using namespace gmx; // TODO: Remove when this file is moved into gmx namespace
-using nbnxn_bb_t = Nbnxm::BoundingBox; // TODO: Remove when refactoring this file
+using BoundingBox = Nbnxm::BoundingBox; // TODO: Remove when refactoring this file
using BoundingBox1D = Nbnxm::BoundingBox1D; // TODO: Remove when refactoring this file
using Grid = Nbnxm::Grid; // TODO: Remove when refactoring this file
/*
static float box_dist2(float bx0, float bx1, float by0,
float by1, float bz0, float bz1,
- const nbnxn_bb_t *bb)
+ const BoundingBox *bb)
{
float d2;
float dl, dh, dm, dm0;
}
*/
-/* Plain C code calculating the distance^2 between two bounding boxes */
-static float subc_bb_dist2(int si,
- const nbnxn_bb_t *bb_i_ci,
- int csj,
- gmx::ArrayRef<const nbnxn_bb_t> bb_j_all)
-{
- const nbnxn_bb_t &bb_i = bb_i_ci[si];
- const nbnxn_bb_t &bb_j = bb_j_all[csj];
-
- float d2 = 0;
- float dl, dh, dm, dm0;
-
- dl = bb_i.lower.x - bb_j.upper.x;
- dh = bb_j.lower.x - bb_i.upper.x;
- dm = std::max(dl, dh);
- dm0 = std::max(dm, 0.0f);
- d2 += dm0*dm0;
-
- dl = bb_i.lower.y - bb_j.upper.y;
- dh = bb_j.lower.y - bb_i.upper.y;
- dm = std::max(dl, dh);
- dm0 = std::max(dm, 0.0f);
- d2 += dm0*dm0;
+#if !NBNXN_SEARCH_BB_SIMD4
- dl = bb_i.lower.z - bb_j.upper.z;
- dh = bb_j.lower.z - bb_i.upper.z;
- dm = std::max(dl, dh);
- dm0 = std::max(dm, 0.0f);
- d2 += dm0*dm0;
+/*! \brief Plain C code calculating the distance^2 between two bounding boxes in xyz0 format
+ *
+ * \param[in] bb_i First bounding box
+ * \param[in] bb_j Second bounding box
+ */
+static float clusterBoundingBoxDistance2(const BoundingBox &bb_i,
+ const BoundingBox &bb_j)
+{
+ float dl = bb_i.lower.x - bb_j.upper.x;
+ float dh = bb_j.lower.x - bb_i.upper.x;
+ float dm = std::max(dl, dh);
+ float dm0 = std::max(dm, 0.0f);
+ float d2 = dm0*dm0;
+
+ dl = bb_i.lower.y - bb_j.upper.y;
+ dh = bb_j.lower.y - bb_i.upper.y;
+ dm = std::max(dl, dh);
+ dm0 = std::max(dm, 0.0f);
+ d2 += dm0*dm0;
+
+ dl = bb_i.lower.z - bb_j.upper.z;
+ dh = bb_j.lower.z - bb_i.upper.z;
+ dm = std::max(dl, dh);
+ dm0 = std::max(dm, 0.0f);
+ d2 += dm0*dm0;
return d2;
}
-#if NBNXN_SEARCH_BB_SIMD4
+#else /* NBNXN_SEARCH_BB_SIMD4 */
-/* 4-wide SIMD code for bb distance for bb format xyz0 */
-static float subc_bb_dist2_simd4(int si,
- const nbnxn_bb_t *bb_i_ci,
- int csj,
- gmx::ArrayRef<const nbnxn_bb_t> bb_j_all)
+/*! \brief 4-wide SIMD code calculating the distance^2 between two bounding boxes in xyz0 format
+ *
+ * \param[in] bb_i First bounding box, should be aligned for 4-wide SIMD
+ * \param[in] bb_j Second bounding box, should be aligned for 4-wide SIMD
+ */
+static float clusterBoundingBoxDistance2(const BoundingBox &bb_i,
+ const BoundingBox &bb_j)
{
// TODO: During SIMDv2 transition only some archs use namespace (remove when done)
using namespace gmx;
- Simd4Float bb_i_S0, bb_i_S1;
- Simd4Float bb_j_S0, bb_j_S1;
- Simd4Float dl_S;
- Simd4Float dh_S;
- Simd4Float dm_S;
- Simd4Float dm0_S;
+ const Simd4Float bb_i_S0 = load4(bb_i.lower.ptr());
+ const Simd4Float bb_i_S1 = load4(bb_i.upper.ptr());
+ const Simd4Float bb_j_S0 = load4(bb_j.lower.ptr());
+ const Simd4Float bb_j_S1 = load4(bb_j.upper.ptr());
- bb_i_S0 = load4(bb_i_ci[si].lower.ptr());
- bb_i_S1 = load4(bb_i_ci[si].upper.ptr());
- bb_j_S0 = load4(bb_j_all[csj].lower.ptr());
- bb_j_S1 = load4(bb_j_all[csj].upper.ptr());
+ const Simd4Float dl_S = bb_i_S0 - bb_j_S1;
+ const Simd4Float dh_S = bb_j_S0 - bb_i_S1;
- dl_S = bb_i_S0 - bb_j_S1;
- dh_S = bb_j_S0 - bb_i_S1;
-
- dm_S = max(dl_S, dh_S);
- dm0_S = max(dm_S, simd4SetZeroF());
+ const Simd4Float dm_S = max(dl_S, dh_S);
+ const Simd4Float dm0_S = max(dm_S, simd4SetZeroF());
return dotProduct(dm0_S, dm0_S);
}
/* Calculate bb bounding distances of bb_i[si,...,si+3] and store them in d2 */
-#define SUBC_BB_DIST2_SIMD4_XXXX_INNER(si, bb_i, d2) \
- { \
- int shi; \
- \
- Simd4Float dx_0, dy_0, dz_0; \
- Simd4Float dx_1, dy_1, dz_1; \
- \
- Simd4Float mx, my, mz; \
- Simd4Float m0x, m0y, m0z; \
- \
- Simd4Float d2x, d2y, d2z; \
- Simd4Float d2s, d2t; \
- \
- shi = (si)*Nbnxm::c_numBoundingBoxBounds1D*DIM; \
- \
- xi_l = load4((bb_i)+shi+0*STRIDE_PBB); \
- yi_l = load4((bb_i)+shi+1*STRIDE_PBB); \
- zi_l = load4((bb_i)+shi+2*STRIDE_PBB); \
- xi_h = load4((bb_i)+shi+3*STRIDE_PBB); \
- yi_h = load4((bb_i)+shi+4*STRIDE_PBB); \
- zi_h = load4((bb_i)+shi+5*STRIDE_PBB); \
- \
- dx_0 = xi_l - xj_h; \
- dy_0 = yi_l - yj_h; \
- dz_0 = zi_l - zj_h; \
- \
- dx_1 = xj_l - xi_h; \
- dy_1 = yj_l - yi_h; \
- dz_1 = zj_l - zi_h; \
- \
- mx = max(dx_0, dx_1); \
- my = max(dy_0, dy_1); \
- mz = max(dz_0, dz_1); \
- \
- m0x = max(mx, zero); \
- m0y = max(my, zero); \
- m0z = max(mz, zero); \
- \
- d2x = m0x * m0x; \
- d2y = m0y * m0y; \
- d2z = m0z * m0z; \
- \
- d2s = d2x + d2y; \
- d2t = d2s + d2z; \
- \
- store4((d2)+(si), d2t); \
- }
+template <int boundingBoxStart>
+static inline void gmx_simdcall
+clusterBoundingBoxDistance2_xxxx_simd4_inner(const float *bb_i,
+ float *d2,
+ const Simd4Float xj_l,
+ const Simd4Float yj_l,
+ const Simd4Float zj_l,
+ const Simd4Float xj_h,
+ const Simd4Float yj_h,
+ const Simd4Float zj_h)
+{
+ const int shi = boundingBoxStart*Nbnxm::c_numBoundingBoxBounds1D*DIM;
+
+ const Simd4Float zero = setZero();
+
+ const Simd4Float xi_l = load4(bb_i + shi + 0*STRIDE_PBB);
+ const Simd4Float yi_l = load4(bb_i + shi + 1*STRIDE_PBB);
+ const Simd4Float zi_l = load4(bb_i + shi + 2*STRIDE_PBB);
+ const Simd4Float xi_h = load4(bb_i + shi + 3*STRIDE_PBB);
+ const Simd4Float yi_h = load4(bb_i + shi + 4*STRIDE_PBB);
+ const Simd4Float zi_h = load4(bb_i + shi + 5*STRIDE_PBB);
+
+ const Simd4Float dx_0 = xi_l - xj_h;
+ const Simd4Float dy_0 = yi_l - yj_h;
+ const Simd4Float dz_0 = zi_l - zj_h;
+
+ const Simd4Float dx_1 = xj_l - xi_h;
+ const Simd4Float dy_1 = yj_l - yi_h;
+ const Simd4Float dz_1 = zj_l - zi_h;
+
+ const Simd4Float mx = max(dx_0, dx_1);
+ const Simd4Float my = max(dy_0, dy_1);
+ const Simd4Float mz = max(dz_0, dz_1);
+
+ const Simd4Float m0x = max(mx, zero);
+ const Simd4Float m0y = max(my, zero);
+ const Simd4Float m0z = max(mz, zero);
+
+ const Simd4Float d2x = m0x * m0x;
+ const Simd4Float d2y = m0y * m0y;
+ const Simd4Float d2z = m0z * m0z;
+
+ const Simd4Float d2s = d2x + d2y;
+ const Simd4Float d2t = d2s + d2z;
+
+ store4(d2 + boundingBoxStart, d2t);
+}
/* 4-wide SIMD code for nsi bb distances for bb format xxxxyyyyzzzz */
-static void subc_bb_dist2_simd4_xxxx(const float *bb_j,
- int nsi, const float *bb_i,
- float *d2)
+static void
+clusterBoundingBoxDistance2_xxxx_simd4(const float *bb_j,
+ const int nsi,
+ const float *bb_i,
+ float *d2)
{
// TODO: During SIMDv2 transition only some archs use namespace (remove when done)
using namespace gmx;
- Simd4Float xj_l, yj_l, zj_l;
- Simd4Float xj_h, yj_h, zj_h;
- Simd4Float xi_l, yi_l, zi_l;
- Simd4Float xi_h, yi_h, zi_h;
-
- Simd4Float zero;
-
- zero = setZero();
-
- xj_l = Simd4Float(bb_j[0*STRIDE_PBB]);
- yj_l = Simd4Float(bb_j[1*STRIDE_PBB]);
- zj_l = Simd4Float(bb_j[2*STRIDE_PBB]);
- xj_h = Simd4Float(bb_j[3*STRIDE_PBB]);
- yj_h = Simd4Float(bb_j[4*STRIDE_PBB]);
- zj_h = Simd4Float(bb_j[5*STRIDE_PBB]);
+ const Simd4Float xj_l = Simd4Float(bb_j[0*STRIDE_PBB]);
+ const Simd4Float yj_l = Simd4Float(bb_j[1*STRIDE_PBB]);
+ const Simd4Float zj_l = Simd4Float(bb_j[2*STRIDE_PBB]);
+ const Simd4Float xj_h = Simd4Float(bb_j[3*STRIDE_PBB]);
+ const Simd4Float yj_h = Simd4Float(bb_j[4*STRIDE_PBB]);
+ const Simd4Float zj_h = Simd4Float(bb_j[5*STRIDE_PBB]);
/* Here we "loop" over si (0,STRIDE_PBB) from 0 to nsi with step STRIDE_PBB.
* But as we know the number of iterations is 1 or 2, we unroll manually.
*/
- SUBC_BB_DIST2_SIMD4_XXXX_INNER(0, bb_i, d2);
+ clusterBoundingBoxDistance2_xxxx_simd4_inner<0>(bb_i, d2,
+ xj_l, yj_l, zj_l,
+ xj_h, yj_h, zj_h);
if (STRIDE_PBB < nsi)
{
- SUBC_BB_DIST2_SIMD4_XXXX_INNER(STRIDE_PBB, bb_i, d2);
+ clusterBoundingBoxDistance2_xxxx_simd4_inner<STRIDE_PBB>(bb_i, d2,
+ xj_l, yj_l, zj_l,
+ xj_h, yj_h, zj_h);
}
}
float rbb2,
int * gmx_restrict numDistanceChecks)
{
- const nbnxn_bb_t * gmx_restrict bb_ci = nbl->work->iClusterData.bb.data();
- const real * gmx_restrict x_ci = nbl->work->iClusterData.x.data();
+ const BoundingBox * gmx_restrict bb_ci = nbl->work->iClusterData.bb.data();
+ const real * gmx_restrict x_ci = nbl->work->iClusterData.x.data();
- gmx_bool InRange;
+ gmx_bool InRange;
InRange = FALSE;
while (!InRange && jclusterFirst <= jclusterLast)
{
- real d2 = subc_bb_dist2(0, bb_ci, jclusterFirst, jGrid.jBoundingBoxes());
+ real d2 = clusterBoundingBoxDistance2(bb_ci[0], jGrid.jBoundingBoxes()[jclusterFirst]);
*numDistanceChecks += 2;
/* Check if the distance is within the distance where
InRange = FALSE;
while (!InRange && jclusterLast > jclusterFirst)
{
- real d2 = subc_bb_dist2(0, bb_ci, jclusterLast, jGrid.jBoundingBoxes());
+ real d2 = clusterBoundingBoxDistance2(bb_ci[0], jGrid.jBoundingBoxes()[jclusterLast]);
*numDistanceChecks += 2;
/* Check if the distance is within the distance where
#if NBNXN_BBXXXX
const float *pbb_ci = work.iSuperClusterData.bbPacked.data();
#else
- const nbnxn_bb_t *bb_ci = work.iSuperClusterData.bb.data();
+ const BoundingBox *bb_ci = work.iSuperClusterData.bb.data();
#endif
assert(c_nbnxnGpuClusterSize == iGrid.geometry().numAtomsICluster);
#if NBNXN_BBXXXX
/* Determine all ci1 bb distances in one call with SIMD4 */
- subc_bb_dist2_simd4_xxxx(jGrid.packedBoundingBoxes().data() + (cj >> STRIDE_PBB_2LOG)*NNBSBB_XXXX + (cj & (STRIDE_PBB-1)),
- ci1, pbb_ci, d2l);
+ clusterBoundingBoxDistance2_xxxx_simd4(jGrid.packedBoundingBoxes().data() + (cj >> STRIDE_PBB_2LOG)*NNBSBB_XXXX + (cj & (STRIDE_PBB-1)),
+ ci1, pbb_ci, d2l);
*numDistanceChecks += c_nbnxnGpuClusterSize*2;
#endif
#if !NBNXN_BBXXXX
/* Determine the bb distance between ci and cj */
- d2l[ci] = subc_bb_dist2(ci, bb_ci, cj, jGrid.jBoundingBoxes());
+ d2l[ci] = clusterBoundingBoxDistance2(bb_ci[ci], jGrid.jBoundingBoxes()[cj]);
*numDistanceChecks += 2;
#endif
float d2 = d2l[ci];
}
/* Sets a simple list i-cell bounding box, including PBC shift */
-static inline void set_icell_bb_simple(gmx::ArrayRef<const nbnxn_bb_t> bb,
+static inline void set_icell_bb_simple(gmx::ArrayRef<const BoundingBox> bb,
int ci,
real shx, real shy, real shz,
- nbnxn_bb_t *bb_ci)
+ BoundingBox *bb_ci)
{
bb_ci->lower.x = bb[ci].lower.x + shx;
bb_ci->lower.y = bb[ci].lower.y + shy;
#endif
/* Sets a super-cell and sub cell bounding boxes, including PBC shift */
-gmx_unused static void set_icell_bb_supersub(gmx::ArrayRef<const nbnxn_bb_t> bb,
+gmx_unused static void set_icell_bb_supersub(gmx::ArrayRef<const BoundingBox> bb,
int ci,
real shx, real shy, real shz,
- nbnxn_bb_t *bb_ci)
+ BoundingBox *bb_ci)
{
for (int i = 0; i < c_gpuNumClusterPerCell; i++)
{
}
}
const bool bSimple = pairlistIsSimple(*nbl);
- gmx::ArrayRef<const nbnxn_bb_t> bb_i;
+ gmx::ArrayRef<const BoundingBox> bb_i;
#if NBNXN_BBXXXX
- gmx::ArrayRef<const float> pbb_i;
+ gmx::ArrayRef<const float> pbb_i;
if (bSimple)
{
bb_i = iGrid.iBoundingBoxes();
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff