src/gromacs/ewald/pme_spline_work.cpp: warning: includes "simd.h" unnecessarily
src/gromacs/ewald/pme_spline_work.h: warning: includes "simd.h" unnecessarily
src/gromacs/ewald/pme_spread.cpp: warning: includes "simd.h" unnecessarily
+src/gromacs/nbnxm/grid.h: warning: includes "simd.h" unnecessarily
src/gromacs/nbnxm/kernels_simd_2xmm/kernel_inner.h: warning: should include "simd.h"
src/gromacs/nbnxm/kernels_simd_2xmm/kernel_outer.h: warning: should include "simd.h"
src/gromacs/nbnxm/kernels_simd_4xm/kernel_inner.h: warning: should include "simd.h"
#include "gromacs/utility/strconvert.h"
#include "gromacs/utility/stringutil.h"
+#include "grid.h"
#include "internal.h"
using namespace gmx; // TODO: Remove when this file is moved into gmx namespace
#include "gmxpre.h"
+#include "grid.h"
+
#include <cmath>
#include <cstring>
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2019, 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version 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.
+ */
+
+/*! \internal \file
+ *
+ * \brief Declares the grid and bounding box objects
+ *
+ * \author Berk Hess <hess@kth.se>
+ *
+ * \ingroup module_nbnxm
+ */
+
+#ifndef GMX_NBNXM_GRID_H
+#define GMX_NBNXM_GRID_H
+
+#include <memory>
+#include <vector>
+
+#include "gromacs/math/vectypes.h"
+#include "gromacs/simd/simd.h"
+#include "gromacs/utility/alignedallocator.h"
+
+
+struct gmx_domdec_zones_t;
+
+
+#ifndef DOXYGEN
+
+/* Pair search box lower and upper corner in x,y,z.
+ * Store this in 4 iso 3 reals, which is useful with 4-wide SIMD.
+ * To avoid complicating the code we also use 4 without 4-wide SIMD.
+ */
+#define NNBSBB_C 4
+/* Pair search box lower and upper bound in z only. */
+#define NNBSBB_D 2
+/* Pair search box lower and upper corner x,y,z indices, entry 3 is unused */
+#define BB_X 0
+#define BB_Y 1
+#define BB_Z 2
+
+#endif // !DOXYGEN
+
+
+/* Bounding box for a nbnxn atom cluster */
+typedef struct {
+ float lower[NNBSBB_C];
+ float upper[NNBSBB_C];
+} nbnxn_bb_t;
+
+
+#ifndef DOXYGEN
+
+/* Bounding box calculations are (currently) always in single precision, so
+ * we only need to check for single precision support here.
+ * This uses less (cache-)memory and SIMD is faster, at least on x86.
+ */
+#if GMX_SIMD4_HAVE_FLOAT
+# define NBNXN_SEARCH_BB_SIMD4 1
+/* Memory alignment in bytes as required by SIMD aligned loads/stores */
+# define NBNXN_SEARCH_BB_MEM_ALIGN (GMX_SIMD4_WIDTH*sizeof(float))
+#else
+# define NBNXN_SEARCH_BB_SIMD4 0
+/* No alignment required, but set it so we can call the same routines */
+# define NBNXN_SEARCH_BB_MEM_ALIGN 32
+#endif
+
+
+#if NBNXN_SEARCH_BB_SIMD4
+/* Always use 4-wide SIMD for bounding box calculations */
+
+# if !GMX_DOUBLE
+/* Single precision BBs + coordinates, we can also load coordinates with SIMD */
+# define NBNXN_SEARCH_SIMD4_FLOAT_X_BB 1
+# else
+# define NBNXN_SEARCH_SIMD4_FLOAT_X_BB 0
+# endif
+
+/* The packed bounding box coordinate stride is always set to 4.
+ * With AVX we could use 8, but that turns out not to be faster.
+ */
+# define STRIDE_PBB GMX_SIMD4_WIDTH
+# define STRIDE_PBB_2LOG 2
+
+/* Store bounding boxes corners as quadruplets: xxxxyyyyzzzz */
+# define NBNXN_BBXXXX 1
+/* Size of bounding box corners quadruplet */
+# define NNBSBB_XXXX (NNBSBB_D*DIM*STRIDE_PBB)
+
+#else /* NBNXN_SEARCH_BB_SIMD4 */
+
+# define NBNXN_SEARCH_SIMD4_FLOAT_X_BB 0
+# define NBNXN_BBXXXX 0
+
+#endif /* NBNXN_SEARCH_BB_SIMD4 */
+
+#endif // !DOXYGEN
+
+
+/* A pair-search grid struct for one domain decomposition zone
+ *
+ * Note that when atom groups, instead of individual atoms, are assigned
+ * to grid cells, individual atoms can be geometrically outside the cell
+ * and grid that they have been assigned to (as determined by the center
+ * or geometry of the atom group they belong to).
+ */
+struct nbnxn_grid_t
+{
+ rvec c0; /* The lower corner of the (local) grid */
+ rvec c1; /* The upper corner of the (local) grid */
+ rvec size; /* c1 - c0 */
+ real atom_density; /* The atom number density for the local grid */
+ real maxAtomGroupRadius; /* The maximum distance an atom can be outside
+ * of a cell and outside of the grid
+ */
+
+ gmx_bool bSimple; /* Is this grid simple or super/sub */
+ int na_c; /* Number of atoms per cluster */
+ int na_cj; /* Number of atoms for list j-clusters */
+ int na_sc; /* Number of atoms per super-cluster */
+ int na_c_2log; /* 2log of na_c */
+
+ int numCells[DIM - 1]; /* Number of cells along x/y */
+ int nc; /* Total number of cells */
+
+ real cellSize[DIM - 1]; /* size of a cell */
+ real invCellSize[DIM - 1]; /* 1/cellSize */
+
+ int cell0; /* Index in nbs->cell corresponding to cell 0 */
+
+ /* Grid data */
+ std::vector<int> cxy_na; /* The number of atoms for each column in x,y */
+ std::vector<int> cxy_ind; /* Grid (super)cell index, offset from cell0 */
+
+ std::vector<int> nsubc; /* The number of sub cells for each super cell */
+
+ /* Bounding boxes */
+ std::vector<float> bbcz; /* Bounding boxes in z for the cells */
+ std::vector < nbnxn_bb_t, gmx::AlignedAllocator < nbnxn_bb_t>> bb; /* 3D bounding boxes for the sub cells */
+ std::vector < nbnxn_bb_t, gmx::AlignedAllocator < nbnxn_bb_t>> bbjStorage; /* 3D j-bounding boxes for the case where
+ * the i- and j-cluster sizes are different */
+ gmx::ArrayRef<nbnxn_bb_t> bbj; /* 3D j-bounding boxes */
+ std::vector < float, gmx::AlignedAllocator < float>> pbb; /* 3D b. boxes in xxxx format per super cell */
+
+ /* Bit-flag information */
+ std::vector<int> flags; /* Flags for properties of clusters in each cell */
+ std::vector<unsigned int> fep; /* FEP signal bits for atoms in each cluster */
+
+ /* Statistics */
+ int nsubc_tot; /* Total number of subcell, used for printing */
+};
+
+#endif
#include "gromacs/utility/real.h"
struct gmx_domdec_zones_t;
+struct nbnxn_grid_t;
// TODO Document after refactoring
#define NBNXN_MEM_ALIGN 32
#endif
-
-/* Bounding box calculations are (currently) always in single precision, so
- * we only need to check for single precision support here.
- * This uses less (cache-)memory and SIMD is faster, at least on x86.
- */
-#if GMX_SIMD4_HAVE_FLOAT
-# define NBNXN_SEARCH_BB_SIMD4 1
-/* Memory alignment in bytes as required by SIMD aligned loads/stores */
-# define NBNXN_SEARCH_BB_MEM_ALIGN (GMX_SIMD4_WIDTH*sizeof(float))
-#else
-# define NBNXN_SEARCH_BB_SIMD4 0
-/* No alignment required, but set it so we can call the same routines */
-# define NBNXN_SEARCH_BB_MEM_ALIGN 32
-#endif
-
-
-/* Pair search box lower and upper corner in x,y,z.
- * Store this in 4 iso 3 reals, which is useful with 4-wide SIMD.
- * To avoid complicating the code we also use 4 without 4-wide SIMD.
- */
-#define NNBSBB_C 4
-/* Pair search box lower and upper bound in z only. */
-#define NNBSBB_D 2
-/* Pair search box lower and upper corner x,y,z indices, entry 3 is unused */
-#define BB_X 0
-#define BB_Y 1
-#define BB_Z 2
-
-
-#if NBNXN_SEARCH_BB_SIMD4
-/* Always use 4-wide SIMD for bounding box calculations */
-
-# if !GMX_DOUBLE
-/* Single precision BBs + coordinates, we can also load coordinates with SIMD */
-# define NBNXN_SEARCH_SIMD4_FLOAT_X_BB 1
-# else
-# define NBNXN_SEARCH_SIMD4_FLOAT_X_BB 0
-# endif
-
-/* The packed bounding box coordinate stride is always set to 4.
- * With AVX we could use 8, but that turns out not to be faster.
- */
-# define STRIDE_PBB GMX_SIMD4_WIDTH
-# define STRIDE_PBB_2LOG 2
-
-/* Store bounding boxes corners as quadruplets: xxxxyyyyzzzz */
-# define NBNXN_BBXXXX 1
-/* Size of bounding box corners quadruplet */
-# define NNBSBB_XXXX (NNBSBB_D*DIM*STRIDE_PBB)
-
-#else /* NBNXN_SEARCH_BB_SIMD4 */
-
-# define NBNXN_SEARCH_SIMD4_FLOAT_X_BB 0
-# define NBNXN_BBXXXX 0
-
-#endif /* NBNXN_SEARCH_BB_SIMD4 */
-
#endif // !DOXYGEN
using AlignedVector = std::vector < T, gmx::AlignedAllocator < T>>;
-/* Bounding box for a nbnxn atom cluster */
-typedef struct {
- float lower[NNBSBB_C];
- float upper[NNBSBB_C];
-} nbnxn_bb_t;
-
-
-/* A pair-search grid struct for one domain decomposition zone
- *
- * Note that when atom groups, instead of individual atoms, are assigned
- * to grid cells, individual atoms can be geometrically outside the cell
- * and grid that they have been assigned to (as determined by the center
- * or geometry of the atom group they belong to).
- */
-struct nbnxn_grid_t
-{
- rvec c0; /* The lower corner of the (local) grid */
- rvec c1; /* The upper corner of the (local) grid */
- rvec size; /* c1 - c0 */
- real atom_density; /* The atom number density for the local grid */
- real maxAtomGroupRadius; /* The maximum distance an atom can be outside
- * of a cell and outside of the grid
- */
-
- gmx_bool bSimple; /* Is this grid simple or super/sub */
- int na_c; /* Number of atoms per cluster */
- int na_cj; /* Number of atoms for list j-clusters */
- int na_sc; /* Number of atoms per super-cluster */
- int na_c_2log; /* 2log of na_c */
-
- int numCells[DIM - 1]; /* Number of cells along x/y */
- int nc; /* Total number of cells */
-
- real cellSize[DIM - 1]; /* size of a cell */
- real invCellSize[DIM - 1]; /* 1/cellSize */
-
- int cell0; /* Index in nbs->cell corresponding to cell 0 */
-
- /* Grid data */
- std::vector<int> cxy_na; /* The number of atoms for each column in x,y */
- std::vector<int> cxy_ind; /* Grid (super)cell index, offset from cell0 */
-
- std::vector<int> nsubc; /* The number of sub cells for each super cell */
-
- /* Bounding boxes */
- std::vector<float> bbcz; /* Bounding boxes in z for the cells */
- std::vector < nbnxn_bb_t, gmx::AlignedAllocator < nbnxn_bb_t>> bb; /* 3D bounding boxes for the sub cells */
- std::vector < nbnxn_bb_t, gmx::AlignedAllocator < nbnxn_bb_t>> bbjStorage; /* 3D j-bounding boxes for the case where
- * the i- and j-cluster sizes are different */
- gmx::ArrayRef<nbnxn_bb_t> bbj; /* 3D j-bounding boxes */
- std::vector < float, gmx::AlignedAllocator < float>> pbb; /* 3D b. boxes in xxxx format per super cell */
-
- /* Bit-flag information */
- std::vector<int> flags; /* Flags for properties of clusters in each cell */
- std::vector<unsigned int> fep; /* FEP signal bits for atoms in each cluster */
-
- /* Statistics */
- int nsubc_tot; /* Total number of subcell, used for printing */
-};
-
-/* Working data for the actual i-supercell during pair search */
-struct NbnxnPairlistCpuWork
-{
- // Struct for storing coordinats and bounding box for an i-entry during search
- struct IClusterData
- {
- IClusterData() :
- bb(1),
- x(c_nbnxnCpuIClusterSize*DIM),
- xSimd(c_nbnxnCpuIClusterSize*DIM*GMX_REAL_MAX_SIMD_WIDTH)
- {
- }
-
- // The bounding boxes, pbc shifted, for each cluster
- AlignedVector<nbnxn_bb_t> bb;
- // The coordinates, pbc shifted, for each atom
- std::vector<real> x;
- // Aligned list for storing 4*DIM*GMX_SIMD_REAL_WIDTH reals
- AlignedVector<real> xSimd;
- };
-
- // Protect data from cache pollution between threads
- gmx_cache_protect_t cp0;
-
- // Work data for generating an IEntry in the pairlist
- IClusterData iClusterData;
- // The current cj_ind index for the current list
- int cj_ind;
- // Temporary j-cluster list, used for sorting on exclusions
- std::vector<nbnxn_cj_t> cj;
-
- // Nr. of cluster pairs without Coulomb for flop counting
- int ncj_noq;
- // Nr. of cluster pairs with 1/2 LJ for flop count
- int ncj_hlj;
-
- // Protect data from cache pollution between threads
- gmx_cache_protect_t cp1;
-};
-
-/* Working data for the actual i-supercell during pair search */
-struct NbnxnPairlistGpuWork
-{
- struct ISuperClusterData
- {
- ISuperClusterData() :
- bb(c_gpuNumClusterPerCell),
-#if NBNXN_SEARCH_BB_SIMD4
- bbPacked(c_gpuNumClusterPerCell/STRIDE_PBB*NNBSBB_XXXX),
-#endif
- x(c_gpuNumClusterPerCell*c_nbnxnGpuClusterSize*DIM),
- xSimd(c_gpuNumClusterPerCell*c_nbnxnGpuClusterSize*DIM)
- {
- }
-
- // The bounding boxes, pbc shifted, for each cluster
- AlignedVector<nbnxn_bb_t> bb;
- // As bb, but in packed xxxx format
- AlignedVector<float> bbPacked;
- // The coordinates, pbc shifted, for each atom
- AlignedVector<real> x;
- // Aligned coordinate list used for 4*DIM*GMX_SIMD_REAL_WIDTH floats
- AlignedVector<real> xSimd;
- };
-
- NbnxnPairlistGpuWork() :
- distanceBuffer(c_gpuNumClusterPerCell),
- sci_sort({}, {gmx::PinningPolicy::PinnedIfSupported})
- {
- }
-
- // Protect data from cache pollution between threads
- gmx_cache_protect_t cp0;
-
- // Work data for generating an i-entry in the pairlist
- ISuperClusterData iSuperClusterData;
- // The current j-cluster index for the current list
- int cj_ind;
- // Bounding box distance work array
- AlignedVector<float> distanceBuffer;
-
- // Buffer for sorting list entries
- std::vector<int> sortBuffer;
-
- // Second sci array, for sorting
- gmx::HostVector<nbnxn_sci_t> sci_sort;
-
- // Protect data from cache pollution between threads
- gmx_cache_protect_t cp1;
-};
-
/* Local cycle count struct for profiling */
typedef struct {
int count;
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/logger.h"
+#include "grid.h"
#include "internal.h"
/*! \brief Returns whether CPU SIMD support exists for the given inputrec
#include "gromacs/utility/gmxomp.h"
#include "gromacs/utility/smalloc.h"
+#include "grid.h"
#include "internal.h"
+#include "pairlistwork.h"
using namespace gmx; // TODO: Remove when this file is moved into gmx namespace
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2019, 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version 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.
+ */
+
+/*! \internal \file
+ *
+ * \brief Declares working data structures for the CPU and GPU pairlists
+ *
+ * \author Berk Hess <hess@kth.se>
+ *
+ * \ingroup module_nbnxn
+ */
+
+#ifndef GMX_NBNXM_PAIRLISTWORK_H
+#define GMX_NBNXM_PAIRLISTWORK_H
+
+#include <memory>
+#include <vector>
+
+#include "gromacs/nbnxm/pairlist.h"
+#include "gromacs/simd/simd.h"
+
+#include "grid.h"
+
+/* Working data for the actual i-supercell during pair search */
+struct NbnxnPairlistCpuWork
+{
+ // Struct for storing coordinats and bounding box for an i-entry during search
+ struct IClusterData
+ {
+ IClusterData() :
+ bb(1),
+ x(c_nbnxnCpuIClusterSize*DIM),
+ xSimd(c_nbnxnCpuIClusterSize*DIM*GMX_REAL_MAX_SIMD_WIDTH)
+ {
+ }
+
+ // The bounding boxes, pbc shifted, for each cluster
+ AlignedVector<nbnxn_bb_t> bb;
+ // The coordinates, pbc shifted, for each atom
+ std::vector<real> x;
+ // Aligned list for storing 4*DIM*GMX_SIMD_REAL_WIDTH reals
+ AlignedVector<real> xSimd;
+ };
+
+ // Protect data from cache pollution between threads
+ gmx_cache_protect_t cp0;
+
+ // Work data for generating an IEntry in the pairlist
+ IClusterData iClusterData;
+ // The current cj_ind index for the current list
+ int cj_ind;
+ // Temporary j-cluster list, used for sorting on exclusions
+ std::vector<nbnxn_cj_t> cj;
+
+ // Nr. of cluster pairs without Coulomb for flop counting
+ int ncj_noq;
+ // Nr. of cluster pairs with 1/2 LJ for flop count
+ int ncj_hlj;
+
+ // Protect data from cache pollution between threads
+ gmx_cache_protect_t cp1;
+};
+
+/* Working data for the actual i-supercell during pair search */
+struct NbnxnPairlistGpuWork
+{
+ struct ISuperClusterData
+ {
+ ISuperClusterData() :
+ bb(c_gpuNumClusterPerCell),
+#if NBNXN_SEARCH_BB_SIMD4
+ bbPacked(c_gpuNumClusterPerCell/STRIDE_PBB*NNBSBB_XXXX),
+#endif
+ x(c_gpuNumClusterPerCell*c_nbnxnGpuClusterSize*DIM),
+ xSimd(c_gpuNumClusterPerCell*c_nbnxnGpuClusterSize*DIM)
+ {
+ }
+
+ // The bounding boxes, pbc shifted, for each cluster
+ AlignedVector<nbnxn_bb_t> bb;
+ // As bb, but in packed xxxx format
+ AlignedVector<float> bbPacked;
+ // The coordinates, pbc shifted, for each atom
+ AlignedVector<real> x;
+ // Aligned coordinate list used for 4*DIM*GMX_SIMD_REAL_WIDTH floats
+ AlignedVector<real> xSimd;
+ };
+
+ NbnxnPairlistGpuWork() :
+ distanceBuffer(c_gpuNumClusterPerCell),
+ sci_sort({}, {gmx::PinningPolicy::PinnedIfSupported})
+ {
+ }
+
+ // Protect data from cache pollution between threads
+ gmx_cache_protect_t cp0;
+
+ // Work data for generating an i-entry in the pairlist
+ ISuperClusterData iSuperClusterData;
+ // The current j-cluster index for the current list
+ int cj_ind;
+ // Bounding box distance work array
+ AlignedVector<float> distanceBuffer;
+
+ // Buffer for sorting list entries
+ std::vector<int> sortBuffer;
+
+ // Second sci array, for sorting
+ gmx::HostVector<nbnxn_sci_t> sci_sort;
+
+ // Protect data from cache pollution between threads
+ gmx_cache_protect_t cp1;
+};
+
+#endif
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff