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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11627 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2014-03-12 16:37:16 +00:00
parent 039af550a0
commit 5bdd5c3c25
16 changed files with 173 additions and 82 deletions
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2
src/accelerator_cuda.h
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@ -32,6 +32,8 @@
// needed for compiling when USER-CUDA is not installed
#include "comm.h"
#include "domain.h"
#include "neighbor.h"
#include "modify.h"
#include "verlet.h"

24
src/accelerator_kokkos.h
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@ -22,6 +22,8 @@
#include "kokkos.h"
#include "atom_kokkos.h"
#include "comm_kokkos.h"
#include "domain_kokkos.h"
#include "neighbor_kokkos.h"
#include "modify_kokkos.h"
#else
@ -29,6 +31,12 @@
// dummy interface to KOKKOS
// needed for compiling when KOKKOS is not installed
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "neighbor.h"
#include "modify.h"
namespace LAMMPS_NS {
class KokkosLMP {
@ -38,29 +46,37 @@ class KokkosLMP {
KokkosLMP(class LAMMPS *, int, char **) {kokkos_exists = 0;}
~KokkosLMP() {}
void accelerator(int, char **) {}
int neigh_list_kokkos(int) {return 0;}
int neigh_count(int) {return 0;}
};
class AtomKokkos : public Atom {
public:
AtomKokkos(class LAMMPS *lmp) : Atom(lmp) {}
AtomKokkos(class LAMMPS *lmp) : Atom(lmp) {}
~AtomKokkos() {}
};
class CommKokkos : public Comm {
public:
CommKokkos(class LAMMPS *lmp) : Comm(lmp) {}
CommKokkos(class LAMMPS *lmp) : Comm(lmp) {}
~CommKokkos() {}
};
class DomainKokkos : public Domain {
public:
DomainKokkos(class LAMMPS *lmp) : Domain(lmp) {}
~DomainKokkos() {}
};
class NeighborKokkos : public Neighbor {
public:
NeighborKokkos(class LAMMPS *lmp) : Neighbor(lmp) {}
NeighborKokkos(class LAMMPS *lmp) : Neighbor(lmp) {}
~NeighborKokkos() {}
};
class ModifyKokkos : public Modify {
public:
ModifyKokkos(class LAMMPS *lmp) : Modify(lmp) {}
ModifyKokkos(class LAMMPS *lmp) : Modify(lmp) {}
~ModifyKokkos() {}
};

4
src/atom.h
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@ -62,8 +62,8 @@ class Atom : protected Pointers {
double *eradius,*ervel,*erforce,*ervelforce;
double *cs,*csforce,*vforce;
int *etag;
double *rho, *drho;
double *e, *de;
double *rho,*drho;
double *e,*de;
double **vest;
double *cv;

38
src/finish.cpp
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@ -16,8 +16,9 @@
#include "string.h"
#include "stdio.h"
#include "finish.h"
#include "timer.h"
#include "lammps.h"
#include "universe.h"
#include "accelerator_kokkos.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
@ -29,6 +30,7 @@
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "timer.h"
#include "output.h"
#include "memory.h"
@ -527,22 +529,28 @@ void Finish::end(int flag)
// find a non-skip neighbor list containing half the pairwise interactions
// count neighbors in that list for stats purposes
// allow it to be Kokkos neigh list as well
for (m = 0; m < neighbor->old_nrequest; m++)
for (m = 0; m < neighbor->old_nrequest; m++) {
if ((neighbor->old_requests[m]->half ||
neighbor->old_requests[m]->gran ||
neighbor->old_requests[m]->respaouter ||
neighbor->old_requests[m]->half_from_full) &&
neighbor->old_requests[m]->skip == 0 &&
neighbor->lists[m]->numneigh) break;
neighbor->old_requests[m]->skip == 0) {
if (neighbor->lists[m] && neighbor->lists[m]->numneigh) break;
if (lmp->kokkos && lmp->kokkos->neigh_list_kokkos(m)) break;
}
}
nneigh = 0;
if (m < neighbor->old_nrequest) {
int inum = neighbor->lists[m]->inum;
int *ilist = neighbor->lists[m]->ilist;
int *numneigh = neighbor->lists[m]->numneigh;
for (i = 0; i < inum; i++)
nneigh += numneigh[ilist[i]];
if (neighbor->lists[m]) {
int inum = neighbor->lists[m]->inum;
int *ilist = neighbor->lists[m]->ilist;
int *numneigh = neighbor->lists[m]->numneigh;
for (i = 0; i < inum; i++)
nneigh += numneigh[ilist[i]];
} else if (lmp->kokkos) nneigh = lmp->kokkos->neigh_count(m);
}
tmp = nneigh;
@ -565,19 +573,23 @@ void Finish::end(int flag)
// find a non-skip neighbor list containing full pairwise interactions
// count neighbors in that list for stats purposes
for (m = 0; m < neighbor->old_nrequest; m++)
for (m = 0; m < neighbor->old_nrequest; m++) {
if (neighbor->old_requests[m]->full &&
neighbor->old_requests[m]->skip == 0) break;
neighbor->old_requests[m]->skip == 0) {
if (neighbor->lists[m] && neighbor->lists[m]->numneigh) break;
if (lmp->kokkos && lmp->kokkos->neigh_list_kokkos(m)) break;
}
}
nneighfull = 0;
if (m < neighbor->old_nrequest) {
if (neighbor->lists[m]->numneigh > 0) {
if (neighbor->lists[m]) {
int inum = neighbor->lists[m]->inum;
int *ilist = neighbor->lists[m]->ilist;
int *numneigh = neighbor->lists[m]->numneigh;
for (i = 0; i < inum; i++)
nneighfull += numneigh[ilist[i]];
}
} else if (lmp->kokkos) nneighfull = lmp->kokkos->neigh_count(m);
tmp = nneighfull;
stats(1,&tmp,&ave,&max,&min,10,histo);

