/*
* This test attempts collective communication after a process in
* the communicator has failed.
*/
int main(int argc, char **argv)
{
int rank, size, i, rc, errclass, toterrs, errs = 0;
char rbuf[100000];
char *sendbuf;
int deadprocs[1] = {1};
MPI_Group world, newgroup;
MPI_Comm newcomm;
MPI_Init(&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &size);
MPI_Comm_set_errhandler(MPI_COMM_WORLD, MPI_ERRORS_RETURN);
if (size < 3) {
fprintf( stderr, "Must run with at least 3 processes\n" );
MPI_Abort( MPI_COMM_WORLD, 1 );
}
MPI_Comm_group(MPI_COMM_WORLD, &world);
MPI_Group_excl(world, 1, deadprocs, &newgroup);
MPI_Comm_create_group(MPI_COMM_WORLD, newgroup, 0, &newcomm);
if (rank == 1) {
exit(EXIT_FAILURE);
}
/* try a small send first */
sendbuf = (char *)malloc(10*size*sizeof(char));
if (rank == 0) {
for (i=0;i<size;i++) {
strcpy(sendbuf + i*10, "No Errors");
}
}
rc = MPI_Scatter(sendbuf, 10, MPI_CHAR, rbuf, 10, MPI_CHAR, 0, MPI_COMM_WORLD);
#if defined (MPICH) && (MPICH_NUMVERSION >= 30100102)
MPI_Error_class(rc, &errclass);
if ((rc) && (errclass != MPIX_ERR_PROC_FAILED)) {
fprintf(stderr, "Wrong error code (%d) returned. Expected MPIX_ERR_PROC_FAILED\n", errclass);
errs++;
}
#endif
/* reset the buffers and try a larger scatter */
free(sendbuf);
memset(rbuf, 0, sizeof(rbuf));
sendbuf = (char *)malloc(100000*size*sizeof(char));
if (rank == 0) {
for (i=0;i<size;i++) {
strcpy(sendbuf + i*100000, "No Errors");
}
}
rc = MPI_Scatter(sendbuf, 100000, MPI_CHAR, rbuf, 100000, MPI_CHAR, 0, MPI_COMM_WORLD);
#if defined (MPICH) && (MPICH_NUMVERSION >= 30100102)
MPI_Error_class(rc, &errclass);
if ((rc) && (errclass != MPIX_ERR_PROC_FAILED)) {
fprintf(stderr, "Wrong error code (%d) returned. Expected MPIX_ERR_PROC_FAILED\n", errclass);
errs++;
}
#endif
rc = MPI_Reduce(&errs, &toterrs, 1, MPI_INT, MPI_SUM, 0, newcomm);
if(rc)
fprintf(stderr, "Failed to get errors from other processes\n");
if (rank == 0) {
if (toterrs) {
printf( " Found %d errors\n", toterrs );
}
else {
printf( " No Errors\n" );
}
fflush(stdout);
}
free(sendbuf);
MPI_Comm_free(&newcomm);
MPI_Group_free(&newgroup);
MPI_Group_free(&world);
MPI_Finalize();
return 0;
}
int main(int argc, char **argv)
{
int rank;
int world_size;
/*
* Initialization
*/
int thread_support;
if (MPI_Init_thread(&argc, &argv, MPI_THREAD_SERIALIZED, &thread_support) != MPI_SUCCESS) {
fprintf(stderr,"MPI_Init_thread failed\n");
exit(1);
}
if (thread_support == MPI_THREAD_FUNNELED)
fprintf(stderr,"Warning: MPI only has funneled thread support, not serialized, hoping this will work\n");
if (thread_support < MPI_THREAD_FUNNELED)
fprintf(stderr,"Warning: MPI does not have thread support!\n");
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &world_size);
starpu_srand48((long int)time(NULL));
parse_args(rank, argc, argv);
int ret = starpu_init(NULL);
STARPU_CHECK_RETURN_VALUE(ret, "starpu_init");
/* We disable sequential consistency in this example */
starpu_data_set_default_sequential_consistency_flag(0);
starpu_mpi_init(NULL, NULL, 0);
STARPU_ASSERT(p*q == world_size);
starpu_cublas_init();
int barrier_ret = MPI_Barrier(MPI_COMM_WORLD);
STARPU_ASSERT(barrier_ret == MPI_SUCCESS);
/*
* Problem Init
*/
init_matrix(rank);
fprintf(stderr, "Rank %d: allocated (%d + %d) MB = %d MB\n", rank,
(int)(allocated_memory/(1024*1024)),
(int)(allocated_memory_extra/(1024*1024)),
(int)((allocated_memory+allocated_memory_extra)/(1024*1024)));
display_grid(rank, nblocks);
TYPE *a_r = NULL;
// STARPU_PLU(display_data_content)(a_r, size);
TYPE *x, *y;
if (check)
{
x = calloc(size, sizeof(TYPE));
STARPU_ASSERT(x);
y = calloc(size, sizeof(TYPE));
STARPU_ASSERT(y);
if (rank == 0)
{
unsigned ind;
for (ind = 0; ind < size; ind++)
x[ind] = (TYPE)starpu_drand48();
}
a_r = STARPU_PLU(reconstruct_matrix)(size, nblocks);
if (rank == 0)
STARPU_PLU(display_data_content)(a_r, size);
// STARPU_PLU(compute_ax)(size, x, y, nblocks, rank);
}
barrier_ret = MPI_Barrier(MPI_COMM_WORLD);
STARPU_ASSERT(barrier_ret == MPI_SUCCESS);
double timing = STARPU_PLU(plu_main)(nblocks, rank, world_size);
/*
* Report performance
*/
int reduce_ret;
double min_timing = timing;
double max_timing = timing;
double sum_timing = timing;
reduce_ret = MPI_Reduce(&timing, &min_timing, 1, MPI_DOUBLE, MPI_MIN, 0, MPI_COMM_WORLD);
STARPU_ASSERT(reduce_ret == MPI_SUCCESS);
reduce_ret = MPI_Reduce(&timing, &max_timing, 1, MPI_DOUBLE, MPI_MAX, 0, MPI_COMM_WORLD);
STARPU_ASSERT(reduce_ret == MPI_SUCCESS);
reduce_ret = MPI_Reduce(&timing, &sum_timing, 1, MPI_DOUBLE, MPI_SUM, 0, MPI_COMM_WORLD);
STARPU_ASSERT(reduce_ret == MPI_SUCCESS);
if (rank == 0)
{
fprintf(stderr, "Computation took: %f ms\n", max_timing/1000);
fprintf(stderr, "\tMIN : %f ms\n", min_timing/1000);
fprintf(stderr, "\tMAX : %f ms\n", max_timing/1000);
fprintf(stderr, "\tAVG : %f ms\n", sum_timing/(world_size*1000));
unsigned n = size;
double flop = (2.0f*n*n*n)/3.0f;
fprintf(stderr, "Synthetic GFlops : %2.2f\n", (flop/max_timing/1000.0f));
}
/*
* Test Result Correctness
*/
if (check)
{
/*
* Compute || A - LU ||
*/
STARPU_PLU(compute_lu_matrix)(size, nblocks, a_r);
#if 0
/*
* Compute || Ax - LUx ||
*/
unsigned ind;
y2 = calloc(size, sizeof(TYPE));
STARPU_ASSERT(y);
if (rank == 0)
{
for (ind = 0; ind < size; ind++)
{
y2[ind] = (TYPE)0.0;
}
}
STARPU_PLU(compute_lux)(size, x, y2, nblocks, rank);
/* Compute y2 = y2 - y */
CPU_AXPY(size, -1.0, y, 1, y2, 1);
TYPE err = CPU_ASUM(size, y2, 1);
int max = CPU_IAMAX(size, y2, 1);
fprintf(stderr, "(A - LU)X Avg error : %e\n", err/(size*size));
fprintf(stderr, "(A - LU)X Max error : %e\n", y2[max]);
#endif
}
/*
* Termination
*/
barrier_ret = MPI_Barrier(MPI_COMM_WORLD);
STARPU_ASSERT(barrier_ret == MPI_SUCCESS);
starpu_cublas_shutdown();
starpu_mpi_shutdown();
starpu_shutdown();
#if 0
MPI_Finalize();
#endif
return 0;
}
int main(int argc, char** argv)
{
int rank;
int size;
MPI_Init(&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &size);
if(argc != 5) {
fprintf(stderr, "argc %d\n", argc);
fprintf(stderr,
"Usage: %s <left> <right> <numSyncFiles> <tolerance>\n"
"where <left> and <right> are different"
"N-procs_case directories\n", argv[0]);
MPI_Finalize();
return 1;
}
char* lpath = argv[1];
char* rpath = argv[2];
int nSyncFiles = atoi(argv[3]);
double tolerance = atof(argv[4]);
int ndof;
int nshg;
int solsize;
double* solution;
std::set<int>* l_timesteps = find_timesteps(lpath, nSyncFiles);
std::set<int>* r_timesteps = find_timesteps(rpath, nSyncFiles);
std::set<int>* timesteps_to_check = new std::set<int>;
std::set_intersection(l_timesteps->begin(), l_timesteps->end(),
r_timesteps->begin(), r_timesteps->end(),
std::inserter(*timesteps_to_check, timesteps_to_check->begin()));
delete l_timesteps;
delete r_timesteps;
if(rank == 0)
printf("Found %d common timesteps\n",
timesteps_to_check->size());
#ifdef DBGONLY
read_solution(&solution, &solsize, &nshg, &ndof,
size, rank, 0, numSyncFiles, "./");
printf("nshg: %d, ndof: %d\n", nshg, ndof);
assert(solsize == ndof*nshg);
#endif
double maxerror = 0.0;
double error;
double gblmaxerror;
for(std::set<int>::iterator i = timesteps_to_check->begin();
i!=timesteps_to_check->end();i++)
{
error = compare_solution(lpath, rpath, *i, size, nSyncFiles);
if(error>maxerror) maxerror = error;
}
delete timesteps_to_check;
MPI_Barrier(MPI_COMM_WORLD);
MPI_Reduce(&maxerror, &gblmaxerror, 1, MPI_DOUBLE, MPI_MAX, 0,
MPI_COMM_WORLD);
if(rank == 0) printf("Maximum difference across all timesteps: %e\n",
gblmaxerror);
MPI_Finalize();
return (gblmaxerror > tolerance);
}
void test_P3DFFT(int *n, std::ofstream& results, int decomp, int * dims){
int nx,ny,nz,procid,nprocs,ndim;
int istart[3],isize[3],iend[3];
int fstart[3],fsize[3],fend[3];
int p3dfft_mem_conf,nrep;
long int Nlocal,Nglob;
double factor;
double l_timers[12]={0},g_timers[12]={0};
double total_time=0*MPI_Wtime(), setup_time=0;
// rtime_local is timings on each process and _global is the max reduced to root
// 0 is the forward FFT time, 1 is the Hadamard multiplication, 2 is the IFFT time, 3 is the sum of 0-2, and 4 is the setup time
// The communication time is measured by l_timers locally on each process and then reduced to g_timers to the root.
