VCluster.hpp 17.5 KB
Newer Older
incardon's avatar
incardon committed
1 2 3 4 5 6 7 8 9
#ifndef VCLUSTER
#define VCLUSTER

#include <mpi.h>
#include "VCluster_object.hpp"
#include "VCluster_object_array.hpp"
#include "Vector/map_vector.hpp"
#include "MPI_IallreduceW.hpp"
#include <exception>
10
#include "Vector/map_vector.hpp"
incardon's avatar
incardon committed
11 12 13

#define MSG_LENGTH 1024
#define MSG_SEND_RECV 1025
14
#define SEND_SPARSE 1026
incardon's avatar
incardon committed
15 16 17 18 19 20 21 22 23 24 25
#define NONE 1
#define NEED_ALL_SIZE 2

#define MPI_SAFE_CALL(call) {\
	int err = call;\
	if (MPI_SUCCESS != err) {\
		std::cerr << "MPI error: "<< __FILE__ << " " << __LINE__ << "\n";\
		error_handler(err);\
	}\
}

incardon's avatar
incardon committed
26 27 28
extern size_t n_vcluster;
extern bool global_mpi_init;

incardon's avatar
incardon committed
29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131
///////////////////// Post functions /////////////

template<typename T> void assign(T * ptr1, T * ptr2)
{
	*ptr1 = *ptr2;
};

//////////////////////////////////////////////////

// temporal buffer for reductions
union red
{
	char c;
	unsigned char uc;
	short s;
	unsigned short us;
	int i;
	unsigned int ui;
	float f;
	double d;
};

/*! \brief Virtual Cluster exception
 *
 * This a a class that signal an exception on MPI_WaitAll
 *
 */

class exec_exception: public std::exception
{
  virtual const char* what() const throw()
  {
    return "One or more request has failed or reported an error";
  }
};

/*! \brief This class is virtualize the cluster as a set of processing unit
 *         and communication unit
 *
 * This class virtualize the cluster as a set of processing unit and communication
 * unit. It can execute any vcluster_exe
 *
 */

class Vcluster
{
	// temporal vector used for meta-communication
	// ( or meta-data before the real communication )
	openfpm::vector<size_t> proc_com;

	// vector that contain the scatter map (it is basically an array of one)
	openfpm::vector<int> map_scatter;

	// vector of MPI requests
	openfpm::vector<MPI_Request> req;

	// vector of MPI status
	openfpm::vector<MPI_Status> stat;

	// vector of functions to execute after all the request has been performed
	std::vector<int> post_exe;

	// Object array


	// Single objects

	// number of processes
	int size;
	// actual rank
	int rank;

	// number of processing unit per process
	int numPE = 1;

	/* This buffer is a temporal buffer for reductions
	 *
	 * MPI_Iallreduce does not accept recv and send buffer to be the same
	 * r is used to overcome this problem (is given as second parameter)
	 * after the execution the data is copied back
	 *
	 */
	std::vector<red> r;


	void error_handler(int error_code)
	{
	   char error_string[BUFSIZ];
	   int length_of_error_string, error_class;

	   MPI_Error_class(error_code, &error_class);
	   MPI_Error_string(error_class, error_string, &length_of_error_string);
	   std::cerr << getProcessUnitID() << ": " << error_string;
	   MPI_Error_string(error_code, error_string, &length_of_error_string);
	   std::cerr << getProcessUnitID() << ": " << error_string;
	}


public:

	// Finalize the MPI program
	~Vcluster()
	{
incardon's avatar
incardon committed
132 133 134 135 136
		n_vcluster--;

		// if there are no other vcluster instances finalize
		if (n_vcluster == 0)
			MPI_Finalize();
incardon's avatar
incardon committed
137 138 139 140 141
	}

	//! \brief Virtual cluster constructor
	Vcluster(int *argc, char ***argv)
	{
incardon's avatar
incardon committed
142 143 144 145 146 147 148 149
		n_vcluster++;

		// Check if MPI is already initialized
		if (global_mpi_init == false)
		{
			MPI_Init(argc,argv);
			global_mpi_init = true;
		}
incardon's avatar
incardon committed
150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218

		//! Get the total number of process
		//! and the rank of this process

		MPI_Comm_size(MPI_COMM_WORLD, &size);
		MPI_Comm_rank(MPI_COMM_WORLD, &rank);

