Commit dbbfacc5 authored by Stan Moore's avatar Stan Moore
Browse files

Fix atomic issues

parent 2fc8da08

src/KOKKOS/fix_qeq_reax_kokkos.cpp

+9 −9
Original line number Diff line number Diff line
@@ -777,7 +777,7 @@ KOKKOS_INLINE_FUNCTION 
void FixQEqReaxKokkos<DeviceType>::sparse13_item(int ii) const

{

  // The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial

  auto a_o = red_o.template access<AtomicDup<NEIGHFLAG>::value>();

  auto a_o = red_o.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();



  const int i = d_ilist[ii];

  if (mask[i] & groupbit) {
@@ -785,9 +785,9 @@ void FixQEqReaxKokkos<DeviceType>::sparse13_item(int ii) const 
    for(int jj = d_firstnbr[i]; jj < d_firstnbr[i] + d_numnbrs[i]; jj++) {

      const int j = d_jlist(jj);

      tmp += d_val(jj) * d_s[j];

      a_o(j) += d_val(jj) * d_s[i];

      a_o[j] += d_val(jj) * d_s[i];

    }

    a_o(i) += tmp;

    a_o[i] += tmp;

  }

}
@@ -829,7 +829,7 @@ KOKKOS_INLINE_FUNCTION 
void FixQEqReaxKokkos<DeviceType>::sparse23_item(int ii) const

{

  // The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial

  auto a_o = red_o.template access<AtomicDup<NEIGHFLAG>::value>();

  auto a_o = red_o.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();



  const int i = d_ilist[ii];

  if (mask[i] & groupbit) {
@@ -837,9 +837,9 @@ void FixQEqReaxKokkos<DeviceType>::sparse23_item(int ii) const 
    for(int jj = d_firstnbr[i]; jj < d_firstnbr[i] + d_numnbrs[i]; jj++) {

      const int j = d_jlist(jj);

      tmp += d_val(jj) * d_d[j];

      a_o(j) += d_val(jj) * d_d[i];

      a_o[j] += d_val(jj) * d_d[i];

    }

    a_o(i) += tmp;

    a_o[i] += tmp;

  }

}
@@ -888,7 +888,7 @@ KOKKOS_INLINE_FUNCTION 
void FixQEqReaxKokkos<DeviceType>::sparse33_item(int ii) const

{

  // The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial

  auto a_o = red_o.template access<AtomicDup<NEIGHFLAG>::value>();

  auto a_o = red_o.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();



  const int i = d_ilist[ii];

  if (mask[i] & groupbit) {
@@ -896,9 +896,9 @@ void FixQEqReaxKokkos<DeviceType>::sparse33_item(int ii) const 
    for(int jj = d_firstnbr[i]; jj < d_firstnbr[i] + d_numnbrs[i]; jj++) {

      const int j = d_jlist(jj);

      tmp += d_val(jj) * d_t[j];

      a_o(j) += d_val(jj) * d_t[i];

      a_o[j] += d_val(jj) * d_t[i];

    }

    a_o(i) += tmp;

    a_o[i] += tmp;

  }

}

src/KOKKOS/pair_kokkos.h

+4 −2
Original line number Diff line number Diff line
@@ -62,15 +62,17 @@ struct AtomicF<HALFTHREAD> { 


// Determine memory traits for force array

// Do atomic trait when running HALFTHREAD neighbor list style

template<int NEIGHFLAG>

template<int NEIGHFLAG, class DeviceType>

struct AtomicDup {

  enum {value = Kokkos::Experimental::ScatterNonAtomic};

};



#ifdef KOKKOS_ENABLE_CUDA

template<>

struct AtomicDup<HALFTHREAD> {

struct AtomicDup<HALFTHREAD,Kokkos::Cuda> {

  enum {value = Kokkos::Experimental::ScatterAtomic};

};

#endif



//Specialisation for Neighborlist types Half, HalfThread, Full

template <class PairStyle, int NEIGHFLAG, bool STACKPARAMS, class Specialisation = void>

src/KOKKOS/pair_reaxc_kokkos.cpp

+28 −28
Original line number Diff line number Diff line
@@ -1073,7 +1073,7 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeLJCoulomb<NEIGHFLAG, 


  // The f array is atomic for Half/Thread neighbor style

  //Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;

  auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG>::value>();

  auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();



  F_FLOAT powr_vdw, powgi_vdw, fn13, dfn13, exp1, exp2, etmp;

