more changes to robustify comm buf_send length (89af88bd) · Commits · 郑智淋 / lammps

src/atom_vec_hybrid.cpp

+3 −0

Original line number	Diff line number	Diff line
		@@ -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;

src/comm.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -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

src/comm_brick.cpp

+16 −11

Original line number	Diff line number	Diff line
		@@ -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)
		{
		if (flag == 0) {
		maxsend = static_cast<int> (BUFFACTOR * n);
		if (flag)
		memory->grow(buf_send,maxsend+bufextra,"comm:buf_send");
		else {
		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");
		}
		}

src/comm_tiled.cpp

+14 −9

Original line number	Diff line number	Diff line
		@@ -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)
		{
		if (flag == 0) {
		maxsend = static_cast<int> (BUFFACTOR * n);
		if (flag)
		memory->grow(buf_send,maxsend+bufextra,"comm:buf_send");
		else {
		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");
		}
		}

src/irregular.cpp

+51 −13

Original line number	Diff line number	Diff line
		@@ -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)
		{
		if (flag == 0) {
		maxsend = static_cast<int> (BUFFACTOR * n);
		if (flag)
		memory->grow(buf_send,maxsend+BUFEXTRA,"comm:buf_send");
		else {
		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)

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