5
src/fix.cpp
View File

@ -79,8 +79,9 @@ Fix::Fix(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
datamask = ALL_MASK;
datamask_ext = ALL_MASK;
datamask_read = datamask_read_ext = ALL_MASK;
datamask_modify = datamask_modify_ext = ALL_MASK;
execution_space = Host;
datamask_read = ALL_MASK;
datamask_modify = ALL_MASK;
}
/* ---------------------------------------------------------------------- */

4
src/fix.h
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@ -84,10 +84,10 @@ class Fix : protected Pointers {
int restart_reset; // 1 if restart just re-initialized fix
// KOKKOS host/device flag and per-fix data masks
// KOKKOS host/device flag and data masks
ExecutionSpace execution_space;
unsigned int datamask_read, datamask_modify;
unsigned int datamask_read,datamask_modify;
// USER-CUDA per-fix data masks

3
src/lammps.cpp
View File

@ -553,9 +553,11 @@ void LAMMPS::create()
else comm = new Comm(this);
if (cuda) neighbor = new NeighborCuda(this);
else if (kokkos) neighbor = new NeighborKokkos(this);
else neighbor = new Neighbor(this);
if (cuda) domain = new DomainCuda(this);
else if (kokkos) domain = new DomainKokkos(this);
#ifdef LMP_USER_OMP
else domain = new DomainOMP(this);
#else
@ -630,6 +632,7 @@ void LAMMPS::destroy()
delete force;
delete group;
delete output;
delete modify; // modify must come after output, force, update
// since they delete fixes
delete domain; // domain must come after modify

4
src/neigh_list.h
View File

@ -78,7 +78,7 @@ class NeighList : protected Pointers {
class CudaNeighList *cuda_list; // CUDA neighbor list
NeighList(class LAMMPS *);
~NeighList();
virtual ~NeighList();
void setup_pages(int, int, int); // setup page data structures
void grow(int); // grow maxlocal
void stencil_allocate(int, int); // allocate stencil arrays
@ -87,7 +87,7 @@ class NeighList : protected Pointers {
int get_maxlocal() {return maxatoms;}
bigint memory_usage();
private:
protected:
int maxatoms; // size of allocated atom arrays
};

2
src/neigh_request.cpp
View File

@ -45,6 +45,7 @@ NeighRequest::NeighRequest(LAMMPS *lmp) : Pointers(lmp)
// default is no neighbors of ghosts
// default is no CUDA neighbor list build
// default is no multi-threaded neighbor list build
// default is no Kokkos neighbor list build
occasional = 0;
newton = 0;
@ -53,6 +54,7 @@ NeighRequest::NeighRequest(LAMMPS *lmp) : Pointers(lmp)
ghost = 0;
cudable = 0;
omp = 0;
kokkos_host = kokkos_device = 0;
// default is no copy or skip

5
src/neigh_request.h
View File

@ -80,6 +80,11 @@ class NeighRequest : protected Pointers {
int omp;
// 1 if using Kokkos neighbor build
int kokkos_host;
int kokkos_device;
// set by neighbor and pair_hybrid after all requests are made
// these settings do not change kind value

132
src/neighbor.cpp
View File

@ -243,7 +243,8 @@ void Neighbor::init()
n = atom->ntypes;
if (cutneighsq == NULL) {
memory->create(cutneighsq,n+1,n+1,"neigh:cutneighsq");
if (lmp->kokkos) init_cutneighsq_kokkos(n);
else memory->create(cutneighsq,n+1,n+1,"neigh:cutneighsq");
memory->create(cutneighghostsq,n+1,n+1,"neigh:cutneighghostsq");
cuttype = new double[n+1];
cuttypesq = new double[n+1];
@ -468,16 +469,27 @@ void Neighbor::init()
delete [] pair_build;
delete [] stencil_create;
nlist = nrequest;
lists = new NeighList*[nlist];
pair_build = new PairPtr[nlist];
stencil_create = new StencilPtr[nlist];
if (lmp->kokkos) nlist = init_lists_kokkos();
else nlist = nrequest;
lists = new NeighList*[nrequest];
pair_build = new PairPtr[nrequest];
stencil_create = new StencilPtr[nrequest];
// initialize to NULL since some may be Kokkos lists
for (i = 0; i < nrequest; i++) {
lists[i] = NULL;
pair_build[i] = NULL;
stencil_create[i] = NULL;
}
// create individual lists, one per request
// pass list ptr back to requestor (except for Command class)
// wait to allocate initial pages until copy lists are detected
for (i = 0; i < nlist; i++) {
for (i = 0; i < nrequest; i++) {
if (requests[i]->kokkos_host || requests[i]->kokkos_device) continue;
lists[i] = new NeighList(lmp);
lists[i]->index = i;
@ -520,7 +532,8 @@ void Neighbor::init()
int processed;
for (i = 0; i < nlist; i++) {
for (i = 0; i < nrequest; i++) {
if (!lists[i]) continue;
processed = 0;
if (requests[i]->copy) {
@ -559,17 +572,20 @@ void Neighbor::init()
if (processed) continue;
if (requests[i]->pair && requests[i]->half) {
for (j = 0; j < nlist; j++)
for (j = 0; j < nrequest; j++) {
if (!lists[j]) continue;
if (requests[j]->full && requests[j]->occasional == 0 &&
requests[j]->skip == 0) break;
if (j < nlist) {
}
if (j < nrequest) {
requests[i]->half = 0;
requests[i]->half_from_full = 1;
lists[i]->listfull = lists[j];
}
} else if (requests[i]->fix || requests[i]->compute) {
for (j = 0; j < nlist; j++) {
for (j = 0; j < nrequest; j++) {
if (!lists[j]) continue;
if (requests[i]->half && requests[j]->pair &&
requests[j]->skip == 0 && requests[j]->half) break;
if (requests[i]->full && requests[j]->pair &&
@ -579,20 +595,21 @@ void Neighbor::init()
if (requests[i]->half && requests[j]->pair &&
requests[j]->skip == 0 && requests[j]->respaouter) break;
}
if (j < nlist && requests[j]->cudable != requests[i]->cudable)
j = nlist;
if (j < nlist) {
if (j < nrequest && requests[j]->cudable != requests[i]->cudable)
j = nrequest;
if (j < nrequest) {
requests[i]->copy = 1;
requests[i]->otherlist = j;
lists[i]->listcopy = lists[j];
} else {
for (j = 0; j < nlist; j++) {
for (j = 0; j < nrequest; j++) {
if (!lists[j]) continue;
if (requests[i]->half && requests[j]->pair &&
requests[j]->skip == 0 && requests[j]->full) break;
}
if (j < nlist && requests[j]->cudable != requests[i]->cudable)
j = nlist;
if (j < nlist) {
if (j < nrequest && requests[j]->cudable != requests[i]->cudable)
j = nrequest;
if (j < nrequest) {
requests[i]->half = 0;
requests[i]->half_from_full = 1;
lists[i]->listfull = lists[j];
@ -603,15 +620,17 @@ void Neighbor::init()
// allocate initial pages for each list, except if listcopy set
for (i = 0; i < nlist; i++)
for (i = 0; i < nrequest; i++) {
if (!lists[i]) continue;
if (!lists[i]->listcopy)
lists[i]->setup_pages(pgsize,oneatom,requests[i]->dnum);
}
// set ptrs to pair_build and stencil_create functions for each list
// ptrs set to NULL if not set explicitly
// also set cudable to 0 if any neigh list request is not cudable
for (i = 0; i < nlist; i++) {
for (i = 0; i < nrequest; i++) {
choose_build(i,requests[i]);
if (style != NSQ) choose_stencil(i,requests[i]);
else stencil_create[i] = NULL;
@ -626,32 +645,37 @@ void Neighbor::init()
// anyghostlist = 1 if any non-occasional list stores neighbors of ghosts
anyghostlist = 0;
for (i = 0; i < nlist; i++) {
lists[i]->buildflag = 1;
if (pair_build[i] == NULL) lists[i]->buildflag = 0;
if (requests[i]->occasional) lists[i]->buildflag = 0;
for (i = 0; i < nrequest; i++) {
if (lists[i]) {
lists[i]->buildflag = 1;
if (pair_build[i] == NULL) lists[i]->buildflag = 0;
if (requests[i]->occasional) lists[i]->buildflag = 0;
lists[i]->growflag = 1;
if (requests[i]->copy) lists[i]->growflag = 0;
lists[i]->growflag = 1;
if (requests[i]->copy) lists[i]->growflag = 0;
lists[i]->stencilflag = 1;
if (style == NSQ) lists[i]->stencilflag = 0;
if (stencil_create[i] == NULL) lists[i]->stencilflag = 0;
lists[i]->stencilflag = 1;
if (style == NSQ) lists[i]->stencilflag = 0;
if (stencil_create[i] == NULL) lists[i]->stencilflag = 0;
lists[i]->ghostflag = 0;
if (requests[i]->ghost) lists[i]->ghostflag = 1;
if (requests[i]->ghost && !requests[i]->occasional) anyghostlist = 1;
lists[i]->ghostflag = 0;
if (requests[i]->ghost) lists[i]->ghostflag = 1;
if (requests[i]->ghost && !requests[i]->occasional) anyghostlist = 1;
} else init_list_flags1_kokkos(i);
}
#ifdef NEIGH_LIST_DEBUG
for (i = 0; i < nlist; i++) lists[i]->print_attributes();
for (i = 0; i < nrequest; i++) lists[i]->print_attributes();
#endif
// allocate atom arrays for neighbor lists that store them
maxatom = atom->nmax;
for (i = 0; i < nlist; i++)
if (lists[i]->growflag) lists[i]->grow(maxatom);
for (i = 0; i < nrequest; i++) {
if (lists[i]) {
if (lists[i]->growflag) lists[i]->grow(maxatom);
} else init_list_grow_kokkos(i);
}
// setup 3 vectors of pairwise neighbor lists
// blist = lists whose pair_build() is invoked every reneighbor
@ -664,16 +688,18 @@ void Neighbor::init()
delete [] blist;
delete [] glist;
delete [] slist;
blist = new int[nlist];
glist = new int[nlist];
slist = new int[nlist];
blist = new int[nrequest];
glist = new int[nrequest];
slist = new int[nrequest];
for (i = 0; i < nlist; i++) {
if (lists[i]->buildflag) blist[nblist++] = i;
if (lists[i]->growflag && requests[i]->occasional == 0)
glist[nglist++] = i;
if (lists[i]->stencilflag && requests[i]->occasional == 0)
slist[nslist++] = i;
for (i = 0; i < nrequest; i++) {
if (lists[i]) {
if (lists[i]->buildflag) blist[nblist++] = i;
if (lists[i]->growflag && requests[i]->occasional == 0)
glist[nglist++] = i;
if (lists[i]->stencilflag && requests[i]->occasional == 0)
slist[nslist++] = i;
} else init_list_flags2_kokkos(i);
}
#ifdef NEIGH_LIST_DEBUG
@ -691,12 +717,13 @@ void Neighbor::init()
while (!done) {
done = 1;
for (i = 0; i < nblist; i++) {
if (!lists[blist[i]]) continue;
NeighList *ptr = NULL;
if (lists[blist[i]]->listfull) ptr = lists[blist[i]]->listfull;
if (lists[blist[i]]->listcopy) ptr = lists[blist[i]]->listcopy;
if (lists[blist[i]]->listskip) ptr = lists[blist[i]]->listskip;
if (ptr == NULL) continue;
for (m = 0; m < nlist; m++)
for (m = 0; m < nrequest; m++)
if (ptr == lists[m]) break;
for (j = 0; j < nblist; j++)
if (m == blist[j]) break;
@ -1399,9 +1426,13 @@ void Neighbor::build(int topoflag)
// invoke building of pair and molecular neighbor lists
// only for pairwise lists with buildflag set
// blist is for standard neigh lists, otherwise is a Kokkos list
for (i = 0; i < nblist; i++)
(this->*pair_build[blist[i]])(lists[blist[i]]);
for (i = 0; i < nblist; i++) {
if (lists[blist[i]])
(this->*pair_build[blist[i]])(lists[blist[i]]);
else build_kokkos(i);
}
if (atom->molecular && topoflag) build_topology();
}
@ -1643,8 +1674,10 @@ void Neighbor::setup_bins()
// only done for lists with stencilflag and buildflag set
for (int i = 0; i < nslist; i++) {
lists[slist[i]]->stencil_allocate(smax,style);
(this->*stencil_create[slist[i]])(lists[slist[i]],sx,sy,sz);
if (lists[slist[i]]) {
lists[slist[i]]->stencil_allocate(smax,style);
(this->*stencil_create[slist[i]])(lists[slist[i]],sx,sy,sz);
} else setup_bins_kokkos(i);
}
}
@ -1971,7 +2004,8 @@ bigint Neighbor::memory_usage()
bytes += memory->usage(binhead,maxhead);
}
for (int i = 0; i < nlist; i++) bytes += lists[i]->memory_usage();
for (int i = 0; i < nrequest; i++)
if (lists[i]) bytes += lists[i]->memory_usage();
bytes += memory->usage(bondlist,maxbond,3);
bytes += memory->usage(anglelist,maxangle,4);

