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Final MPI version

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This commit is contained in:
JairoBuitrago
2024-04-15 16:53:25 +02:00
parent a6a269703d
commit a13a0f3bae
33 changed files with 3568 additions and 624 deletions
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22
common/includes/box.h Normal file
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/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.
*/
#include <parameter.h>
#ifndef __BOX_H_
#define __BOX_H_
typedef struct {
int id;
MD_FLOAT xprd, yprd, zprd; //Domain Dimension
MD_FLOAT lo[3]; //smallest coordinate of my subdomain
MD_FLOAT hi[3]; //Highest coordinate of my subdomain
} Box;
int overlapBox(int, int , const Box*, const Box* , Box* , MD_FLOAT , MD_FLOAT);
int overlapFullBox(Parameter*, MD_FLOAT*, const Box*, const Box*);
void expandBox(int , const Box*, const Box* , Box* , MD_FLOAT);
#endif

104
common/includes/comm.h Normal file
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#include <atom.h>
#include <parameter.h>
#include <box.h>
#include <grid.h>
#ifndef COMM_H
#define COMM_H
#ifdef GROMACS
#define FORWARD_SIZE (3*CLUSTER_N)
#define REVERSE_SIZE (3*CLUSTER_N)
#define GHOST_SIZE (4*CLUSTER_N+10)
#define EXCHANGE_SIZE 7
#define JFAC MAX(1, CLUSTER_N / CLUSTER_M)
#define LOCAL atom->Nclusters_local / JFAC
#define GHOST atom->Nclusters_ghost
#define IsinRegionToSend(cj) \
((atom->jclusters[(cj)].bbminx >= xlo || atom->jclusters[(cj)].bbmaxx >= xlo) && \
(atom->jclusters[(cj)].bbminx < xhi || atom->jclusters[(cj)].bbmaxx < xhi) && \
(atom->jclusters[(cj)].bbminy >= ylo || atom->jclusters[(cj)].bbmaxy >= ylo) && \
(atom->jclusters[(cj)].bbminy < yhi || atom->jclusters[(cj)].bbmaxy < yhi) && \
(atom->jclusters[(cj)].bbminz >= zlo || atom->jclusters[(cj)].bbmaxz >= zlo) && \
(atom->jclusters[(cj)].bbminz < zhi || atom->jclusters[(cj)].bbmaxz < zhi))
#else
#define FORWARD_SIZE 3
#define REVERSE_SIZE 3
#define GHOST_SIZE 4
#define EXCHANGE_SIZE 7
#define LOCAL atom->Nlocal
#define GHOST atom->Nghost
#define IsinRegionToSend(i) \
((atom_x((i)) >= xlo && atom_x((i)) < xhi) && \
(atom_y((i)) >= ylo && atom_y((i)) < yhi) && \
(atom_z((i)) >= zlo && atom_z((i)) < zhi))
#endif
typedef struct {
int myproc; // my proc ID
int numproc; // # of processors
int numneigh; // # of all my neighs along all swaps
int maxneigh; // Buffer size for my neighs
int sendfrom[6]; //return the lowest neigh index to send in each swap
int sendtill[6]; //return the highest neigh index to send in each swao
int recvfrom[6]; //return the lowest neigh index to recv in each swap
int recvtill[6]; //return the highest neigh index to recv in each swap
int* nsend; // neigh whose I want to send
int* nrecv; // neigh whose I want to recv
int* pbc_x; // if pbc in x
int* pbc_y; // if pbc in y
int* pbc_z; // if pbc in z
int* atom_send, *atom_recv; // # of atoms to send/recv for each of my neighs
int* off_atom_send; // atom offset to send, inside of a swap
int* off_atom_recv; // atom offset to recv, inside of a swap
int* nexch; //procs to exchange
int numneighexch; //# of neighbours to exchange
int maxneighexch; //max buff size to store neighbours
int numswap; // # of swaps to perform, it is 6
int swapdim[6]; // dimension of the swap (_x, _y or _z)
int swapdir[6]; // direction of the swap 0 or 1
int swap[3][2]; // given a dim and dir, knows the swap
int othersend[6]; // Determine if a proc interact with more procs in a given swap
int firstrecv[6]; // where to put 1st recv atom in each swap
int** sendlist; // list of atoms to send in each swap
int* maxsendlist; // max # of atoms send in each list-swap
int maxsend; // max elements in buff sender
int maxrecv; // max elements in buff receiver
MD_FLOAT* buf_send; // sender buffer for all comm
MD_FLOAT* buf_recv; // receicer buffer for all comm
int forwardSize; // # of paramaters per atom in forward comm.
int reverseSize; // # of parameters per atom in reverse
int exchangeSize; // # of parameters per atom in exchange
int ghostSize; // # of parameters per atom in ghost list
int iterAtom; //last atom to iterate in each swap.
Box* boxes; // Boundaries to be sent to other procs as ghost.
} Comm;
void initComm(int*, char***, Comm*); //Init MPI
void endComm(Comm*); //End MPI
void setupComm(Comm*,Parameter*,Grid*); //Creates a 3d grid or rcb grid
void neighComm(Comm*,Parameter*,Grid*); //Find neighbours within cut-off and defines ghost regions
void forwardComm(Comm*,Atom*,int); //Send info in one direction
void reverseComm(Comm*,Atom*,int); //Return info after forward communication
void exchangeComm(Comm*,Atom*); //Exchange info between procs
void ghostComm(Comm*, Atom*,int); //Build the ghost neighbours to send during next forwards
void growSend(Comm*,int); //Grows the size of the buffer sender
void growRecv(Comm*,int); //Grows the size of the buffer receiver
void growList(Comm*, int, int); //Grows the size of the list to send
#endif

51
common/includes/grid.h Normal file
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/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.
*/
#include <parameter.h>
#include <box.h>
#include <atom.h>
#include <mpi.h>
#ifndef __MAP_H_
#define __MAP_H_
#define world MPI_COMM_WORLD
#define atom_pos(i) ((dim == _x) ? atom_x((i)) : (dim == _y) ? atom_y((i)) : atom_z((i)))
enum {RCB=1, meanTimeRCB, Staggered};
typedef struct {
int balance_every;
int map_size;
MD_FLOAT* map;
//===Param for Staggerd balance
int nprocs[3];
int coord[3];
MD_FLOAT cutneigh[3];
double Timer;
//===Param for RCB balance
MD_FLOAT* buf_send;
MD_FLOAT* buf_recv;
int maxsend;
int maxrecv;
} Grid;
typedef MD_FLOAT(*RCB_Method)(Atom*,MPI_Comm,int,double);
void setupGrid(Grid*, Atom*, Parameter*);
void cartisian3d(Grid*, Parameter*, Box*);
void rcbBalance(Grid*, Atom*, Parameter* ,RCB_Method, int, double);
void staggeredBalance(Grid*, Atom*, Parameter*, double);
void printGrid(Grid*);
//rcb methods
MD_FLOAT meanBisect(Atom* , MPI_Comm, int, double);
MD_FLOAT meanTimeBisect(Atom*, MPI_Comm, int, double);
#endif

4
common/includes/parameter.h
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@@ -53,6 +53,10 @@ typedef struct {
MD_FLOAT k_dn;
MD_FLOAT gx, gy, gz;
MD_FLOAT reflect_x, reflect_y, reflect_z;
//MPI implementation
int balance;
int method;
int balance_every;
} Parameter;
void initParameter(Parameter*);

71
common/includes/shell_methods.h Normal file
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@@ -0,0 +1,71 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.
*/
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <unistd.h>
#include <limits.h>
#include <math.h>
#include <comm.h>
#include <atom.h>
#include <timing.h>
#include <parameter.h>
#include <util.h>
//static void addDummyCluster(Atom*);
double forward(Comm* comm, Atom *atom, Parameter* param){
double S, E;
S = getTimeStamp();
if(param->method == halfShell){
for(int iswap = 0; iswap < 5; iswap++)
forwardComm(comm, atom, iswap);
} else if(param->method == eightShell){
for(int iswap = 0; iswap < 6; iswap+=2)
forwardComm(comm, atom, iswap);
} else {
for(int iswap = 0; iswap < 6; iswap++)
forwardComm(comm, atom, iswap);
}
E = getTimeStamp();
return E-S;
}
double reverse(Comm* comm, Atom *atom, Parameter* param){
double S, E;
S = getTimeStamp();
if(param->method == halfShell){
for(int iswap = 4; iswap >= 0; iswap--)
reverseComm(comm, atom, iswap);
} else if(param->method == eightShell){
for(int iswap = 4; iswap >= 0; iswap-=2)
reverseComm(comm, atom, iswap);
} else if(param->method == halfStencil){
for(int iswap = 5; iswap >= 0; iswap--)
reverseComm(comm, atom, iswap);
} else { } //Full Shell Reverse does nothing
E = getTimeStamp();
return E-S;
}
void ghostNeighbor(Comm* comm, Atom* atom, Parameter* param)
{
#ifdef GROMACS
atom->Nclusters_ghost = 0;
#endif
atom->Nghost = 0;
if(param->method == halfShell){
for(int iswap=0; iswap<5; iswap++)
ghostComm(comm,atom,iswap);
} else if(param->method == eightShell){
for(int iswap = 0; iswap<6; iswap+=2)
ghostComm(comm, atom,iswap);
} else {
for(int iswap=0; iswap<6; iswap++)
ghostComm(comm,atom,iswap);
}
}

10
common/includes/timers.h
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@@ -9,9 +9,15 @@
typedef enum {
TOTAL = 0,
NEIGH,
FORCE,
NEIGH,
FORWARD,
REVERSE,
UPDATE,
BALANCE,
SETUP,
REST,
NUMTIMER
} timertype;
} timerComm;
#endif

9
common/includes/util.h
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@@ -4,6 +4,8 @@
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.
*/
#include <math.h>
#ifndef __UTIL_H_
#define __UTIL_H_
@@ -35,6 +37,13 @@
# define PRECISION_STRING "double"
#endif
#define BigOrEqual(a,b) (fabs((a)-(b))<1e-9 || (a)>(b))
#define Equal(a,b) (fabs((a)-(b))<1e-9)
enum {_x=0, _y, _z};
enum {fullShell=0, halfShell, eightShell, halfStencil};
extern double myrandom(int*);
extern void random_reset(int *seed, int ibase, double *coord);
extern int str2ff(const char *string);