// the sum of first four elements give the comm time
unsigned char op_f[4]="fft", op_b[4]="tff";
int memsize[3];
MPI_Comm_size(MPI_COMM_WORLD,&nprocs);
MPI_Comm_rank(MPI_COMM_WORLD,&procid);
nx=n[0]; ny=n[1]; nz=n[2]; ndim=1; nrep=NREP;
if(decomp==1){
dims[0] = 1; dims[1] = nprocs;
}
if(procid == 0)
printf("Using processor grid %d x %d\n",dims[0],dims[1]);
/* Initialize P3DFFT */
MPI_Barrier(MPI_COMM_WORLD);
setup_time -= MPI_Wtime(); //Compute Setup Time.
Cp3dfft_setup(dims,nx,ny,nz,MPI_Comm_c2f(MPI_COMM_WORLD),nx,ny,nz,1,memsize);
setup_time += MPI_Wtime(); //Compute Setup Time.
PCOUT<<"done with setup"<<std::endl;
Cp3dfft_get_dims(istart,iend,isize,1);
Cp3dfft_get_dims(fstart,fend,fsize,2);
/* Allocate and initialize */
double *A; // Input matrix A
A=(double*)fftw_malloc(sizeof(double)*(memsize[0]*memsize[1]*memsize[2]*2));
//B=(double*)fftw_malloc(sizeof(double)*(memsize[0]*memsize[1]*memsize[2]*2));
/* Warmup */
Cp3dfft_ftran_r2c(A,A,op_f);
Cp3dfft_ftran_r2c(A,A,op_f);
MPI_Barrier(MPI_COMM_WORLD);
Cset_timers();
for (int rep=0; rep<nrep; rep++){
initialize_p3dfft(A,n);
MPI_Barrier(MPI_COMM_WORLD);
/* Forward transform */
total_time -= MPI_Wtime();
Cp3dfft_ftran_r2c(A,A,op_f);
total_time += MPI_Wtime();
MPI_Barrier(MPI_COMM_WORLD);
}
Cget_timers(l_timers);
Cp3dfft_btran_c2r(A,A,op_b);
/* Compute Error */
//PCOUT<<"Done With FFTs computing error"<<std::endl;
compute_error_p3dfft(A,n);
/* Gather timing statistics */
double g_total_time, g_comm_time, g_setup_time;
MPI_Reduce(&total_time,&g_total_time,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD);
MPI_Reduce(&setup_time,&g_setup_time,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD);
MPI_Reduce(&l_timers,&g_timers,12,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD);
g_total_time=g_total_time/nrep;
g_comm_time=(g_timers[0]+g_timers[1]+g_timers[2]+g_timers[3])/((double) nrep);
//g_total_time=g_total_time/((double)nrep);
ptrdiff_t size=n[0];size*=n[1]; size*=n[2];
double gflops=2.5*size*( log2(n[2]) + log2(n[0])+ log2(n[1]) )/(g_total_time)/1e9;
if(procid == 0){
std::cout.precision(4);
std::cout<<"P3DFFT Size="<<n[0]<<" "<<n[1]<<" "<<n[2]<<std::endl;;
std::cout<<"0= "<<g_timers[0]<<" 1= "<<g_timers[1]<<" 2= "<<g_timers[2]<<" 3= "<<g_timers[3]<<" 4= "<<g_timers[4]<<std::endl;
std::cout<<"5= "<<g_timers[5]<<" 6= "<<g_timers[6]<<" 7= "<<g_timers[7]<<" 8= "<<g_timers[8]<<" 9= "<<g_timers[9]<<std::endl;
std::cout<<"10= "<<g_timers[10]<<" 11= "<<g_timers[11]<<std::endl;
std::cout<<"\033[1;31m";
std::cout<<"\t"<<"np"<<"\t"<<"Grid"<<"\t"<<"Total"<<'\t'<<"Comm Time"<<"\t"<<"Setup Time"<<"\t"<<"\t"<<"Reps"<<'\t'<<"GFlops"<<std::endl;
std::cout<<"\t"<<nprocs<<"\t"<<dims[1]<<"*"<<dims[0]<<"\t"<<g_total_time<<'\t'<<g_comm_time<<"\t"<<g_setup_time<<"\t"<<nrep<<'\t'<<gflops<<std::endl;
std::cout<<"\033[0m\n"<<std::endl;
results<<"\t"<<nprocs<<"\t"<<dims[1]<<"*"<<dims[0]<<"\t"<<g_total_time<<'\t'<<g_comm_time<<"\t"<<g_setup_time<<"\t"<<nrep<<'\t'<<gflops<<std::endl;
}
/* Free work space */
fftw_free(A);
Cp3dfft_clean();
}
int olsr_main(int argc, char *argv[])
{
int i;
char log[32];
tw_opt_add(olsr_opts);
tw_init(&argc, &argv);
#if DEBUG
sprintf( log, "olsr-log.%ld", g_tw_mynode );
olsr_event_log = fopen( log, "w+");
if( olsr_event_log == nullptr )
tw_error( TW_LOC, "Failed to Open OLSR Event Log file \n");
#endif
g_tw_mapping = CUSTOM;
g_tw_custom_initial_mapping = &olsr_custom_mapping;
g_tw_custom_lp_global_to_local_map = &olsr_mapping_to_lp;
// nlp_per_pe = OLSR_MAX_NEIGHBORS;// / tw_nnodes();
//g_tw_lookahead = SA_INTERVAL;
SA_range_start = nlp_per_pe;
// Increase nlp_per_pe by nlp_per_pe / OMN
nlp_per_pe += nlp_per_pe / OLSR_MAX_NEIGHBORS;
g_tw_events_per_pe = OLSR_MAX_NEIGHBORS / 2 * nlp_per_pe + 65536;
tw_define_lps(nlp_per_pe, sizeof(olsr_msg_data));
for(i = 0; i < OLSR_END_EVENT; i++)
g_olsr_event_stats[i] = 0;
for (i = 0; i < SA_range_start; i++) {
tw_lp_settype(i, &olsr_lps[0]);
}
for (i = SA_range_start; i < nlp_per_pe; i++) {
tw_lp_settype(i, &olsr_lps[1]);
}
#if DEBUG
printf("g_tw_nlp is %llu\n", g_tw_nlp);
#endif
tw_run();
if( g_tw_synchronization_protocol != 1 )
{
MPI_Reduce( g_olsr_event_stats, g_olsr_root_event_stats, OLSR_END_EVENT, MPI_LONG_LONG, MPI_SUM, 0, MPI_COMM_WORLD);
}
else {
for (i = 0; i < OLSR_END_EVENT; i++) {
g_olsr_root_event_stats[i] = g_olsr_event_stats[i];
}
}
if (tw_ismaster()) {
for( i = 0; i < OLSR_END_EVENT; i++ )
printf("OLSR Type %s Event Count = %llu \n", event_names[i], g_olsr_root_event_stats[i]);
printf("Complete.\n");
}
tw_end();
return 0;
}
int main( int argc, char *argv[] )
{
int opt;
extern char *optarg;
extern int optind;
int is_output_timing=0, is_print_usage = 0;
int _debug=0, use_gen_file = 0, use_actsto = 0, use_normalsto=0;
char *token;
MPI_Offset disp, offset, file_size;
MPI_Datatype etype, ftype, buftype;
int errs = 0;
int size, rank, i, count;
char *fname = NULL;
double *buf;
MPI_File fh;
MPI_Comm comm;
MPI_Status status;
int64_t nitem = 0;
int fsize = 0, type_size;
double stime, etime, iotime, comptime, elapsed_time;
double max_iotime, max_comptime;
double max, min, sum=0.0, global_sum;
MPI_Init( &argc, &argv );
comm = MPI_COMM_WORLD;
MPI_Comm_size( comm, &size );
MPI_Comm_rank( comm, &rank );
while ( (opt=getopt(argc,argv,"i:s:godhxt"))!= EOF) {
switch (opt) {
case 'i': fname = optarg;
break;
case 'o': is_output_timing = 1;
break;
case 'g': use_gen_file = 1;
break;
case 'd': _debug = 1;
break;
case 'h': is_print_usage = 1;
break;
case 's':
token = strtok(optarg, ":");
//if (rank == 0) printf("token=%s\n", token);
if(token == NULL) {
if (rank == 0) printf("1: Wrong file size format!\n");
MPI_Finalize();
exit(1);
}
fsize = atoi(token);
token = strtok(NULL, ":");
//if (rank == 0) printf("token=%s\n", token);
if(token == NULL) {
if (rank == 0) printf("2: Wrong file size format!\n");
MPI_Finalize();
exit(1);
}
if(*token != 'm' && *token != 'g') {
if (rank == 0) printf("3: Wrong file size format!\n");
MPI_Finalize();
exit(1);
}
if (rank ==0) printf("fsize = %d (%s)\n", fsize, (*token=='m'?"MB":"GB"));
if (fsize == 0)
nitem = 0;
else {
MPI_Type_size(MPI_DOUBLE, &type_size);
nitem = fsize*1024; /* KB */
nitem = nitem*1024; /* MB */
if(*token == 'g') {
//if(rank == 0) printf("data in GB\n");
nitem = nitem*1024; /* GB */
}
nitem = nitem/type_size;
//printf("nitem=%lld\n", nitem);
nitem = nitem/size; /* size means comm size */
}
if (rank == 0) printf("nitem = %d\n", nitem);
break;
case 'x': use_actsto = 1;
break;
case 't': use_normalsto = 1;
break;
default: is_print_usage = 1;
break;
}
}
if (fname == NULL || is_print_usage == 1 || nitem == 0) {
if (rank == 0) usage(argv[0]);
MPI_Finalize();
exit(1);
}
int sizeof_mpi_offset;
sizeof_mpi_offset = (int)(sizeof(MPI_Offset)); // 8
//if (rank == 0) printf ("size_of_mpi_offset=%d\n", sizeof_mpi_offset);
if(use_normalsto == 1 && use_actsto == 1) {
if(rank == 0)
printf("Can't test both: either normalsto or actsto\n");
MPI_Finalize();
exit(1);
}
#if 0
if(use_actsto == 1) {
if (size != 1) {
if(rank == 0)
printf("active storage should be run with only 1 process!!!\n");
MPI_Finalize();
exit(1);
}
}
#endif
/* initialize random seed: */
srand(time(NULL));
if(use_gen_file == 1) {
int t, result;
MPI_File_open( comm, fname, MPI_MODE_RDWR | MPI_MODE_CREATE, MPI_INFO_NULL, &fh );
/* Set the file view */
disp = rank * nitem * type_size;
printf("%d: disp = %lld\n", rank, disp);
etype = MPI_DOUBLE;
ftype = MPI_DOUBLE;
result = MPI_File_set_view(fh, disp, etype, ftype, "native", MPI_INFO_NULL);
if(result != MPI_SUCCESS)
sample_error(result, "MPI_File_set_view");
buf = (double *)malloc( nitem * sizeof(double) );
if (buf == NULL) {
if(rank == 0) printf("malloc() failed\n");
MPI_Finalize();
exit(1);
}
buf[0] = rand()%4096;
if(rank==0) printf("%lf\n", buf[0]);
max = min = sum = buf[0];
for(i=1; i<nitem; i++) {
t = rand()%4096;
if (t>max) max = t;
if (t<min) min = t;
sum += t;
buf[i] = t;
if (i<10 && rank == 0) printf("%lf\n", buf[i]);
}
if(rank == 0) {
printf("MPI_Type_size(MPI_DOUBLE)=%d\n", type_size);
printf ("max=%lf, min=%lf, sum=%lf\n", max, min, sum);
}
stime = MPI_Wtime();
/* Write to file */
MPI_File_write_all( fh, buf, nitem, MPI_DOUBLE, &status );
etime = MPI_Wtime();
iotime = etime - stime;
printf("%d: iotime (write) = %10.4f\n", rank, iotime);
MPI_Get_count( &status, MPI_DOUBLE, &count );
//printf("count = %lld\n", count);
if (count != nitem) {
fprintf( stderr, "%d: Wrong count (%lld) on write\n", rank, count );
fflush(stderr);
/* exit */
MPI_Finalize();
exit(1);
}
MPI_File_close(&fh);
MPI_Barrier(MPI_COMM_WORLD);
if(rank == 0) printf("File is written\n\n");
}
double *tmp = (double *)malloc( nitem * sizeof(double) );
memset (tmp, 0, nitem*sizeof(double));
if(use_normalsto == 1) {
MPI_File_open( comm, fname, MPI_MODE_RDWR, MPI_INFO_NULL, &fh );
/* Read nothing (check status) */
memset( &status, 0xff, sizeof(MPI_Status) );
offset = rank * nitem * type_size;
/* start I/O */
stime = MPI_Wtime();
MPI_File_read_at(fh, offset, tmp, nitem, MPI_DOUBLE, &status);
etime = MPI_Wtime();
/* end I/O */
iotime = etime - stime;
if(_debug==1) printf("%d: iotime = %10.4f\n", rank, iotime);
MPI_Reduce(&iotime, &max_iotime, 1, MPI_DOUBLE, MPI_MAX, 0, MPI_COMM_WORLD);
sum = 0.0; /* reset sum */
/* start computation */
stime = MPI_Wtime();
for(i=0; i<nitem; i++) {
sum += tmp[i];
}
MPI_Reduce(&sum, &global_sum, 1, MPI_DOUBLE, MPI_MAX, 0, MPI_COMM_WORLD);
etime = MPI_Wtime();
/* end computation */
comptime = etime - stime;
if(_debug==1) printf("%d: comptime = %10.4f\n", rank, comptime);
MPI_Reduce(&comptime, &max_comptime, 1, MPI_DOUBLE, MPI_MAX, 0, MPI_COMM_WORLD);
if(rank == 0) {
elapsed_time = max_comptime + max_iotime;
printf("<<Result (SUM) with normal read>>\n"
"SUM = %10.4f \n"
"Computation time = %10.4f sec\n"
"I/O time = %10.4f sec\n"
"total time = %10.4f sec\n\n",
global_sum, max_comptime, max_iotime, elapsed_time);
}
MPI_File_close(&fh);
}
#if 0
if(use_actsto == 1) {
#if 0
/* MPI_MAX */
MPI_File_open( comm, fname, MPI_MODE_RDWR, MPI_INFO_NULL, &fh );
stime = MPI_Wtime();
MPI_File_read_at_ex( fh, offset, tmp, nitem, MPI_DOUBLE, MPI_MAX, &status );
etime = MPI_Wtime();
elapsed_time = etime-stime;
printf ("<<Result with active storage>>\n"
"max=%lf (in %10.4f sec)\n", tmp[0], elapsed_time);
MPI_File_close(&fh);
/* MPI_MIN */
MPI_File_open( comm, fname, MPI_MODE_RDWR, MPI_INFO_NULL, &fh );
stime = MPI_Wtime();
MPI_File_read_at_ex( fh, offset, tmp, nitem, MPI_DOUBLE, MPI_MIN, &status );
etime = MPI_Wtime();
elapsed_time = etime - stime;
printf ("min=%lf (in %10.4f sec)\n", tmp[0], elapsed_time);
MPI_File_close(&fh);
#endif
/* MPI_SUM */
MPI_File_open( comm, fname, MPI_MODE_RDWR, MPI_INFO_NULL, &fh );
memset(&status, 0xff, sizeof(MPI_Status));
offset = rank * nitem * type_size;
stime = MPI_Wtime();
MPI_File_read_at_ex( fh, offset, tmp, nitem, MPI_DOUBLE, MPI_SUM, &status );
etime = MPI_Wtime();
elapsed_time = etime - stime;
printf ("<<Result with active storage>>\n"
"sum=%lf (in %10.4f sec)\n", tmp[0], elapsed_time);
MPI_File_close( &fh );
}
#endif
MPI_Barrier(MPI_COMM_WORLD);
if (use_gen_file == 1) free( buf );
free( tmp );
MPI_Finalize();
return errs;
}
void trainOneEpochDenseCPU(int itask, float *data, float *numerator,
float *denominator, float *codebook,
unsigned int nSomX, unsigned int nSomY,
unsigned int nDimensions, unsigned int nVectors,
unsigned int nVectorsPerRank, float radius,
float scale, string mapType, string gridType,
bool compact_support, bool gaussian, int *globalBmus) {
unsigned int p1[2] = {0, 0};
unsigned int *bmus = new unsigned int[nVectorsPerRank * 2];
#ifdef _OPENMP
#pragma omp parallel default(shared) private(p1)
#endif
{
#ifdef _OPENMP
#pragma omp for
#endif
#ifdef _WIN32
for (int n = 0; n < nVectorsPerRank; n++) {
#else
for (unsigned int n = 0; n < nVectorsPerRank; n++) {
#endif
if (itask * nVectorsPerRank + n < nVectors) {
/// get the best matching unit
get_bmu_coord(codebook, data, nSomY, nSomX,
nDimensions, p1, n);
bmus[2 * n] = p1[0];
bmus[2 * n + 1] = p1[1];
}
}
}
float *localNumerator = new float[nSomY * nSomX * nDimensions];
float *localDenominator = new float[nSomY * nSomX];
#ifdef _OPENMP
#pragma omp parallel default(shared)
#endif
{
#ifdef _OPENMP
#pragma omp for
#endif
#ifdef _WIN32
for (int som_y = 0; som_y < nSomY; som_y++) {
#else
for (unsigned int som_y = 0; som_y < nSomY; som_y++) {
#endif
for (unsigned int som_x = 0; som_x < nSomX; som_x++) {
localDenominator[som_y * nSomX + som_x] = 0.0;
for (unsigned int d = 0; d < nDimensions; d++)
localNumerator[som_y * nSomX * nDimensions + som_x * nDimensions + d] = 0.0;
}
}
/// Accumulate denoms and numers
#ifdef _OPENMP
#pragma omp for
#endif
#ifdef _WIN32
for (int som_y = 0; som_y < nSomY; som_y++) {
#else
for (unsigned int som_y = 0; som_y < nSomY; som_y++) {
#endif
for (unsigned int som_x = 0; som_x < nSomX; som_x++) {
for (unsigned int n = 0; n < nVectorsPerRank; n++) {
if (itask * nVectorsPerRank + n < nVectors) {
float dist = 0.0f;
if (gridType == "rectangular") {
if (mapType == "planar") {
dist = euclideanDistanceOnPlanarMap(som_x, som_y, bmus[2 * n], bmus[2 * n + 1]);
}
else if (mapType == "toroid") {
dist = euclideanDistanceOnToroidMap(som_x, som_y, bmus[2 * n], bmus[2 * n + 1], nSomX, nSomY);
}
}
else {
if (mapType == "planar") {
dist = euclideanDistanceOnHexagonalPlanarMap(som_x, som_y, bmus[2 * n], bmus[2 * n + 1]);
}
else if (mapType == "toroid") {
dist = euclideanDistanceOnHexagonalToroidMap(som_x, som_y, bmus[2 * n], bmus[2 * n + 1], nSomX, nSomY);