  F_FLOAT evdwl, fvdwl;
@@ -1233,7 +1233,7 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeTabulatedLJCoulomb<N 


  // The f array is atomic for Half/Thread neighbor style

  //Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;

  auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG>::value>();

  auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();



  const int i = d_ilist[ii];

  const X_FLOAT xtmp = x(i,0);
@@ -1616,8 +1616,8 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxBuildListsHalf<NEIGHFLAG>, 


  //Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_dDeltap_self = d_dDeltap_self;

  //Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_total_bo = d_total_bo;

  auto a_dDeltap_self = dup_dDeltap_self.template access<AtomicDup<NEIGHFLAG>::value>();

  auto a_total_bo = dup_total_bo.template access<AtomicDup<NEIGHFLAG>::value>();

  auto a_dDeltap_self = dup_dDeltap_self.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();

  auto a_total_bo = dup_total_bo.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();



  const int i = d_ilist[ii];

  const X_FLOAT xtmp = x(i,0);
@@ -2312,10 +2312,10 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeMulti2<NEIGHFLAG,EVF 
  Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;

  Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbopi = d_Cdbopi;

  Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbopi2 = d_Cdbopi2;

  auto a_CdDelta = dup_CdDelta.template access<AtomicDup<NEIGHFLAG>::value>();

  //auto a_Cdbo = dup_Cdbo.template access<AtomicDup<NEIGHFLAG>::value>();

  //auto a_Cdbopi = dup_Cdbopi.template access<AtomicDup<NEIGHFLAG>::value>();

  //auto a_Cdbopi2 = dup_Cdbopi2.template access<AtomicDup<NEIGHFLAG>::value>();

  auto a_CdDelta = dup_CdDelta.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();

  //auto a_Cdbo = dup_Cdbo.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();

  //auto a_Cdbopi = dup_Cdbopi.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();

  //auto a_Cdbopi2 = dup_Cdbopi2.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();



  const int i = d_ilist[ii];

  const int itype = type(i);
@@ -2469,9 +2469,9 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeAngular<NEIGHFLAG,EV 
  //Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;

  Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;

  //Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_CdDelta = d_CdDelta;

  auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG>::value>();

  //auto a_Cdbo = dup_Cdbo.template access<AtomicDup<NEIGHFLAG>::value>();

  auto a_CdDelta = dup_CdDelta.template access<AtomicDup<NEIGHFLAG>::value>();

  auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();

  //auto a_Cdbo = dup_Cdbo.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();

  auto a_CdDelta = dup_CdDelta.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();





  const int i = d_ilist[ii];
@@ -2782,9 +2782,9 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeTorsion<NEIGHFLAG,EV 
  //Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;

  //Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_CdDelta = d_CdDelta;

  Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;

  auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG>::value>();

  auto a_CdDelta = dup_CdDelta.template access<AtomicDup<NEIGHFLAG>::value>();

  //auto a_Cdbo = dup_Cdbo.template access<AtomicDup<NEIGHFLAG>::value>();

  auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();

  auto a_CdDelta = dup_CdDelta.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();

  //auto a_Cdbo = dup_Cdbo.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();



  // in reaxc_torsion_angles: j = i, k = j, i = k;
@@ -3155,7 +3155,7 @@ KOKKOS_INLINE_FUNCTION 
void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeHydrogen<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT_REAX& ev) const {



  //Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;

  auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG>::value>();

  auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();



  int hblist[MAX_BONDS];

  F_FLOAT theta, cos_theta, sin_xhz4, cos_xhz1, sin_theta2;
@@ -3305,9 +3305,9 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxUpdateBond<NEIGHFLAG>, cons 
  Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;

  Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbopi = d_Cdbopi;

  Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbopi2 = d_Cdbopi2;

  //auto a_Cdbo = dup_Cdbo.template access<AtomicDup<NEIGHFLAG>::value>();

  //auto a_Cdbopi = dup_Cdbopi.template access<AtomicDup<NEIGHFLAG>::value>();

  //auto a_Cdbopi2 = dup_Cdbopi2.template access<AtomicDup<NEIGHFLAG>::value>();

  //auto a_Cdbo = dup_Cdbo.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();

  //auto a_Cdbopi = dup_Cdbopi.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();

  //auto a_Cdbopi2 = dup_Cdbopi2.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();



  const int i = d_ilist[ii];

  const tagint itag = tag(i);
@@ -3356,8 +3356,8 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeBond1<NEIGHFLAG,EVFL 


  //Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;

  //Kokkos::View<F_FLOAT*, typename DAT::t_ffloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_CdDelta = d_CdDelta;

  auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG>::value>();

  auto a_CdDelta = dup_CdDelta.template access<AtomicDup<NEIGHFLAG>::value>();

  auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();

  auto a_CdDelta = dup_CdDelta.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();



  F_FLOAT delij[3];

  F_FLOAT p_be1, p_be2, De_s, De_p, De_pp, pow_BOs_be2, exp_be12, CEbo, ebond;
@@ -3495,7 +3495,7 @@ KOKKOS_INLINE_FUNCTION 
void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeBond2<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT_REAX& ev) const {



  //Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;

  auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG>::value>();

  auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();



  F_FLOAT delij[3], delik[3], deljk[3], tmpvec[3];

  F_FLOAT dBOp_i[3], dBOp_k[3], dln_BOp_pi[3], dln_BOp_pi2[3];
@@ -3710,8 +3710,8 @@ void PairReaxCKokkos<DeviceType>::ev_tally(EV_FLOAT_REAX &ev, const int &i, cons 
  // The eatom and vatom arrays are atomic for Half/Thread neighbor style

  //Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_eatom = v_eatom;

  //Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_vatom = v_vatom;

  auto a_eatom = dup_eatom.template access<AtomicDup<NEIGHFLAG>::value>();

  auto a_vatom = dup_vatom.template access<AtomicDup<NEIGHFLAG>::value>();

  auto a_eatom = dup_eatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();

  auto a_vatom = dup_vatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();



  if (eflag_atom) {

    const E_FLOAT epairhalf = 0.5 * epair;
@@ -3778,7 +3778,7 @@ void PairReaxCKokkos<DeviceType>::e_tally(EV_FLOAT_REAX &ev, const int &i, const 


  if (eflag_atom) {

    //Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_eatom = v_eatom;

    auto a_eatom = dup_eatom.template access<AtomicDup<NEIGHFLAG>::value>();

    auto a_eatom = dup_eatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();



    const E_FLOAT epairhalf = 0.5 * epair;

    a_eatom[i] += epairhalf;
@@ -3796,7 +3796,7 @@ void PairReaxCKokkos<DeviceType>::e_tally_single(EV_FLOAT_REAX &ev, const int &i 
{

  // The eatom array is atomic for Half/Thread neighbor style

  //Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_eatom = v_eatom;

  auto a_eatom = dup_eatom.template access<AtomicDup<NEIGHFLAG>::value>();

  auto a_eatom = dup_eatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();



  a_eatom[i] += epair;

}
@@ -3830,7 +3830,7 @@ void PairReaxCKokkos<DeviceType>::v_tally(EV_FLOAT_REAX &ev, const int &i, 


  if (vflag_atom) {

    //Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_vatom = v_vatom;

    auto a_vatom = dup_vatom.template access<AtomicDup<NEIGHFLAG>::value>();

    auto a_vatom = dup_vatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();



    a_vatom(i,0) += v[0]; a_vatom(i,1) += v[1]; a_vatom(i,2) += v[2];

    a_vatom(i,3) += v[3]; a_vatom(i,4) += v[4]; a_vatom(i,5) += v[5];
@@ -3848,7 +3848,7 @@ void PairReaxCKokkos<DeviceType>::v_tally3(EV_FLOAT_REAX &ev, const int &i, cons 


  // The eatom and vatom arrays are atomic for Half/Thread neighbor style

  //Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_vatom = v_vatom;

  auto a_vatom = dup_vatom.template access<AtomicDup<NEIGHFLAG>::value>();

  auto a_vatom = dup_vatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();



  F_FLOAT v[6];
@@ -3909,7 +3909,7 @@ void PairReaxCKokkos<DeviceType>::v_tally4(EV_FLOAT_REAX &ev, const int &i, cons 


  if (vflag_atom) {

    //Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_vatom = v_vatom;

    auto a_vatom = dup_vatom.template access<AtomicDup<NEIGHFLAG>::value>();

    auto a_vatom = dup_vatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();



    a_vatom(i,0) += 0.25 * v[0]; a_vatom(i,1) += 0.25 * v[1]; a_vatom(i,2) += 0.25 * v[2];

    a_vatom(i,3) += 0.25 * v[3]; a_vatom(i,4) += 0.25 * v[4]; a_vatom(i,5) += 0.25 * v[5];

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