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Add Kokkos threaded reverse comm option

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This commit is contained in:
Stan Moore
2017-10-03 10:14:24 -06:00
parent 529eeb6039
commit ca032f21fb
17 changed files with 748 additions and 1850 deletions
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444
src/KOKKOS/atom_vec_atomic_kokkos.cpp
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@ -136,450 +136,6 @@ void AtomVecAtomicKokkos::copy(int i, int j, int delflag)
/* ---------------------------------------------------------------------- */
template<class DeviceType,int PBC_FLAG,int TRICLINIC>
struct AtomVecAtomicKokkos_PackComm {
typedef DeviceType device_type;
typename ArrayTypes<DeviceType>::t_x_array_randomread _x;
typename ArrayTypes<DeviceType>::t_xfloat_2d_um _buf;
typename ArrayTypes<DeviceType>::t_int_2d_const _list;
const int _iswap;
X_FLOAT _xprd,_yprd,_zprd,_xy,_xz,_yz;
X_FLOAT _pbc[6];
AtomVecAtomicKokkos_PackComm(
const typename DAT::tdual_x_array &x,
const typename DAT::tdual_xfloat_2d &buf,
const typename DAT::tdual_int_2d &list,
const int & iswap,
const X_FLOAT &xprd, const X_FLOAT &yprd, const X_FLOAT &zprd,
const X_FLOAT &xy, const X_FLOAT &xz, const X_FLOAT &yz, const int* const pbc):
_x(x.view<DeviceType>()),_list(list.view<DeviceType>()),_iswap(iswap),
_xprd(xprd),_yprd(yprd),_zprd(zprd),
_xy(xy),_xz(xz),_yz(yz) {
const size_t maxsend = (buf.view<DeviceType>().dimension_0()*buf.view<DeviceType>().dimension_1())/3;
const size_t elements = 3;
buffer_view<DeviceType>(_buf,buf,maxsend,elements);
_pbc[0] = pbc[0]; _pbc[1] = pbc[1]; _pbc[2] = pbc[2];
_pbc[3] = pbc[3]; _pbc[4] = pbc[4]; _pbc[5] = pbc[5];
};
KOKKOS_INLINE_FUNCTION
void operator() (const int& i) const {
const int j = _list(_iswap,i);
if (PBC_FLAG == 0) {
_buf(i,0) = _x(j,0);
_buf(i,1) = _x(j,1);
_buf(i,2) = _x(j,2);
} else {
if (TRICLINIC == 0) {
_buf(i,0) = _x(j,0) + _pbc[0]*_xprd;
_buf(i,1) = _x(j,1) + _pbc[1]*_yprd;
_buf(i,2) = _x(j,2) + _pbc[2]*_zprd;
} else {
_buf(i,0) = _x(j,0) + _pbc[0]*_xprd + _pbc[5]*_xy + _pbc[4]*_xz;
_buf(i,1) = _x(j,1) + _pbc[1]*_yprd + _pbc[3]*_yz;
_buf(i,2) = _x(j,2) + _pbc[2]*_zprd;
}
}
}
};
/* ---------------------------------------------------------------------- */
int AtomVecAtomicKokkos::pack_comm_kokkos(const int &n,
const DAT::tdual_int_2d &list,
const int & iswap,
const DAT::tdual_xfloat_2d &buf,
const int &pbc_flag,
const int* const pbc)
{
// Check whether to always run forward communication on the host
// Choose correct forward PackComm kernel
if(commKK->forward_comm_on_host) {
sync(Host,X_MASK);
if(pbc_flag) {
if(domain->triclinic) {
struct AtomVecAtomicKokkos_PackComm<LMPHostType,1,1> f(atomKK->k_x,buf,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
} else {
struct AtomVecAtomicKokkos_PackComm<LMPHostType,1,0> f(atomKK->k_x,buf,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
}
} else {
if(domain->triclinic) {
struct AtomVecAtomicKokkos_PackComm<LMPHostType,0,1> f(atomKK->k_x,buf,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
} else {
struct AtomVecAtomicKokkos_PackComm<LMPHostType,0,0> f(atomKK->k_x,buf,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
}
}
} else {
sync(Device,X_MASK);
if(pbc_flag) {
if(domain->triclinic) {
struct AtomVecAtomicKokkos_PackComm<LMPDeviceType,1,1> f(atomKK->k_x,buf,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
} else {
struct AtomVecAtomicKokkos_PackComm<LMPDeviceType,1,0> f(atomKK->k_x,buf,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
}
} else {
if(domain->triclinic) {
struct AtomVecAtomicKokkos_PackComm<LMPDeviceType,0,1> f(atomKK->k_x,buf,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
} else {
struct AtomVecAtomicKokkos_PackComm<LMPDeviceType,0,0> f(atomKK->k_x,buf,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
}
}
}
return n*size_forward;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType,int PBC_FLAG,int TRICLINIC>
struct AtomVecAtomicKokkos_PackCommSelf {
typedef DeviceType device_type;
typename ArrayTypes<DeviceType>::t_x_array_randomread _x;
typename ArrayTypes<DeviceType>::t_x_array _xw;
int _nfirst;
typename ArrayTypes<DeviceType>::t_int_2d_const _list;
const int _iswap;
X_FLOAT _xprd,_yprd,_zprd,_xy,_xz,_yz;
X_FLOAT _pbc[6];
AtomVecAtomicKokkos_PackCommSelf(
const typename DAT::tdual_x_array &x,
const int &nfirst,
const typename DAT::tdual_int_2d &list,
const int & iswap,
const X_FLOAT &xprd, const X_FLOAT &yprd, const X_FLOAT &zprd,
const X_FLOAT &xy, const X_FLOAT &xz, const X_FLOAT &yz, const int* const pbc):
_x(x.view<DeviceType>()),_xw(x.view<DeviceType>()),_nfirst(nfirst),_list(list.view<DeviceType>()),_iswap(iswap),
_xprd(xprd),_yprd(yprd),_zprd(zprd),
_xy(xy),_xz(xz),_yz(yz) {
_pbc[0] = pbc[0]; _pbc[1] = pbc[1]; _pbc[2] = pbc[2];
_pbc[3] = pbc[3]; _pbc[4] = pbc[4]; _pbc[5] = pbc[5];
};
KOKKOS_INLINE_FUNCTION
void operator() (const int& i) const {
const int j = _list(_iswap,i);
if (PBC_FLAG == 0) {
_xw(i+_nfirst,0) = _x(j,0);
_xw(i+_nfirst,1) = _x(j,1);
_xw(i+_nfirst,2) = _x(j,2);
} else {
if (TRICLINIC == 0) {
_xw(i+_nfirst,0) = _x(j,0) + _pbc[0]*_xprd;
_xw(i+_nfirst,1) = _x(j,1) + _pbc[1]*_yprd;
_xw(i+_nfirst,2) = _x(j,2) + _pbc[2]*_zprd;
} else {
_xw(i+_nfirst,0) = _x(j,0) + _pbc[0]*_xprd + _pbc[5]*_xy + _pbc[4]*_xz;
_xw(i+_nfirst,1) = _x(j,1) + _pbc[1]*_yprd + _pbc[3]*_yz;
_xw(i+_nfirst,2) = _x(j,2) + _pbc[2]*_zprd;
}
}
}
};
/* ---------------------------------------------------------------------- */
int AtomVecAtomicKokkos::pack_comm_self(const int &n, const DAT::tdual_int_2d &list, const int & iswap,
const int nfirst, const int &pbc_flag, const int* const pbc) {
if(commKK->forward_comm_on_host) {
sync(Host,X_MASK);
modified(Host,X_MASK);
if(pbc_flag) {
if(domain->triclinic) {
struct AtomVecAtomicKokkos_PackCommSelf<LMPHostType,1,1> f(atomKK->k_x,nfirst,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
} else {
struct AtomVecAtomicKokkos_PackCommSelf<LMPHostType,1,0> f(atomKK->k_x,nfirst,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
}
} else {
if(domain->triclinic) {
struct AtomVecAtomicKokkos_PackCommSelf<LMPHostType,0,1> f(atomKK->k_x,nfirst,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
} else {
struct AtomVecAtomicKokkos_PackCommSelf<LMPHostType,0,0> f(atomKK->k_x,nfirst,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
}
}
} else {
sync(Device,X_MASK);
modified(Device,X_MASK);
if(pbc_flag) {
if(domain->triclinic) {
struct AtomVecAtomicKokkos_PackCommSelf<LMPDeviceType,1,1> f(atomKK->k_x,nfirst,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
} else {
struct AtomVecAtomicKokkos_PackCommSelf<LMPDeviceType,1,0> f(atomKK->k_x,nfirst,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
}
} else {
if(domain->triclinic) {
struct AtomVecAtomicKokkos_PackCommSelf<LMPDeviceType,0,1> f(atomKK->k_x,nfirst,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
} else {
struct AtomVecAtomicKokkos_PackCommSelf<LMPDeviceType,0,0> f(atomKK->k_x,nfirst,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
}
}
}
return n*3;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
struct AtomVecAtomicKokkos_UnpackComm {
typedef DeviceType device_type;
typename ArrayTypes<DeviceType>::t_x_array _x;
typename ArrayTypes<DeviceType>::t_xfloat_2d_const _buf;
int _first;
AtomVecAtomicKokkos_UnpackComm(
const typename DAT::tdual_x_array &x,
const typename DAT::tdual_xfloat_2d &buf,
const int& first):_x(x.view<DeviceType>()),_buf(buf.view<DeviceType>()),
_first(first) {};
KOKKOS_INLINE_FUNCTION
void operator() (const int& i) const {
_x(i+_first,0) = _buf(i,0);
_x(i+_first,1) = _buf(i,1);
_x(i+_first,2) = _buf(i,2);
}
};
/* ---------------------------------------------------------------------- */
void AtomVecAtomicKokkos::unpack_comm_kokkos(const int &n, const int &first,
const DAT::tdual_xfloat_2d &buf ) {
if(commKK->forward_comm_on_host) {
sync(Host,X_MASK);
modified(Host,X_MASK);
struct AtomVecAtomicKokkos_UnpackComm<LMPHostType> f(atomKK->k_x,buf,first);
Kokkos::parallel_for(n,f);
} else {
sync(Device,X_MASK);
modified(Device,X_MASK);
struct AtomVecAtomicKokkos_UnpackComm<LMPDeviceType> f(atomKK->k_x,buf,first);
Kokkos::parallel_for(n,f);
}
}
/* ---------------------------------------------------------------------- */
int AtomVecAtomicKokkos::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = h_x(j,0);
buf[m++] = h_x(j,1);
buf[m++] = h_x(j,2);
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = h_x(j,0) + dx;
buf[m++] = h_x(j,1) + dy;
buf[m++] = h_x(j,2) + dz;
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecAtomicKokkos::pack_comm_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = h_x(j,0);
buf[m++] = h_x(j,1);
buf[m++] = h_x(j,2);
buf[m++] = h_v(j,0);
buf[m++] = h_v(j,1);
buf[m++] = h_v(j,2);
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = h_x(j,0) + dx;
buf[m++] = h_x(j,1) + dy;
buf[m++] = h_x(j,2) + dz;
buf[m++] = h_v(j,0);
buf[m++] = h_v(j,1);
buf[m++] = h_v(j,2);
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = h_x(j,0) + dx;
buf[m++] = h_x(j,1) + dy;
buf[m++] = h_x(j,2) + dz;
if (mask[i] & deform_groupbit) {
buf[m++] = h_v(j,0) + dvx;
buf[m++] = h_v(j,1) + dvy;
buf[m++] = h_v(j,2) + dvz;
} else {
buf[m++] = h_v(j,0);
buf[m++] = h_v(j,1);
buf[m++] = h_v(j,2);
}
}
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecAtomicKokkos::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
h_x(i,0) = buf[m++];
h_x(i,1) = buf[m++];
h_x(i,2) = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void AtomVecAtomicKokkos::unpack_comm_vel(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
h_x(i,0) = buf[m++];
h_x(i,1) = buf[m++];
h_x(i,2) = buf[m++];
h_v(i,0) = buf[m++];
h_v(i,1) = buf[m++];
h_v(i,2) = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecAtomicKokkos::pack_reverse(int n, int first, double *buf)
{
if(n > 0)
sync(Host,F_MASK);
int m = 0;
const int last = first + n;
for (int i = first; i < last; i++) {
buf[m++] = h_f(i,0);
buf[m++] = h_f(i,1);
buf[m++] = h_f(i,2);
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecAtomicKokkos::unpack_reverse(int n, int *list, double *buf)
{
if(n > 0) {
sync(Host,F_MASK);
modified(Host,F_MASK);
}
int m = 0;
for (int i = 0; i < n; i++) {
const int j = list[i];
h_f(j,0) += buf[m++];
h_f(j,1) += buf[m++];
h_f(j,2) += buf[m++];
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType,int PBC_FLAG>
struct AtomVecAtomicKokkos_PackBorder {
typedef DeviceType device_type;