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more changes to robustify comm buf_send length

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This commit is contained in:
Steve Plimpton
2019-07-10 08:41:27 -06:00
parent 2fd327d057
commit 89af88bd10
6 changed files with 87 additions and 34 deletions
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3
src/atom_vec_hybrid.cpp
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@ -95,6 +95,7 @@ void AtomVecHybrid::process_args(int narg, char **arg)
size_data_atom = 5;
size_data_vel = 4;
xcol_data = 3;
maxexchange = 0;
for (int k = 0; k < nstyles; k++) {
if ((styles[k]->molecular == 1 && molecular == 2) ||
@ -120,6 +121,8 @@ void AtomVecHybrid::process_args(int narg, char **arg)
size_border += styles[k]->size_border - 6;
size_data_atom += styles[k]->size_data_atom - 5;
size_data_vel += styles[k]->size_data_vel - 4;
maxexchange += styles[k]->maxexchange;
}
size_velocity = 3;

2
src/comm.h
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@ -134,7 +134,7 @@ class Comm : protected Pointers {
int maxexchange_atom; // contribution to maxexchange from AtomVec
int maxexchange_fix; // static contribution to maxexchange from Fixes
int maxexchange_fix_dynamic; // 1 if a fix has a dynamic contribution
int bufextra; // augment size of send buf for an exchange atom
int bufextra; // augment send buf size for an exchange atom
int gridflag; // option for creating 3d grid

27
src/comm_brick.cpp
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@ -109,9 +109,9 @@ void CommBrick::init_buffers()
multilo = multihi = NULL;
cutghostmulti = NULL;
maxsend = BUFMIN;
memory->create(buf_send,maxsend+bufextra,"comm:buf_send");
maxrecv = BUFMIN;
buf_send = buf_recv = NULL;
maxsend = maxrecv = BUFMIN;
grow_send(maxsend,2);
memory->create(buf_recv,maxrecv,"comm:buf_recv");
nswap = 0;
@ -134,7 +134,7 @@ void CommBrick::init()
int bufextra_old = bufextra;
init_exchange();
if (bufextra > bufextra_old) grow_send(maxsend+bufextra,0);
if (bufextra > bufextra_old) grow_send(maxsend+bufextra,2);
// memory for multi-style communication
@ -604,7 +604,7 @@ void CommBrick::exchange()
if (maxexchange_fix_dynamic) {
int bufextra_old = bufextra;
init_exchange();
if (bufextra > bufextra_old) grow_send(maxsend+bufextra,0);
if (bufextra > bufextra_old) grow_send(maxsend+bufextra,2);
}
// subbox bounds for orthogonal or triclinic
@ -1346,18 +1346,23 @@ int CommBrick::exchange_variable(int n, double *inbuf, double *&outbuf)
/* ----------------------------------------------------------------------
realloc the size of the send buffer as needed with BUFFACTOR and bufextra
if flag = 1, realloc
if flag = 0, don't need to realloc with copy, just free/malloc
flag = 0, don't need to realloc with copy, just free/malloc w/ BUFFACTOR
flag = 1, realloc with BUFFACTOR
flag = 2, free/malloc w/out BUFFACTOR
------------------------------------------------------------------------- */
void CommBrick::grow_send(int n, int flag)
{
maxsend = static_cast<int> (BUFFACTOR * n);
if (flag)
memory->grow(buf_send,maxsend+bufextra,"comm:buf_send");
else {
if (flag == 0) {
maxsend = static_cast<int> (BUFFACTOR * n);
memory->destroy(buf_send);
memory->create(buf_send,maxsend+bufextra,"comm:buf_send");
} else if (flag == 1) {
maxsend = static_cast<int> (BUFFACTOR * n);
memory->grow(buf_send,maxsend+bufextra,"comm:buf_send");
} else {
memory->destroy(buf_send);
memory->grow(buf_send,maxsend+bufextra,"comm:buf_send");
}
}

23
src/comm_tiled.cpp
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@ -79,9 +79,9 @@ CommTiled::~CommTiled()
void CommTiled::init_buffers()
{
maxsend = BUFMIN;
memory->create(buf_send,maxsend+bufextra,"comm:buf_send");
maxrecv = BUFMIN;
buf_send = buf_recv = NULL;
maxsend = maxrecv = BUFMIN;
grow_send(maxsend,2);
memory->create(buf_recv,maxrecv,"comm:buf_recv");
maxoverlap = 0;
@ -1804,18 +1804,23 @@ int CommTiled::coord2proc(double *x, int &igx, int &igy, int &igz)
/* ----------------------------------------------------------------------
realloc the size of the send buffer as needed with BUFFACTOR and bufextra
if flag = 1, realloc
if flag = 0, don't need to realloc with copy, just free/malloc
flag = 0, don't need to realloc with copy, just free/malloc w/ BUFFACTOR
flag = 1, realloc with BUFFACTOR
flag = 2, free/malloc w/out BUFFACTOR
------------------------------------------------------------------------- */
void CommTiled::grow_send(int n, int flag)
{
maxsend = static_cast<int> (BUFFACTOR * n);
if (flag)
memory->grow(buf_send,maxsend+bufextra,"comm:buf_send");
else {
if (flag == 0) {
maxsend = static_cast<int> (BUFFACTOR * n);
memory->destroy(buf_send);
memory->create(buf_send,maxsend+bufextra,"comm:buf_send");
} else if (flag == 1) {
maxsend = static_cast<int> (BUFFACTOR * n);
memory->grow(buf_send,maxsend+bufextra,"comm:buf_send");
} else {
memory->destroy(buf_send);
memory->grow(buf_send,maxsend+bufextra,"comm:buf_send");
}
}

64
src/irregular.cpp
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@ -19,6 +19,8 @@
#include "atom_vec.h"
#include "domain.h"
#include "comm.h"
#include "modify.h"
#include "fix.h"
#include "memory.h"
using namespace LAMMPS_NS;
@ -35,8 +37,8 @@ static int compare_standalone(const int, const int, void *);
#endif
#define BUFFACTOR 1.5
#define BUFMIN 1000
#define BUFEXTRA 1000
#define BUFMIN 1024
#define BUFEXTRA 1024
/* ---------------------------------------------------------------------- */
@ -69,9 +71,10 @@ Irregular::Irregular(LAMMPS *lmp) : Pointers(lmp)
// initialize buffers for migrate atoms, not used for datum comm
// these can persist for multiple irregular operations
maxsend = BUFMIN;
memory->create(buf_send,maxsend+BUFEXTRA,"comm:buf_send");
maxrecv = BUFMIN;
buf_send = buf_recv = NULL;
maxsend = maxrecv = BUFMIN;
bufextra = BUFEXTRA;
grow_send(maxsend,2);
memory->create(buf_recv,maxrecv,"comm:buf_recv");
}
@ -103,6 +106,13 @@ Irregular::~Irregular()
void Irregular::migrate_atoms(int sortflag, int preassign, int *procassign)
{
// check if buf_send needs to be extended due to atom style or per-atom fixes
// same as in Comm::exchange()
int bufextra_old = bufextra;
init_exchange();
if (bufextra > bufextra_old) grow_send(maxsend+bufextra,2);
// clear global->local map since atoms move to new procs
// clear old ghosts so map_set() at end will operate only on local atoms
// exchange() doesn't need to clear ghosts b/c borders()
@ -983,24 +993,52 @@ void Irregular::destroy_data()
}
/* ----------------------------------------------------------------------
realloc the size of the send buffer as needed with BUFFACTOR & BUFEXTRA
if flag = 1, realloc
if flag = 0, don't need to realloc with copy, just free/malloc
set bufextra based on AtomVec and fixes
similar to Comm::init_exchange()
------------------------------------------------------------------------- */
void Irregular::init_exchange()
{
int nfix = modify->nfix;
Fix **fix = modify->fix;
int onefix;
int maxexchange_fix = 0;
for (int i = 0; i < nfix; i++) {
onefix = fix[i]->maxexchange;
maxexchange_fix = MAX(maxexchange_fix,onefix);
}
int maxexchange = atom->avec->maxexchange + maxexchange_fix;
bufextra = maxexchange + BUFEXTRA;
}
/* ----------------------------------------------------------------------
realloc the size of the send buffer as needed with BUFFACTOR and bufextra
flag = 0, don't need to realloc with copy, just free/malloc w/ BUFFACTOR
flag = 1, realloc with BUFFACTOR
flag = 2, free/malloc w/out BUFFACTOR
same as Comm::grow_send()
------------------------------------------------------------------------- */
void Irregular::grow_send(int n, int flag)
{
maxsend = static_cast<int> (BUFFACTOR * n);
if (flag)
memory->grow(buf_send,maxsend+BUFEXTRA,"comm:buf_send");
else {
if (flag == 0) {
maxsend = static_cast<int> (BUFFACTOR * n);
memory->destroy(buf_send);
memory->create(buf_send,maxsend+BUFEXTRA,"comm:buf_send");
memory->create(buf_send,maxsend+bufextra,"comm:buf_send");
} else if (flag == 1) {
maxsend = static_cast<int> (BUFFACTOR * n);
memory->grow(buf_send,maxsend+bufextra,"comm:buf_send");
} else {
memory->destroy(buf_send);
memory->grow(buf_send,maxsend+bufextra,"comm:buf_send");
}
}
/* ----------------------------------------------------------------------
free/malloc the size of the recv buffer as needed with BUFFACTOR
same as Comm::grow_recv()
------------------------------------------------------------------------- */
void Irregular::grow_recv(int n)

2
src/irregular.h
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@ -43,6 +43,7 @@ class Irregular : protected Pointers {
int triclinic;
int map_style;
int bufextra; // augment send buf size for a migrating atom
int maxsend,maxrecv; // size of buf send/recv in # of doubles
double *buf_send,*buf_recv; // bufs used in migrate_atoms
int maxdbuf; // size of double buf in bytes
@ -91,6 +92,7 @@ class Irregular : protected Pointers {
int binary(double, int, double *);
void init_exchange(); // reset bufxtra
void grow_send(int,int); // reallocate send buffer
void grow_recv(int); // free/allocate recv buffer
};