#include "config.h"
-#include <assert.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-
+#include <cassert>
#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include <algorithm>
+#include <list>
+#include "gromacs/domdec/domdec.h"
#include "gromacs/ewald/ewald-utils.h"
#include "gromacs/fft/parallel_3dfft.h"
#include "gromacs/fileio/pdbio.h"
#include "gromacs/timing/cyclecounter.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/topology/topology.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.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 foundErrorReasons = errorReasons.empty();
+ if (!foundErrorReasons && error)
+ {
+ std::string regressionTestMarker = "PME GPU does not support";
+ // this prefix is tested for in the regression tests script gmxtest.pl
+ *error = regressionTestMarker + ": " + gmx::joinStrings(errorReasons, "; ") + ".";
+ }
+ return foundErrorReasons;
+}
+
+bool pme_gpu_supports_build(std::string *error)
+{
+ std::list<std::string> errorReasons;
+ if (GMX_DOUBLE)
+ {
+ errorReasons.emplace_back("double precision");
+ }
+ if (GMX_GPU == GMX_GPU_NONE)
+ {
+ errorReasons.emplace_back("non-GPU build of GROMACS");
+ }
+ return addMessageIfNotSupported(errorReasons, error);
+}
+
+bool pme_gpu_supports_input(const t_inputrec &ir, const gmx_mtop_t &mtop, 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 (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 (ir.cutoff_scheme == ecutsGROUP)
+ {
+ errorReasons.emplace_back("group cutoff scheme");
+ }
+ if (!EI_DYNAMICS(ir.eI))
+ {
+ errorReasons.emplace_back("not a dynamical integrator");
+ }
+ return addMessageIfNotSupported(errorReasons, error);
+}
+
+/*! \brief \libinternal
+ * Finds out if PME with given inputs is possible to run on GPU.
+ * This function is an internal final check, validating the whole PME structure on creation,
+ * but it still duplicates the preliminary checks from the above (externally exposed) pme_gpu_supports_input() - just in case.
+ *
+ * \param[in] pme The PME structure.
+ * \param[out] error The error message if the input is not supported on GPU.
+ * \returns True if this PME input is possible to run on GPU, false otherwise.
+ */
+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->bFEP)
+ {
+ errorReasons.emplace_back("free energy calculations (multiple grids)");
+ }
+ if (pme->doLJ)
+ {
+ errorReasons.emplace_back("Lennard-Jones PME");
+ }
+ if (GMX_DOUBLE)
+ {
+ errorReasons.emplace_back("double precision");
+ }
+ if (GMX_GPU == GMX_GPU_NONE)
+ {
+ errorReasons.emplace_back("non-GPU build of GROMACS");
+ }
+
+ return addMessageIfNotSupported(errorReasons, error);
+}
+
+PmeRunMode pme_run_mode(const gmx_pme_t *pme)
+{
+ GMX_ASSERT(pme != nullptr, "Expecting valid PME data pointer");
+ return pme->runMode;
+}
+
+gmx::PinningPolicy pme_get_pinning_policy()
+{
+ return gmx::PinningPolicy::PinnedIfSupported;
+}
+
/*! \brief Number of bytes in a cache line.
*
* Must also be a multiple of the SIMD and SIMD4 register size, to
/* pme_solve is roughly double the cost of an fft */
- return (n1 + n2 + 3*n3)/(double)(6*pme->nkx*pme->nky*pme->nkz);
+ return (n1 + n2 + 3*n3)/static_cast<double>(6*pme->nkx*pme->nky*pme->nkz);
}
/*! \brief Initialize atom communication data structure */
int ndata,
int commplainsize)
{
- int b, i;
- pme_grid_comm_t *pgc;
gmx_bool bCont;
- int fft_start, fft_end, send_index1, recv_index1;
#if GMX_MPI
MPI_Status stat;
* that belong to higher nodes (modulo nnodes)
*/
- snew(ol->s2g0, ol->nnodes+1);
- snew(ol->s2g1, ol->nnodes);
+ ol->s2g0.resize(ol->nnodes + 1);
+ ol->s2g1.resize(ol->nnodes);
if (debug)
{
fprintf(debug, "PME slab boundaries:");
}
- for (i = 0; i < nnodes; i++)
+ for (int i = 0; i < nnodes; i++)
{
/* s2g0 the local interpolation grid start.
* s2g1 the local interpolation grid end.
* spatially uniform along dimension x or y, we need to round
* s2g0 down and s2g1 up.
*/
- ol->s2g0[i] = ( i *ndata + 0 )/nnodes;
- ol->s2g1[i] = ((i+1)*ndata + nnodes-1)/nnodes + norder - 1;
+ ol->s2g0[i] = (i * ndata + 0) / nnodes;
+ ol->s2g1[i] = ((i + 1) * ndata + nnodes - 1) / nnodes + norder - 1;
if (debug)
{
}
/* Determine with how many nodes we need to communicate the grid overlap */
- b = 0;
+ int testRankCount = 0;
do
{
- b++;
+ testRankCount++;
bCont = FALSE;
- for (i = 0; i < nnodes; i++)
+ for (int i = 0; i < nnodes; i++)
{
- if ((i+b < nnodes && ol->s2g1[i] > ol->s2g0[i+b]) ||
- (i+b >= nnodes && ol->s2g1[i] > ol->s2g0[i+b-nnodes] + ndata))
+ if ((i + testRankCount < nnodes && ol->s2g1[i] > ol->s2g0[i + testRankCount]) ||
+ (i + testRankCount >= nnodes && ol->s2g1[i] > ol->s2g0[i + testRankCount - nnodes] + ndata))
{
bCont = TRUE;
}
}
}
- while (bCont && b < nnodes);
- ol->noverlap_nodes = b - 1;
-
- snew(ol->send_id, ol->noverlap_nodes);
- snew(ol->recv_id, ol->noverlap_nodes);
- for (b = 0; b < ol->noverlap_nodes; b++)
- {
- ol->send_id[b] = (ol->nodeid + (b + 1)) % ol->nnodes;
- ol->recv_id[b] = (ol->nodeid - (b + 1) + ol->nnodes) % ol->nnodes;
- }
- snew(ol->comm_data, ol->noverlap_nodes);
+ while (bCont && testRankCount < nnodes);
+ ol->comm_data.resize(testRankCount - 1);
ol->send_size = 0;
- for (b = 0; b < ol->noverlap_nodes; b++)
+
+ for (size_t b = 0; b < ol->comm_data.size(); b++)
{
- pgc = &ol->comm_data[b];
+ pme_grid_comm_t *pgc = &ol->comm_data[b];
+
/* Send */
- fft_start = ol->s2g0[ol->send_id[b]];
- fft_end = ol->s2g0[ol->send_id[b]+1];
- if (ol->send_id[b] < nodeid)
+ pgc->send_id = (ol->nodeid + (b + 1)) % ol->nnodes;
+ int fft_start = ol->s2g0[pgc->send_id];
+ int fft_end = ol->s2g0[pgc->send_id + 1];
+ if (pgc->send_id < nodeid)
{
fft_start += ndata;
fft_end += ndata;
}
- send_index1 = ol->s2g1[nodeid];
- send_index1 = std::min(send_index1, fft_end);
- pgc->send_index0 = fft_start;
- pgc->send_nindex = std::max(0, send_index1 - pgc->send_index0);
- ol->send_size += pgc->send_nindex;
+ int send_index1 = ol->s2g1[nodeid];
+ send_index1 = std::min(send_index1, fft_end);
+ pgc->send_index0 = fft_start;
+ pgc->send_nindex = std::max(0, send_index1 - pgc->send_index0);
+ ol->send_size += pgc->send_nindex;
/* We always start receiving to the first index of our slab */
+ pgc->recv_id = (ol->nodeid - (b + 1) + ol->nnodes) % ol->nnodes;
fft_start = ol->s2g0[ol->nodeid];
- fft_end = ol->s2g0[ol->nodeid+1];
- recv_index1 = ol->s2g1[ol->recv_id[b]];
- if (ol->recv_id[b] > nodeid)
+ fft_end = ol->s2g0[ol->nodeid + 1];
+ int recv_index1 = ol->s2g1[pgc->recv_id];
+ if (pgc->recv_id > nodeid)
{
recv_index1 -= ndata;
}
#if GMX_MPI
/* Communicate the buffer sizes to receive */
- for (b = 0; b < ol->noverlap_nodes; b++)
+ for (size_t b = 0; b < ol->comm_data.size(); b++)
{
- MPI_Sendrecv(&ol->send_size, 1, MPI_INT, ol->send_id[b], b,
- &ol->comm_data[b].recv_size, 1, MPI_INT, ol->recv_id[b], 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);
}
#endif
/* For non-divisible grid we need pme_order iso pme_order-1 */
- snew(ol->sendbuf, norder*commplainsize);
- snew(ol->recvbuf, norder*commplainsize);
-}
-
-/*! \brief Destroy data structure for communication */
-static void
-destroy_overlap_comm(const pme_overlap_t *ol)
-{
- sfree(ol->s2g0);
- sfree(ol->s2g1);
- sfree(ol->send_id);
- sfree(ol->recv_id);
- sfree(ol->comm_data);
- sfree(ol->sendbuf);
- sfree(ol->recvbuf);
+ ol->sendbuf.resize(norder * commplainsize);
+ ol->recvbuf.resize(norder * commplainsize);
}
int minimalPmeGridSize(int pmeOrder)
bool gmx_pme_check_restrictions(int pme_order,
int nkx, int nky, int nkz,
- int nnodes_major,
+ int numPmeDomainsAlongX,
bool useThreads,
bool errorsAreFatal)
{
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);
- GMX_THROW(InconsistentInputError(message));
+ GMX_THROW(gmx::InconsistentInputError(message));
}
const int minGridSize = minimalPmeGridSize(pme_order);
std::string message = gmx::formatString(
"The PME grid sizes need to be >= 2*(pme_order-1) (%d)",
minGridSize);
- GMX_THROW(InconsistentInputError(message));
+ GMX_THROW(gmx::InconsistentInputError(message));
}
/* Check for a limitation of the (current) sum_fftgrid_dd code.
* We only allow multiple communication pulses in dim 1, not in dim 0.
*/
- if (useThreads && (nkx < nnodes_major*pme_order &&
- nkx != nnodes_major*(pme_order - 1)))
+ if (useThreads && (nkx < numPmeDomainsAlongX*pme_order &&
+ nkx != numPmeDomainsAlongX*(pme_order - 1)))
{
if (!errorsAreFatal)
{
return false;
}
gmx_fatal(FARGS, "The number of PME grid lines per rank along x is %g. But when using OpenMP 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/(double)nnodes_major, pme_order);
+ nkx/static_cast<double>(numPmeDomainsAlongX), pme_order);
}
return true;
return (enumerator + denominator - 1)/denominator;
}
-gmx_pme_t *gmx_pme_init(const t_commrec *cr,
- int nnodes_major,
- int nnodes_minor,
- const t_inputrec *ir,
- int homenr,
- gmx_bool bFreeEnergy_q,
- gmx_bool bFreeEnergy_lj,
- gmx_bool bReproducible,
- real ewaldcoeff_q,
- real ewaldcoeff_lj,
- int nthread,
- PmeRunMode runMode,
- PmeGpu *pmeGpu,
- gmx_device_info_t *gpuInfo,
- const gmx::MDLogger & /*mdlog*/)
+gmx_pme_t *gmx_pme_init(const t_commrec *cr,
+ const NumPmeDomains &numPmeDomains,
+ const t_inputrec *ir,
+ int homenr,
+ 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,
+ PmeGpuProgramHandle pmeGpuProgram,
+ const gmx::MDLogger & /*mdlog*/)
{
int use_threads, sum_use_threads, i;
ivec ndata;
fprintf(debug, "Creating PME data structures.\n");
}
- unique_cptr<gmx_pme_t, gmx_pme_destroy> pme(new gmx_pme_t());
+ 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->nnodes = 1;
pme->bPPnode = TRUE;
- pme->nnodes_major = nnodes_major;
- pme->nnodes_minor = nnodes_minor;
+ pme->nnodes_major = numPmeDomains.x;
+ pme->nnodes_minor = numPmeDomains.y;
#if GMX_MPI
- if (nnodes_major*nnodes_minor > 1)
+ if (numPmeDomains.x*numPmeDomains.y > 1)
{
pme->mpi_comm = cr->mpi_comm_mygroup;
MPI_Comm_rank(pme->mpi_comm, &pme->nodeid);
MPI_Comm_size(pme->mpi_comm, &pme->nnodes);
- if (pme->nnodes != nnodes_major*nnodes_minor)
+ if (pme->nnodes != numPmeDomains.x*numPmeDomains.y)
{
gmx_incons("PME rank count mismatch");
}
}
else
{
- if (nnodes_minor == 1)
+ if (numPmeDomains.y == 1)
{
#if GMX_MPI
pme->mpi_comm_d[0] = pme->mpi_comm;
pme->nodeid_minor = 0;
}
- else if (nnodes_major == 1)
+ else if (numPmeDomains.x == 1)
{
#if GMX_MPI
pme->mpi_comm_d[0] = MPI_COMM_NULL;
}
else
{
- if (pme->nnodes % nnodes_major != 0)
+ if (pme->nnodes % numPmeDomains.x != 0)
{
- gmx_incons("For 2D PME decomposition, #PME ranks must be divisible by the number of ranks in the major dimension");
+ gmx_incons("For 2D PME decomposition, #PME ranks must be divisible by the number of domains along x");
}
pme->ndecompdim = 2;
#if GMX_MPI
- MPI_Comm_split(pme->mpi_comm, pme->nodeid % nnodes_minor,
+ 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/nnodes_minor,
+ 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);
" 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",
- (int)((imbal-1)*100 + 0.5),
+ gmx::roundToInt((imbal-1)*100),
pme->nkx, pme->nky, pme->nnodes_major,
pme->nky, pme->nkz, pme->nnodes_minor);
}
/* Double-check for a limitation of the (current) sum_fftgrid_dd code.
* Note that gmx_pme_check_restrictions checked for this already.
*/
- if (pme->bUseThreads && pme->overlap[0].noverlap_nodes > 1)
+ if (pme->bUseThreads && (pme->overlap[0].comm_data.size() > 1))
{
gmx_incons("More than one communication pulse required for grid overlap communication along the major dimension while using threads");
}
pme->overlap[0].s2g1[pme->nodeid_major]-pme->overlap[0].s2g0[pme->nodeid_major+1],
pme->overlap[1].s2g1[pme->nodeid_minor]-pme->overlap[1].s2g0[pme->nodeid_minor+1]);
/* This routine will allocate the grid data to fit the FFTs */
- const auto allocateRealGridForGpu = (pme->runMode == PmeRunMode::Mixed) ? gmx::PinningPolicy::CanBePinned : gmx::PinningPolicy::CannotBePinned;
+ 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,
}
/* Use atc[0] for spreading */
- init_atomcomm(pme.get(), &pme->atc[0], nnodes_major > 1 ? 0 : 1, TRUE);
+ init_atomcomm(pme.get(), &pme->atc[0], numPmeDomains.x > 1 ? 0 : 1, TRUE);
if (pme->ndecompdim >= 2)
{
init_atomcomm(pme.get(), &pme->atc[1], 1, FALSE);
pme->lb_buf2 = nullptr;
pme->lb_buf_nalloc = 0;
- pme_gpu_reinit(pme.get(), gpuInfo);
+ if (pme_gpu_active(pme.get()))
+ {
+ if (!pme->gpu)
+ {
+ // Initial check of validity of the data
+ std::string errorString;
+ bool canRunOnGpu = pme_gpu_check_restrictions(pme.get(), &errorString);
+ if (!canRunOnGpu)
+ {
+ GMX_THROW(gmx::NotImplementedError(errorString));
+ }
+ }
+
+ pme_gpu_reinit(pme.get(), gpuInfo, pmeGpuProgram);
+ }
pme_init_all_work(&pme->solve_work, pme->nthread, pme->nkx);
}
void gmx_pme_reinit(struct gmx_pme_t **pmedata,
- t_commrec * cr,
+ const t_commrec *cr,
struct gmx_pme_t * pme_src,
const t_inputrec * ir,
const ivec grid_size,
// 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");
- *pmedata = gmx_pme_init(cr, pme_src->nnodes_major, pme_src->nnodes_minor,
+ NumPmeDomains numPmeDomains = { pme_src->nnodes_major, pme_src->nnodes_minor };
+ *pmedata = gmx_pme_init(cr, numPmeDomains,
&irc, homenr, pme_src->bFEP_q, pme_src->bFEP_lj, FALSE, ewaldcoeff_q, ewaldcoeff_lj,
- pme_src->nthread, pme_src->runMode, pme_src->gpu, nullptr, dummyLogger);
+ pme_src->nthread, pme_src->runMode, pme_src->gpu, nullptr, nullptr, dummyLogger);
//TODO this is mostly passing around current values
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
{
gmx_incons("gmx_pme_calc_energy called in parallel");
}
- if (pme->bFEP_q > 1)
+ if (pme->bFEP_q)
{
gmx_incons("gmx_pme_calc_energy with free energy");
}
/*! \brief Calculate initial Lorentz-Berthelot coefficients for LJ-PME */
static void
-calc_initial_lb_coeffs(struct gmx_pme_t *pme, real *local_c6, real *local_sigma)
+calc_initial_lb_coeffs(struct gmx_pme_t *pme, const real *local_c6, const real *local_sigma)
{
int i;
for (i = 0; i < pme->atc[0].n; ++i)
/*! \brief Calculate next Lorentz-Berthelot coefficients for LJ-PME */
static void
-calc_next_lb_coeffs(struct gmx_pme_t *pme, real *local_sigma)
+calc_next_lb_coeffs(struct gmx_pme_t *pme, const real *local_sigma)
{
int i;
real chargeA[], real chargeB[],
real c6A[], real c6B[],
real sigmaA[], real sigmaB[],
- matrix box, t_commrec *cr,
+ matrix box, const t_commrec *cr,
int maxshift_x, int maxshift_y,
- t_nrnb *nrnb, gmx_wallcycle_t wcycle,
+ t_nrnb *nrnb, gmx_wallcycle *wcycle,
matrix vir_q, matrix vir_lj,
real *energy_q, real *energy_lj,
real lambda_q, real lambda_lj,
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;
- const gmx_bool bBackFFT = flags & (GMX_PME_CALC_F | GMX_PME_CALC_POT);
- const gmx_bool bCalcF = flags & GMX_PME_CALC_F;
+ 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;
/* We could be passing lambda!=1 while no q or LJ is actually perturbed */
if (!pme->bFEP_q)
{
fprintf(debug, "PME: number of ranks = %d, rank = %d\n",
cr->nnodes, cr->nodeid);
- fprintf(debug, "Grid = %p\n", (void*)grid);
+ fprintf(debug, "Grid = %p\n", static_cast<void*>(grid));
if (grid == nullptr)
{
gmx_fatal(FARGS, "No grid!");
}
}
- where();
if (pme->nnodes == 1)
{
{
wallcycle_start(wcycle, ewcPME_REDISTXF);
do_redist_pos_coeffs(pme, cr, start, homenr, bFirst, x, coefficient);
- where();
wallcycle_stop(wcycle, ewcPME_REDISTXF);
}
if (pme->nnodes > 1)
{
gmx_sum_qgrid_dd(pme, grid, GMX_SUM_GRID_FORWARD);
- where();
}
#endif
{
wallcycle_stop(wcycle, ewcPME_FFT);
}
- where();
/* solve in k-space for our local cells */
if (thread == 0)
if (thread == 0)
{
wallcycle_stop(wcycle, (grid_index < DO_Q ? ewcPME_SOLVE : ewcLJPME));
- where();
inc_nrnb(nrnb, eNR_SOLVEPME, loop_count);
}
}
/* do 3d-invfft */
if (thread == 0)
{
- where();
wallcycle_start(wcycle, ewcPME_FFT);
}
gmx_parallel_3dfft_execute(pfft_setup, GMX_FFT_COMPLEX_TO_REAL,
{
wallcycle_stop(wcycle, ewcPME_FFT);
- where();
if (pme->nodeid == 0)
{
gmx_sum_qgrid_dd(pme, grid, GMX_SUM_GRID_BACKWARD);
}
#endif
- where();
unwrap_periodic_pmegrid(pme, grid);
}
{
/* interpolate forces for our local atoms */
- where();
/* If we are running without parallelization,
* atc->f is the actual force array, not a buffer,
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
}
- where();
inc_nrnb(nrnb, eNR_GATHERFBSP,
pme->pme_order*pme->pme_order*pme->pme_order*pme->atc[0].n);
{
local_c6[i] = atc->coefficient[i];
}
- where();
do_redist_pos_coeffs(pme, cr, start, homenr, FALSE, x, RedistSigma);
local_sigma = pme->lb_buf2;
{
local_sigma[i] = atc->coefficient[i];
}
- where();
wallcycle_stop(wcycle, ewcPME_REDISTXF);
}
pfft_setup = pme->pfft_setup[grid_index];
calc_next_lb_coeffs(pme, local_sigma);
grid = pmegrid->grid.grid;
- where();
if (flags & GMX_PME_SPREAD)
{
if (pme->nnodes > 1)
{
gmx_sum_qgrid_dd(pme, grid, GMX_SUM_GRID_FORWARD);
- where();
}
#endif
copy_pmegrid_to_fftgrid(pme, grid, fftgrid, grid_index);
{
wallcycle_stop(wcycle, ewcPME_FFT);
}
- where();
}
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
if (thread == 0)
{
wallcycle_stop(wcycle, ewcLJPME);
- where();
inc_nrnb(nrnb, eNR_SOLVEPME, loop_count);
}
}
pfft_setup = pme->pfft_setup[grid_index];
grid = pmegrid->grid.grid;
calc_next_lb_coeffs(pme, local_sigma);
- where();
#pragma omp parallel num_threads(pme->nthread) private(thread)
{
try
/* do 3d-invfft */
if (thread == 0)
{
- where();
wallcycle_start(wcycle, ewcPME_FFT);
}
{
wallcycle_stop(wcycle, ewcPME_FFT);
- where();
if (pme->nodeid == 0)
{
gmx_sum_qgrid_dd(pme, grid, GMX_SUM_GRID_BACKWARD);
}
#endif
- where();
unwrap_periodic_pmegrid(pme, grid);
if (bCalcF)
{
/* interpolate forces for our local atoms */
- where();
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];
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
}
- where();
inc_nrnb(nrnb, eNR_GATHERFBSP,
pme->pme_order*pme->pme_order*pme->pme_order*pme->atc[0].n);
wallcycle_stop(wcycle, ewcPME_REDISTXF);
}
- where();
if (bCalcEnerVir)
{
sfree(pme->bsp_mod[i]);
}
- destroy_overlap_comm(&pme->overlap[0]);
- destroy_overlap_comm(&pme->overlap[1]);
-
sfree(pme->lb_buf1);
sfree(pme->lb_buf2);
sfree(pme->sum_qgrid_tmp);
sfree(pme->sum_qgrid_dd_tmp);
+ destroy_pme_spline_work(pme->spline_work);
+
if (pme_gpu_active(pme) && pme->gpu)
{
pme_gpu_destroy(pme->gpu);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff