Intel Package: Bug fix when using LRT with minimize. Bug fix for virial... (2fe0eabc) · Commits · 郑智淋 / lammps

src/USER-INTEL/fix_intel.h

+2 −1

Original line number	Diff line number	Diff line
		@@ -82,7 +82,8 @@ class FixIntel : public Fix {
		}
		inline void set_reduce_flag() { if (_nthreads > 1) _need_reduce = 1; }
		inline int lrt() {
		if (force->kspace_match("pppm/intel", 0)) return _lrt;
		if (force->kspace_match("pppm/intel", 0) && update->whichflag == 1)
		return _lrt;
		else return 0;
		}
		inline int pppm_table() {

src/USER-INTEL/intel_preprocess.h

+50 −3

Original line number	Diff line number	Diff line
		@@ -134,6 +134,20 @@ enum {TIME_PACK, TIME_HOST_NEIGHBOR, TIME_HOST_PAIR, TIME_OFFLOAD_NEIGHBOR,
		#define INTEL_HTHREADS 2
		#endif

		#if INTEL_DATA_ALIGN > 1

		#define IP_PRE_edge_align(n, esize) \
		{ \
		const int pad_mask = ~static_cast<int>(INTEL_DATA_ALIGN/esize-1); \
		n = (n + INTEL_DATA_ALIGN / esize - 1) & pad_mask; \
		}

		#else

		#define IP_PRE_edge_align(n, esize) \

		#endif

		#define IP_PRE_get_stride(stride, n, datasize, torque) \
		{ \
		int blength = n; \
		@@ -303,7 +317,7 @@ enum {TIME_PACK, TIME_HOST_NEIGHBOR, TIME_HOST_PAIR, TIME_OFFLOAD_NEIGHBOR,
		{ \
		tid = 0; \
		ifrom = 0; \
		ip = 1; \
		ip = vecsize; \
		ito = inum; \
		}

		@@ -316,7 +330,7 @@ enum {TIME_PACK, TIME_HOST_NEIGHBOR, TIME_HOST_PAIR, TIME_OFFLOAD_NEIGHBOR,
		acc_t *f_scalar = &f_start[0].x; \
		flt_t *x_scalar = &pos[minlocal].x; \
		int f_stride4 = f_stride * 4; \
		_alignvar(acc_t ovv[INTEL_COMPILE_WIDTH],64); \
		_alignvar(acc_t ovv[16],64); \
		int vwidth; \
		if (sizeof(acc_t) == sizeof(double)) \
		vwidth = INTEL_COMPILE_WIDTH/2; \
		@@ -516,6 +530,22 @@ inline double MIC_Wtime() {
		return time;
		}

		#define IP_PRE_neighbor_pad(jnum, offload) \
		{ \
		const int opad_mask = ~static_cast<int>(INTEL_MIC_NBOR_PAD * \
		sizeof(float) / \
		sizeof(flt_t) - 1); \
		const int pad_mask = ~static_cast<int>(INTEL_NBOR_PAD * \
		sizeof(float) / \
		sizeof(flt_t) - 1); \
		if (offload && INTEL_MIC_NBOR_PAD > 1) \
		jnum = (jnum + INTEL_MIC_NBOR_PAD * sizeof(float) / \
		sizeof(flt_t) - 1) & opad_mask; \
		else if (INTEL_NBOR_PAD > 1) \
		jnum = (jnum + INTEL_NBOR_PAD * sizeof(float) / \
		sizeof(flt_t) - 1) & pad_mask; \
		}

		#define IP_PRE_pack_separate_buffers(fix, buffers, ago, offload, \
		nlocal, nall) \
		{ \
		@@ -644,6 +674,23 @@ inline double MIC_Wtime() {

		#else

		#if INTEL_NBOR_PAD > 1

		#define IP_PRE_neighbor_pad(jnum, offload) \
		{ \
		const int pad_mask = ~static_cast<int>(INTEL_NBOR_PAD * \
		sizeof(float) / \
		sizeof(flt_t) - 1); \
		jnum = (jnum + INTEL_NBOR_PAD * sizeof(float) / \
		sizeof(flt_t) - 1) & pad_mask; \
		}

		#else

		#define IP_PRE_neighbor_pad(jnum, offload)

		#endif

		#define MIC_Wtime MPI_Wtime
		#define IP_PRE_pack_separate_buffers(fix, buffers, ago, offload, \
		nlocal, nall)

src/USER-INTEL/npair_full_bin_ghost_intel.cpp

+98 −97

Original line number	Diff line number	Diff line
		@@ -112,7 +112,6 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
		if (pend-pstart == 0) return;

		const int nall = atom->nlocal + atom->nghost;
		int pad = 1;
		int nall_t = nall;
		const int aend = nall;

		@@ -207,6 +206,17 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
		const int mbinz = this->mbinz;
		const int * const stencilxyz = &this->stencilxyz[0][0];

		int sb = 1;
		if (special_flag[1] == 0) {
		sb = 2;
		if (special_flag[2] == 0) {
		sb = 3;
		if (special_flag[3] == 0)
		sb = 4;
		}
		}
		const int special_bound = sb;

		#ifdef _LMP_INTEL_OFFLOAD
		const int * _noalias const binhead = this->binhead;
		const int * _noalias const bins = this->bins;
		@@ -230,7 +240,7 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
		in(ncachex,ncachey,ncachez,ncachej:length(0) alloc_if(0) free_if(0)) \
		in(ncachejtype,ncachetag:length(0) alloc_if(0) free_if(0)) \
		in(ncache_stride,maxnbors,nthreads,maxspecial,nstencil,e_nall,offload) \
		in(separate_buffers,aend,nlocal,molecular,ntypes,mbinx,mbiny) \
		in(separate_buffers,aend,nlocal,molecular,ntypes,mbinx,mbiny,special_bound)\
		in(mbinz,xperiodic,yperiodic,zperiodic,xprd_half,yprd_half,zprd_half) \
		in(stencilxyz:length(3*nstencil)) \
		out(overflow:length(5) alloc_if(0) free_if(0)) \
		@@ -287,8 +297,6 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
		int e_ito = ito;
		const int list_size = (e_ito + tid * 2 + 2) * maxnbors;

		int which;

		int pack_offset = maxnbors;
		int ct = (ifrom + tid * 2) * maxnbors;
		int *neighptr = firstneigh + ct;
		@@ -418,41 +426,109 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
		}
		} // for u

		if (molecular && i < nlocal) {
		int alln = n;
		n = 0;
		#if defined(LMP_SIMD_COMPILER)
		#pragma vector aligned
		#ifdef LMP_INTEL_NBOR_COMPAT
		#pragma ivdep
		#else
		#pragma simd
		#endif
		#endif
		for (int u = 0; u < alln; u++) {
		int which;
		int addme = 1;
		int j = neighptr[u];
		if (need_ic && j < 0) {
		which = 0;
		j = -j - 1;
		} else
		ofind_special(which, special, nspecial, i, tag[j]);
		if (which) {
		j = j ^ (which << SBBITS);
		if (which < special_bound) addme = 0;
		}
		#ifdef LMP_INTEL_NBOR_COMPAT
		if (addme) neighptr2[n++] = j;
		#else
		neighptr2[n++] = j;
		#endif
		}
		alln = n2;
		n2 = maxnbors * 2;
		#if defined(LMP_SIMD_COMPILER)
		#pragma vector aligned
		#ifdef LMP_INTEL_NBOR_COMPAT
		#pragma ivdep
		#else
		#pragma simd
		#endif
		#endif
		for (int u = n2; u < alln; u++) {
		int which;
		int addme = 1;
		int j = neighptr[u];
		if (need_ic && j < 0) {
		which = 0;
		j = -j - 1;
		} else
		ofind_special(which, special, nspecial, i, tag[j]);
		if (which) {
		j = j ^ (which << SBBITS);
		if (which < special_bound) addme = 0;
		}
		#ifdef LMP_INTEL_NBOR_COMPAT
		if (addme) neighptr2[n2++] = j;
		#else
		neighptr2[n2++] = j;
		#endif
		}
		}

		#ifndef _LMP_INTEL_OFFLOAD
		if (exclude) {
		int alln = n;
		n = maxnbors;
		for (int u = pack_offset; u < alln; u++) {
		const int j = neighptr[u];
		int pj = j;
		if (need_ic)
		if (pj < 0) pj = -j - 1;
		const int jtype = x[pj].w;
		if (exclusion(i,pj,itype,jtype,mask,molecule)) continue;
		neighptr[n++] = j;
		#if defined(LMP_SIMD_COMPILER)
		#pragma vector aligned
		#pragma ivdep
		#endif
		for (int u = n; u < alln; u++) {
		int addme = 1;
		const int js = neighptr[u];
		const int j = js & NEIGHMASK;
		const int jtype = x[j].w;
		if (exclusion(i,j,itype,jtype,mask,molecule)) addme = 0;
		if (addme) neighptr2[n++] = js;
		}
		alln = n2;
		n2 = maxnbors * 2;
		#if defined(LMP_SIMD_COMPILER)
		#pragma vector aligned
		#pragma ivdep
		#endif
		for (int u = n2; u < alln; u++) {
		const int j = neighptr[u];
		int pj = j;
		if (need_ic)
		if (pj < 0) pj = -j - 1;
		const int jtype = x[pj].w;
		if (exclusion(i,pj,itype,jtype,mask,molecule)) continue;
		neighptr[n2++] = j;
		int addme = 1;
		const int js = neighptr[u];
		const int j = js & NEIGHMASK;
		const int jtype = x[j].w;
		if (exclusion(i,j,itype,jtype,mask,molecule)) addme = 0;
		if (addme) neighptr2[n2++] = js;
		}
		}
		#endif

		int ns = n - maxnbors;
		int alln = n;
		atombin[i] = ns;
		n = 0;
		for (int u = maxnbors; u < alln; u++)
		neighptr[n++] = neighptr[u];
		neighptr[n++] = neighptr2[u];
		ns += n2 - maxnbors * 2;
		for (int u = maxnbors * 2; u < n2; u++)
		neighptr[n++] = neighptr[u];
		neighptr[n++] = neighptr2[u];
		if (ns > maxnbors) *overflow = 1;

		ilist[i] = i;
		@@ -460,9 +536,7 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
		numneigh[i] = ns;

		ct += ns;
		const int alignb = (INTEL_DATA_ALIGN / sizeof(int));
		const int edge = ct & (alignb - 1);
		if (edge) ct += alignb - edge;
		IP_PRE_edge_align(ct, sizeof(int));
		neighptr = firstneigh + ct;
		if (ct + obound > list_size) {
		if (i < ito - 1) {
		@@ -477,84 +551,11 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
		numneigh[i] = 0;

		#ifdef _LMP_INTEL_OFFLOAD
		int ghost_offset = 0, nall_offset = e_nall;
		if (separate_buffers) {
		for (int i = ifrom; i < ito; ++i) {
		int * _noalias jlist = firstneigh + cnumneigh[i];
		const int jnum = numneigh[i];
		#if __INTEL_COMPILER+0 > 1499
		#pragma vector aligned
		#pragma simd
		#endif
		for (int jj = 0; jj < jnum; jj++) {
		int j = jlist[jj];
		if (need_ic && j < 0) j = -j - 1;
		}
		}

		overflow[LMP_LOCAL_MIN] = 0;
		overflow[LMP_LOCAL_MAX] = nlocal - 1;
		overflow[LMP_GHOST_MIN] = nlocal;
		overflow[LMP_GHOST_MAX] = e_nall - 1;

		int nghost = overflow[LMP_GHOST_MAX] + 1 - overflow[LMP_GHOST_MIN];
		if (nghost < 0) nghost = 0;
		if (offload) {
		ghost_offset = overflow[LMP_GHOST_MIN] - overflow[LMP_LOCAL_MAX] - 1;
		nall_offset = overflow[LMP_LOCAL_MAX] + 1 + nghost;
		} else {
		ghost_offset = overflow[LMP_GHOST_MIN] - nlocal;
		nall_offset = nlocal + nghost;
		}
		} // if separate_buffers
		#endif

		if (molecular) {
		int ito_m = ito;
		if (ito >= nlocal) ito_m = nlocal;
		for (int i = ifrom; i < ito_m; ++i) {
		int * _noalias jlist = firstneigh + cnumneigh[i];
		const int jnum = numneigh[i];

		#if defined(LMP_SIMD_COMPILER)
		#pragma vector aligned
		#pragma simd
		#endif
		for (int jj = 0; jj < jnum; jj++) {
		const int j = jlist[jj];
		if (need_ic && j < 0) {
		which = 0;
		jlist[jj] = -j - 1;
		} else
		ofind_special(which, special, nspecial, i, tag[j]);
		#ifdef _LMP_INTEL_OFFLOAD
		if (j >= nlocal) {
		if (j == e_nall)
		jlist[jj] = nall_offset;
		else if (which)
		jlist[jj] = (j-ghost_offset) ^ (which << SBBITS);
		else jlist[jj]-=ghost_offset;
		} else
		#endif
		if (which) jlist[jj] = j ^ (which << SBBITS);
		}
		} // for i
		} // if molecular
		#ifdef _LMP_INTEL_OFFLOAD
		else if (separate_buffers) {
		for (int i = ifrom; i < ito; ++i) {
		int * _noalias jlist = firstneigh + cnumneigh[i];
		const int jnum = numneigh[i];
		int jj = 0;
		#pragma vector aligned
		#pragma simd
		for (jj = 0; jj < jnum; jj++) {
		if (jlist[jj] >= nlocal) {
		if (jlist[jj] == e_nall) jlist[jj] = nall_offset;
		else jlist[jj] -= ghost_offset;
		}
		}
		}
		}
		#endif
		} // end omp

src/USER-INTEL/npair_intel.cpp

+165 −122

File changed.

Preview size limit exceeded, changes collapsed.

src/USER-INTEL/pair_buck_coul_cut_intel.cpp

+7 −3

Original line number	Diff line number	Diff line
		@@ -142,6 +142,7 @@ void PairBuckCoulCutIntel::eval(const int offload, const int vflag,
		ATOM_T * _noalias const x = buffers->get_x(offload);
		flt_t * _noalias const q = buffers->get_q(offload);

		const int * _noalias const ilist = list->ilist;
		const int * _noalias const numneigh = list->numneigh;
		const int * _noalias const cnumneigh = buffers->cnumneigh(list);
		const int * _noalias const firstneigh = buffers->firstneigh(list);
		@@ -185,6 +186,7 @@ void PairBuckCoulCutIntel::eval(const int offload, const int vflag,
		in(numneigh:length(0) alloc_if(0) free_if(0)) \
		in(x:length(x_size) alloc_if(0) free_if(0)) \
		in(q:length(q_size) alloc_if(0) free_if(0)) \
		in(ilist:length(0) alloc_if(0) free_if(0)) \
		in(overflow:length(0) alloc_if(0) free_if(0)) \
		in(astart,nthreads,qqrd2e,inum,nall,ntypes,vflag,eatom) \
		in(f_stride,nlocal,minlocal,separate_flag,offload) \
		@@ -221,15 +223,17 @@ void PairBuckCoulCutIntel::eval(const int offload, const int vflag,
		FORCE_T * _noalias const f = f_start + foff;
		if (NEWTON_PAIR) memset(f + minlocal, 0, f_stride * sizeof(FORCE_T));

		for (int i = iifrom; i < iito; i += iip) {
		for (int ii = iifrom; ii < iito; ii += iip) {
		const int i = ilist[ii];
		const int itype = x[i].w;

		const int ptr_off = itype * ntypes;
		const C_FORCE_T * _noalias const c_forcei = c_force + ptr_off;
		const C_ENERGY_T * _noalias const c_energyi = c_energy + ptr_off;
		const C_CUT_T * _noalias const c_cuti = c_cut + ptr_off;
		const int * _noalias const jlist = firstneigh + cnumneigh[i];
		const int jnum = numneigh[i];
		const int * _noalias const jlist = firstneigh + cnumneigh[ii];
		int jnum = numneigh[ii];
		IP_PRE_neighbor_pad(jnum, offload);

		acc_t fxtmp,fytmp,fztmp,fwtmp;
		acc_t sevdwl, secoul, sv0, sv1, sv2, sv3, sv4, sv5;

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