#include "gromacs/utility/logger.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/message_string_collector.h"
#include "gromacs/utility/unique_cptr.h"
#include "calculate_spline_moduli.h"
#include "pme_spline_work.h"
#include "pme_spread.h"
-/*! \brief Help build a descriptive message in \c error if there are
- * \c errorReasons why PME on GPU is not supported.
- *
- * \returns Whether the lack of errorReasons indicate there is support. */
-static bool addMessageIfNotSupported(const std::list<std::string>& errorReasons, std::string* error)
-{
- bool isSupported = errorReasons.empty();
- if (!isSupported && error)
- {
- std::string regressionTestMarker = "PME GPU does not support";
- // this prefix is tested for in the regression tests script gmxtest.pl
- *error = regressionTestMarker;
- if (errorReasons.size() == 1)
- {
- *error += " " + errorReasons.back();
- }
- else
- {
- *error += ": " + gmx::joinStrings(errorReasons, "; ");
- }
- *error += ".";
- }
- return isSupported;
-}
+//NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
+bool g_allowPmeWithSyclForTesting = false;
bool pme_gpu_supports_build(std::string* error)
{
- std::list<std::string> errorReasons;
- if (GMX_DOUBLE)
- {
- errorReasons.emplace_back("a double-precision build");
- }
- 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);
+ gmx::MessageStringCollector errorReasons;
+ // Before changing the prefix string, make sure that it is not searched for in regression tests.
+ errorReasons.startContext("PME GPU does not support:");
+ errorReasons.appendIf(GMX_DOUBLE, "Double-precision build of GROMACS.");
+ errorReasons.appendIf(!GMX_GPU, "Non-GPU build of GROMACS.");
+ errorReasons.appendIf(GMX_GPU_SYCL && !g_allowPmeWithSyclForTesting, "SYCL build."); // SYCL-TODO
+ errorReasons.finishContext();
+ if (error != nullptr)
+ {
+ *error = errorReasons.toString();
+ }
+ return errorReasons.isEmpty();
}
bool pme_gpu_supports_hardware(const gmx_hw_info_t gmx_unused& hwinfo, std::string* error)
{
- std::list<std::string> errorReasons;
-
- if (GMX_GPU_OPENCL)
- {
+ gmx::MessageStringCollector errorReasons;
+ // Before changing the prefix string, make sure that it is not searched for in regression tests.
+ errorReasons.startContext("PME GPU does not support:");
#ifdef __APPLE__
- errorReasons.emplace_back("Apple OS X operating system");
+ errorReasons.appendIf(GMX_GPU_OPENCL, "Apple OS X operating system");
#endif
+ errorReasons.finishContext();
+ if (error != nullptr)
+ {
+ *error = errorReasons.toString();
}
- return addMessageIfNotSupported(errorReasons, error);
+ return errorReasons.isEmpty();
}
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("systems that do not use PME for electrostatics");
- }
- if (ir.pme_order != 4)
- {
- errorReasons.emplace_back("interpolation orders other than 4");
- }
- if (EVDW_PME(ir.vdwtype))
- {
- errorReasons.emplace_back("Lennard-Jones PME");
- }
- if (!EI_DYNAMICS(ir.eI))
- {
- errorReasons.emplace_back(
- "Cannot compute PME interactions on a GPU, because PME GPU requires a dynamical "
- "integrator (md, sd, etc).");
- }
- return addMessageIfNotSupported(errorReasons, error);
+ gmx::MessageStringCollector errorReasons;
+ // Before changing the prefix string, make sure that it is not searched for in regression tests.
+ errorReasons.startContext("PME GPU does not support:");
+ errorReasons.appendIf(!EEL_PME(ir.coulombtype),
+ "Systems that do not use PME for electrostatics.");
+ errorReasons.appendIf((ir.pme_order != 4), "Interpolation orders other than 4.");
+ errorReasons.appendIf(EVDW_PME(ir.vdwtype), "Lennard-Jones PME.");
+ errorReasons.appendIf(!EI_DYNAMICS(ir.eI), "Non-dynamical integrator (use md, sd, etc).");
+ errorReasons.finishContext();
+ if (error != nullptr)
+ {
+ *error = errorReasons.toString();
+ }
+ return errorReasons.isEmpty();
}
bool pme_gpu_mixed_mode_supports_input(const t_inputrec& ir, std::string* error)
{
- std::list<std::string> errorReasons;
- if (ir.efep != efepNO)
+ gmx::MessageStringCollector errorReasons;
+ // Before changing the prefix string, make sure that it is not searched for in regression tests.
+ errorReasons.startContext("PME GPU in Mixed mode does not support:");
+ errorReasons.appendIf(ir.efep != FreeEnergyPerturbationType::No, "Free Energy Perturbation.");
+ errorReasons.finishContext();
+ if (error != nullptr)
{
- errorReasons.emplace_back("Free Energy Perturbation (in PME GPU mixed mode)");
+ *error = errorReasons.toString();
}
- return addMessageIfNotSupported(errorReasons, error);
+ return errorReasons.isEmpty();
}
/*! \brief \libinternal
*/
static bool pme_gpu_check_restrictions(const gmx_pme_t* pme, std::string* error)
{
- std::list<std::string> errorReasons;
- if (pme->nnodes != 1)
- {
- errorReasons.emplace_back("PME decomposition");
- }
- if (pme->pme_order != 4)
- {
- errorReasons.emplace_back("interpolation orders other than 4");
- }
- if (pme->doLJ)
- {
- errorReasons.emplace_back("Lennard-Jones PME");
- }
- if (GMX_DOUBLE)
- {
- errorReasons.emplace_back("double precision");
- }
- 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);
+ gmx::MessageStringCollector errorReasons;
+ // Before changing the prefix string, make sure that it is not searched for in regression tests.
+ errorReasons.startContext("PME GPU does not support:");
+ errorReasons.appendIf((pme->nnodes != 1), "PME decomposition.");
+ errorReasons.appendIf((pme->pme_order != 4), "interpolation orders other than 4.");
+ errorReasons.appendIf(pme->doLJ, "Lennard-Jones PME.");
+ errorReasons.appendIf(GMX_DOUBLE, "Double precision build of GROMACS.");
+ errorReasons.appendIf(!GMX_GPU, "Non-GPU build of GROMACS.");
+ errorReasons.appendIf(GMX_GPU_SYCL && !g_allowPmeWithSyclForTesting, "SYCL build of GROMACS."); // SYCL-TODO
+ errorReasons.finishContext();
+ if (error != nullptr)
+ {
+ *error = errorReasons.toString();
+ }
+ return errorReasons.isEmpty();
}
PmeRunMode pme_run_mode(const gmx_pme_t* pme)
const int pmeOrder,
const int dimIndex,
const bool doSpread) :
- dimind(dimIndex),
- bSpread(doSpread),
- pme_order(pmeOrder),
- nthread(numThreads),
- spline(nthread)
+ dimind(dimIndex), bSpread(doSpread), pme_order(pmeOrder), nthread(numThreads), spline(nthread)
{
if (PmeMpiCommunicator != MPI_COMM_NULL)
{
MPI_Status stat;
for (size_t b = 0; b < ol->comm_data.size(); b++)
{
- MPI_Sendrecv(&ol->send_size, 1, MPI_INT, ol->comm_data[b].send_id, b, &ol->comm_data[b].recv_size,
- 1, MPI_INT, ol->comm_data[b].recv_id, b, ol->mpi_comm, &stat);
+ MPI_Sendrecv(&ol->send_size,
+ 1,
+ MPI_INT,
+ ol->comm_data[b].send_id,
+ b,
+ &ol->comm_data[b].recv_size,
+ 1,
+ MPI_INT,
+ ol->comm_data[b].recv_id,
+ b,
+ ol->mpi_comm,
+ &stat);
}
#endif
std::string message = gmx::formatString(
"pme_order (%d) is larger than the maximum allowed value (%d). Modify and "
"recompile the code if you really need such a high order.",
- pme_order, PME_ORDER_MAX);
+ pme_order,
+ PME_ORDER_MAX);
GMX_THROW(gmx::InconsistentInputError(message));
}
"threads, the number of grid lines per rank along x should be >= pme_order (%d) "
"or = pmeorder-1. To resolve this issue, use fewer ranks along x (and possibly "
"more along y and/or z) by specifying -dd manually.",
- nkx / static_cast<double>(numPmeDomainsAlongX), pme_order);
+ nkx / static_cast<double>(numPmeDomainsAlongX),
+ pme_order);
}
return true;
gmx::unique_cptr<gmx_pme_t, gmx_pme_destroy> pme(new gmx_pme_t());
- pme->sum_qgrid_tmp = nullptr;
- pme->sum_qgrid_dd_tmp = nullptr;
-
pme->buf_nalloc = 0;
pme->nnodes = 1;
pme->ndecompdim = 2;
#if GMX_MPI
- MPI_Comm_split(pme->mpi_comm, pme->nodeid % numPmeDomains.y, pme->nodeid,
+ MPI_Comm_split(pme->mpi_comm,
+ pme->nodeid % numPmeDomains.y,
+ pme->nodeid,
&pme->mpi_comm_d[0]); /* My communicator along major dimension */
- MPI_Comm_split(pme->mpi_comm, pme->nodeid / numPmeDomains.y, pme->nodeid,
+ MPI_Comm_split(pme->mpi_comm,
+ pme->nodeid / numPmeDomains.y,
+ pme->nodeid,
&pme->mpi_comm_d[1]); /* My communicator along minor dimension */
MPI_Comm_rank(pme->mpi_comm_d[0], &pme->nodeid_major);
* not calculating free-energy for Coulomb and/or LJ while gmx_pme_init()
* configures with free-energy, but that has never been tested.
*/
- pme->doCoulomb = EEL_PME(ir->coulombtype);
- pme->doLJ = EVDW_PME(ir->vdwtype);
- pme->bFEP_q = ((ir->efep != efepNO) && bFreeEnergy_q);
- pme->bFEP_lj = ((ir->efep != efepNO) && bFreeEnergy_lj);
- pme->bFEP = (pme->bFEP_q || pme->bFEP_lj);
- pme->nkx = ir->nkx;
- pme->nky = ir->nky;
- pme->nkz = ir->nkz;
- pme->bP3M = (ir->coulombtype == eelP3M_AD || getenv("GMX_PME_P3M") != nullptr);
+ pme->doCoulomb = EEL_PME(ir->coulombtype);
+ pme->doLJ = EVDW_PME(ir->vdwtype);
+ pme->bFEP_q = ((ir->efep != FreeEnergyPerturbationType::No) && bFreeEnergy_q);
+ pme->bFEP_lj = ((ir->efep != FreeEnergyPerturbationType::No) && bFreeEnergy_lj);
+ pme->bFEP = (pme->bFEP_q || pme->bFEP_lj);
+ pme->nkx = ir->nkx;
+ pme->nky = ir->nky;
+ pme->nkz = ir->nkz;
+ pme->bP3M = (ir->coulombtype == CoulombInteractionType::P3mAD || getenv("GMX_PME_P3M") != nullptr);
pme->pme_order = ir->pme_order;
pme->ewaldcoeff_q = ewaldcoeff_q;
pme->ewaldcoeff_lj = ewaldcoeff_lj;
// The box requires scaling with nwalls = 2, we store that condition as well
// as the scaling factor
- delete pme->boxScaler;
- pme->boxScaler = new EwaldBoxZScaler(*ir);
+ pme->boxScaler = std::make_unique<EwaldBoxZScaler>(
+ EwaldBoxZScaler(inputrecPbcXY2Walls(ir), ir->wall_ewald_zfac));
/* If we violate restrictions, generate a fatal error here */
- gmx_pme_check_restrictions(pme->pme_order, pme->nkx, pme->nky, pme->nkz, pme->nnodes_major,
- pme->bUseThreads, true);
+ gmx_pme_check_restrictions(
+ pme->pme_order, pme->nkx, pme->nky, pme->nkz, pme->nnodes_major, pme->bUseThreads, true);
if (pme->nnodes > 1)
{
" 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::roundToInt((imbal - 1) * 100),
+ pme->nkx,
+ pme->nky,
+ pme->nnodes_major,
+ pme->nky,
+ pme->nkz,
+ pme->nnodes_minor);
}
}
* y is always copied through a buffer: we don't need padding in z,
* but we do need the overlap in x because of the communication order.
*/
- init_overlap_comm(&pme->overlap[0], pme->pme_order, pme->mpi_comm_d[0], pme->nnodes_major,
- pme->nodeid_major, pme->nkx,
+ init_overlap_comm(&pme->overlap[0],
+ pme->pme_order,
+ pme->mpi_comm_d[0],
+ pme->nnodes_major,
+ pme->nodeid_major,
+ pme->nkx,
(div_round_up(pme->nky, pme->nnodes_minor) + pme->pme_order)
* (pme->nkz + pme->pme_order - 1));
* We do this with an offset buffer of equal size, so we need to allocate
* extra for the offset. That's what the (+1)*pme->nkz is for.
*/
- init_overlap_comm(&pme->overlap[1], pme->pme_order, pme->mpi_comm_d[1], pme->nnodes_minor,
- pme->nodeid_minor, pme->nky,
+ init_overlap_comm(&pme->overlap[1],
+ pme->pme_order,
+ pme->mpi_comm_d[1],
+ pme->nnodes_minor,
+ pme->nodeid_minor,
+ pme->nky,
(div_round_up(pme->nkx, pme->nnodes_major) + pme->pme_order + 1) * pme->nkz);
/* Double-check for a limitation of the (current) sum_fftgrid_dd code.
pme->pmegrid_start_iy = pme->overlap[1].s2g0[pme->nodeid_minor];
pme->pmegrid_start_iz = 0;
- make_gridindex_to_localindex(pme->nkx, pme->pmegrid_start_ix,
- pme->pmegrid_nx - (pme->pme_order - 1), &pme->nnx, &pme->fshx);
- make_gridindex_to_localindex(pme->nky, pme->pmegrid_start_iy,
- pme->pmegrid_ny - (pme->pme_order - 1), &pme->nny, &pme->fshy);
- make_gridindex_to_localindex(pme->nkz, pme->pmegrid_start_iz, pme->pmegrid_nz_base, &pme->nnz,
- &pme->fshz);
+ make_gridindex_to_localindex(
+ pme->nkx, pme->pmegrid_start_ix, pme->pmegrid_nx - (pme->pme_order - 1), &pme->nnx, &pme->fshx);
+ make_gridindex_to_localindex(
+ pme->nky, pme->pmegrid_start_iy, pme->pmegrid_ny - (pme->pme_order - 1), &pme->nny, &pme->fshy);
+ make_gridindex_to_localindex(
+ pme->nkz, pme->pmegrid_start_iz, pme->pmegrid_nz_base, &pme->nnz, &pme->fshz);
pme->spline_work = make_pme_spline_work(pme->pme_order);
*/
if (pme->doLJ)
{
- pme->ngrids = ((ir->ljpme_combination_rule == eljpmeLB) ? DO_Q_AND_LJ_LB : DO_Q_AND_LJ);
+ pme->ngrids = ((ir->ljpme_combination_rule == LongRangeVdW::LB) ? DO_Q_AND_LJ_LB : DO_Q_AND_LJ);
}
else
{
{
if ((i < DO_Q && pme->doCoulomb && (i == 0 || bFreeEnergy_q))
|| (i >= DO_Q && pme->doLJ
- && (i == 2 || bFreeEnergy_lj || ir->ljpme_combination_rule == eljpmeLB)))
+ && (i == 2 || bFreeEnergy_lj || ir->ljpme_combination_rule == LongRangeVdW::LB)))
{
- pmegrids_init(&pme->pmegrid[i], pme->pmegrid_nx, pme->pmegrid_ny, pme->pmegrid_nz,
- pme->pmegrid_nz_base, pme->pme_order, pme->bUseThreads, pme->nthread,
+ pmegrids_init(&pme->pmegrid[i],
+ pme->pmegrid_nx,
+ pme->pmegrid_ny,
+ pme->pmegrid_nz,
+ pme->pmegrid_nz_base,
+ pme->pme_order,
+ pme->bUseThreads,
+ pme->nthread,
pme->overlap[0].s2g1[pme->nodeid_major]
- pme->overlap[0].s2g0[pme->nodeid_major + 1],
pme->overlap[1].s2g1[pme->nodeid_minor]
const auto allocateRealGridForGpu = (pme->runMode == PmeRunMode::Mixed)
? gmx::PinningPolicy::PinnedIfSupported
: gmx::PinningPolicy::CannotBePinned;
- gmx_parallel_3dfft_init(&pme->pfft_setup[i], ndata, &pme->fftgrid[i], &pme->cfftgrid[i],
- pme->mpi_comm_d, bReproducible, pme->nthread, allocateRealGridForGpu);
+ gmx_parallel_3dfft_init(&pme->pfft_setup[i],
+ ndata,
+ &pme->fftgrid[i],
+ &pme->cfftgrid[i],
+ pme->mpi_comm_d,
+ bReproducible,
+ pme->nthread,
+ allocateRealGridForGpu);
}
}
const gmx::MDLogger dummyLogger;
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, nullptr, dummyLogger);
+ *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,
+ 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, nullptr);
+ gmx_pme_reinit_atoms(*pmedata, pme_src->atc[0].numAtoms(), {}, {});
}
// TODO this is mostly passing around current values
}
/* We would like to reuse the fft grids, but that's harder */
}
-void gmx_pme_calc_energy(gmx_pme_t* pme, gmx::ArrayRef<const gmx::RVec> x, gmx::ArrayRef<const real> q, real* V)
+real gmx_pme_calc_energy(gmx_pme_t* pme, gmx::ArrayRef<const gmx::RVec> x, gmx::ArrayRef<const real> q)
{
pmegrids_t* grid;
/* Only calculate the spline coefficients, don't actually spread */
spread_on_grid(pme, atc, nullptr, TRUE, FALSE, pme->fftgrid[PME_GRID_QA], FALSE, PME_GRID_QA);
- *V = gather_energy_bsplines(pme, grid->grid.grid, atc);
+ return gather_energy_bsplines(pme, grid->grid.grid, atc);
}
/*! \brief Calculate initial Lorentz-Berthelot coefficients for LJ-PME */
-static void calc_initial_lb_coeffs(gmx::ArrayRef<real> coefficient, const real* local_c6, const real* local_sigma)
+static void calc_initial_lb_coeffs(gmx::ArrayRef<real> coefficient,
+ gmx::ArrayRef<const real> local_c6,
+ gmx::ArrayRef<const real> local_sigma)
{
for (gmx::index i = 0; i < coefficient.ssize(); ++i)
{
}
/*! \brief Calculate next Lorentz-Berthelot coefficients for LJ-PME */
-static void calc_next_lb_coeffs(gmx::ArrayRef<real> coefficient, const real* local_sigma)
+static void calc_next_lb_coeffs(gmx::ArrayRef<real> coefficient, gmx::ArrayRef<const real> local_sigma)
{
for (gmx::index i = 0; i < coefficient.ssize(); ++i)
{
int gmx_pme_do(struct gmx_pme_t* pme,
gmx::ArrayRef<const gmx::RVec> coordinates,
gmx::ArrayRef<gmx::RVec> forces,
- real chargeA[],
- real chargeB[],
- real c6A[],
- real c6B[],
- real sigmaA[],
- real sigmaB[],
+ gmx::ArrayRef<const real> chargeA,
+ gmx::ArrayRef<const real> chargeB,
+ gmx::ArrayRef<const real> c6A,
+ gmx::ArrayRef<const real> c6B,
+ gmx::ArrayRef<const real> sigmaA,
+ gmx::ArrayRef<const real> sigmaB,
const matrix box,
const t_commrec* cr,
int maxshift_x,
GMX_ASSERT(pme->runMode == PmeRunMode::CPU,
"gmx_pme_do should not be called on the GPU PME run.");
- int d, npme, grid_index, max_grid_index;
- PmeAtomComm& atc = pme->atc[0];
- pmegrids_t* pmegrid = nullptr;
- real* grid = nullptr;
- real* coefficient = nullptr;
- PmeOutput output[2]; // The second is used for the B state with FEP
- real scale, lambda;
- gmx_bool bClearF;
- gmx_parallel_3dfft_t pfft_setup;
- real* fftgrid;
- t_complex* cfftgrid;
- int thread;
- gmx_bool bFirst, bDoSplines;
- int fep_state;
- int fep_states_lj = pme->bFEP_lj ? 2 : 1;
+ PmeAtomComm& atc = pme->atc[0];
+ pmegrids_t* pmegrid = nullptr;
+ real* grid = nullptr;
+ gmx::ArrayRef<const real> coefficient;
+ std::array<PmeOutput, 2> output; // The second is used for the B state with FEP
+ gmx_parallel_3dfft_t pfft_setup;
+ real* fftgrid;
+ t_complex* cfftgrid;
+ int thread;
+ const int fep_states_lj = pme->bFEP_lj ? 2 : 1;
// There's no support for computing energy without virial, or vice versa
const bool computeEnergyAndVirial = (stepWork.computeEnergy || stepWork.computeVirial);
pme->boxScaler->scaleBox(box, scaledBox);
gmx::invertBoxMatrix(scaledBox, pme->recipbox);
- bFirst = TRUE;
+ bool bFirst = true;
/* For simplicity, we construct the splines for all particles if
* more than one PME calculations is needed. Some optimization
* that don't yet have them.
*/
- bDoSplines = pme->bFEP || (pme->doCoulomb && pme->doLJ);
+ bool bDoSplines = pme->bFEP || (pme->doCoulomb && pme->doLJ);
/* We need a maximum of four separate PME calculations:
* grid_index=0: Coulomb PME with charges from state A
*/
/* If we are doing LJ-PME with LB, we only do Q here */
- max_grid_index = (pme->ljpme_combination_rule == eljpmeLB) ? DO_Q : DO_Q_AND_LJ;
-
- for (grid_index = 0; grid_index < max_grid_index; ++grid_index)
+ const int max_grid_index = (pme->ljpme_combination_rule == LongRangeVdW::LB) ? DO_Q : DO_Q_AND_LJ;
+ bool bClearF;
+ for (int grid_index = 0; grid_index < max_grid_index; ++grid_index)
{
/* Check if we should do calculations at this grid_index
* If grid_index is odd we should be doing FEP
grid = pmegrid->grid.grid;
- if (debug)
- {
- fprintf(debug, "PME: number of ranks = %d, rank = %d\n", cr->nnodes, cr->nodeid);
- fprintf(debug, "Grid = %p\n", static_cast<void*>(grid));
- if (grid == nullptr)
- {
- gmx_fatal(FARGS, "No grid!");
- }
- }
-
if (pme->nnodes == 1)
{
- atc.coefficient = gmx::arrayRefFromArray(coefficient, coordinates.size());
+ atc.coefficient = coefficient;
}
else
{
- wallcycle_start(wcycle, ewcPME_REDISTXF);
+ wallcycle_start(wcycle, WallCycleCounter::PmeRedistXF);
do_redist_pos_coeffs(pme, cr, bFirst, coordinates, coefficient);
- wallcycle_stop(wcycle, ewcPME_REDISTXF);
+ wallcycle_stop(wcycle, WallCycleCounter::PmeRedistXF);
}
- if (debug)
- {
- fprintf(debug, "Rank= %6d, pme local particles=%6d\n", cr->nodeid, atc.numAtoms());
- }
-
- wallcycle_start(wcycle, ewcPME_SPREAD);
+ wallcycle_start(wcycle, WallCycleCounter::PmeSpread);
/* Spread the coefficients on a grid */
spread_on_grid(pme, &atc, pmegrid, bFirst, TRUE, fftgrid, bDoSplines, grid_index);
copy_pmegrid_to_fftgrid(pme, grid, fftgrid, grid_index);
}
- wallcycle_stop(wcycle, ewcPME_SPREAD);
+ wallcycle_stop(wcycle, WallCycleCounter::PmeSpread);
/* TODO If the OpenMP and single-threaded implementations
converge, then spread_on_grid() and
/* do 3d-fft */
if (thread == 0)
{
- wallcycle_start(wcycle, ewcPME_FFT);
+ wallcycle_start(wcycle, WallCycleCounter::PmeFft);
}
gmx_parallel_3dfft_execute(pfft_setup, GMX_FFT_REAL_TO_COMPLEX, thread, wcycle);
if (thread == 0)
{
- wallcycle_stop(wcycle, ewcPME_FFT);
+ wallcycle_stop(wcycle, WallCycleCounter::PmeFft);
}
/* solve in k-space for our local cells */
if (thread == 0)
{
- wallcycle_start(wcycle, (grid_index < DO_Q ? ewcPME_SOLVE : ewcLJPME));
+ wallcycle_start(
+ wcycle,
+ (grid_index < DO_Q ? WallCycleCounter::PmeSolve : WallCycleCounter::LJPme));
}
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);
+ 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,
+ solve_pme_lj_yzx(pme,
+ &cfftgrid,
+ FALSE,
scaledBox[XX][XX] * scaledBox[YY][YY] * scaledBox[ZZ][ZZ],
- computeEnergyAndVirial, pme->nthread, thread);
+ computeEnergyAndVirial,
+ pme->nthread,
+ thread);
}
if (thread == 0)
{
- wallcycle_stop(wcycle, (grid_index < DO_Q ? ewcPME_SOLVE : ewcLJPME));
+ wallcycle_stop(
+ wcycle,
+ (grid_index < DO_Q ? WallCycleCounter::PmeSolve : WallCycleCounter::LJPme));
inc_nrnb(nrnb, eNR_SOLVEPME, loop_count);
}
/* do 3d-invfft */
if (thread == 0)
{
- wallcycle_start(wcycle, ewcPME_FFT);
+ wallcycle_start(wcycle, WallCycleCounter::PmeFft);
}
gmx_parallel_3dfft_execute(pfft_setup, GMX_FFT_COMPLEX_TO_REAL, thread, wcycle);
if (thread == 0)
{
- wallcycle_stop(wcycle, ewcPME_FFT);
+ wallcycle_stop(wcycle, WallCycleCounter::PmeFft);
if (pme->nodeid == 0)
{
- real ntot = pme->nkx * pme->nky * pme->nkz;
- npme = static_cast<int>(ntot * std::log(ntot) / std::log(2.0));
+ real ntot = pme->nkx * pme->nky * pme->nkz;
+ const int 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);
+ wallcycle_start(wcycle, WallCycleCounter::PmeGather);
}
copy_fftgrid_to_pmegrid(pme, fftgrid, grid, grid_index, pme->nthread, thread);
* atc->f is the actual force array, not a buffer,
* therefore we should not clear it.
*/
- lambda = grid_index < DO_Q ? lambda_q : lambda_lj;
- bClearF = (bFirst && PAR(cr));
+ real lambda = grid_index < DO_Q ? lambda_q : lambda_lj;
+ bClearF = (bFirst && PAR(cr));
#pragma omp parallel for num_threads(pme->nthread) schedule(static)
for (thread = 0; thread < pme->nthread; thread++)
{
try
{
- gather_f_bsplines(pme, grid, bClearF, &atc, &atc.spline[thread],
+ gather_f_bsplines(pme,
+ grid,
+ bClearF,
+ &atc,
+ &atc.spline[thread],
pme->bFEP ? (grid_index % 2 == 0 ? 1.0 - lambda : lambda) : 1.0);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
- inc_nrnb(nrnb, eNR_GATHERFBSP,
- pme->pme_order * pme->pme_order * pme->pme_order * atc.numAtoms());
+ inc_nrnb(nrnb, eNR_GATHERFBSP, pme->pme_order * pme->pme_order * pme->pme_order * atc.numAtoms());
/* Note: this wallcycle region is opened above inside an OpenMP
region, so take care if refactoring code here. */
- wallcycle_stop(wcycle, ewcPME_GATHER);
+ wallcycle_stop(wcycle, WallCycleCounter::PmeGather);
}
if (computeEnergyAndVirial)
/* For Lorentz-Berthelot combination rules in LJ-PME, we need to calculate
* seven terms. */
- if (pme->doLJ && pme->ljpme_combination_rule == eljpmeLB)
+ if (pme->doLJ && pme->ljpme_combination_rule == LongRangeVdW::LB)
{
/* Loop over A- and B-state if we are doing FEP */
- for (fep_state = 0; fep_state < fep_states_lj; ++fep_state)
+ for (int fep_state = 0; fep_state < fep_states_lj; ++fep_state)
{
- real *local_c6 = nullptr, *local_sigma = nullptr, *RedistC6 = nullptr, *RedistSigma = nullptr;
- gmx::ArrayRef<real> coefficientBuffer;
+ std::vector<real> local_c6;
+ std::vector<real> local_sigma;
+ gmx::ArrayRef<const real> RedistC6;
+ gmx::ArrayRef<const real> RedistSigma;
+ gmx::ArrayRef<real> coefficientBuffer;
if (pme->nnodes == 1)
{
pme->lb_buf1.resize(atc.numAtoms());
switch (fep_state)
{
case 0:
- local_c6 = c6A;
- local_sigma = sigmaA;
+ local_c6.assign(c6A.begin(), c6A.end());
+ local_sigma.assign(sigmaA.begin(), sigmaA.end());
break;
case 1:
- local_c6 = c6B;
- local_sigma = sigmaB;
+ local_c6.assign(c6B.begin(), c6B.end());
+ local_sigma.assign(sigmaB.begin(), sigmaB.end());
break;
default: gmx_incons("Trying to access wrong FEP-state in LJ-PME routine");
}
break;
default: gmx_incons("Trying to access wrong FEP-state in LJ-PME routine");
}
- wallcycle_start(wcycle, ewcPME_REDISTXF);
+ wallcycle_start(wcycle, WallCycleCounter::PmeRedistXF);
do_redist_pos_coeffs(pme, cr, bFirst, coordinates, RedistC6);
pme->lb_buf1.resize(atc.numAtoms());
pme->lb_buf2.resize(atc.numAtoms());
- local_c6 = pme->lb_buf1.data();
+ local_c6.assign(pme->lb_buf1.begin(), pme->lb_buf1.end());
for (int i = 0; i < atc.numAtoms(); ++i)
{
local_c6[i] = atc.coefficient[i];
}
do_redist_pos_coeffs(pme, cr, FALSE, coordinates, RedistSigma);
- local_sigma = pme->lb_buf2.data();
+ local_sigma.assign(pme->lb_buf2.begin(), pme->lb_buf2.end());
for (int i = 0; i < atc.numAtoms(); ++i)
{
local_sigma[i] = atc.coefficient[i];
}
- wallcycle_stop(wcycle, ewcPME_REDISTXF);
+ wallcycle_stop(wcycle, WallCycleCounter::PmeRedistXF);
}
atc.coefficient = coefficientBuffer;
calc_initial_lb_coeffs(coefficientBuffer, local_c6, local_sigma);
/*Seven terms in LJ-PME with LB, grid_index < 2 reserved for electrostatics*/
- for (grid_index = 2; grid_index < 9; ++grid_index)
+ for (int grid_index = 2; grid_index < 9; ++grid_index)
{
/* Unpack structure */
pmegrid = &pme->pmegrid[grid_index];
calc_next_lb_coeffs(coefficientBuffer, local_sigma);
grid = pmegrid->grid.grid;
- wallcycle_start(wcycle, ewcPME_SPREAD);
+ wallcycle_start(wcycle, WallCycleCounter::PmeSpread);
/* Spread the c6 on a grid */
spread_on_grid(pme, &atc, pmegrid, bFirst, TRUE, fftgrid, bDoSplines, grid_index);
inc_nrnb(nrnb, eNR_WEIGHTS, DIM * atc.numAtoms());
}
- inc_nrnb(nrnb, eNR_SPREADBSP,
+ inc_nrnb(nrnb,
+ eNR_SPREADBSP,
pme->pme_order * pme->pme_order * pme->pme_order * atc.numAtoms());
if (pme->nthread == 1)
{
}
copy_pmegrid_to_fftgrid(pme, grid, fftgrid, grid_index);
}
- wallcycle_stop(wcycle, ewcPME_SPREAD);
+ wallcycle_stop(wcycle, WallCycleCounter::PmeSpread);
/*Here we start a large thread parallel region*/
#pragma omp parallel num_threads(pme->nthread) private(thread)
/* do 3d-fft */
if (thread == 0)
{
- wallcycle_start(wcycle, ewcPME_FFT);
+ wallcycle_start(wcycle, WallCycleCounter::PmeFft);
}
gmx_parallel_3dfft_execute(pfft_setup, GMX_FFT_REAL_TO_COMPLEX, thread, wcycle);
if (thread == 0)
{
- wallcycle_stop(wcycle, ewcPME_FFT);
+ wallcycle_stop(wcycle, WallCycleCounter::PmeFft);
}
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
thread = gmx_omp_get_thread_num();
if (thread == 0)
{
- wallcycle_start(wcycle, ewcLJPME);
+ wallcycle_start(wcycle, WallCycleCounter::LJPme);
}
loop_count =
- solve_pme_lj_yzx(pme, &pme->cfftgrid[2], TRUE,
+ solve_pme_lj_yzx(pme,
+ &pme->cfftgrid[2],
+ TRUE,
scaledBox[XX][XX] * scaledBox[YY][YY] * scaledBox[ZZ][ZZ],
- computeEnergyAndVirial, pme->nthread, thread);
+ computeEnergyAndVirial,
+ pme->nthread,
+ thread);
if (thread == 0)
{
- wallcycle_stop(wcycle, ewcLJPME);
+ wallcycle_stop(wcycle, WallCycleCounter::LJPme);
inc_nrnb(nrnb, eNR_SOLVEPME, loop_count);
}
}
bFirst = !pme->doCoulomb;
calc_initial_lb_coeffs(coefficientBuffer, local_c6, local_sigma);
- for (grid_index = 8; grid_index >= 2; --grid_index)
+ for (int grid_index = 8; grid_index >= 2; --grid_index)
{
/* Unpack structure */
pmegrid = &pme->pmegrid[grid_index];
/* do 3d-invfft */
if (thread == 0)
{
- wallcycle_start(wcycle, ewcPME_FFT);
+ wallcycle_start(wcycle, WallCycleCounter::PmeFft);
}
gmx_parallel_3dfft_execute(pfft_setup, GMX_FFT_COMPLEX_TO_REAL, thread, wcycle);
if (thread == 0)
{
- wallcycle_stop(wcycle, ewcPME_FFT);
+ wallcycle_stop(wcycle, WallCycleCounter::PmeFft);
if (pme->nodeid == 0)
{
- real ntot = pme->nkx * pme->nky * pme->nkz;
- npme = static_cast<int>(ntot * std::log(ntot) / std::log(2.0));
+ real ntot = pme->nkx * pme->nky * pme->nkz;
+ const int npme = static_cast<int>(ntot * std::log(ntot) / std::log(2.0));
inc_nrnb(nrnb, eNR_FFT, 2 * npme);
}
- wallcycle_start(wcycle, ewcPME_GATHER);
+ wallcycle_start(wcycle, WallCycleCounter::PmeGather);
}
copy_fftgrid_to_pmegrid(pme, fftgrid, grid, grid_index, pme->nthread, thread);
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;
+ bClearF = (bFirst && PAR(cr));
+ real 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)
{
try
{
- gather_f_bsplines(pme, grid, bClearF, &pme->atc[0],
- &pme->atc[0].spline[thread], scale);
+ 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,
+ inc_nrnb(nrnb,
+ eNR_GATHERFBSP,
pme->pme_order * pme->pme_order * pme->pme_order * pme->atc[0].numAtoms());
}
- wallcycle_stop(wcycle, ewcPME_GATHER);
+ wallcycle_stop(wcycle, WallCycleCounter::PmeGather);
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 (pme->doLJ && pme->ljpme_combination_rule == LongRangeVdW::LB) */
if (stepWork.computeForces && pme->nnodes > 1)
{
- wallcycle_start(wcycle, ewcPME_REDISTXF);
- for (d = 0; d < pme->ndecompdim; d++)
+ wallcycle_start(wcycle, WallCycleCounter::PmeRedistXF);
+ for (int d = 0; d < pme->ndecompdim; d++)
{
gmx::ArrayRef<gmx::RVec> forcesRef;
if (d == pme->ndecompdim - 1)
{
forcesRef = pme->atc[d + 1].f;
}
- if (DOMAINDECOMP(cr))
+ if (haveDDAtomOrdering(*cr))
{
dd_pmeredist_f(pme, &pme->atc[d], forcesRef, d == pme->ndecompdim - 1 && pme->bPPnode);
}
}
- wallcycle_stop(wcycle, ewcPME_REDISTXF);
+ wallcycle_stop(wcycle, WallCycleCounter::PmeRedistXF);
}
if (computeEnergyAndVirial)
}
}
}
- if (debug)
- {
- fprintf(debug, "Electrostatic PME mesh energy: %g\n", *energy_q);
- }
}
else
{
}
}
}
- if (debug)
- {
- fprintf(debug, "Lennard-Jones PME mesh energy: %g\n", *energy_lj);
- }
}
else
{
return;
}
- delete pme->boxScaler;
-
sfree(pme->nnx);
sfree(pme->nny);
sfree(pme->nnz);
pme_free_all_work(&pme->solve_work, pme->nthread);
}
- sfree(pme->sum_qgrid_tmp);
- sfree(pme->sum_qgrid_dd_tmp);
-
destroy_pme_spline_work(pme->spline_work);
if (pme->gpu != nullptr)
delete pme;
}
-void gmx_pme_reinit_atoms(gmx_pme_t* pme, const int numAtoms, const real* chargesA, const real* chargesB)
+void gmx_pme_reinit_atoms(gmx_pme_t* pme,
+ const int numAtoms,
+ gmx::ArrayRef<const real> chargesA,
+ gmx::ArrayRef<const real> chargesB)
{
if (pme->gpu != nullptr)
{
- GMX_ASSERT(!(pme->bFEP_q && chargesB == nullptr),
+ GMX_ASSERT(!(pme->bFEP_q && chargesB.empty()),
"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);
+ pme_gpu_reinit_atoms(pme->gpu, numAtoms, chargesA.data(), pme->bFEP_q ? chargesB.data() : nullptr);
}
else
{
{
return (pme.nkx == grid_size[XX] && pme.nky == grid_size[YY] && pme.nkz == grid_size[ZZ]);
}
+
+void gmx::SeparatePmeRanksPermitted::disablePmeRanks(const std::string& reason)
+{
+ permitSeparatePmeRanks_ = false;
+
+ if (!reason.empty())
+ {
+ reasons_.push_back(reason);
+ }
+}
+
+bool gmx::SeparatePmeRanksPermitted::permitSeparatePmeRanks() const
+{
+ return permitSeparatePmeRanks_;
+}
+
+std::string gmx::SeparatePmeRanksPermitted::reasonsWhyDisabled() const
+{
+ return joinStrings(reasons_, "; ");
+}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff