"%d OpenMP threads were requested. Since the non-bonded force buffer reduction "
"is prohibitively slow with more than %d threads, we do not allow this. Use %d "
"or less OpenMP threads.",
- numLists, NBNXN_BUFFERFLAG_MAX_THREADS, NBNXN_BUFFERFLAG_MAX_THREADS);
+ numLists,
+ NBNXN_BUFFERFLAG_MAX_THREADS,
+ NBNXN_BUFFERFLAG_MAX_THREADS);
}
if (isCpuType_)
fprintf(fp, "nbl nci %zu ncj %d\n", nbl.ci.size(), nbl.ncjInUse);
const int numAtomsJCluster = grid.geometry().numAtomsJCluster;
const double numAtomsPerCell = nbl.ncjInUse / static_cast<double>(grid.numCells()) * numAtomsJCluster;
- fprintf(fp, "nbl na_cj %d rl %g ncp %d per cell %.1f atoms %.1f ratio %.2f\n", nbl.na_cj, rl,
- nbl.ncjInUse, nbl.ncjInUse / static_cast<double>(grid.numCells()), numAtomsPerCell,
+ fprintf(fp,
+ "nbl na_cj %d rl %g ncp %d per cell %.1f atoms %.1f ratio %.2f\n",
+ nbl.na_cj,
+ rl,
+ nbl.ncjInUse,
+ nbl.ncjInUse / static_cast<double>(grid.numCells()),
+ numAtomsPerCell,
numAtomsPerCell
/ (0.5 * 4.0 / 3.0 * M_PI * rl * rl * rl * grid.numCells() * numAtomsJCluster
/ (dims.gridSize[XX] * dims.gridSize[YY] * dims.gridSize[ZZ])));
- fprintf(fp, "nbl average j cell list length %.1f\n",
+ fprintf(fp,
+ "nbl average j cell list length %.1f\n",
0.25 * nbl.ncjInUse / std::max(static_cast<double>(nbl.ci.size()), 1.0));
int cs[SHIFTS] = { 0 };
j++;
}
}
- fprintf(fp, "nbl cell pairs, total: %zu excl: %d %.1f%%\n", nbl.cj.size(), npexcl,
+ fprintf(fp,
+ "nbl cell pairs, total: %zu excl: %d %.1f%%\n",
+ nbl.cj.size(),
+ npexcl,
100 * npexcl / std::max(static_cast<double>(nbl.cj.size()), 1.0));
for (int s = 0; s < SHIFTS; s++)
{
const Grid& grid = gridSet.grids()[0];
const Grid::Dimensions& dims = grid.dimensions();
- fprintf(fp, "nbl nsci %zu ncj4 %zu nsi %d excl4 %zu\n", nbl.sci.size(), nbl.cj4.size(),
- nbl.nci_tot, nbl.excl.size());
+ fprintf(fp,
+ "nbl nsci %zu ncj4 %zu nsi %d excl4 %zu\n",
+ nbl.sci.size(),
+ nbl.cj4.size(),
+ nbl.nci_tot,
+ nbl.excl.size());
const int numAtomsCluster = grid.geometry().numAtomsICluster;
const double numAtomsPerCell = nbl.nci_tot / static_cast<double>(grid.numClusters()) * numAtomsCluster;
- fprintf(fp, "nbl na_c %d rl %g ncp %d per cell %.1f atoms %.1f ratio %.2f\n", nbl.na_ci, rl,
- nbl.nci_tot, nbl.nci_tot / static_cast<double>(grid.numClusters()), numAtomsPerCell,
+ fprintf(fp,
+ "nbl na_c %d rl %g ncp %d per cell %.1f atoms %.1f ratio %.2f\n",
+ nbl.na_ci,
+ rl,
+ nbl.nci_tot,
+ nbl.nci_tot / static_cast<double>(grid.numClusters()),
+ numAtomsPerCell,
numAtomsPerCell
/ (0.5 * 4.0 / 3.0 * M_PI * rl * rl * rl * grid.numClusters() * numAtomsCluster
/ (dims.gridSize[XX] * dims.gridSize[YY] * dims.gridSize[ZZ])));
sum_nsp /= nbl.sci.size();
sum_nsp2 /= nbl.sci.size();
}
- fprintf(fp, "nbl #cluster-pairs: av %.1f stddev %.1f max %d\n", sum_nsp,
- std::sqrt(sum_nsp2 - sum_nsp * sum_nsp), nsp_max);
+ fprintf(fp,
+ "nbl #cluster-pairs: av %.1f stddev %.1f max %d\n",
+ sum_nsp,
+ std::sqrt(sum_nsp2 - sum_nsp * sum_nsp),
+ nsp_max);
if (!nbl.cj4.empty())
{
for (int b = 0; b <= c_gpuNumClusterPerCell; b++)
{
- fprintf(fp, "nbl j-list #i-subcell %d %7d %4.1f\n", b, c[b],
+ fprintf(fp,
+ "nbl j-list #i-subcell %d %7d %4.1f\n",
+ b,
+ c[b],
100.0 * c[b] / size_t{ nbl.cj4.size() * c_nbnxnGpuJgroupSize });
}
}
#if NBNXN_BBXXXX
/* Determine all ci1 bb distances in one call with SIMD4 */
const int offset = packedBoundingBoxesIndex(cj) + (cj & (c_packedBoundingBoxesDimSize - 1));
- clusterBoundingBoxDistance2_xxxx_simd4(jGrid.packedBoundingBoxes().data() + offset, ci1,
- pbb_ci, d2l);
+ clusterBoundingBoxDistance2_xxxx_simd4(
+ jGrid.packedBoundingBoxes().data() + offset, ci1, pbb_ci, d2l);
*numDistanceChecks += c_nbnxnGpuClusterSize * 2;
#endif
{
fprintf(debug,
"reallocating neigborlist (ielec=%d, ivdw=%d, igeometry=%d, type=%d), maxnri=%d\n",
- nl->ielec, nl->ivdw, nl->igeometry, nl->type, nl->maxnri);
+ nl->ielec,
+ nl->ivdw,
+ nl->igeometry,
+ nl->type,
+ nl->maxnri);
}
srenew(nl->iinr, nl->maxnri);
srenew(nl->gid, nl->maxnri);
gmx_fatal(FARGS,
"The Verlet scheme with %dx%d kernels and free-energy only supports up to %zu "
"energy groups",
- iGrid.geometry().numAtomsICluster, numAtomsJCluster,
+ iGrid.geometry().numAtomsICluster,
+ numAtomsJCluster,
(sizeof(gid_cj) * 8) / numAtomsJCluster);
}
* Note that here we can not use cj4_ind_end, since the last cj4
* can be only partially filled, so we use cj_ind.
*/
- const JListRanges ranges(iEntry.cj4_ind_start * c_nbnxnGpuJgroupSize, nbl->work->cj_ind,
+ const JListRanges ranges(iEntry.cj4_ind_start * c_nbnxnGpuJgroupSize,
+ nbl->work->cj_ind,
gmx::makeConstArrayRef(nbl->cj4));
GMX_ASSERT(nbl->na_ci == c_nbnxnGpuClusterSize, "na_ci should match the GPU cluster size");
gmx_unused static void set_icell_bb(const Grid& iGrid, int ci, real shx, real shy, real shz, NbnxnPairlistGpuWork* work)
{
#if NBNXN_BBXXXX
- set_icell_bbxxxx_supersub(iGrid.packedBoundingBoxes(), ci, shx, shy, shz,
- work->iSuperClusterData.bbPacked.data());
+ set_icell_bbxxxx_supersub(
+ iGrid.packedBoundingBoxes(), ci, shx, shy, shz, work->iSuperClusterData.bbPacked.data());
#else
set_icell_bb_supersub(iGrid.iBoundingBoxes(), ci, shx, shy, shz, work->iSuperClusterData.bb.data());
#endif
{
for (const nbnxn_ci_t& ciEntry : nbl.ci)
{
- fprintf(fp, "ci %4d shift %2d ncj %3d\n", ciEntry.ci, ciEntry.shift,
- ciEntry.cj_ind_end - ciEntry.cj_ind_start);
+ fprintf(fp, "ci %4d shift %2d ncj %3d\n", ciEntry.ci, ciEntry.shift, ciEntry.cj_ind_end - ciEntry.cj_ind_start);
for (int j = ciEntry.cj_ind_start; j < ciEntry.cj_ind_end; j++)
{
}
}
}
- fprintf(fp, "ci %4d shift %2d ncj4 %2d ncp %3d\n", sci.sci, sci.shift,
- sci.numJClusterGroups(), ncp);
+ fprintf(fp, "ci %4d shift %2d ncj4 %2d ncp %3d\n", sci.sci, sci.shift, sci.numJClusterGroups(), ncp);
}
}
switch (kernelType)
{
case ClusterDistanceKernelType::CpuPlainC:
- makeClusterListSimple(jGrid, nbl, ci, firstCell, lastCell, excludeSubDiagonal,
- nbat->x().data(), rlist2, rbb2, numDistanceChecks);
+ makeClusterListSimple(
+ jGrid, nbl, ci, firstCell, lastCell, excludeSubDiagonal, nbat->x().data(), rlist2, rbb2, numDistanceChecks);
break;
#ifdef GMX_NBNXN_SIMD_4XN
case ClusterDistanceKernelType::CpuSimd_4xM:
- makeClusterListSimd4xn(jGrid, nbl, ci, firstCell, lastCell, excludeSubDiagonal,
- nbat->x().data(), rlist2, rbb2, numDistanceChecks);
+ makeClusterListSimd4xn(
+ jGrid, nbl, ci, firstCell, lastCell, excludeSubDiagonal, nbat->x().data(), rlist2, rbb2, numDistanceChecks);
break;
#endif
#ifdef GMX_NBNXN_SIMD_2XNN
case ClusterDistanceKernelType::CpuSimd_2xMM:
- makeClusterListSimd2xnn(jGrid, nbl, ci, firstCell, lastCell, excludeSubDiagonal,
- nbat->x().data(), rlist2, rbb2, numDistanceChecks);
+ makeClusterListSimd2xnn(
+ jGrid, nbl, ci, firstCell, lastCell, excludeSubDiagonal, nbat->x().data(), rlist2, rbb2, numDistanceChecks);
break;
#endif
default: GMX_ASSERT(false, "Unhandled kernel type");
{
for (int cj = firstCell; cj <= lastCell; cj++)
{
- make_cluster_list_supersub(iGrid, jGrid, nbl, ci, cj, excludeSubDiagonal, nbat->xstride,
- nbat->x().data(), rlist2, rbb2, numDistanceChecks);
+ make_cluster_list_supersub(
+ iGrid, jGrid, nbl, ci, cj, excludeSubDiagonal, nbat->xstride, nbat->x().data(), rlist2, rbb2, numDistanceChecks);
}
}
if (debug)
{
- fprintf(debug, "nbl nc_i %d col.av. %.1f ci_block %d\n", iGrid.numCells(),
- iGrid.numCells() / static_cast<double>(iGrid.numColumns()), ci_block);
+ fprintf(debug,
+ "nbl nc_i %d col.av. %.1f ci_block %d\n",
+ iGrid.numCells(),
+ iGrid.numCells() / static_cast<double>(iGrid.numColumns()),
+ ci_block);
}
numDistanceChecks = 0;
set_icell_bb(iGrid, ci, shx, shy, shz, nbl->work.get());
- icell_set_x(cell0_i + ci, shx, shy, shz, nbat->xstride, nbat->x().data(),
- kernelType, nbl->work.get());
+ icell_set_x(cell0_i + ci,
+ shx,
+ shy,
+ shz,
+ nbat->xstride,
+ nbat->x().data(),
+ kernelType,
+ nbl->work.get());
for (int cx = cxf; cx <= cxl; cx++)
{
/* For f buffer flags with simple lists */
ncj_old_j = getNumSimpleJClustersInList(*nbl);
- makeClusterListWrapper(nbl, iGrid, ci, jGrid, firstCell, lastCell,
- excludeSubDiagonal, nbat, rlist2, rbb2,
- kernelType, &numDistanceChecks);
+ makeClusterListWrapper(nbl,
+ iGrid,
+ ci,
+ jGrid,
+ firstCell,
+ lastCell,
+ excludeSubDiagonal,
+ nbat,
+ rlist2,
+ rbb2,
+ kernelType,
+ &numDistanceChecks);
if (bFBufferFlag)
{
if (!exclusions.empty())
{
/* Set the exclusions for this ci list */
- setExclusionsForIEntry(gridSet, nbl, excludeSubDiagonal, na_cj_2log,
- *getOpenIEntry(nbl), exclusions);
+ setExclusionsForIEntry(
+ gridSet, nbl, excludeSubDiagonal, na_cj_2log, *getOpenIEntry(nbl), exclusions);
}
if (haveFep)
{
- make_fep_list(gridSet.atomIndices(), nbat, nbl, excludeSubDiagonal,
- getOpenIEntry(nbl), shx, shy, shz, rl_fep2, iGrid, jGrid, nbl_fep);
+ make_fep_list(gridSet.atomIndices(),
+ nbat,
+ nbl,
+ excludeSubDiagonal,
+ getOpenIEntry(nbl),
+ shx,
+ shy,
+ shz,
+ rl_fep2,
+ iGrid,
+ jGrid,
+ nbl_fep);
}
/* Close this ci list */
const auto numFlags = static_cast<double>(flags.size());
fprintf(debug,
"nbnxn reduction: #flag %zu #list %d elem %4.2f, keep %4.2f copy %4.2f red %4.2f\n",
- flags.size(), nout, nelem / numFlags, nkeep / numFlags, ncopy / numFlags, nred / numFlags);
+ flags.size(),
+ nout,
+ nelem / numFlags,
+ nkeep / numFlags,
+ ncopy / numFlags,
+ nred / numFlags);
}
/* Copies the list entries from src to dest when cjStart <= *cjGlobal < cjEnd.
}
else
{
- copySelectedListRange<false>(srcCi, src, &dest, flag, iFlagShift,
- jFlagShift, t);
+ copySelectedListRange<false>(
+ srcCi, src, &dest, flag, iFlagShift, jFlagShift, t);
}
}
cjGlobal += ncj;
if (!isCpuType_ && minimumIlistCountForGpuBalancing > 0)
{
- get_nsubpair_target(gridSet, locality_, rlist, minimumIlistCountForGpuBalancing,
- &nsubpair_target, &nsubpair_tot_est);
+ get_nsubpair_target(
+ gridSet, locality_, rlist, minimumIlistCountForGpuBalancing, &nsubpair_target, &nsubpair_tot_est);
}
else
{
/* Divide the i cells equally over the pairlists */
if (isCpuType_)
{
- nbnxn_make_pairlist_part(gridSet, iGrid, jGrid, &work, nbat, exclusions, rlist,
- params_.pairlistType, ci_block, nbat->bUseBufferFlags,
- nsubpair_target, progBal, nsubpair_tot_est, th,
- numLists, &cpuLists_[th], fepListPtr);
+ nbnxn_make_pairlist_part(gridSet,
+ iGrid,
+ jGrid,
+ &work,
+ nbat,
+ exclusions,
+ rlist,
+ params_.pairlistType,
+ ci_block,
+ nbat->bUseBufferFlags,
+ nsubpair_target,
+ progBal,
+ nsubpair_tot_est,
+ th,
+ numLists,
+ &cpuLists_[th],
+ fepListPtr);
}
else
{
- nbnxn_make_pairlist_part(gridSet, iGrid, jGrid, &work, nbat, exclusions, rlist,
- params_.pairlistType, ci_block, nbat->bUseBufferFlags,
- nsubpair_target, progBal, nsubpair_tot_est, th,
- numLists, &gpuLists_[th], fepListPtr);
+ nbnxn_make_pairlist_part(gridSet,
+ iGrid,
+ jGrid,
+ &work,
+ nbat,
+ exclusions,
+ rlist,
+ params_.pairlistType,
+ ci_block,
+ nbat->bUseBufferFlags,
+ nsubpair_target,
+ progBal,
+ nsubpair_tot_est,
+ th,
+ numLists,
+ &gpuLists_[th],
+ fepListPtr);
}
work.cycleCounter.stop();
"exclusions should either be empty or the number of lists should match the number of "
"local i-atoms");
- pairlistSet(iLocality).constructPairlists(gridSet, pairSearch->work(), nbat, exclusions,
- minimumIlistCountForGpuBalancing_, nrnb,
+ pairlistSet(iLocality).constructPairlists(gridSet,
+ pairSearch->work(),
+ nbat,
+ exclusions,
+ minimumIlistCountForGpuBalancing_,
+ nrnb,
&pairSearch->cycleCounting_);
if (iLocality == InteractionLocality::Local)
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff