOLVEPME, loop_count);
+ }
+ /* do 3d-invfft */
+ if (thread == 0)
+ {
+ wallcycle_start(wcycle, ewcPME_FFT);
+ }
+ gmx_parallel_3dfft_execute(pfft_setup, GMX_FFT_COMPLEX_TO_REAL, thread, wcycle);
+ if (thread == 0)
+ {
+ wallcycle_stop(wcycle, ewcPME_FFT);
- if (pme->nodeid == 0)
- {
- real ntot = pme->nkx * pme->nky * pme->nkz;
- npme = static_cast<int>(ntot * std::log(ntot) / std::log(2.0));
- inc_nrnb(nrnb, eNR_FFT, 2 * npme);
- }
- /* Note: this wallcycle region is closed below
- outside an OpenMP region, so take care if
- refactoring code here. */
- wallcycle_start(wcycle, ewcPME_GATHER);
+ if (pme->nodeid == 0)
+ {
+ real ntot = pme->nkx * pme->nky * pme->nkz;
+ npme = static_cast<int>(ntot * std::log(ntot) / std::log(2.0));
+ inc_nrnb(nrnb, eNR_FFT, 2 * npme);
}
- copy_fftgrid_to_pmegrid(pme, fftgrid, grid, grid_index, pme->nthread, thread);
+ /* Note: this wallcycle region is closed below
+ outside an OpenMP region, so take care if
+ refactoring code here. */
+ wallcycle_start(wcycle, ewcPME_GATHER);
}
+
+ copy_fftgrid_to_pmegrid(pme, fftgrid, grid, grid_index, pme->nthread, thread);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
* With MPI we have to synchronize here before gmx_sum_qgrid_dd.
*/
- if (bBackFFT)
+ /* distribute local grid to all nodes */
+ if (pme->nnodes > 1)
{
- /* distribute local grid to all nodes */
- if (pme->nnodes > 1)
- {
- gmx_sum_qgrid_dd(pme, grid, GMX_SUM_GRID_BACKWARD);
- }
-
- unwrap_periodic_pmegrid(pme, grid);
+ gmx_sum_qgrid_dd(pme, grid, GMX_SUM_GRID_BACKWARD);
}
- if (bCalcF)
+ unwrap_periodic_pmegrid(pme, grid);
+
+ if (stepWork.computeForces)
{
/* interpolate forces for our local atoms */
wallcycle_stop(wcycle, ewcPME_GATHER);
}
- if (bCalcEnerVir)
+ if (computeEnergyAndVirial)
{
/* This should only be called on the master thread
* and after the threads have synchronized.
calc_next_lb_coeffs(coefficientBuffer, local_sigma);
grid = pmegrid->grid.grid;
- if (flags & GMX_PME_SPREAD)
- {
- wallcycle_start(wcycle, ewcPME_SPREAD);
- /* Spread the c6 on a grid */
- spread_on_grid(pme, &atc, pmegrid, bFirst, TRUE, fftgrid, bDoSplines, grid_index);
+ wallcycle_start(wcycle, ewcPME_SPREAD);
+ /* Spread the c6 on a grid */
+ spread_on_grid(pme, &atc, pmegrid, bFirst, TRUE, fftgrid, bDoSplines, grid_index);
- if (bFirst)
- {
- inc_nrnb(nrnb, eNR_WEIGHTS, DIM * atc.numAtoms());
- }
+ if (bFirst)
+ {
+ inc_nrnb(nrnb, eNR_WEIGHTS, DIM * atc.numAtoms());
+ }
- inc_nrnb(nrnb, eNR_SPREADBSP,
- pme->pme_order * pme->pme_order * pme->pme_order * atc.numAtoms());
- if (pme->nthread == 1)
+ inc_nrnb(nrnb, eNR_SPREADBSP,
+ pme->pme_order * pme->pme_order * pme->pme_order * atc.numAtoms());
+ if (pme->nthread == 1)
+ {
+ wrap_periodic_pmegrid(pme, grid);
+ /* sum contributions to local grid from other nodes */
+ if (pme->nnodes > 1)
{
- wrap_periodic_pmegrid(pme, grid);
- /* sum contributions to local grid from other nodes */
- if (pme->nnodes > 1)
- {
- gmx_sum_qgrid_dd(pme, grid, GMX_SUM_GRID_FORWARD);
- }
- copy_pmegrid_to_fftgrid(pme, grid, fftgrid, grid_index);
+ gmx_sum_qgrid_dd(pme, grid, GMX_SUM_GRID_FORWARD);
}
- wallcycle_stop(wcycle, ewcPME_SPREAD);
+ copy_pmegrid_to_fftgrid(pme, grid, fftgrid, grid_index);
}
+ wallcycle_stop(wcycle, ewcPME_SPREAD);
+
/*Here we start a large thread parallel region*/
#pragma omp parallel num_threads(pme->nthread) private(thread)
{
try
{
thread = gmx_omp_get_thread_num();
- if (flags & GMX_PME_SOLVE)
+ /* do 3d-fft */
+ if (thread == 0)
{
- /* do 3d-fft */
- if (thread == 0)
- {
- wallcycle_start(wcycle, ewcPME_FFT);
- }
+ wallcycle_start(wcycle, ewcPME_FFT);
+ }
- gmx_parallel_3dfft_execute(pfft_setup, GMX_FFT_REAL_TO_COMPLEX, thread, wcycle);
- if (thread == 0)
- {
- wallcycle_stop(wcycle, ewcPME_FFT);
- }
+ gmx_parallel_3dfft_execute(pfft_setup, GMX_FFT_REAL_TO_COMPLEX, thread, wcycle);
+ if (thread == 0)
+ {
+ wallcycle_stop(wcycle, ewcPME_FFT);
}
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
bFirst = FALSE;
}
- if (flags & GMX_PME_SOLVE)
- {
- /* solve in k-space for our local cells */
+ /* solve in k-space for our local cells */
#pragma omp parallel num_threads(pme->nthread) private(thread)
+ {
+ try
{
- try
+ int loop_count;
+ thread = gmx_omp_get_thread_num();
+ if (thread == 0)
{
- int loop_count;
- thread = gmx_omp_get_thread_num();
- if (thread == 0)
- {
- wallcycle_start(wcycle, ewcLJPME);
- }
+ wallcycle_start(wcycle, ewcLJPME);
+ }
- loop_count = solve_pme_lj_yzx(
- pme, &pme->cfftgrid[2], TRUE,
- scaledBox[XX][XX] * scaledBox[YY][YY] * scaledBox[ZZ][ZZ],
- bCalcEnerVir, pme->nthread, thread);
- if (thread == 0)
- {
- wallcycle_stop(wcycle, ewcLJPME);
- inc_nrnb(nrnb, eNR_SOLVEPME, loop_count);
- }
+ loop_count =
+ solve_pme_lj_yzx(pme, &pme->cfftgrid[2], TRUE,
+ scaledBox[XX][XX] * scaledBox[YY][YY] * scaledBox[ZZ][ZZ],
+ computeEnergyAndVirial, pme->nthread, thread);
+ if (thread == 0)
+ {
+ wallcycle_stop(wcycle, ewcLJPME);
+ inc_nrnb(nrnb, eNR_SOLVEPME, loop_count);
}
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
- if (bCalcEnerVir)
+ if (computeEnergyAndVirial)
{
/* This should only be called on the master thread and
* after the threads have synchronized.
get_pme_ener_vir_lj(pme->solve_work, pme->nthread, &output[fep_state]);
}
- if (bBackFFT)
+ bFirst = !pme->doCoulomb;
+ calc_initial_lb_coeffs(coefficientBuffer, local_c6, local_sigma);
+ for (grid_index = 8; grid_index >= 2; --grid_index)
{
- bFirst = !pme->doCoulomb;
- calc_initial_lb_coeffs(coefficientBuffer, local_c6, local_sigma);
- for (grid_index = 8; grid_index >= 2; --grid_index)
- {
- /* Unpack structure */
- pmegrid = &pme->pmegrid[grid_index];
- fftgrid = pme->fftgrid[grid_index];
- pfft_setup = pme->pfft_setup[grid_index];
- grid = pmegrid->grid.grid;
- calc_next_lb_coeffs(coefficientBuffer, local_sigma);
+ /* Unpack structure */
+ pmegrid = &pme->pmegrid[grid_index];
+ fftgrid = pme->fftgrid[grid_index];
+ pfft_setup = pme->pfft_setup[grid_index];
+ grid = pmegrid->grid.grid;
+ calc_next_lb_coeffs(coefficientBuffer, local_sigma);
#pragma omp parallel num_threads(pme->nthread) private(thread)
+ {
+ try
{
- try
+ thread = gmx_omp_get_thread_num();
+ /* do 3d-invfft */
+ if (thread == 0)
{
- thread = gmx_omp_get_thread_num();
- /* do 3d-invfft */
- if (thread == 0)
- {
- wallcycle_start(wcycle, ewcPME_FFT);
- }
+ wallcycle_start(wcycle, ewcPME_FFT);
+ }
- gmx_parallel_3dfft_execute(pfft_setup, GMX_FFT_COMPLEX_TO_REAL, thread, wcycle);
- if (thread == 0)
- {
- wallcycle_stop(wcycle, ewcPME_FFT);
+ gmx_parallel_3dfft_execute(pfft_setup, GMX_FFT_COMPLEX_TO_REAL, thread, wcycle);
+ if (thread == 0)
+ {
+ wallcycle_stop(wcycle, ewcPME_FFT);
- if (pme->nodeid == 0)
- {
- real ntot = pme->nkx * pme->nky * pme->nkz;
- npme = static_cast<int>(ntot * std::log(ntot) / std::log(2.0));
- inc_nrnb(nrnb, eNR_FFT, 2 * npme);
- }
- wallcycle_start(wcycle, ewcPME_GATHER);
+ if (pme->nodeid == 0)
+ {
+ real ntot = pme->nkx * pme->nky * pme->nkz;
+ npme = static_cast<int>(ntot * std::log(ntot) / std::log(2.0));
+ inc_nrnb(nrnb, eNR_FFT, 2 * npme);
}
-
- copy_fftgrid_to_pmegrid(pme, fftgrid, grid, grid_index, pme->nthread, thread);
+ wallcycle_start(wcycle, ewcPME_GATHER);
}
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
- } /*#pragma omp parallel*/
- /* distribute local grid to all nodes */
- if (pme->nnodes > 1)
- {
- gmx_sum_qgrid_dd(pme, grid, GMX_SUM_GRID_BACKWARD);
+ copy_fftgrid_to_pmegrid(pme, fftgrid, grid, grid_index, pme->nthread, thread);
}
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
+ } /*#pragma omp parallel*/
- unwrap_periodic_pmegrid(pme, grid);
+ /* distribute local grid to all nodes */
+ if (pme->nnodes > 1)
+ {
+ gmx_sum_qgrid_dd(pme, grid, GMX_SUM_GRID_BACKWARD);
+ }
- if (bCalcF)
- {
- /* interpolate forces for our local atoms */
- bClearF = (bFirst && PAR(cr));
- scale = pme->bFEP ? (fep_state < 1 ? 1.0 - lambda_lj : lambda_lj) : 1.0;
- scale *= lb_scale_factor[grid_index - 2];
+ unwrap_periodic_pmegrid(pme, grid);
+
+ if (stepWork.computeForces)
+ {
+ /* interpolate forces for our local atoms */
+ bClearF = (bFirst && PAR(cr));
+ scale = pme->bFEP ? (fep_state < 1 ? 1.0 - lambda_lj : lambda_lj) : 1.0;
+ scale *= lb_scale_factor[grid_index - 2];
#pragma omp parallel for num_threads(pme->nthread) schedule(static)
- for (thread = 0; thread < pme->nthread; thread++)
+ for (thread = 0; thread < pme->nthread; thread++)
+ {
+ try
{
- try
- {
- gather_f_bsplines(pme, grid, bClearF, &pme->atc[0],
- &pme->atc[0].spline[thread], scale);
- }
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
+ gather_f_bsplines(pme, grid, bClearF, &pme->atc[0],
+ &pme->atc[0].spline[thread], scale);
}
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
+ }
- inc_nrnb(nrnb, eNR_GATHERFBSP,
- pme->pme_order * pme->pme_order * pme->pme_order * pme->atc[0].numAtoms());
- }
- wallcycle_stop(wcycle, ewcPME_GATHER);
+ inc_nrnb(nrnb, eNR_GATHERFBSP,
+ pme->pme_order * pme->pme_order * pme->pme_order * pme->atc[0].numAtoms());
+ }
+ wallcycle_stop(wcycle, ewcPME_GATHER);
- bFirst = FALSE;
- } /* for (grid_index = 8; grid_index >= 2; --grid_index) */
- } /* if (bCalcF) */
- } /* for (fep_state = 0; fep_state < fep_states_lj; ++fep_state) */
- } /* if ((flags & GMX_PME_DO_LJ) && pme->ljpme_combination_rule == eljpmeLB) */
+ bFirst = FALSE;
+ } /* for (grid_index = 8; grid_index >= 2; --grid_index) */
+ } /* for (fep_state = 0; fep_state < fep_states_lj; ++fep_state) */
+ } /* if (pme->doLJ && pme->ljpme_combination_rule == eljpmeLB) */
- if (bCalcF && pme->nnodes > 1)
+ if (stepWork.computeForces && pme->nnodes > 1)
{
wallcycle_start(wcycle, ewcPME_REDISTXF);
for (d = 0; d < pme->ndecompdim; d++)
wallcycle_stop(wcycle, ewcPME_REDISTXF);
}
- if (bCalcEnerVir)
+ if (computeEnergyAndVirial)
{
if (pme->doCoulomb)
{
delete pme;
}
-void gmx_pme_reinit_atoms(gmx_pme_t* pme, const int numAtoms, const real* charges)
+void gmx_pme_reinit_atoms(gmx_pme_t* pme, const int numAtoms, const real* chargesA, const real* chargesB)
{
if (pme->gpu != nullptr)
{
- pme_gpu_reinit_atoms(pme->gpu, numAtoms, charges);
+ GMX_ASSERT(!(pme->bFEP_q && chargesB == nullptr),
+ "B state charges must be specified if running Coulomb FEP on the GPU");
+ pme_gpu_reinit_atoms(pme->gpu, numAtoms, chargesA, pme->bFEP_q ? chargesB : nullptr);
}
else
{
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff