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Merge branch 'master' of github.com:lammps/lammps into kk_snap_host

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This commit is contained in:
Stan Gerald Moore
2021-07-14 14:49:16 -06:00
parent 2295745318 5af74edcc0
commit 1ce5e3bd00
25 changed files with 566 additions and 224 deletions
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1
cmake/Modules/Packages/KOKKOS.cmake
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@ -79,6 +79,7 @@ target_compile_definitions(lammps PRIVATE -DLMP_KOKKOS)
set(KOKKOS_PKG_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/KOKKOS)
set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/atom_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/atom_map_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/atom_vec_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/comm_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/comm_tiled_kokkos.cpp

1
src/KOKKOS/Install.sh
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@ -55,6 +55,7 @@ action angle_harmonic_kokkos.cpp angle_harmonic.cpp
action angle_harmonic_kokkos.h angle_harmonic.h
action atom_kokkos.cpp
action atom_kokkos.h
action atom_map_kokkos.cpp
action atom_vec_angle_kokkos.cpp atom_vec_angle.cpp
action atom_vec_angle_kokkos.h atom_vec_angle.h
action atom_vec_atomic_kokkos.cpp

133
src/KOKKOS/atom_kokkos.cpp
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@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -13,23 +12,25 @@
------------------------------------------------------------------------- */
#include "atom_kokkos.h"
#include <mpi.h>
#include "atom_masks.h"
#include "atom_vec.h"
#include "atom_vec_kokkos.h"
#include "comm_kokkos.h"
#include "update.h"
#include "domain.h"
#include "atom_masks.h"
#include "memory_kokkos.h"
#include "error.h"
#include "kokkos.h"
#include "atom_masks.h"
#include "memory_kokkos.h"
#include "update.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
AtomKokkos::AtomKokkos(LAMMPS *lmp) : Atom(lmp) {}
AtomKokkos::AtomKokkos(LAMMPS *lmp) : Atom(lmp)
{
k_error_flag = DAT::tdual_int_scalar("atom:error_flag");
}
/* ---------------------------------------------------------------------- */
@ -77,6 +78,8 @@ AtomKokkos::~AtomKokkos()
memoryKK->destroy_kokkos(k_improper_atom3, improper_atom3);
memoryKK->destroy_kokkos(k_improper_atom4, improper_atom4);
AtomKokkos::map_delete();
// SPIN package
memoryKK->destroy_kokkos(k_sp, sp);
@ -84,16 +87,16 @@ AtomKokkos::~AtomKokkos()
memoryKK->destroy_kokkos(k_fm_long, fm_long);
// DPD-REACT package
memoryKK->destroy_kokkos(k_uCond,uCond);
memoryKK->destroy_kokkos(k_uMech,uMech);
memoryKK->destroy_kokkos(k_uChem,uChem);
memoryKK->destroy_kokkos(k_uCG,uCG);
memoryKK->destroy_kokkos(k_uCGnew,uCGnew);
memoryKK->destroy_kokkos(k_rho,rho);
memoryKK->destroy_kokkos(k_dpdTheta,dpdTheta);
memoryKK->destroy_kokkos(k_duChem,duChem);
memoryKK->destroy_kokkos(k_uCond, uCond);
memoryKK->destroy_kokkos(k_uMech, uMech);
memoryKK->destroy_kokkos(k_uChem, uChem);
memoryKK->destroy_kokkos(k_uCG, uCG);
memoryKK->destroy_kokkos(k_uCGnew, uCGnew);
memoryKK->destroy_kokkos(k_rho, rho);
memoryKK->destroy_kokkos(k_dpdTheta, dpdTheta);
memoryKK->destroy_kokkos(k_duChem, duChem);
memoryKK->destroy_kokkos(k_dvector,dvector);
memoryKK->destroy_kokkos(k_dvector, dvector);
dvector = nullptr;
}
@ -101,34 +104,32 @@ AtomKokkos::~AtomKokkos()
void AtomKokkos::sync(const ExecutionSpace space, unsigned int mask)
{
if (space == Device && lmp->kokkos->auto_sync)
((AtomVecKokkos *) avec)->modified(Host,mask);
if (space == Device && lmp->kokkos->auto_sync) ((AtomVecKokkos *) avec)->modified(Host, mask);
((AtomVecKokkos *) avec)->sync(space,mask);
((AtomVecKokkos *) avec)->sync(space, mask);
}
/* ---------------------------------------------------------------------- */
void AtomKokkos::modified(const ExecutionSpace space, unsigned int mask)
{
((AtomVecKokkos *) avec)->modified(space,mask);
((AtomVecKokkos *) avec)->modified(space, mask);
if (space == Device && lmp->kokkos->auto_sync)
((AtomVecKokkos *) avec)->sync(Host,mask);
if (space == Device && lmp->kokkos->auto_sync) ((AtomVecKokkos *) avec)->sync(Host, mask);
}
void AtomKokkos::sync_overlapping_device(const ExecutionSpace space, unsigned int mask)
{
((AtomVecKokkos *) avec)->sync_overlapping_device(space,mask);
((AtomVecKokkos *) avec)->sync_overlapping_device(space, mask);
}
/* ---------------------------------------------------------------------- */
void AtomKokkos::allocate_type_arrays()
{
if (avec->mass_type == AtomVec::PER_TYPE) {
k_mass = DAT::tdual_float_1d("Mass",ntypes+1);
k_mass = DAT::tdual_float_1d("Mass", ntypes + 1);
mass = k_mass.h_view.data();
mass_setflag = new int[ntypes+1];
mass_setflag = new int[ntypes + 1];
for (int itype = 1; itype <= ntypes; itype++) mass_setflag[itype] = 0;
k_mass.modify<LMPHostType>();
}
@ -138,11 +139,11 @@ void AtomKokkos::allocate_type_arrays()
void AtomKokkos::sort()
{
int i,m,n,ix,iy,iz,ibin,empty;
int i, m, n, ix, iy, iz, ibin, empty;
// set next timestep for sorting to take place
nextsort = (update->ntimestep/sortfreq)*sortfreq + sortfreq;
nextsort = (update->ntimestep / sortfreq) * sortfreq + sortfreq;
// re-setup sort bins if needed
@ -155,33 +156,33 @@ void AtomKokkos::sort()
memory->destroy(next);
memory->destroy(permute);
maxnext = atom->nmax;
memory->create(next,maxnext,"atom:next");
memory->create(permute,maxnext,"atom:permute");
memory->create(next, maxnext, "atom:next");
memory->create(permute, maxnext, "atom:permute");
}
// insure there is one extra atom location at end of arrays for swaps
if (nlocal == nmax) avec->grow(0);
sync(Host,ALL_MASK);
modified(Host,ALL_MASK);
sync(Host, ALL_MASK);
modified(Host, ALL_MASK);
// bin atoms in reverse order so linked list will be in forward order
for (i = 0; i < nbins; i++) binhead[i] = -1;
HAT::t_x_array_const h_x = k_x.view<LMPHostType>();
for (i = nlocal-1; i >= 0; i--) {
ix = static_cast<int> ((h_x(i,0)-bboxlo[0])*bininvx);
iy = static_cast<int> ((h_x(i,1)-bboxlo[1])*bininvy);
iz = static_cast<int> ((h_x(i,2)-bboxlo[2])*bininvz);
ix = MAX(ix,0);
iy = MAX(iy,0);
iz = MAX(iz,0);
ix = MIN(ix,nbinx-1);
iy = MIN(iy,nbiny-1);
iz = MIN(iz,nbinz-1);
ibin = iz*nbiny*nbinx + iy*nbinx + ix;
for (i = nlocal - 1; i >= 0; i--) {
ix = static_cast<int>((h_x(i, 0) - bboxlo[0]) * bininvx);
iy = static_cast<int>((h_x(i, 1) - bboxlo[1]) * bininvy);
iz = static_cast<int>((h_x(i, 2) - bboxlo[2]) * bininvz);
ix = MAX(ix, 0);
iy = MAX(iy, 0);
iz = MAX(iz, 0);
ix = MIN(ix, nbinx - 1);
iy = MIN(iy, nbiny - 1);
iz = MIN(iz, nbinz - 1);
ibin = iz * nbiny * nbinx + iy * nbinx + ix;
next[i] = binhead[ibin];
binhead[ibin] = i;
}
@ -213,13 +214,13 @@ void AtomKokkos::sort()
for (i = 0; i < nlocal; i++) {
if (current[i] == permute[i]) continue;
avec->copy(i,nlocal,0);
avec->copy(i, nlocal, 0);
empty = i;
while (permute[empty] != i) {
avec->copy(permute[empty],empty,0);
avec->copy(permute[empty], empty, 0);
empty = current[empty] = permute[empty];
}
avec->copy(nlocal,empty,0);
avec->copy(nlocal, empty, 0);
current[empty] = permute[empty];
}
@ -237,13 +238,14 @@ void AtomKokkos::sort()
reallocate memory to the pointer selected by the mask
------------------------------------------------------------------------- */
void AtomKokkos::grow(unsigned int mask) {
void AtomKokkos::grow(unsigned int mask)
{
if (mask & SPECIAL_MASK) {
memoryKK->destroy_kokkos(k_special, special);
sync(Device, mask);
modified(Device, mask);
memoryKK->grow_kokkos(k_special,special,nmax,maxspecial,"atom:special");
memoryKK->grow_kokkos(k_special, special, nmax, maxspecial, "atom:special");
avec->grow_pointers();
sync(Host, mask);
}
@ -262,22 +264,18 @@ int AtomKokkos::add_custom(const char *name, int flag)
if (flag == 0) {
index = nivector;
nivector++;
iname = (char **) memory->srealloc(iname,nivector*sizeof(char *),
"atom:iname");
iname = (char **) memory->srealloc(iname, nivector * sizeof(char *), "atom:iname");
iname[index] = utils::strdup(name);
ivector = (int **) memory->srealloc(ivector,nivector*sizeof(int *),
"atom:ivector");
memory->create(ivector[index],nmax,"atom:ivector");
ivector = (int **) memory->srealloc(ivector, nivector * sizeof(int *), "atom:ivector");
memory->create(ivector[index], nmax, "atom:ivector");
} else {
index = ndvector;
ndvector++;
dname = (char **) memory->srealloc(dname,ndvector*sizeof(char *),
"atom:dname");
dname = (char **) memory->srealloc(dname, ndvector * sizeof(char *), "atom:dname");
dname[index] = utils::strdup(name);
this->sync(Device,DVECTOR_MASK);
memoryKK->grow_kokkos(k_dvector,dvector,ndvector,nmax,
"atom:dvector");
this->modified(Device,DVECTOR_MASK);
this->sync(Device, DVECTOR_MASK);
memoryKK->grow_kokkos(k_dvector, dvector, ndvector, nmax, "atom:dvector");
this->modified(Device, DVECTOR_MASK);
}
return index;
@ -294,12 +292,12 @@ void AtomKokkos::remove_custom(int flag, int index)
if (flag == 0) {
memory->destroy(ivector[index]);
ivector[index] = nullptr;
delete [] iname[index];
delete[] iname[index];
iname[index] = nullptr;
} else {
//memoryKK->destroy_kokkos(dvector);
dvector[index] = nullptr;
delete [] dname[index];
delete[] dname[index];
dname[index] = nullptr;
}
}
@ -335,19 +333,16 @@ void AtomKokkos::deallocate_topology()
done at higher levels (Verlet,Modify,etc)
------------------------------------------------------------------------- */
void AtomKokkos::sync_modify(ExecutionSpace execution_space,
unsigned int datamask_read,
void AtomKokkos::sync_modify(ExecutionSpace execution_space, unsigned int datamask_read,
unsigned int datamask_modify)
{
sync(execution_space,datamask_read);
modified(execution_space,datamask_modify);
sync(execution_space, datamask_read);
modified(execution_space, datamask_modify);
}
AtomVec *AtomKokkos::new_avec(const std::string &style,
int trysuffix, int &sflag)
AtomVec *AtomKokkos::new_avec(const std::string &style, int trysuffix, int &sflag)
{
AtomVec* avec = Atom::new_avec(style,trysuffix,sflag);
if (!avec->kokkosable)
error->all(FLERR,"KOKKOS package requires a kokkos enabled atom_style");
AtomVec *avec = Atom::new_avec(style, trysuffix, sflag);
if (!avec->kokkosable) error->all(FLERR, "KOKKOS package requires a kokkos enabled atom_style");
return avec;
}

38
src/KOKKOS/atom_kokkos.h
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@ -67,7 +67,43 @@ class AtomKokkos : public Atom {
AtomKokkos(class LAMMPS *);
~AtomKokkos();
virtual ~AtomKokkos();
void map_init(int check = 1);
void map_set();
void map_delete();
DAT::tdual_int_1d k_sametag;
DAT::tdual_int_1d k_map_array;
DAT::tdual_int_scalar k_error_flag;
dual_hash_type k_map_hash;
// map lookup function inlined for efficiency
// return -1 if no map defined
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
static int map_kokkos(tagint global, int map_style, DAT::tdual_int_1d k_map_array, dual_hash_type k_map_hash)
{
if (map_style == 1)
return k_map_array.view<DeviceType>()(global);
else if (map_style == 2)
return AtomKokkos::map_find_hash_kokkos<DeviceType>(global,k_map_hash);
else
return -1;
}
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
static int map_find_hash_kokkos(tagint global, dual_hash_type &k_map_hash)
{
int local = -1;
auto d_map_hash = k_map_hash.view<DeviceType>();
auto index = d_map_hash.find(global);
if (d_map_hash.valid_at(index))
local = d_map_hash.value_at(index);
return local;
}
virtual void allocate_type_arrays();
void sync(const ExecutionSpace space, unsigned int mask);