#ifdef MEMLEAK_CHECK
			process_v_cl = rank;
#endif

		//! create and fill map scatter with one
		map_scatter.resize(size);

		for (size_t i = 0 ; i < map_scatter.size() ; i++)
		{
			map_scatter.get(i) = 1;
		}
	}

	//! Get the total number of processing units
	size_t getProcessingUnits()
	{
		return size*numPE;
	}

	//! Get the process unit id
	size_t getProcessUnitID()
	{
		return rank;
	}

	/*! \brief Allocate a set of objects
	 *
	 * \tparam obj
	 * \param n number of object
	 *
	 * \return an object representing an array of objects
	 *
	 */
	template <typename obj> Vcluster_object_array<obj> allocate(size_t n)
	{
		// Vcluster object array
		Vcluster_object_array<obj> vo;

		// resize the array
		vo.resize(n);

		// Create the object on memory and return a Vcluster_object_array
		return vo;
	}

	/*! \brief Sum the number across all processors and get the result
	 *
	 * \param num to reduce, input and output
	 *
	 */

	template<typename T> void reduce(T & num)
	{
		// reduce over MPI

		// Create one request
		req.add();

		// reduce
		MPI_IallreduceW<T>::reduce(num,MPI_SUM,req.last());
	}

incardon's avatar
incardon committed
219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235
	/*! \brief Get the maximum number across all processors (or reduction with insinity norm)
	 *
	 * \param num to reduce
	 *
	 */

	template<typename T> void max(T & num)
	{
		// reduce over MPI

		// Create one request
		req.add();

		// reduce
		MPI_IallreduceW<T>::reduce(num,MPI_MAX,req.last());
	}

incardon's avatar
incardon committed
236 237 238 239 240 241 242 243 244
	// vector of pointers of send buffers
	openfpm::vector<void *> ptr_send;

	// vector of the size of send buffers
	openfpm::vector<size_t> sz_send;

	// sending map
	openfpm::vector<size_t> map;

245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320
	// Distributed processor graph
	MPI_Comm proc_comm_graph;

	/*! \brief
	 *
	 * Set the near processor of this processors
	 *
	 */

	openfpm::vector<size_t> NN_proc;

	void setLocality(openfpm::vector<size_t> NN_proc)
	{
		// Number of sources in the graph, and sources processors
		size_t sources = NN_proc.size();
		openfpm::vector<int> src_proc;

		// number of destination in the graph
		size_t dest = NN_proc.size();
		openfpm::vector<int> dest_proc;

		// insert in sources and out sources
		for (size_t i = 0; i < NN_proc.size() ; i++)
		{
			src_proc.add(NN_proc.get(i));
			dest_proc.add(NN_proc.get(i));
			// Copy the vector
			this->NN_proc.get(i) = NN_proc.get(i);
		}

		MPI_Dist_graph_create_adjacent(MPI_COMM_WORLD,sources,&src_proc.get(0),(const int *)MPI_UNWEIGHTED,dest,&dest_proc.get(0),(const int *)MPI_UNWEIGHTED,MPI_INFO_NULL,true,&proc_comm_graph);
	}

	/*! \brief Send and receive multiple messages within local processors
	 *
	 * It send multiple messages and receive
	 * other multiple messages, all the processor must call this
	 * function
	 *
	 * \param prc list of processors with which it should communicate
	 *
	 * \param v vector containing the data to send
	 *
	 * \param msg_alloc This is a call-back with the purpose of allocate space
	 *        for the incoming message and give back a valid pointer, the 6 parameters
	 *        in the call-back are in order:
	 *        1) message size required to receive from i
	 *        2) total message size to receive from all the processors
	 *        3) the total number of processor want to communicate with you
	 *        4) processor id
	 *        5) ri request id (it is an id that goes from 0 to total_p, and is unique
	 *           every time message_alloc is called)
	 *        6) void pointer parameter for additional data to pass to the call-back
	 *
	 * \param opt options, NONE or NEED_ALL_SIZE, with NEED_ALL_SIZE the allocation
	 *        callback will not be called until all the message size will be
	 *        gathered, [usefull for example with you want to allocate one big buffer
	 *        to gather all the messages]
	 *
	 */

	template<typename T> void sendrecvMultipleMessagesNBX(openfpm::vector< size_t > & prc, openfpm::vector< T > & data, void * (* msg_alloc)(size_t,size_t,size_t,size_t,size_t,void *), void * ptr_arg, long int opt=NONE)
	{
		// resize the pointer list
		ptr_send.resize(prc.size());
		sz_send.resize(prc.size());

		for (size_t i = 0 ; i < prc.size() ; i++)
		{
			ptr_send.get(i) = data.get(i).getPointer();
			sz_send.get(i) = data.get(i).size() * sizeof(typename T::value_type);
		}

		sendrecvMultipleMessagesNBX(prc.size(),(size_t *)sz_send.getPointer(),(size_t *)prc.getPointer(),(void **)ptr_send.getPointer(),msg_alloc,ptr_arg,opt);
	}

incardon's avatar
incardon committed
321 322 323

	/*! \brief Send and receive multiple messages
	 *
324
	 * It send multiple messages and receive
incardon's avatar
incardon committed
325 326 327 328 329
	 * other multiple messages, all the processor must call this
	 * function
	 *
	 * \param prc list of processors with which it should communicate
	 *
330 331
	 * \param nn_prc near processors
	 *
incardon's avatar
incardon committed
332 333 334
	 * \param v vector containing the data to send
	 *
	 * \param msg_alloc This is a call-back with the purpose of allocate space
335 336 337 338 339 340 341 342 343
	 *        for the incoming message and give back a valid pointer, the 6 parameters
	 *        in the call-back are in order:
	 *        1) message size required to receive from i
	 *        2) total message size to receive from all the processors
	 *        3) the total number of processor want to communicate with you
	 *        4) processor id
	 *        5) ri request id (it is an id that goes from 0 to total_p, and is unique
	 *           every time message_alloc is called)
	 *        6) void pointer parameter for additional data to pass to the call-back
incardon's avatar
incardon committed
344 345 346 347 348 349 350 351
	 *
	 * \param opt options, NONE or NEED_ALL_SIZE, with NEED_ALL_SIZE the allocation
	 *        callback will not be called until all the message size will be
	 *        gathered, [usefull for example with you want to allocate one big buffer
	 *        to gather all the messages]
	 *
	 */

352
	template<typename T> void sendrecvMultipleMessagesPCX(openfpm::vector< size_t > & prc, openfpm::vector< T > & data, void * (* msg_alloc)(size_t,size_t,size_t,size_t,size_t,void *), void * ptr_arg, long int opt=NONE)
incardon's avatar
incardon committed
353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373
	{
		// resize map with the number of processors
		map.resize(size);

		// reset the sending buffer
		map.fill(0);

		// create sending map
		for (size_t i = 0 ; i < prc.size() ; i++)
		{map.get(prc.get(i)) = 1;}

		// resize the pointer list
		ptr_send.resize(prc.size());
		sz_send.resize(prc.size());

		for (size_t i = 0 ; i < prc.size() ; i++)
		{
			ptr_send.get(i) = data.get(i).getPointer();
			sz_send.get(i) = data.get(i).size() * sizeof(typename T::value_type);
		}

374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476
		sendrecvMultipleMessagesPCX(prc.size(),(size_t *)map.getPointer(),(size_t *)sz_send.getPointer(),(size_t *)prc.getPointer(),(void **)ptr_send.getPointer(),msg_alloc,ptr_arg,opt);
	}

	/*! \brief Send and receive multiple messages local
	 *
	 * It send multiple messages to the near processor the and receive
	 * other multiple messages from the, all the processor must call this
	 * function
	 *
	 * \param n_send number of send this processor must do
	 *
	 * \param sz the array contain the size of the message for each processor
	 *        (zeros must be omitted)
	 *
	 *        [Example] for the previous patter 5 10 15 4 mean processor 1
	 *        message size 5 byte, processor 6 message size 10 , ......
	 *
	 * \param prc list of processor with which it should communicate
	 *        [Example] for the previous case should be
	 *        1 6 7 8 (prc and mp contain the same information in different
	 *        format, giving both reduce the computation)
	 *
	 * \param ptr array that contain the messages pointers
	 *
	 * \param msg_alloc This is a call-back with the purpose of allocate space
	 *        for the incoming message and give back a valid pointer, the 6 parameters
	 *        in the call-back are in order:
	 *        1) message size required to receive from i
	 *        2) total message size to receive from all the processors
	 *        3) the total number of processor want to communicate with you
	 *        4) processor id
	 *        5) ri request id (it is an id that goes from 0 to total_p, and is unique
	 *           every time message_alloc is called)
	 *        6) void pointer parameter for additional data to pass to the call-back
	 *
	 * \param opt options, NONE (ignored in this moment)
	 *
	 */

	void sendrecvMultipleMessagesNBX(size_t n_send , size_t sz[], size_t prc[] , void * ptr[], void * (* msg_alloc)(size_t,size_t,size_t,size_t,size_t,void *), void * ptr_arg, long int opt)
	{
		req.clear();
		// Do MPI_Issend

		for (size_t i = 0 ; i < n_send ; i++)
		{
			req.add();
			MPI_SAFE_CALL(MPI_Issend(ptr[i], sz[i], MPI_BYTE, prc[i], SEND_SPARSE, MPI_COMM_WORLD,&req.last()));
		}

		size_t rid = 0;
		int flag = false;

		bool reached_bar_req = false;
		MPI_Request bar_req;

		// Wait that all the send are acknowledge
		do
		{
			// flag that notify that this processor reach the barrier
			// Barrier request

			MPI_Status stat_t;
			int stat = false;
			MPI_SAFE_CALL(MPI_Iprobe(MPI_ANY_SOURCE,SEND_SPARSE,MPI_COMM_WORLD,&stat,&stat_t));

			// If I have received a message

			if (stat == true)
			{
				// Get the message size
				int msize;
				MPI_SAFE_CALL(MPI_Get_count(&stat_t,MPI_BYTE,&msize));

				// Get the pointer to receive the message
				void * ptr = msg_alloc(msize,0,0,stat_t.MPI_SOURCE,rid,ptr_arg);

				rid++;

				MPI_SAFE_CALL(MPI_Recv(ptr,msize,MPI_BYTE,stat_t.MPI_SOURCE,SEND_SPARSE,MPI_COMM_WORLD,&stat_t));
			}

			// Check the status of all the MPI_issend and call the barrier if finished

			if (reached_bar_req == false)
			{
				int flag = false;
				MPI_SAFE_CALL(MPI_Testall(req.size(),&req.get(0),&flag,MPI_STATUSES_IGNORE));

				// If all send has been completed
				if (flag == true)
				{MPI_SAFE_CALL(MPI_Ibarrier(MPI_COMM_WORLD,&bar_req));reached_bar_req = true;}
			}

			// Check if all processor reach the async barrier
			if (reached_bar_req)
				MPI_Test(&bar_req,&flag,MPI_STATUSES_IGNORE);
		} while (flag == false);

		// Remove the executed request

		req.clear();
		stat.clear();
incardon's avatar
incardon committed
477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517
	}

	/*! \brief Send and receive multiple messages
	 *
	 * It send multiple (to more than one) messages and receive
	 * other multiple messages, all the processor must call this
	 * function
	 *
	 * \param n_send number of send this processor must do
	 *
	 * \param map array containing an array of unsigned chars that
	 *        specify the communication pattern of the processor
	 *
	 *        [Example]   0 1 0 0 0 0 1 1 1 mean that the processor
	 *        communicate with the processor 1 6 7 8
	 *
	 * \param sz the array contain the size of the message for each processor
	 *        (zeros must be omitted)
	 *
	 *        [Example] for the previous patter 5 10 15 4 mean processor 1
	 *        message size 5 byte, processor 6 message size 10 , ......
	 *
	 * \param prc list of processor with which it should communicate
	 *        [Example] for the previous case should be
	 *        1 6 7 8 (prc and mp contain the same information in different
	 *        format, giving both reduce the computation)
	 *
	 * \param ptr array that contain the message (zero lengh must be omitted)
	 *
	 * \param msg_alloc This is a call-back with the purpose of allocate space
	 *        for the incoming message and give back a valid pointer, the 3 parameters
	 *        in the call-back are  , total message to receive, i processor id from witch
	 *        to receive
	 *
	 * \param opt options, NONE or NEED_ALL_SIZE, with NEED_ALL_SIZE the allocation
	 *        callback will not be called until all the message size will be
	 *        gathered, [usefull for example with you want to allocate one big buffer
	 *        to gather all the messages]
	 *
	 */

518
	void sendrecvMultipleMessagesPCX(size_t n_send, size_t * map, size_t sz[], size_t prc[] , void * ptr[], void * (* msg_alloc)(size_t,size_t,size_t,size_t,size_t,void *), void * ptr_arg, long int opt)
incardon's avatar
incardon committed
519 520 521
	{
		req.clear();
		req.add();
incardon's avatar
incardon committed
522
		stat.add();
incardon's avatar
incardon committed
523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582

		proc_com.resize(1);

		MPI_SAFE_CALL(MPI_Ireduce_scatter(map,&proc_com.get(0),&map_scatter.get(0),MPI_UNSIGNED_LONG,MPI_SUM,MPI_COMM_WORLD,&req.last()));
		MPI_SAFE_CALL(MPI_Waitall(req.size(),&req.get(0),&stat.get(0)));

		// Remove the executed request

		req.clear();
		stat.clear();

		// Allocate the temporal buffer to store the message size for each processor

		size_t n_proc_com = proc_com.get(0);
		proc_com.resize(n_proc_com * 2);

		// queue n_proc_com MPI_Irecv with source ANY_SOURCE to get
		// the message length from each processor and
		//  send the message length to each processor

		for (size_t i = 0 ; i < n_proc_com ; i++)
		{
			req.add();
			MPI_SAFE_CALL(MPI_Irecv(&proc_com.get(i),1,MPI_UNSIGNED_LONG,MPI_ANY_SOURCE,MSG_LENGTH,MPI_COMM_WORLD,&req.last()));
		}

		for (size_t i = 0 ; i < n_send ; i++)
		{
			req.add();
			MPI_SAFE_CALL(MPI_Isend(&sz[i],1,MPI_UNSIGNED_LONG,prc[i],MSG_LENGTH,MPI_COMM_WORLD,&req.last()));
		}

		stat.resize(req.size());
		MPI_SAFE_CALL(MPI_Waitall(req.size(),&req.get(0),&stat.get(0)));

		// Use proc_com to get the processor id that try to communicate

		for (size_t i = 0 ; i < n_proc_com ; i++)
		{
			proc_com.get(n_proc_com+i) = stat.get(i).MPI_SOURCE;
		}

		// Remove the executed request

		req.clear();
		stat.clear();

		// Calculate the total size of the message

		size_t total_msg = 0;

		for (size_t i = 0 ; i < n_proc_com ; i++)
		{
			total_msg += proc_com.get(i);
		}

		// Receive the message

		for (size_t i = 0 ; i < n_proc_com ; i++)
		{
incardon's avatar
incardon committed
583
			void * ptr = msg_alloc(proc_com.get(i),total_msg,n_proc_com,proc_com.get(n_proc_com+i),i,ptr_arg);
incardon's avatar
incardon committed
584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612

			req.add();
			MPI_SAFE_CALL(MPI_Irecv(ptr,proc_com.get(i),MPI_BYTE,proc_com.get(i+n_proc_com),MSG_SEND_RECV,MPI_COMM_WORLD,&req.last()));
		}

		// Send all the messages this processor must send

		for (size_t i = 0 ; i < n_send ; i++)
		{
			req.add();
			MPI_SAFE_CALL(MPI_Isend(ptr[i],sz[i],MPI_BYTE,prc[i],MSG_SEND_RECV,MPI_COMM_WORLD,&req.last()));
		}

		stat.resize(req.size());
		MPI_SAFE_CALL(MPI_Waitall(req.size(),&req.get(0),&stat.get(0)));

		// Remove the executed request

		req.clear();
		stat.clear();
	}

	/*! \brief Execute all the request
	 *
	 */
	void execute()
	{
		int err = 0;

613 614 615 616
		// if req == 0 return
		if (req.size() == 0)
			return;

incardon's avatar
incardon committed
617
		// Wait for all the requests
618
		stat.resize(req.size());
incardon's avatar
incardon committed
619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644
		err = MPI_Waitall(req.size(),&req.get(0),&stat.get(0));

		// MPI error get the message and abort MPI
		if (err != MPI_SUCCESS)
		{
			char * error_msg = NULL;
			int len;
			MPI_Error_string(err,error_msg,&len);

			std::cerr << "Error MPI rank " << rank << ": " << error_msg << "\n";

			MPI_Abort(MPI_COMM_WORLD,1);
		}

		//! Remove executed request and status
		req.clear();
		stat.clear();
	}
};

void init_global_v_cluster(int *argc, char ***argv);

extern Vcluster * global_v_cluster;

#endif