10
src/neighbor.h
View File

@ -176,6 +176,16 @@ class Neighbor : protected Pointers {
virtual void choose_build(int, class NeighRequest *);
void choose_stencil(int, class NeighRequest *);
// dummy functions provided by NeighborKokkos
virtual void init_cutneighsq_kokkos(int) {}
virtual int init_lists_kokkos() {return 0;}
virtual void init_list_flags1_kokkos(int) {}
virtual void init_list_flags2_kokkos(int) {}
virtual void init_list_grow_kokkos(int) {}
virtual void build_kokkos(int) {}
virtual void setup_bins_kokkos(int) {}
// pairwise build functions
typedef void (Neighbor::*PairPtr)(class NeighList *);

6
src/pair.cpp
View File

@ -89,8 +89,14 @@ Pair::Pair(LAMMPS *lmp) : Pointers(lmp)
eatom = NULL;
vatom = NULL;
// CUDA and KOKKOS per-fix data masks
datamask = ALL_MASK;
datamask_ext = ALL_MASK;
execution_space = Host;
datamask_read = ALL_MASK;
datamask_modify = ALL_MASK;
}
/* ---------------------------------------------------------------------- */

5
src/pair.h
View File

@ -97,6 +97,11 @@ class Pair : protected Pointers {
int compute_flag; // 0 if skip compute()
// KOKKOS host/device flag and data masks
ExecutionSpace execution_space;
unsigned int datamask_read,datamask_modify;
Pair(class LAMMPS *);
virtual ~Pair();

2
src/pair_lj_cut.h
View File

@ -54,7 +54,7 @@ class PairLJCut : public Pair {
double **lj1,**lj2,**lj3,**lj4,**offset;
double *cut_respa;
void allocate();
virtual void allocate();
};
}

9
src/update.cpp
View File

@ -60,13 +60,8 @@ Update::Update(LAMMPS *lmp) : Pointers(lmp)
minimize_style = NULL;
minimize = NULL;
if (lmp->cuda) {
str = (char *) "verlet/cuda";
create_integrate(1,&str,NULL);
} else {
str = (char *) "verlet";
create_integrate(1,&str,NULL);
}
str = (char *) "verlet";
create_integrate(1,&str,lmp->suffix);
str = (char *) "cg";
create_minimize(1,&str);