288
src/KOKKOS/atom_map_kokkos.cpp Normal file
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@ -0,0 +1,288 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "atom_kokkos.h"
#include "atom_masks.h"
#include "comm.h"
#include "error.h"
#include "fix.h"
#include "memory_kokkos.h"
#include "modify.h"
#include "neighbor_kokkos.h"
#include <cmath>
using namespace LAMMPS_NS;
#define EXTRA 1000
/* ----------------------------------------------------------------------
allocate and initialize array or hash table for global -> local map
for array option:
array length = 1 to map_tag_max
set entire array to -1 as initial values
for hash option:
map_nhash = length of hash table
map_nbucket = # of hash buckets, prime larger than map_nhash * 2
so buckets will only be filled with 0 or 1 atoms on average
------------------------------------------------------------------------- */
void AtomKokkos::map_init(int check)
{
// check for new map style if max atomID changed (check = 1 = default)
// recreate = 1 if must delete old map and create new map
// recreate = 0 if can re-use old map w/out realloc and just adjust settings
// map_maxarray/map_nhash initially -1, to force recreate even when no atoms
int recreate = 0;
if (check) recreate = map_style_set();
if (map_style == MAP_ARRAY && map_tag_max > map_maxarray)
recreate = 1;
else if (map_style == MAP_HASH && nlocal + nghost > map_nhash)
recreate = 1;
// if not recreating:
// for array, initialize current map_tag_max values
// for hash, set all buckets to empty, put all entries in free list
if (!recreate) {
if (map_style == MAP_ARRAY) {
for (int i = 0; i <= map_tag_max; i++) map_array[i] = -1;
} else {
for (int i = 0; i < map_nbucket; i++) map_bucket[i] = -1;
map_nused = 0;
map_free = 0;
for (int i = 0; i < map_nhash; i++) map_hash[i].next = i + 1;
if (map_nhash > 0) map_hash[map_nhash - 1].next = -1;
}
// recreating: delete old map and create new one for array or hash
} else {
map_delete();
if (map_style == MAP_ARRAY) {
map_maxarray = map_tag_max;
memoryKK->create_kokkos(k_map_array, map_array, map_maxarray + 1, "atom:map_array");
for (int i = 0; i <= map_tag_max; i++) map_array[i] = -1;
} else {
// map_nhash = max # of atoms that can be hashed on this proc
// set to max of ave atoms/proc or atoms I can store
// multiply by 2, require at least 1000
// doubling means hash table will need to be re-init only rarely
int nper = static_cast<int>(natoms / comm->nprocs);
map_nhash = MAX(nper, nmax);
map_nhash *= 2;
map_nhash = MAX(map_nhash, 1000);
// map_nbucket = prime just larger than map_nhash
// next_prime() should be fast enough,
// about 10% of odd integers are prime above 1M
map_nbucket = next_prime(map_nhash);
// set all buckets to empty
// set hash to map_nhash in length
// put all hash entries in free list and point them to each other
map_bucket = new int[map_nbucket];
for (int i = 0; i < map_nbucket; i++) map_bucket[i] = -1;
map_hash = new HashElem[map_nhash];
map_nused = 0;
map_free = 0;
for (int i = 0; i < map_nhash; i++) map_hash[i].next = i + 1;
map_hash[map_nhash - 1].next = -1;
// use "view" template method to avoid unnecessary deep_copy
auto h_map_hash = k_map_hash.view<LMPHostType>(); // get type
h_map_hash = decltype(h_map_hash)(map_nhash);
k_map_hash.view<LMPHostType>() = h_map_hash;
}
}
k_sametag.modify_host();
if (map_style == Atom::MAP_ARRAY) k_map_array.modify_host();
}
/* ----------------------------------------------------------------------
set global -> local map for all of my own and ghost atoms
loop in reverse order so that nearby images take precedence over far ones
and owned atoms take precedence over images
this enables valid lookups of bond topology atoms
for hash table option:
if hash table too small, re-init
global ID may already be in table if image atom was set
------------------------------------------------------------------------- */
void AtomKokkos::map_set()
{
int nall = nlocal + nghost;
atomKK->sync(Host, TAG_MASK);
k_sametag.sync_host();
if (map_style == Atom::MAP_ARRAY) k_map_array.sync_host();
if (map_style == MAP_ARRAY) {
// possible reallocation of sametag must come before loop over atoms
// since loop sets sametag
if (nall > max_same) {
max_same = nall + EXTRA;
memoryKK->destroy_kokkos(k_sametag, sametag);
memoryKK->create_kokkos(k_sametag, sametag, max_same, "atom:sametag");
}
for (int i = nall - 1; i >= 0; i--) {
sametag[i] = map_array[tag[i]];
map_array[tag[i]] = i;
}
} else {
// if this proc has more atoms than hash table size, call map_init()
// call with 0 since max atomID in system has not changed
// possible reallocation of sametag must come after map_init(),
// b/c map_init() may invoke map_delete(), whacking sametag
if (nall > map_nhash) map_init(0);
if (nall > max_same) {
max_same = nall + EXTRA;
memoryKK->destroy_kokkos(k_sametag, sametag);
memoryKK->create_kokkos(k_sametag, sametag, max_same, "atom:sametag");
}
int previous, ibucket, index;
tagint global;
for (int i = nall - 1; i >= 0; i--) {
sametag[i] = map_find_hash(tag[i]);
// search for key
// if found it, just overwrite local value with index
previous = -1;
global = tag[i];
ibucket = global % map_nbucket;
index = map_bucket[ibucket];
while (index > -1) {
if (map_hash[index].global == global) break;
previous = index;
index = map_hash[index].next;
}
if (index > -1) {
map_hash[index].local = i;
continue;
}
// take one entry from free list
// add the new global/local pair as entry at end of bucket list
// special logic if this entry is 1st in bucket
index = map_free;
map_free = map_hash[map_free].next;
if (previous == -1)
map_bucket[ibucket] = index;
else
map_hash[previous].next = index;
map_hash[index].global = global;
map_hash[index].local = i;
map_hash[index].next = -1;
map_nused++;
}
// Copy to Kokkos hash
// use "view" template method to avoid unnecessary deep_copy
auto h_map_hash = k_map_hash.view<LMPHostType>();
h_map_hash.clear();
for (int i = nall - 1; i >= 0; i--) {
// search for key
// if don't find it, done
previous = -1;
global = tag[i];
ibucket = global % map_nbucket;
index = map_bucket[ibucket];
while (index > -1) {
if (map_hash[index].global == global) break;
previous = index;
index = map_hash[index].next;
}
if (index == -1) continue;
int local = map_hash[index].local;
auto insert_result = h_map_hash.insert(global, local);
if (insert_result.failed()) error->one(FLERR, "Kokkos::UnorderedMap insertion failed");
}
}
k_sametag.modify_host();
if (map_style == Atom::MAP_ARRAY)
k_map_array.modify_host();
else if (map_style == Atom::MAP_HASH) {
// use "view" template method to avoid unnecessary deep_copy
auto h_map_hash = k_map_hash.view<LMPHostType>();
auto d_map_hash = k_map_hash.view<LMPDeviceType>();
// check if fix shake or neigh bond needs a device hash
int device_hash_flag = 0;
auto neighborKK = (NeighborKokkos *) neighbor;
if (neighborKK->device_flag) device_hash_flag = 1;
for (int n = 0; n < modify->nfix; n++)
if (utils::strmatch(modify->fix[n]->style, "^shake"))
if (modify->fix[n]->execution_space == Device) device_hash_flag = 1;
if (device_hash_flag) {
Kokkos::deep_copy(d_map_hash,h_map_hash);
k_map_hash.view<LMPDeviceType>() = d_map_hash;
}
}
}
/* ----------------------------------------------------------------------
free the array or hash table for global to local mapping
------------------------------------------------------------------------- */
void AtomKokkos::map_delete()
{
memoryKK->destroy_kokkos(k_sametag, sametag);
sametag = nullptr;
if (map_style == MAP_ARRAY) {
memoryKK->destroy_kokkos(k_map_array, map_array);
map_array = nullptr;
} else {
k_map_hash.h_view = host_hash_type();
k_map_hash.d_view = hash_type();
}
Atom::map_delete();
}

10
src/KOKKOS/atom_vec_dpd_kokkos.cpp
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@ -13,15 +13,15 @@
------------------------------------------------------------------------- */
#include "atom_vec_dpd_kokkos.h"
#include "atom_kokkos.h"
#include "atom_masks.h"
#include "comm_kokkos.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "atom_masks.h"
#include "memory_kokkos.h"
#include "error.h"
#include "fix.h"
#include "memory_kokkos.h"
#include "modify.h"
using namespace LAMMPS_NS;

10
src/KOKKOS/atom_vec_full_kokkos.cpp
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@ -13,15 +13,15 @@
------------------------------------------------------------------------- */
#include "atom_vec_full_kokkos.h"
#include "atom_kokkos.h"
#include "atom_masks.h"
#include "comm_kokkos.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "atom_masks.h"
#include "memory_kokkos.h"
#include "error.h"
#include "fix.h"
#include "memory_kokkos.h"
#include "modify.h"
using namespace LAMMPS_NS;

3
src/KOKKOS/comm_kokkos.cpp
View File

@ -1128,9 +1128,10 @@ void CommKokkos::borders_device() {
max = MAX(maxforward*rmax,maxreverse*smax);
if (max > maxrecv) grow_recv_kokkos(max);
atomKK->modified(exec_space,ALL_MASK);
// reset global->local map
atomKK->modified(exec_space,ALL_MASK);
if (map_style != Atom::MAP_NONE) {
atomKK->sync(Host,TAG_MASK);
atom->map_set();

83
src/KOKKOS/fix_shake_kokkos.cpp
View File

@ -201,6 +201,14 @@ void FixShakeKokkos<DeviceType>::pre_neighbor()
type = atom->type;
nlocal = atom->nlocal;
map_style = atom->map_style;
if (map_style == Atom::MAP_ARRAY) {
k_map_array = atomKK->k_map_array;
k_map_array.template sync<DeviceType>();
} else if (map_style == Atom::MAP_HASH) {
k_map_hash = atomKK->k_map_hash;
}
k_shake_flag.sync<DeviceType>();
k_shake_atom.sync<DeviceType>();
@ -213,21 +221,16 @@ void FixShakeKokkos<DeviceType>::pre_neighbor()
d_list = k_list.view<DeviceType>();
}
// don't yet have atom_map_kokkos routines, so move data from host to device
// Atom Map
if (atom->map_style != Atom::MAP_ARRAY)
error->all(FLERR,"Must use atom map style array with Kokkos");
map_style = atom->map_style;
int* map_array_host = atom->get_map_array();
int map_size = atom->get_map_size();
int map_maxarray = atom->get_map_maxarray();
if (map_maxarray > (int)k_map_array.extent(0))
k_map_array = DAT::tdual_int_1d("NeighBond:map_array",map_maxarray);
for (int i=0; i<map_size; i++)
k_map_array.h_view[i] = map_array_host[i];
k_map_array.template modify<LMPHostType>();
k_map_array.template sync<DeviceType>();
map_array = k_map_array.view<DeviceType>();
if (map_style == Atom::MAP_ARRAY) {
k_map_array = atomKK->k_map_array;
k_map_array.template sync<DeviceType>();
} else if (map_style == Atom::MAP_HASH) {
k_map_hash = atomKK->k_map_hash;
}
// build list of SHAKE clusters I compute
@ -241,14 +244,16 @@ void FixShakeKokkos<DeviceType>::pre_neighbor()
auto d_list = this->d_list;
auto d_error_flag = this->d_error_flag;
auto d_nlist = this->d_nlist;
auto map_array = this->map_array;
auto map_style = atom->map_style;
auto k_map_array = this->k_map_array;
auto k_map_hash = this->k_map_hash;
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType>(0,nlocal),
LAMMPS_LAMBDA(const int& i) {
if (d_shake_flag[i]) {
if (d_shake_flag[i] == 2) {
const int atom1 = map_array(d_shake_atom(i,0));
const int atom2 = map_array(d_shake_atom(i,1));
const int atom1 = AtomKokkos::map_kokkos<DeviceType>(d_shake_atom(i,0),map_style,k_map_array,k_map_hash);
const int atom2 = AtomKokkos::map_kokkos<DeviceType>(d_shake_atom(i,1),map_style,k_map_array,k_map_hash);
if (atom1 == -1 || atom2 == -1) {
d_error_flag() = 1;
}
@ -257,9 +262,9 @@ void FixShakeKokkos<DeviceType>::pre_neighbor()
d_list[nlist] = i;
}
} else if (d_shake_flag[i] % 2 == 1) {
const int atom1 = map_array(d_shake_atom(i,0));
const int atom2 = map_array(d_shake_atom(i,1));
const int atom3 = map_array(d_shake_atom(i,2));
const int atom1 = AtomKokkos::map_kokkos<DeviceType>(d_shake_atom(i,0),map_style,k_map_array,k_map_hash);
const int atom2 = AtomKokkos::map_kokkos<DeviceType>(d_shake_atom(i,1),map_style,k_map_array,k_map_hash);
const int atom3 = AtomKokkos::map_kokkos<DeviceType>(d_shake_atom(i,2),map_style,k_map_array,k_map_hash);
if (atom1 == -1 || atom2 == -1 || atom3 == -1)
d_error_flag() = 1;
if (i <= atom1 && i <= atom2 && i <= atom3) {
@ -267,10 +272,10 @@ void FixShakeKokkos<DeviceType>::pre_neighbor()
d_list[nlist] = i;
}
} else {
const int atom1 = map_array(d_shake_atom(i,0));
const int atom2 = map_array(d_shake_atom(i,1));
const int atom3 = map_array(d_shake_atom(i,2));
const int atom4 = map_array(d_shake_atom(i,3));
const int atom1 = AtomKokkos::map_kokkos<DeviceType>(d_shake_atom(i,0),map_style,k_map_array,k_map_hash);
const int atom2 = AtomKokkos::map_kokkos<DeviceType>(d_shake_atom(i,1),map_style,k_map_array,k_map_hash);
const int atom3 = AtomKokkos::map_kokkos<DeviceType>(d_shake_atom(i,2),map_style,k_map_array,k_map_hash);
const int atom4 = AtomKokkos::map_kokkos<DeviceType>(d_shake_atom(i,3),map_style,k_map_array,k_map_hash);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1)
d_error_flag() = 1;
if (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4) {
@ -307,6 +312,14 @@ void FixShakeKokkos<DeviceType>::post_force(int vflag)
d_mass = atomKK->k_mass.view<DeviceType>();
nlocal = atomKK->nlocal;
map_style = atom->map_style;
if (map_style == Atom::MAP_ARRAY) {
k_map_array = atomKK->k_map_array;
k_map_array.template sync<DeviceType>();
} else if (map_style == Atom::MAP_HASH) {
k_map_hash = atomKK->k_map_hash;
}
if (d_rmass.data())
atomKK->sync(execution_space,X_MASK|F_MASK|RMASS_MASK);
else
@ -586,8 +599,8 @@ void FixShakeKokkos<DeviceType>::shake(int m, EV_FLOAT& ev) const
// local atom IDs and constraint distances
int i0 = map_array(d_shake_atom(m,0));
int i1 = map_array(d_shake_atom(m,1));
int i0 = AtomKokkos::map_kokkos<DeviceType>(d_shake_atom(m,0),map_style,k_map_array,k_map_hash);
int i1 = AtomKokkos::map_kokkos<DeviceType>(d_shake_atom(m,1),map_style,k_map_array,k_map_hash);
double bond1 = d_bond_distance[d_shake_type(m,0)];
// r01 = distance vec between atoms, with PBC
@ -697,9 +710,9 @@ void FixShakeKokkos<DeviceType>::shake3(int m, EV_FLOAT& ev) const
// local atom IDs and constraint distances
int i0 = map_array(d_shake_atom(m,0));
int i1 = map_array(d_shake_atom(m,1));
int i2 = map_array(d_shake_atom(m,2));
int i0 = AtomKokkos::map_kokkos<DeviceType>(d_shake_atom(m,0),map_style,k_map_array,k_map_hash);
int i1 = AtomKokkos::map_kokkos<DeviceType>(d_shake_atom(m,1),map_style,k_map_array,k_map_hash);
int i2 = AtomKokkos::map_kokkos<DeviceType>(d_shake_atom(m,2),map_style,k_map_array,k_map_hash);
double bond1 = d_bond_distance[d_shake_type(m,0)];
double bond2 = d_bond_distance[d_shake_type(m,1)];
@ -880,10 +893,10 @@ void FixShakeKokkos<DeviceType>::shake4(int m, EV_FLOAT& ev) const
// local atom IDs and constraint distances
int i0 = map_array(d_shake_atom(m,0));
int i1 = map_array(d_shake_atom(m,1));
int i2 = map_array(d_shake_atom(m,2));
int i3 = map_array(d_shake_atom(m,3));
int i0 = AtomKokkos::map_kokkos<DeviceType>(d_shake_atom(m,0),map_style,k_map_array,k_map_hash);
int i1 = AtomKokkos::map_kokkos<DeviceType>(d_shake_atom(m,1),map_style,k_map_array,k_map_hash);
int i2 = AtomKokkos::map_kokkos<DeviceType>(d_shake_atom(m,2),map_style,k_map_array,k_map_hash);
int i3 = AtomKokkos::map_kokkos<DeviceType>(d_shake_atom(m,3),map_style,k_map_array,k_map_hash);
double bond1 = d_bond_distance[d_shake_type(m,0)];
double bond2 = d_bond_distance[d_shake_type(m,1)];
double bond3 = d_bond_distance[d_shake_type(m,2)];
@ -1142,9 +1155,9 @@ void FixShakeKokkos<DeviceType>::shake3angle(int m, EV_FLOAT& ev) const
// local atom IDs and constraint distances
int i0 = map_array(d_shake_atom(m,0));
int i1 = map_array(d_shake_atom(m,1));
int i2 = map_array(d_shake_atom(m,2));
int i0 = AtomKokkos::map_kokkos<DeviceType>(d_shake_atom(m,0),map_style,k_map_array,k_map_hash);
int i1 = AtomKokkos::map_kokkos<DeviceType>(d_shake_atom(m,1),map_style,k_map_array,k_map_hash);
int i2 = AtomKokkos::map_kokkos<DeviceType>(d_shake_atom(m,2),map_style,k_map_array,k_map_hash);
double bond1 = d_bond_distance[d_shake_type(m,0)];
double bond2 = d_bond_distance[d_shake_type(m,1)];
double bond12 = d_angle_distance[d_shake_type(m,2)];

8
src/KOKKOS/fix_shake_kokkos.h
View File

@ -26,6 +26,7 @@ FixStyle(shake/kk/host,FixShakeKokkos<LMPHostType>);
#include "fix_shake.h"
#include "kokkos_type.h"
#include "kokkos_base.h"
#include <Kokkos_UnorderedMap.hpp>
namespace LAMMPS_NS {
@ -172,9 +173,6 @@ class FixShakeKokkos : public FixShake, public KokkosBase {
KOKKOS_INLINE_FUNCTION
void v_tally(EV_FLOAT&, int, int *, double, double *) const;
DAT::tdual_int_1d k_map_array;
typename AT::t_int_1d_randomread map_array;
int iswap;
int first;
typename AT::t_int_2d d_sendlist;
@ -185,6 +183,10 @@ class FixShakeKokkos : public FixShake, public KokkosBase {
tagint **shake_atom_tmp;
int **shake_type_tmp;
int map_style;
DAT::tdual_int_1d k_map_array;
dual_hash_type k_map_hash;
// copied from Domain
KOKKOS_INLINE_FUNCTION

22
src/KOKKOS/kokkos_type.h
View File

@ -23,6 +23,7 @@
#include <impl/Kokkos_Timer.hpp>
#include <Kokkos_Vectorization.hpp>
#include <Kokkos_ScatterView.hpp>
#include <Kokkos_UnorderedMap.hpp>
enum{FULL=1u,HALFTHREAD=2u,HALF=4u};
@ -45,7 +46,9 @@ enum{FULL=1u,HALFTHREAD=2u,HALF=4u};
static constexpr LAMMPS_NS::bigint LMP_KOKKOS_AV_DELTA = 10;
namespace Kokkos {
using NoInit = ViewAllocateWithoutInitializing;
static auto NoInit = [](std::string const& label) {
return Kokkos::view_alloc(Kokkos::WithoutInitializing, label);
};
}
struct lmp_float3 {
@ -551,6 +554,23 @@ typedef int T_INT;
// LAMMPS types
typedef Kokkos::UnorderedMap<LAMMPS_NS::tagint,int,LMPDeviceType> hash_type;
typedef hash_type::HostMirror host_hash_type;
struct dual_hash_type {
hash_type d_view;
host_hash_type h_view;
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
std::enable_if_t<(std::is_same<DeviceType,LMPDeviceType>::value || Kokkos::SpaceAccessibility<LMPDeviceType::memory_space,LMPHostType::memory_space>::accessible),hash_type&> view() {return d_view;}
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
std::enable_if_t<!(std::is_same<DeviceType,LMPDeviceType>::value || Kokkos::SpaceAccessibility<LMPDeviceType::memory_space,LMPHostType::memory_space>::accessible),host_hash_type&> view() {return h_view;}
};
template <class DeviceType>
struct ArrayTypes;

101
src/KOKKOS/neigh_bond_kokkos.cpp
View File

@ -197,8 +197,6 @@ template<class DeviceType>
void NeighBondKokkos<DeviceType>::build_topology_kk()
{
atomKK->sync(execution_space, X_MASK | TAG_MASK);
int nall = atom->nlocal + atom->nghost;
int nmax = atom->nmax;
nlocal = atom->nlocal;
x = atomKK->k_x.view<DeviceType>();
@ -207,30 +205,7 @@ void NeighBondKokkos<DeviceType>::build_topology_kk()
lostbond = output->thermo->lostbond;
// don't yet have atom_map_kokkos routines, so move data from host to device
if (atom->map_style != Atom::MAP_ARRAY)
error->all(FLERR,"Must use atom map style array with Kokkos");
int* map_array_host = atom->get_map_array();
int map_size = atom->get_map_size();
int map_maxarray = atom->get_map_maxarray();
if (map_maxarray > (int)k_map_array.extent(0))
k_map_array = DAT::tdual_int_1d("NeighBond:map_array",map_maxarray);
for (int i=0; i<map_size; i++)
k_map_array.h_view[i] = map_array_host[i];
k_map_array.template modify<LMPHostType>();
k_map_array.template sync<DeviceType>();
map_array = k_map_array.view<DeviceType>();
int* sametag_host = atomKK->sametag;
if (nmax > (int)k_sametag.extent(0))
k_sametag = DAT::tdual_int_1d("NeighBond:sametag",nmax);
for (int i=0; i<nall; i++)
k_sametag.h_view[i] = sametag_host[i];
k_sametag.template modify<LMPHostType>();
k_sametag.template sync<DeviceType>();
sametag = k_sametag.view<DeviceType>();
update_class_variables();
if (force->bond) (this->*bond_build_kk)();
if (force->angle) (this->*angle_build_kk)();
@ -306,7 +281,7 @@ template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void NeighBondKokkos<DeviceType>::operator()(TagNeighBondBondAll, const int &i, int &nmissing) const {
for (int m = 0; m < num_bond[i]; m++) {
int atom1 = map_array(bond_atom(i,m));
int atom1 = AtomKokkos::map_kokkos<DeviceType>(bond_atom(i,m),map_style,k_map_array,k_map_hash);
if (atom1 == -1) {
nmissing++;
if (lostbond == Thermo::ERROR) return;
@ -394,7 +369,7 @@ KOKKOS_INLINE_FUNCTION
void NeighBondKokkos<DeviceType>::operator()(TagNeighBondBondPartial, const int &i, int &nmissing) const {
for (int m = 0; m < num_bond[i]; m++) {
if (bond_type(i,m) <= 0) continue;
int atom1 = map_array(bond_atom(i,m));
int atom1 = AtomKokkos::map_kokkos<DeviceType>(bond_atom(i,m),map_style,k_map_array,k_map_hash);
if (atom1 == -1) {
nmissing++;
if (lostbond == Thermo::ERROR) return;
@ -420,7 +395,6 @@ void NeighBondKokkos<DeviceType>::bond_check()
{
int flag = 0;
update_domain_variables();
atomKK->sync(execution_space, X_MASK);
k_bondlist.sync<DeviceType>();
@ -507,9 +481,9 @@ template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void NeighBondKokkos<DeviceType>::operator()(TagNeighBondAngleAll, const int &i, int &nmissing) const {
for (int m = 0; m < num_angle[i]; m++) {
int atom1 = map_array(angle_atom1(i,m));
int atom2 = map_array(angle_atom2(i,m));
int atom3 = map_array(angle_atom3(i,m));
int atom1 = AtomKokkos::map_kokkos<DeviceType>(angle_atom1(i,m),map_style,k_map_array,k_map_hash);
int atom2 = AtomKokkos::map_kokkos<DeviceType>(angle_atom2(i,m),map_style,k_map_array,k_map_hash);
int atom3 = AtomKokkos::map_kokkos<DeviceType>(angle_atom3(i,m),map_style,k_map_array,k_map_hash);
if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
nmissing++;
if (lostbond == Thermo::ERROR) return;
@ -602,9 +576,9 @@ KOKKOS_INLINE_FUNCTION
void NeighBondKokkos<DeviceType>::operator()(TagNeighBondAnglePartial, const int &i, int &nmissing) const {
for (int m = 0; m < num_angle[i]; m++) {
if (angle_type(i,m) <= 0) continue;
int atom1 = map_array(angle_atom1(i,m));
int atom2 = map_array(angle_atom2(i,m));
int atom3 = map_array(angle_atom3(i,m));
int atom1 = AtomKokkos::map_kokkos<DeviceType>(angle_atom1(i,m),map_style,k_map_array,k_map_hash);
int atom2 = AtomKokkos::map_kokkos<DeviceType>(angle_atom2(i,m),map_style,k_map_array,k_map_hash);
int atom3 = AtomKokkos::map_kokkos<DeviceType>(angle_atom3(i,m),map_style,k_map_array,k_map_hash);
if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
nmissing++;
if (lostbond == Thermo::ERROR) return;
@ -636,7 +610,6 @@ void NeighBondKokkos<DeviceType>::angle_check()
// check all 3 distances
// in case angle potential computes any of them
update_domain_variables();
atomKK->sync(execution_space, X_MASK);
k_anglelist.sync<DeviceType>();
@ -735,10 +708,10 @@ template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void NeighBondKokkos<DeviceType>::operator()(TagNeighBondDihedralAll, const int &i, int &nmissing) const {
for (int m = 0; m < num_dihedral[i]; m++) {
int atom1 = map_array(dihedral_atom1(i,m));
int atom2 = map_array(dihedral_atom2(i,m));
int atom3 = map_array(dihedral_atom3(i,m));
int atom4 = map_array(dihedral_atom4(i,m));
int atom1 = AtomKokkos::map_kokkos<DeviceType>(dihedral_atom1(i,m),map_style,k_map_array,k_map_hash);
int atom2 = AtomKokkos::map_kokkos<DeviceType>(dihedral_atom2(i,m),map_style,k_map_array,k_map_hash);
int atom3 = AtomKokkos::map_kokkos<DeviceType>(dihedral_atom3(i,m),map_style,k_map_array,k_map_hash);
int atom4 = AtomKokkos::map_kokkos<DeviceType>(dihedral_atom4(i,m),map_style,k_map_array,k_map_hash);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
nmissing++;
if (lostbond == Thermo::ERROR) return;
@ -835,10 +808,10 @@ KOKKOS_INLINE_FUNCTION
void NeighBondKokkos<DeviceType>::operator()(TagNeighBondDihedralPartial, const int &i, int &nmissing) const {
for (int m = 0; m < num_dihedral[i]; m++) {
if (dihedral_type(i,m) <= 0) continue;
int atom1 = map_array(dihedral_atom1(i,m));
int atom2 = map_array(dihedral_atom2(i,m));
int atom3 = map_array(dihedral_atom3(i,m));
int atom4 = map_array(dihedral_atom4(i,m));
int atom1 = AtomKokkos::map_kokkos<DeviceType>(dihedral_atom1(i,m),map_style,k_map_array,k_map_hash);
int atom2 = AtomKokkos::map_kokkos<DeviceType>(dihedral_atom2(i,m),map_style,k_map_array,k_map_hash);
int atom3 = AtomKokkos::map_kokkos<DeviceType>(dihedral_atom3(i,m),map_style,k_map_array,k_map_hash);
int atom4 = AtomKokkos::map_kokkos<DeviceType>(dihedral_atom4(i,m),map_style,k_map_array,k_map_hash);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
nmissing++;
if (lostbond == Thermo::ERROR) return;
@ -874,7 +847,6 @@ void NeighBondKokkos<DeviceType>::dihedral_check(int nlist, typename AT::t_int_2
// check all 6 distances
// in case dihedral/improper potential computes any of them
update_domain_variables();
atomKK->sync(execution_space, X_MASK);
k_dihedrallist.sync<DeviceType>();
@ -990,10 +962,10 @@ template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void NeighBondKokkos<DeviceType>::operator()(TagNeighBondImproperAll, const int &i, int &nmissing) const {
for (int m = 0; m < num_improper[i]; m++) {
int atom1 = map_array(improper_atom1(i,m));
int atom2 = map_array(improper_atom2(i,m));
int atom3 = map_array(improper_atom3(i,m));
int atom4 = map_array(improper_atom4(i,m));
int atom1 = AtomKokkos::map_kokkos<DeviceType>(improper_atom1(i,m),map_style,k_map_array,k_map_hash);
int atom2 = AtomKokkos::map_kokkos<DeviceType>(improper_atom2(i,m),map_style,k_map_array,k_map_hash);
int atom3 = AtomKokkos::map_kokkos<DeviceType>(improper_atom3(i,m),map_style,k_map_array,k_map_hash);
int atom4 = AtomKokkos::map_kokkos<DeviceType>(improper_atom4(i,m),map_style,k_map_array,k_map_hash);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
nmissing++;
if (lostbond == Thermo::ERROR) return;
@ -1090,10 +1062,10 @@ KOKKOS_INLINE_FUNCTION
void NeighBondKokkos<DeviceType>::operator()(TagNeighBondImproperPartial, const int &i, int &nmissing) const {
for (int m = 0; m < num_improper[i]; m++) {
if (improper_type(i,m) <= 0) continue;
int atom1 = map_array(improper_atom1(i,m));
int atom2 = map_array(improper_atom2(i,m));
int atom3 = map_array(improper_atom3(i,m));
int atom4 = map_array(improper_atom4(i,m));
int atom1 = AtomKokkos::map_kokkos<DeviceType>(improper_atom1(i,m),map_style,k_map_array,k_map_hash);
int atom2 = AtomKokkos::map_kokkos<DeviceType>(improper_atom2(i,m),map_style,k_map_array,k_map_hash);
int atom3 = AtomKokkos::map_kokkos<DeviceType>(improper_atom3(i,m),map_style,k_map_array,k_map_hash);
int atom4 = AtomKokkos::map_kokkos<DeviceType>(improper_atom4(i,m),map_style,k_map_array,k_map_hash);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
nmissing++;
if (lostbond == Thermo::ERROR) return;
@ -1137,8 +1109,8 @@ int NeighBondKokkos<DeviceType>::closest_image(const int i, int j) const
X_FLOAT rsqmin = delx*delx + dely*dely + delz*delz;
X_FLOAT rsq;
while (sametag[j] >= 0) {
j = sametag[j];
while (d_sametag[j] >= 0) {
j = d_sametag[j];
delx = xi0 - x(j,0);
dely = xi1 - x(j,1);
delz = xi2 - x(j,2);
@ -1218,8 +1190,10 @@ void NeighBondKokkos<DeviceType>::minimum_image(X_FLOAT &dx, X_FLOAT &dy, X_FLOA
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void NeighBondKokkos<DeviceType>::update_domain_variables()
void NeighBondKokkos<DeviceType>::update_class_variables()
{
// Domain
triclinic = domain->triclinic;
xperiodic = domain->xperiodic;
xprd_half = domain->xprd_half;
@ -1233,6 +1207,21 @@ void NeighBondKokkos<DeviceType>::update_domain_variables()
xy = domain->xy;
xz = domain->xz;
yz = domain->yz;
// Atom Map
map_style = atom->map_style;
k_sametag = atomKK->k_sametag;
k_sametag.template sync<DeviceType>();
d_sametag = k_sametag.view<DeviceType>();
if (map_style == Atom::MAP_ARRAY) {
k_map_array = atomKK->k_map_array;
k_map_array.template sync<DeviceType>();
} else if (map_style == Atom::MAP_HASH) {
k_map_hash = atomKK->k_map_hash;
}
}
/* ---------------------------------------------------------------------- */

17
src/KOKKOS/neigh_bond_kokkos.h
View File

@ -19,6 +19,7 @@
#include "kokkos_type.h"
#include "domain_kokkos.h"
#include "pointers.h"
#include <Kokkos_UnorderedMap.hpp>
namespace LAMMPS_NS {
@ -81,13 +82,11 @@ class NeighBondKokkos : protected Pointers {
int me,nprocs;
private:
DAT::tdual_int_1d k_map_array;
typename AT::t_int_1d_randomread map_array;
int map_style;
DAT::tdual_int_1d k_sametag;
typename AT::t_int_1d_randomread sametag;
typename AT::t_int_1d d_sametag;
DAT::tdual_int_1d k_map_array;
dual_hash_type k_map_hash;
typename AT::t_int_2d v_bondlist;
typename AT::t_int_2d v_anglelist;
@ -130,7 +129,7 @@ class NeighBondKokkos : protected Pointers {
KOKKOS_INLINE_FUNCTION
void minimum_image(X_FLOAT &dx, X_FLOAT &dy, X_FLOAT &dz) const;
void update_domain_variables();
void update_class_variables();
// topology build functions
@ -174,10 +173,6 @@ class NeighBondKokkos : protected Pointers {
/* ERROR/WARNING messages:
E: Must use atom map style array with Kokkos
See the atom_modify map command.
E: Bond atoms missing on proc %d at step %ld
The 2nd atom needed to compute a particular bond is missing on this

3
src/KOKKOS/neighbor_kokkos.h
View File

@ -64,13 +64,14 @@ class NeighborKokkos : public Neighbor {
DAT::tdual_int_2d k_dihedrallist;
DAT::tdual_int_2d k_improperlist;
int device_flag;
private:
DAT::tdual_x_array x;
DAT::tdual_x_array xhold;
X_FLOAT deltasq;
int device_flag;
void init_cutneighsq_kokkos(int);
void create_kokkos_list(int);

2
src/OPENMP/reaxc_init_md_omp.cpp
View File

@ -111,7 +111,7 @@ int Init_ListsOMP(reax_system *system, control_params *control,
free(hb_top);
free(bond_top);
return SUCCESS;
return REAXC_SUCCESS;
}
/* ---------------------------------------------------------------------- */

12
src/REAXFF/reaxc_allocate.cpp
View File

@ -66,7 +66,7 @@ int PreAllocate_Space( reax_system *system, control_params * /*control*/,
LMP_UNUSED_PARAM(workspace);
#endif
return SUCCESS;
return REAXC_SUCCESS;
}
@ -78,7 +78,7 @@ int Allocate_System( reax_system *system, int /*local_cap*/, int total_cap,
system->my_atoms = (reax_atom*)
realloc( system->my_atoms, total_cap*sizeof(reax_atom) );
return SUCCESS;
return REAXC_SUCCESS;
}
@ -315,7 +315,7 @@ int Allocate_Workspace( reax_system * /*system*/, control_params * control,
LMP_UNUSED_PARAM(control);
#endif
return SUCCESS;
return REAXC_SUCCESS;
}
@ -392,7 +392,7 @@ static int Reallocate_Bonds_List( reax_system *system, reax_list *bonds,
(double*) smalloc(system->error_ptr, sizeof(double)*nthreads, "CdboReduction");
#endif
return SUCCESS;
return REAXC_SUCCESS;
}
@ -426,7 +426,7 @@ void ReAllocate( reax_system *system, control_params *control,
if (Nflag) {
/* system */
ret = Allocate_System( system, system->local_cap, system->total_cap, msg );
if (ret != SUCCESS) {
if (ret != REAXC_SUCCESS) {
char errmsg[256];
snprintf(errmsg, 256, "Not enough space for atom_list: total_cap=%d", system->total_cap);
system->error_ptr->one(FLERR, errmsg);
@ -436,7 +436,7 @@ void ReAllocate( reax_system *system, control_params *control,
DeAllocate_Workspace( control, workspace );
ret = Allocate_Workspace( system, control, workspace, system->local_cap,
system->total_cap, msg );
if (ret != SUCCESS) {
if (ret != REAXC_SUCCESS) {
char errmsg[256];
snprintf(errmsg, 256, "Not enough space for workspace: local_cap=%d total_cap=%d", system->local_cap, system->total_cap);
system->error_ptr->one(FLERR, errmsg);

2
src/REAXFF/reaxc_control.cpp
View File

@ -387,5 +387,5 @@ char Read_Control_File( char *control_file, control_params* control,
fclose(fp);
return SUCCESS;
return REAXC_SUCCESS;
}

4
src/REAXFF/reaxc_defs.h
View File

@ -34,8 +34,8 @@
#define inline __inline__
#endif /*IBMC*/
#ifndef SUCCESS
#define SUCCESS 1
#ifndef REAXC_SUCCESS
#define REAXC_SUCCESS 1
#endif
#ifndef FAILURE
#define FAILURE 0

2
src/REAXFF/reaxc_ffield.cpp
View File

@ -736,5 +736,5 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax,
fclose(fp);
return SUCCESS;
return REAXC_SUCCESS;
}

12
src/REAXFF/reaxc_init_md.cpp
View File

@ -67,7 +67,7 @@ int Init_System(reax_system *system, control_params *control, char * /*msg*/)
}
system->Hcap = (int)(MAX(system->numH * saferzone, mincap));
return SUCCESS;
return REAXC_SUCCESS;
}
@ -83,7 +83,7 @@ int Init_Simulation_Data(reax_system *system, control_params *control,
data->step = data->prev_steps = 0;
return SUCCESS;
return REAXC_SUCCESS;
}
void Init_Taper(control_params *control, storage *workspace)
@ -134,7 +134,7 @@ int Init_Workspace(reax_system *system, control_params *control,
ret = Allocate_Workspace(system, control, workspace,
system->local_cap, system->total_cap, msg);
if (ret != SUCCESS)
if (ret != REAXC_SUCCESS)
return ret;
memset(&(workspace->realloc), 0, sizeof(reallocate_data));
@ -143,7 +143,7 @@ int Init_Workspace(reax_system *system, control_params *control,
/* Initialize the Taper function */
Init_Taper(control, workspace);
return SUCCESS;
return REAXC_SUCCESS;
}
@ -156,7 +156,7 @@ int Init_MPI_Datatypes(reax_system *system, storage * /*workspace*/,
mpi_data->world = comm;
MPI_Comm_size(comm, &(system->wsize));
return SUCCESS;
return REAXC_SUCCESS;
}
int Init_Lists(reax_system *system, control_params *control,
@ -216,7 +216,7 @@ int Init_Lists(reax_system *system, control_params *control,
free(hb_top);
free(bond_top);
return SUCCESS;
return REAXC_SUCCESS;
}
void Initialize(reax_system *system, control_params *control,

4
src/REAXFF/reaxc_io_tools.cpp
View File

@ -78,7 +78,7 @@ int Init_Output_Files( reax_system *system, control_params *control,
}
}
return SUCCESS;
return REAXC_SUCCESS;
}
@ -101,7 +101,7 @@ int Close_Output_Files( reax_system *system, control_params * /* control */,
}
}
return SUCCESS;
return REAXC_SUCCESS;
}

2
src/REAXFF/reaxc_list.cpp
View File

@ -95,7 +95,7 @@ int Make_List(int n, int num_intrs, int type, reax_list *l )
l->error_ptr->one(FLERR,errmsg);
}
return SUCCESS;
return REAXC_SUCCESS;
}

20
src/REAXFF/reaxc_traj.cpp
View File

@ -48,7 +48,7 @@ int Reallocate_Output_Buffer( LAMMPS_NS::Error *error_ptr, output_controls *out_
error_ptr->one(FLERR,errmsg);
}
return SUCCESS;
return REAXC_SUCCESS;
}
@ -259,7 +259,7 @@ int Write_Header( reax_system *system, control_params *control,
if (system->my_rank == MASTER_NODE)
fprintf( out_control->strj, "%s", out_control->buffer );
return SUCCESS;
return REAXC_SUCCESS;
}
@ -311,7 +311,7 @@ int Write_Init_Desc( reax_system *system, control_params * /*control*/,
fprintf( out_control->strj, "%s", out_control->buffer );
}
return SUCCESS;
return REAXC_SUCCESS;
}
@ -355,7 +355,7 @@ int Init_Traj( reax_system *system, control_params *control,
Write_Header( system, control, out_control, mpi_data );
Write_Init_Desc( system, control, out_control, mpi_data );
return SUCCESS;
return REAXC_SUCCESS;
}
@ -480,7 +480,7 @@ int Write_Frame_Header( reax_system *system, control_params *control,
if (system->my_rank == MASTER_NODE)
fprintf( out_control->strj, "%s", out_control->buffer );
return SUCCESS;
return REAXC_SUCCESS;
}
@ -557,7 +557,7 @@ int Write_Atoms( reax_system *system, control_params * /*control*/,
fprintf( out_control->strj, "%s", out_control->buffer );
}
return SUCCESS;
return REAXC_SUCCESS;
}
@ -646,7 +646,7 @@ int Write_Bonds(reax_system *system, control_params *control, reax_list *bonds,
fprintf( out_control->strj, "%s", out_control->buffer );
}
return SUCCESS;
return REAXC_SUCCESS;
}
@ -741,7 +741,7 @@ int Write_Angles( reax_system *system, control_params *control,
fprintf( out_control->strj, "%s", out_control->buffer );
}
return SUCCESS;
return REAXC_SUCCESS;
}
@ -761,7 +761,7 @@ int Append_Frame( reax_system *system, control_params *control,
Write_Angles( system, control, (*lists + BONDS), (*lists + THREE_BODIES),
out_control, mpi_data );
return SUCCESS;
return REAXC_SUCCESS;
}
@ -773,5 +773,5 @@ int End_Traj( int my_rank, output_controls *out_control )
free( out_control->buffer );
free( out_control->line );
return SUCCESS;
return REAXC_SUCCESS;
}

10
src/atom.h
View File

@ -275,7 +275,7 @@ class Atom : protected Pointers {
// functions
Atom(class LAMMPS *);
~Atom();
virtual ~Atom();
void settings(class Atom *);
void peratom_create();
@ -364,12 +364,12 @@ class Atom : protected Pointers {
return -1;
};
void map_init(int check = 1);
void map_clear();
void map_set();
virtual void map_init(int check = 1);
virtual void map_clear();
virtual void map_set();
void map_one(tagint, int);
int map_style_set();
void map_delete();
virtual void map_delete();
int map_find_hash(tagint);
protected:

2
src/atom_map.cpp
View File

@ -309,7 +309,7 @@ int Atom::map_style_set()
if (map_user == MAP_ARRAY || map_user == MAP_HASH) {
map_style = map_user;
} else { // map_user == MAP_YES
if (map_tag_max > 1000000 && !lmp->kokkos) map_style = MAP_HASH;
if (map_tag_max > 1000000) map_style = MAP_HASH;
else map_style = MAP_ARRAY;
}