}
}
float neighbor_fuct = getWeight(dist, radius, scale, compact_support, gaussian);
for (unsigned int d = 0; d < nDimensions; d++) {
localNumerator[som_y * nSomX * nDimensions + som_x * nDimensions + d] +=
1.0f * neighbor_fuct
* (*(data + n * nDimensions + d));
}
localDenominator[som_y * nSomX + som_x] += neighbor_fuct;
}
}
}
}
}
#ifdef HAVE_MPI
MPI_Reduce(localNumerator, numerator,
nSomY * nSomX * nDimensions, MPI_FLOAT, MPI_SUM, 0, MPI_COMM_WORLD);
MPI_Reduce(localDenominator, denominator,
nSomY * nSomX, MPI_FLOAT, MPI_SUM, 0, MPI_COMM_WORLD);
MPI_Gather(bmus, nVectorsPerRank * 2, MPI_INT, globalBmus, nVectorsPerRank * 2, MPI_INT, 0, MPI_COMM_WORLD);
#else
for (unsigned int i = 0; i < nSomY * nSomX * nDimensions; ++i) {
numerator[i] = localNumerator[i];
}
for (unsigned int i = 0; i < nSomY * nSomX; ++i) {
denominator[i] = localDenominator[i];
}
for (unsigned int i = 0; i < 2 * nVectorsPerRank; ++i) {
globalBmus[i] = bmus[i];
}
#endif
delete [] bmus;
delete [] localNumerator;
delete [] localDenominator;
}
int main( int argc, char *argv[] )
{
int num_errors = 0, total_num_errors = 0;
int rank, size;
char port1[MPI_MAX_PORT_NAME];
char port2[MPI_MAX_PORT_NAME];
char port3[MPI_MAX_PORT_NAME];
MPI_Status status;
MPI_Comm comm1, comm2, comm3;
int verbose = 0;
int data = 0;
if (getenv("MPITEST_VERBOSE"))
{
verbose = 1;
}
MPI_Init(&argc, &argv);
MPI_Comm_size(MPI_COMM_WORLD, &size);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
if (size < 4)
{
printf("Four processes needed to run this test.\n");
MPI_Finalize();
return 0;
}
if (rank == 0)
{
IF_VERBOSE(("0: opening ports.\n"));
MPI_Open_port(MPI_INFO_NULL, port1);
MPI_Open_port(MPI_INFO_NULL, port2);
MPI_Open_port(MPI_INFO_NULL, port3);
IF_VERBOSE(("0: opened port1: <%s>\n", port1));
IF_VERBOSE(("0: opened port2: <%s>\n", port2));
IF_VERBOSE(("0: opened port3: <%s>\n", port3));
IF_VERBOSE(("0: sending ports.\n"));
MPI_Send(port1, MPI_MAX_PORT_NAME, MPI_CHAR, 1, 0, MPI_COMM_WORLD);
MPI_Send(port2, MPI_MAX_PORT_NAME, MPI_CHAR, 2, 0, MPI_COMM_WORLD);
MPI_Send(port3, MPI_MAX_PORT_NAME, MPI_CHAR, 3, 0, MPI_COMM_WORLD);
IF_VERBOSE(("0: accepting port3.\n"));
MPI_Comm_accept(port3, MPI_INFO_NULL, 0, MPI_COMM_SELF, &comm3);
IF_VERBOSE(("0: accepting port2.\n"));
MPI_Comm_accept(port2, MPI_INFO_NULL, 0, MPI_COMM_SELF, &comm2);
IF_VERBOSE(("0: accepting port1.\n"));
MPI_Comm_accept(port1, MPI_INFO_NULL, 0, MPI_COMM_SELF, &comm1);
IF_VERBOSE(("0: closing ports.\n"));
MPI_Close_port(port1);
MPI_Close_port(port2);
MPI_Close_port(port3);
IF_VERBOSE(("0: sending 1 to process 1.\n"));
data = 1;
MPI_Send(&data, 1, MPI_INT, 0, 0, comm1);
IF_VERBOSE(("0: sending 2 to process 2.\n"));
data = 2;
MPI_Send(&data, 1, MPI_INT, 0, 0, comm2);
IF_VERBOSE(("0: sending 3 to process 3.\n"));
data = 3;
MPI_Send(&data, 1, MPI_INT, 0, 0, comm3);
IF_VERBOSE(("0: disconnecting.\n"));
MPI_Comm_disconnect(&comm1);
MPI_Comm_disconnect(&comm2);
MPI_Comm_disconnect(&comm3);
}
else if (rank == 1)
{
IF_VERBOSE(("1: receiving port.\n"));
MPI_Recv(port1, MPI_MAX_PORT_NAME, MPI_CHAR, 0, 0, MPI_COMM_WORLD, &status);
IF_VERBOSE(("1: received port1: <%s>\n", port1));
IF_VERBOSE(("1: connecting.\n"));
MPI_Comm_connect(port1, MPI_INFO_NULL, 0, MPI_COMM_SELF, &comm1);
MPI_Recv(&data, 1, MPI_INT, 0, 0, comm1, &status);
if (data != 1)
{
printf("Received %d from root when expecting 1\n", data);
fflush(stdout);
num_errors++;
}
IF_VERBOSE(("1: disconnecting.\n"));
MPI_Comm_disconnect(&comm1);
}
else if (rank == 2)
{
IF_VERBOSE(("2: receiving port.\n"));
MPI_Recv(port2, MPI_MAX_PORT_NAME, MPI_CHAR, 0, 0, MPI_COMM_WORLD, &status);
IF_VERBOSE(("2: received port2: <%s>\n", port2));
/* make sure process 1 has time to do the connect before this process
attempts to connect */
MTestSleep(2);
IF_VERBOSE(("2: connecting.\n"));
MPI_Comm_connect(port2, MPI_INFO_NULL, 0, MPI_COMM_SELF, &comm2);
MPI_Recv(&data, 1, MPI_INT, 0, 0, comm2, &status);
if (data != 2)
{
printf("Received %d from root when expecting 2\n", data);
fflush(stdout);
num_errors++;
}
IF_VERBOSE(("2: disconnecting.\n"));
MPI_Comm_disconnect(&comm2);
}
else if (rank == 3)
{
IF_VERBOSE(("3: receiving port.\n"));
MPI_Recv(port3, MPI_MAX_PORT_NAME, MPI_CHAR, 0, 0, MPI_COMM_WORLD, &status);
IF_VERBOSE(("2: received port2: <%s>\n", port2));
/* make sure process 1 and 2 have time to do the connect before this
process attempts to connect */
MTestSleep(4);
IF_VERBOSE(("3: connecting.\n"));
MPI_Comm_connect(port3, MPI_INFO_NULL, 0, MPI_COMM_SELF, &comm3);
MPI_Recv(&data, 1, MPI_INT, 0, 0, comm3, &status);
if (data != 3)
{
printf("Received %d from root when expecting 3\n", data);
fflush(stdout);
num_errors++;
}
IF_VERBOSE(("3: disconnecting.\n"));
MPI_Comm_disconnect(&comm3);
}
MPI_Barrier(MPI_COMM_WORLD);
MPI_Reduce(&num_errors, &total_num_errors, 1, MPI_INT, MPI_SUM, 0, MPI_COMM_WORLD);
if (rank == 0)
{
if (total_num_errors)
{
printf(" Found %d errors\n", total_num_errors);
}
else
{
printf(" No Errors\n");
}
fflush(stdout);
}
MPI_Finalize();
return total_num_errors;
}
int main(int argc, char *argv[])
{
int i, numprocs, rank, size, align_size, disp;
int skip;
double latency = 0.0, t_start = 0.0, t_stop = 0.0;
double timer=0.0;
double avg_time = 0.0, max_time = 0.0, min_time = 0.0;
char *sendbuf, *recvbuf, *s_buf1, *r_buf1;
int *rdispls=NULL, *recvcounts=NULL;
int max_msg_size = 1048576, full = 0;
MPI_Init(&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &numprocs);
if (process_args(argc, argv, rank, &max_msg_size, &full)) {
MPI_Finalize();
return EXIT_SUCCESS;
}
if(numprocs < 2) {
if(rank == 0) {
fprintf(stderr, "This test requires at least two processes\n");
}
MPI_Finalize();
return EXIT_FAILURE;
}
print_header(rank, full);
recvcounts=rdispls=NULL;
recvcounts = (int *) malloc (numprocs*sizeof(int));
if(NULL == recvcounts) {
fprintf(stderr, "malloc failed.\n");
exit(1);
}
rdispls = (int *) malloc (numprocs*sizeof(int));
if(NULL == rdispls) {
fprintf(stderr, "malloc failed.\n");
exit(1);
}
s_buf1 = r_buf1 = NULL;
s_buf1 = (char *) malloc(sizeof(char)*max_msg_size + MAX_ALIGNMENT);
if(NULL == s_buf1) {
fprintf(stderr, "malloc failed.\n");
exit(1);
}
r_buf1 = (char *) malloc(sizeof(char)*max_msg_size * numprocs + MAX_ALIGNMENT);
if(NULL == r_buf1) {
fprintf(stderr, "malloc failed.\n");
exit(1);
}
align_size = getpagesize();
sendbuf = (char *)(((unsigned long) s_buf1 + (align_size - 1)) / align_size
* align_size);
recvbuf = (char *)(((unsigned long) r_buf1 + (align_size - 1)) / align_size
* align_size);
memset(sendbuf, 1, max_msg_size);
memset(recvbuf, 0, max_msg_size * numprocs);
for(size=1; size <= max_msg_size; size *= 2) {
if(size > LARGE_MESSAGE_SIZE) {
skip = SKIP_LARGE;
iterations = iterations_large;
} else {
skip = SKIP;
}
MPI_Barrier(MPI_COMM_WORLD);
disp =0;
for ( i = 0; i < numprocs; i++) {
recvcounts[i] = size;
rdispls[i] = disp;
disp += size;
}
MPI_Barrier(MPI_COMM_WORLD);
timer=0.0;
for(i=0; i < iterations + skip ; i++) {
t_start = MPI_Wtime();
MPI_Allgatherv(sendbuf, size, MPI_CHAR, recvbuf, recvcounts, rdispls, MPI_CHAR, MPI_COMM_WORLD);
t_stop = MPI_Wtime();
if(i >= skip) {
timer+= t_stop-t_start;
}
MPI_Barrier(MPI_COMM_WORLD);
}
MPI_Barrier(MPI_COMM_WORLD);
latency = (double)(timer * 1e6) / iterations;
MPI_Reduce(&latency, &min_time, 1, MPI_DOUBLE, MPI_MIN, 0,
MPI_COMM_WORLD);
MPI_Reduce(&latency, &max_time, 1, MPI_DOUBLE, MPI_MAX, 0,
MPI_COMM_WORLD);
MPI_Reduce(&latency, &avg_time, 1, MPI_DOUBLE, MPI_SUM, 0,
MPI_COMM_WORLD);
avg_time = avg_time/numprocs;
print_data(rank, full, size, avg_time, min_time, max_time, iterations);
MPI_Barrier(MPI_COMM_WORLD);
}
free(s_buf1);
free(r_buf1);
free(recvcounts);
free(rdispls);
MPI_Finalize();
return EXIT_SUCCESS;
}
int main(int argc, char **argv)
{
int size , rank, number;
MPI_Init(&argc, &argv);
MPI_Comm_size(MPI_COMM_WORLD , &size);
MPI_Comm_rank(MPI_COMM_WORLD , &rank);
double start = MPI_Wtime(); //Starter klokka
double umaxglob=0; //Max feil for alle tråder
if (argc < 2) {
printf("Usage:\n");
printf(" poisson n\n\n");
printf("Arguments:\n");
printf(" n: the problem size (must be a power of 2)\n");
}
// The number of grid points in each direction is n+1
// The number of degrees of freedom in each direction is n-1
int n = atoi(argv[1]);
int m = n - 1; // ant punk hver vei i B
int *cnt = (int *) malloc(size * sizeof(int)); //loakal ant kolonner i matrix
int *displs = (int *) malloc((size+1) * sizeof(int)); //lokal displacement for de andre prosessorene sine punkter i sendbuf
displs[size] = m;
displs[0]=0; //Displacement til første prosessor er alltid 0
int overflow = m % size; //ant kolonner som blir til overs
for(int i = 0;i<size;i++){
cnt[i] = m / size; // nrColon for hver prosessor
if (overflow != 0){
cnt[i]++; //fordeler de ekstra kolonnene
overflow--;
}
if (i < size-1){
displs[i+1] = displs[i]+cnt[i];
}
}
int nrColon = cnt[rank]; //ant kolonner "jeg" har
int pros_dof = nrColon*m; //ant lementer jeg har
int nn = 4 * n;
double h = 1.0 / n;
// Grid points
double *grid = mk_1D_array(n+1, false);
double **b = mk_2D_array(nrColon, m, false);
double **bt = mk_2D_array(nrColon, m,false);
int trad = omp_get_max_threads(); //ant tråder
double **z = mk_2D_array(trad,nn, false); //z er 2D pga paralellisering med OpenMP, da FST ikke skal overskrive andre tråders z
double *diag = mk_1D_array(m, false);
double *sendbuf = mk_1D_array(nrColon*m, false);
double *recbuf = mk_1D_array(nrColon*m, false);
int *sendcnt = (int *) malloc((size+1) * sizeof(int)); //ant elementer jeg skal sende hver prosessor
int *sdispls = (int *) malloc((size+1) * sizeof(int)); //index i sendbuf for hver prosessor
sdispls[0]=0; //prosessor 0 skal alltid ha fra index 0
for(int i = 0;i<size;i++){
sendcnt[i] = cnt[i]*cnt[rank]; // antt elementer jeg eier * ant element den eier
sdispls[i] = displs[i]*cnt[rank]; //displacement for hver prosessor
}
// GRID
#pragma omp parallel for schedule(static)
for (int i = 0; i < n+1; i++) {
grid[i] = i * h;
}
#pragma omp parallel for schedule(static)
for (size_t i = 0; i < m; i++) {
diag[i] = 2.0 * (1.0 - cos((i+1) * PI / n)); //Eigenvalue
}
// Initialize the right hand side data
#pragma omp parallel for schedule(static)
for (size_t i = 0; i < nrColon; i++) {
for (size_t j = 0; j < m; j++) {
// b[i][j] = h * h;
b[i][j] = h * h * func1(grid[i+displs[rank]], grid[j]); //evaluerer funksjoen * h*h
}
}
// Calculate Btilde^T = S^-1 * (S * B)^T
#pragma omp parallel for schedule(guided, 5)
for (size_t i = 0; i < nrColon; i++) {
fst_(b[i], &n, z[omp_get_thread_num()], &nn);
}
MPItranspose (b, bt,nrColon,m, sendbuf,recbuf,sendcnt,sdispls, size, rank, displs);
#pragma omp parallel for schedule(static)
for (size_t i = 0; i < nrColon; i++) {
fstinv_(bt[i], &n, z[omp_get_thread_num()], &nn);
}
// Solve Lambda * Xtilde = Btilde
#pragma omp parallel for schedule(static)
for (int j=0; j < nrColon; j++) {
for (int i=0; i < m; i++) {
bt[j][i] /= (diag[j+displs[rank]]+diag[i]);
}
}
// Calculate X = S^-1 * (S * Xtilde^T)
#pragma omp parallel for schedule(static)
for (size_t i = 0; i < nrColon; i++) {
fst_(bt[i], &n, z[omp_get_thread_num()], &nn);
}
MPItranspose (bt, b, nrColon,m, sendbuf,recbuf,sendcnt,sdispls, size, rank, displs);
#pragma omp parallel for schedule(static)
for (size_t i = 0; i < nrColon; i++) {
fstinv_(b[i], &n, z[omp_get_thread_num()], &nn);
}
// Calculate maximal value of solution
double u_max = 0.0, temp;
#pragma omp parallel for schedule(static)
for (size_t i = 0; i < nrColon; i++) {
for (size_t j = 0; j < m; j++) {
temp = b[i][j] - func2(grid[displs[rank]+i], grid[j]); //tester resultat - kjent funksjon, skal bli = 0
if (temp > u_max){
u_max = temp;
}
}
}
MPI_Reduce (&u_max, &umaxglob, 1, MPI_DOUBLE, MPI_MAX, 0, MPI_COMM_WORLD); //Finner den største u_max fra de forskjellige prosessorene og setter den til umaxglob
MPI_Finalize();
if (rank == 0) {
printf("Nodes = %d \n", size);
printf("Threads per node = %d \n", omp_get_max_threads());
printf("u_max = %e\n", umaxglob); //Printer max feil
double times = MPI_Wtime()-start; //Stopper klokka
printf("Time elapsed = %1.16f \n", times); //Pinter tid
}
return 0;
}
void PetscVector<Complex>::localize_to_one (std::vector<Complex>& v_local,
const processor_id_type pid) const
{
this->_restore_array();
PetscErrorCode ierr=0;
const PetscInt n = size();
const PetscInt nl = local_size();
PetscScalar *values;
v_local.resize(n);
for (PetscInt i=0; i<n; i++)
v_local[i] = 0.;
// only one processor
if (n == nl)
{
ierr = VecGetArray (_vec, &values);
CHKERRABORT(libMesh::COMM_WORLD,ierr);
for (PetscInt i=0; i<n; i++)
v_local[i] = static_cast<Complex>(values[i]);
ierr = VecRestoreArray (_vec, &values);
CHKERRABORT(libMesh::COMM_WORLD,ierr);
}
// otherwise multiple processors
else
{
numeric_index_type ioff = this->first_local_index();
/* in here the local values are stored, acting as send buffer for MPI
* initialize to zero, since we collect using MPI_SUM
*/
std::vector<Real> real_local_values(n, 0.);
std::vector<Real> imag_local_values(n, 0.);
{
ierr = VecGetArray (_vec, &values);
CHKERRABORT(libMesh::COMM_WORLD,ierr);
// provide my local share to the real and imag buffers
for (PetscInt i=0; i<nl; i++)
{
real_local_values[i+ioff] = static_cast<Complex>(values[i]).real();
imag_local_values[i+ioff] = static_cast<Complex>(values[i]).imag();
}
ierr = VecRestoreArray (_vec, &values);
CHKERRABORT(libMesh::COMM_WORLD,ierr);
}
/* have buffers of the real and imaginary part of v_local.
* Once MPI_Reduce() collected all the real and imaginary
* parts in these std::vector<Real>, the values can be
* copied to v_local
*/
std::vector<Real> real_v_local(n);
std::vector<Real> imag_v_local(n);
// collect entries from other proc's in real_v_local, imag_v_local
MPI_Reduce (&real_local_values[0], &real_v_local[0], n,
MPI_REAL, MPI_SUM,
pid, libMesh::COMM_WORLD);
MPI_Reduce (&imag_local_values[0], &imag_v_local[0], n,
MPI_REAL, MPI_SUM,
pid, libMesh::COMM_WORLD);
// copy real_v_local and imag_v_local to v_local
for (PetscInt i=0; i<n; i++)
v_local[i] = Complex(real_v_local[i], imag_v_local[i]);
}
}
void grad(int *n, int nthreads) {
int nprocs, procid;
MPI_Comm_rank(MPI_COMM_WORLD, &procid);
MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
/* Create Cartesian Communicator */
int c_dims[2]={0};
MPI_Comm c_comm;
accfft_create_comm(MPI_COMM_WORLD,c_dims,&c_comm);
double *data;
Complex *data_hat;
double f_time=0*MPI_Wtime(),i_time=0, setup_time=0;
int alloc_max=0;
int isize[3],osize[3],istart[3],ostart[3];
/* Get the local pencil size and the allocation size */
alloc_max=accfft_local_size_dft_r2c(n,isize,istart,osize,ostart,c_comm);
//data=(double*)accfft_alloc(isize[0]*isize[1]*isize[2]*sizeof(double));
data=(double*)accfft_alloc(alloc_max);
data_hat=(Complex*)accfft_alloc(alloc_max);
accfft_init(nthreads);
/* Create FFT plan */
setup_time=-MPI_Wtime();
accfft_plan * plan=accfft_plan_dft_3d_r2c(n,data,(double*)data_hat,c_comm,ACCFFT_MEASURE);
setup_time+=MPI_Wtime();
/* Initialize data */
initialize(data,n,c_comm);
MPI_Barrier(c_comm);
double * gradx=(double*)accfft_alloc(isize[0]*isize[1]*isize[2]*sizeof(double));
double * grady=(double*)accfft_alloc(isize[0]*isize[1]*isize[2]*sizeof(double));
double * gradz=(double*)accfft_alloc(isize[0]*isize[1]*isize[2]*sizeof(double));
double timings[5]={0};
std::bitset<3> XYZ=0;
XYZ[0]=1;
XYZ[1]=1;
XYZ[2]=1;
double exec_time=-MPI_Wtime();
accfft_grad(gradx,grady,gradz,data,plan,XYZ,timings);
exec_time+=MPI_Wtime();
/* Check err*/
PCOUT<<">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>"<<std::endl;
PCOUT<<">>>>>>>>Checking Gradx>>>>>>>>"<<std::endl;
check_err_grad(gradx,n,c_comm,0);
PCOUT<<"<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<"<<std::endl;
PCOUT<<"<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n"<<std::endl;
PCOUT<<">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>"<<std::endl;
PCOUT<<">>>>>>>>Checking Grady>>>>>>>>"<<std::endl;
check_err_grad(grady,n,c_comm,1);
PCOUT<<"<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<"<<std::endl;
PCOUT<<"<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n"<<std::endl;
PCOUT<<">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>"<<std::endl;
PCOUT<<">>>>>>>>Checking Gradz>>>>>>>>"<<std::endl;
check_err_grad(gradz,n,c_comm,2);
PCOUT<<"<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<"<<std::endl;
PCOUT<<"<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n"<<std::endl;
/* Compute some timings statistics */
double g_setup_time,g_timings[5],g_exec_time;
MPI_Reduce(timings,g_timings,5, MPI_DOUBLE, MPI_MAX,0, c_comm);
MPI_Reduce(&setup_time,&g_setup_time,1, MPI_DOUBLE, MPI_MAX,0, c_comm);
MPI_Reduce(&exec_time,&g_exec_time,1, MPI_DOUBLE, MPI_MAX,0, c_comm);
PCOUT<<"Timing for Grad Computation for size "<<n[0]<<"*"<<n[1]<<"*"<<n[2]<<std::endl;
PCOUT<<"Setup \t\t"<<g_setup_time<<std::endl;
PCOUT<<"Evaluation \t"<<g_exec_time<<std::endl;
accfft_free(data);
accfft_free(data_hat);
MPI_Barrier(c_comm);
accfft_free(gradx);
accfft_free(grady);
accfft_free(gradz);
accfft_destroy_plan(plan);
accfft_cleanup();
MPI_Comm_free(&c_comm);
PCOUT<<"-------------------------------------------------------"<<std::endl;
PCOUT<<"-------------------------------------------------------"<<std::endl;
PCOUT<<"-------------------------------------------------------\n"<<std::endl;
return ;
} // end grad
int
main(int argc, char *argv[])
{
GRID *g;
DOF *u_h;
MAT *A, *A0, *B;
MAP *map;
INT i;
size_t nnz, mem, mem_peak;
VEC *x, *y0, *y1, *y2;
double t0, t1, dnz, dnz1, mflops, mop;
char *fn = "../test/cube.dat";
FLOAT mem_max = 300;
INT refine = 0;
phgOptionsRegisterFilename("-mesh_file", "Mesh file", (char **)&fn);
phgOptionsRegisterInt("-loop_count", "Loop count", &loop_count);
phgOptionsRegisterInt("-refine", "Refinement level", &refine);
phgOptionsRegisterFloat("-mem_max", "Maximum memory", &mem_max);
phgInit(&argc, &argv);
g = phgNewGrid(-1);
if (!phgImport(g, fn, FALSE))
phgError(1, "can't read file \"%s\".\n", fn);
phgRefineAllElements(g, refine);
u_h = phgDofNew(g, DOF_DEFAULT, 1, "u_h", DofNoAction);
while (TRUE) {
phgPrintf("\n");
if (phgBalanceGrid(g, 1.2, 1, NULL, 0.))
phgPrintf("Repartition mesh, %d submeshes, load imbalance: %lg\n",
g->nprocs, (double)g->lif);
map = phgMapCreate(u_h, NULL);
A = phgMapCreateMat(map, map);
A->handle_bdry_eqns = TRUE;
build_matrix(A, u_h);
phgMatAssemble(A);
/* Note: A is unsymmetric (A' != A) if boundary entries not removed */
phgMatRemoveBoundaryEntries(A);
#if 0
/* test block matrix operation */
A0 = phgMatCreateBlockMatrix(g->comm, 1, 1, &A, NULL);
#else
A0 = A;
#endif
phgPrintf("%d DOF, %d elems, %d submeshes, matrix size: %d, LIF: %lg\n",
DofGetDataCountGlobal(u_h), g->nleaf_global,
g->nprocs, A->rmap->nglobal, (double)g->lif);
/* test PHG mat-vec multiply */
x = phgMapCreateVec(A->cmap, 1);
y1 = phgMapCreateVec(A->rmap, 1);
phgVecRandomize(x, 123);
phgMatVec(MAT_OP_N, 1.0, A0, x, 0.0, &y1);
phgPerfGetMflops(g, NULL, NULL); /* reset flops counter */
t0 = phgGetTime(NULL);
for (i = 0; i < loop_count; i++) {
phgMatVec(MAT_OP_N, 1.0, A0, x, 0.0, &y1);
}
t1 = phgGetTime(NULL);
mflops = phgPerfGetMflops(g, NULL, NULL);
y0 = phgVecCopy(y1, NULL);
nnz = A->nnz_d + A->nnz_o;
#if USE_MPI
dnz1 = nnz;
MPI_Reduce(&dnz1, &dnz, 1, MPI_DOUBLE, MPI_SUM, 0, g->comm);
#else
dnz = nnz;
#endif
mop = loop_count * (dnz + dnz - A->rmap->nlocal) * 1e-6;
phgPrintf("\n");
t1 -= t0;
phgPrintf(" PHG: time %0.4lf, nnz %0.16lg, %0.2lfMF (%0.2lfMF)\n",
t1, dnz, mop / (t1 == 0 ? 1. : t1), mflops);
/* test trans(A)*x */
phgPerfGetMflops(g, NULL, NULL); /* reset flops counter */
t0 = phgGetTime(NULL);
for (i = 0; i < loop_count; i++) {
phgMatVec(MAT_OP_T, 1.0, A0, x, 0.0, &y1);
}
t1 = phgGetTime(NULL);
mflops = phgPerfGetMflops(g, NULL, NULL);
t1 -= t0;
phgPrintf(" A'*x: time %0.4lf, nnz %0.16lg, %0.2lfMF (%0.2lfMF), "
"err: %le\n", t1, dnz, mop / (t1 == 0 ? 1. : t1), mflops,
(double)phgVecNorm2(phgVecAXPBY(-1.0, y0, 1.0, &y1), 0, NULL));
/* time A * trans(A) */
phgPerfGetMflops(g, NULL, NULL); /* reset flops counter */
t0 = phgGetTime(NULL);
B = phgMatMat(MAT_OP_N, MAT_OP_N, 1.0, A, A, 0.0, NULL);
t1 = phgGetTime(NULL);
mflops = phgPerfGetMflops(g, NULL, NULL);
nnz = B->nnz_d + B->nnz_o;
#if USE_MPI
dnz1 = nnz;
MPI_Reduce(&dnz1, &dnz, 1, MPI_DOUBLE, MPI_SUM, 0, g->comm);
#else
dnz = nnz;
#endif
/* compare B*x <--> A*A*x */
y2 = phgMatVec(MAT_OP_N, 1.0, B, x, 0.0, NULL);
phgMatVec(MAT_OP_N, 1.0, A0, y0, 0.0, &y1);
phgMatDestroy(&B);
t1 -= t0;
phgPrintf(" A*A: time %0.4lf, nnz %0.16lg, %0.2lfMF, err: %le\n",
t1, dnz, mflops,
(double)phgVecNorm2(phgVecAXPBY(-1.0, y1, 1.0, &y2), 0, NULL));
#if USE_PETSC
{
Mat ma, mb;
MatInfo info;
Vec va, vb, vc;
PetscScalar *vec;
ma = phgPetscCreateMatAIJ(A);
MatGetVecs(ma, PETSC_NULL, &va);
VecDuplicate(va, &vb);
VecGetArray(va, &vec);
memcpy(vec, x->data, x->map->nlocal * sizeof(*vec));
VecRestoreArray(va, &vec);
MatMult(ma, va, vb);
phgPerfGetMflops(g, NULL, NULL); /* reset flops counter */
t0 = phgGetTime(NULL);
for (i = 0; i < loop_count; i++) {
MatMult(ma, va, vb);
}
t1 = phgGetTime(NULL);
mflops = phgPerfGetMflops(g, NULL, NULL);
VecGetArray(vb, &vec);
memcpy(y1->data, vec, x->map->nlocal * sizeof(*vec));
VecRestoreArray(vb, &vec);
MatGetInfo(ma, MAT_GLOBAL_SUM, &info);
/*phgPrintf(" --------------------------------------------"
"-------------------------\n");*/
phgPrintf("\n");
t1 -= t0;
dnz = info.nz_used;
phgPrintf(" PETSc: time %0.4lf, nnz %0.16lg, %0.2lfMF (%0.2lfMF), "
"err: %le\n", t1, dnz, mop / (t1==0 ? 1.:t1), mflops,
(double)phgVecNorm2(phgVecAXPBY(-1.0, y0, 1.0, &y1), 0, NULL));
phgPerfGetMflops(g, NULL, NULL); /* reset flops counter */
t0 = phgGetTime(NULL);
for (i = 0; i < loop_count; i++) {
MatMultTranspose(ma, va, vb);
}
t1 = phgGetTime(NULL);
mflops = phgPerfGetMflops(g, NULL, NULL);
VecGetArray(vb, &vec);
memcpy(y1->data, vec, x->map->nlocal * sizeof(*vec));
VecRestoreArray(vb, &vec);
t1 -= t0;
phgPrintf(" A'*x: time %0.4lf, nnz %0.16lg, %0.2lfMF (%0.2lfMF), "
"err: %le\n", t1, dnz, mop / (t1==0 ? 1.:t1), mflops,
(double)phgVecNorm2(phgVecAXPBY(-1.0, y0, 1.0, &y1), 0, NULL));
phgPerfGetMflops(g, NULL, NULL); /* reset flops counter */
t0 = phgGetTime(NULL);
MatMatMult(ma, ma, MAT_INITIAL_MATRIX, PETSC_DEFAULT, &mb);
t1 = phgGetTime(NULL);
mflops = phgPerfGetMflops(g, NULL, NULL);
t1 -= t0;
MatGetInfo(mb, MAT_GLOBAL_SUM, &info);
dnz = info.nz_used;
VecDuplicate(va, &vc);
/* compare B*x <--> A*A*x */
MatMult(ma, vb, vc);
MatMult(mb, va, vb);
VecGetArray(vb, &vec);
memcpy(y1->data, vec, x->map->nlocal * sizeof(*vec));
VecRestoreArray(vb, &vec);
VecGetArray(vc, &vec);
memcpy(y2->data, vec, x->map->nlocal * sizeof(*vec));
VecRestoreArray(vc, &vec);
phgPrintf(" A*A: time %0.4lf, nnz %0.16lg, %0.2lfMF, err: %le\n",
t1, dnz, mflops,
(double)phgVecNorm2(phgVecAXPBY(-1.0, y1, 1.0, &y2), 0, NULL));
phgPetscMatDestroy(&mb);
phgPetscMatDestroy(&ma);
phgPetscVecDestroy(&va);
phgPetscVecDestroy(&vb);
phgPetscVecDestroy(&vc);
}
#endif /* USE_PETSC */
#if USE_HYPRE
{
HYPRE_IJMatrix ma;
HYPRE_IJVector va, vb, vc;
HYPRE_ParCSRMatrix par_ma;
hypre_ParCSRMatrix *par_mb;
HYPRE_ParVector par_va, par_vb, par_vc;
HYPRE_Int offset, *ni, start, end;
assert(sizeof(INT)==sizeof(int) && sizeof(FLOAT)==sizeof(double));
setup_hypre_mat(A, &ma);
ni = phgAlloc(2 * A->rmap->nlocal * sizeof(*ni));
offset = A->cmap->partition[A->cmap->rank];
for (i = 0; i < A->rmap->nlocal; i++)
ni[i] = i + offset;
HYPRE_IJVectorCreate(g->comm, offset, offset + A->rmap->nlocal - 1,
&va);
HYPRE_IJVectorCreate(g->comm, offset, offset + A->rmap->nlocal - 1,
&vb);
HYPRE_IJVectorCreate(g->comm, offset, offset + A->rmap->nlocal - 1,
&vc);
HYPRE_IJVectorSetObjectType(va, HYPRE_PARCSR);
HYPRE_IJVectorSetObjectType(vb, HYPRE_PARCSR);
HYPRE_IJVectorSetObjectType(vc, HYPRE_PARCSR);
HYPRE_IJVectorSetMaxOffProcElmts(va, 0);
HYPRE_IJVectorSetMaxOffProcElmts(vb, 0);
HYPRE_IJVectorSetMaxOffProcElmts(vc, 0);
HYPRE_IJVectorInitialize(va);
HYPRE_IJVectorInitialize(vb);
HYPRE_IJVectorInitialize(vc);
HYPRE_IJMatrixGetObject(ma, (void **)(void *)&par_ma);
HYPRE_IJVectorGetObject(va, (void **)(void *)&par_va);
HYPRE_IJVectorGetObject(vb, (void **)(void *)&par_vb);
HYPRE_IJVectorGetObject(vc, (void **)(void *)&par_vc);
HYPRE_IJVectorSetValues(va, A->cmap->nlocal, ni, (double *)x->data);
HYPRE_IJVectorAssemble(va);
HYPRE_IJVectorAssemble(vb);
HYPRE_IJVectorAssemble(vc);
HYPRE_IJMatrixGetRowCounts(ma, A->cmap->nlocal,
ni, ni + A->rmap->nlocal);
for (i = 0, nnz = 0; i < A->rmap->nlocal; i++)
nnz += ni[A->rmap->nlocal + i];
#if USE_MPI
dnz1 = nnz;
MPI_Reduce(&dnz1, &dnz, 1, MPI_DOUBLE, MPI_SUM, 0, g->comm);
#else
dnz = nnz;
#endif
HYPRE_ParCSRMatrixMatvec(1.0, par_ma, par_va, 0.0, par_vb);
phgPerfGetMflops(g, NULL, NULL); /* reset flops counter */
t0 = phgGetTime(NULL);
for (i = 0; i < loop_count; i++) {
HYPRE_ParCSRMatrixMatvec(1.0, par_ma, par_va, 0.0, par_vb);
}
t1 = phgGetTime(NULL);
mflops = phgPerfGetMflops(g, NULL, NULL);
HYPRE_IJVectorGetValues(vb, A->rmap->nlocal, ni, (double*)y1->data);
/*phgPrintf(" --------------------------------------------"
"-------------------------\n");*/
phgPrintf("\n");
t1 -= t0;
phgPrintf(" HYPRE: time %0.4lf, nnz %0.16lg, %0.2lfMF (%0.2lfMF), "
"err: %le\n", t1, dnz, mop / (t1==0 ? 1.:t1), mflops,
(double)phgVecNorm2(phgVecAXPBY(-1.0, y0, 1.0, &y1), 0, NULL));
phgPerfGetMflops(g, NULL, NULL); /* reset flops counter */
t0 = phgGetTime(NULL);
for (i = 0; i < loop_count; i++) {
HYPRE_ParCSRMatrixMatvecT(1.0, par_ma, par_va, 0.0, par_vb);
}
t1 = phgGetTime(NULL);
mflops = phgPerfGetMflops(g, NULL, NULL);
HYPRE_IJVectorGetValues(vb, A->rmap->nlocal, ni, (double*)y1->data);
t1 -= t0;
phgPrintf(" A'*x: time %0.4lf, nnz %0.16lg, %0.2lfMF (%0.2lfMF), "
"err: %le\n", t1, dnz, mop / (t1==0 ? 1.:t1), mflops,
(double)phgVecNorm2(phgVecAXPBY(-1.0, y0, 1.0, &y1), 0, NULL));
phgPerfGetMflops(g, NULL, NULL); /* reset flops counter */
t0 = phgGetTime(NULL);
/* Note: 'HYPRE_ParCSRMatrix' is currently typedef'ed to
* 'hypre_ParCSRMatrix *' */
par_mb = hypre_ParMatmul((hypre_ParCSRMatrix *)par_ma,
(hypre_ParCSRMatrix *)par_ma);
t1 = phgGetTime(NULL);
mflops = phgPerfGetMflops(g, NULL, NULL);
start = hypre_ParCSRMatrixFirstRowIndex(par_mb);
end = hypre_ParCSRMatrixLastRowIndex(par_mb) + 1;
for (i = start, nnz = 0; i < end; i++) {
HYPRE_Int ncols;
hypre_ParCSRMatrixGetRow(par_mb, i, &ncols, NULL, NULL);
hypre_ParCSRMatrixRestoreRow(par_mb, i, &ncols, NULL, NULL);
nnz += ncols;
}
#if USE_MPI
dnz1 = nnz;
MPI_Reduce(&dnz1, &dnz, 1, MPI_DOUBLE, MPI_SUM, 0, g->comm);
#else
dnz = nnz;
#endif
/* compare B*x <--> A*A*x */
HYPRE_ParCSRMatrixMatvec(1.0, par_ma, par_vb, 0.0, par_vc);
HYPRE_ParCSRMatrixMatvec(1.0, (void *)par_mb, par_va, 0.0, par_vb);
HYPRE_IJVectorGetValues(vb, A->rmap->nlocal, ni, (double*)y1->data);
HYPRE_IJVectorGetValues(vc, A->rmap->nlocal, ni, (double*)y2->data);
hypre_ParCSRMatrixDestroy((par_mb));
t1 -= t0;
phgPrintf(" A*A: time %0.4lf, nnz %0.16lg, %0.2lfMF, err: %le\n",
t1, dnz, mflops,
(double)phgVecNorm2(phgVecAXPBY(-1.0, y1, 1.0, &y2), 0, NULL));
phgFree(ni);
HYPRE_IJMatrixDestroy(ma);
HYPRE_IJVectorDestroy(va);
HYPRE_IJVectorDestroy(vb);
HYPRE_IJVectorDestroy(vc);
}
#endif /* USE_HYPRE */
if (A0 != A)
phgMatDestroy(&A0);
#if 0
if (A->rmap->nglobal > 1000) {
VEC *v = phgMapCreateVec(A->rmap, 3);
for (i = 0; i < v->map->nlocal; i++) {
v->data[i + 0 * v->map->nlocal] = 1 * (i + v->map->partition[g->rank]);
v->data[i + 1 * v->map->nlocal] = 2 * (i + v->map->partition[g->rank]);
v->data[i + 2 * v->map->nlocal] = 3 * (i + v->map->partition[g->rank]);
}
phgMatDumpMATLAB(A, "A", "A.m");
phgVecDumpMATLAB(v, "v", "v.m");
phgFinalize();
exit(0);
}
#endif
phgMatDestroy(&A);
phgVecDestroy(&x);
phgVecDestroy(&y0);
phgVecDestroy(&y1);
phgVecDestroy(&y2);
phgMapDestroy(&map);
mem = phgMemoryUsage(g, &mem_peak);
dnz = mem / (1024.0 * 1024.0);
dnz1 = mem_peak / (1024.0 * 1024.0);
/*phgPrintf(" --------------------------------------------"
"-------------------------\n");*/
phgPrintf("\n");
phgPrintf(" Memory: current %0.4lgMB, peak %0.4lgMB\n", dnz, dnz1);
#if 0
{
static int loop_count = 0;
if (++loop_count == 4)
break;
}
#endif
if (mem_peak > 1024 * (size_t)1024 * mem_max)
break;
phgRefineAllElements(g, 1);
}
phgDofFree(&u_h);
phgFreeGrid(&g);
phgFinalize();
return 0;
}
void Master::collectStats() {
int64_t dummy = 0;
MPI_Reduce(&dummy, &engine.conflicts, 1, MPI_LONG_LONG_INT, MPI_SUM, 0, MPI_COMM_WORLD);
MPI_Reduce(&dummy, &engine.propagations, 1, MPI_LONG_LONG_INT, MPI_SUM, 0, MPI_COMM_WORLD);
MPI_Reduce(&dummy, &engine.opt_time, 1, MPI_DOUBLE, MPI_MAX, 0, MPI_COMM_WORLD);
}
int main(int argc, char ** argv)
{
int Block_order;
size_t Block_size;
size_t Colblock_size;
int Tile_order=32;
int tiling;
int Num_procs; /* Number of ranks */
int order; /* overall matrix order */
int send_to, recv_from; /* communicating ranks */
size_t bytes; /* total amount of data to be moved */
int my_ID; /* rank */
int root=0; /* root rank of a communicator */
int iterations; /* number of times to run the pipeline algorithm */
int i, j, it, jt, ID;/* dummies */
int iter; /* index of iteration */
int phase; /* phase in the staged communication */
size_t colstart; /* sequence number of first column owned by calling rank */
int error=0; /* error flag */
double *A_p; /* original matrix column block */
double *B_p; /* transposed matrix column block */
double *Work_in_p; /* workspace for the transpose function */
double *Work_out_p;/* workspace for the transpose function */
double abserr, abserr_tot; /* computed error */
double epsilon = 1.e-8; /* error tolerance */
double local_trans_time, /* timing parameters */
trans_time,
avgtime;
MPI_Status status; /* completion status of message */
MPI_Win shm_win_A; /* Shared Memory window object */
MPI_Win shm_win_B; /* Shared Memory window object */
MPI_Win shm_win_Work_in; /* Shared Memory window object */
MPI_Win shm_win_Work_out; /* Shared Memory window object */
MPI_Info rma_winfo;/* info for window */
MPI_Comm shm_comm_prep;/* Shared Memory prep Communicator */
MPI_Comm shm_comm; /* Shared Memory Communicator */
int shm_procs; /* # of ranks in shared domain */
int shm_ID; /* MPI rank within coherence domain */
int group_size; /* number of ranks per shared memory group */
int Num_groups; /* number of shared memory group */
int group_ID; /* sequence number of shared memory group */
int size_mul; /* size multiplier; 0 for non-root ranks in coherence domain*/
int istart;
MPI_Request send_req, recv_req;
/*********************************************************************************
** Initialize the MPI environment
**********************************************************************************/
MPI_Init(&argc,&argv);
MPI_Comm_rank(MPI_COMM_WORLD, &my_ID);
MPI_Comm_size(MPI_COMM_WORLD, &Num_procs);
root = 0;
/*********************************************************************
** process, test and broadcast input parameter
*********************************************************************/
if (my_ID == root){
if (argc != 4 && argc !=5){
printf("Usage: %s <#ranks per coherence domain> <# iterations> <matrix order> [tile size]\n",
*argv);
error = 1;
goto ENDOFTESTS;
}
group_size = atoi(*++argv);
if (group_size < 1) {
printf("ERROR: # ranks per coherence domain must be >= 1 : %d \n",group_size);
error = 1;
goto ENDOFTESTS;
}
if (Num_procs%group_size) {
printf("ERROR: toal # %d ranks not divisible by ranks per coherence domain %d\n",
Num_procs, group_size);
error = 1;
goto ENDOFTESTS;
}
iterations = atoi(*++argv);
if (iterations < 1){
printf("ERROR: iterations must be >= 1 : %d \n",iterations);
error = 1;
goto ENDOFTESTS;
}
order = atoi(*++argv);
if (order < Num_procs) {
printf("ERROR: matrix order %d should at least # procs %d\n",
order, Num_procs);
error = 1; goto ENDOFTESTS;
}
if (order%Num_procs) {
printf("ERROR: matrix order %d should be divisible by # procs %d\n",
order, Num_procs);
error = 1; goto ENDOFTESTS;
}
if (argc == 5) Tile_order = atoi(*++argv);
ENDOFTESTS:;
}
bail_out(error);
/* Broadcast input data to all ranks */
MPI_Bcast(&order, 1, MPI_INT, root, MPI_COMM_WORLD);
MPI_Bcast(&iterations, 1, MPI_INT, root, MPI_COMM_WORLD);
MPI_Bcast(&Tile_order, 1, MPI_INT, root, MPI_COMM_WORLD);
MPI_Bcast(&group_size, 1, MPI_INT, root, MPI_COMM_WORLD);
if (my_ID == root) {
printf("Parallel Research Kernels version %s\n", PRKVERSION);
printf("MPI+SHM Matrix transpose: B = A^T\n");
printf("Number of ranks = %d\n", Num_procs);
printf("Rank group size = %d\n", group_size);
printf("Matrix order = %d\n", order);
printf("Number of iterations = %d\n", iterations);
if ((Tile_order > 0) && (Tile_order < order))
printf("Tile size = %d\n", Tile_order);
else printf("Untiled\n");
#ifndef SYNCHRONOUS
printf("Non-");
#endif
printf("Blocking messages\n");
}
/* Setup for Shared memory regions */
/* first divide WORLD in groups of size group_size */
MPI_Comm_split(MPI_COMM_WORLD, my_ID/group_size, my_ID%group_size, &shm_comm_prep);
/* derive from that a SHM communicator */
MPI_Comm_split_type(shm_comm_prep, MPI_COMM_TYPE_SHARED, 0, MPI_INFO_NULL, &shm_comm);
MPI_Comm_rank(shm_comm, &shm_ID);
MPI_Comm_size(shm_comm, &shm_procs);
/* do sanity check, making sure groups did not shrink in second comm split */
if (shm_procs != group_size) MPI_Abort(MPI_COMM_WORLD, 666);
/* a non-positive tile size means no tiling of the local transpose */
tiling = (Tile_order > 0) && (Tile_order < order);
bytes = 2 * sizeof(double) * order * order;
/*********************************************************************
** The matrix is broken up into column blocks that are mapped one to a
** rank. Each column block is made up of Num_procs smaller square
** blocks of order block_order.
*********************************************************************/
Num_groups = Num_procs/group_size;
Block_order = order/Num_groups;
group_ID = my_ID/group_size;
colstart = Block_order * group_ID;
Colblock_size = order * Block_order;
Block_size = Block_order * Block_order;
/*********************************************************************
** Create the column block of the test matrix, the column block of the
** transposed matrix, and workspace (workspace only if #procs>1)
*********************************************************************/
/* RMA win info */
MPI_Info_create(&rma_winfo);
/* This key indicates that passive target RMA will not be used.
* It is the one info key that MPICH actually uses for optimization. */
MPI_Info_set(rma_winfo, "no_locks", "true");
/* only the root of each SHM domain specifies window of nonzero size */
size_mul = (shm_ID==0);
int offset = 32;
MPI_Aint size= (Colblock_size+offset)*sizeof(double)*size_mul; int disp_unit;
MPI_Win_allocate_shared(size, sizeof(double), rma_winfo, shm_comm,
(void *) &A_p, &shm_win_A);
MPI_Win_shared_query(shm_win_A, MPI_PROC_NULL, &size, &disp_unit, (void *)&A_p);
if (A_p == NULL){
printf(" Error allocating space for original matrix on node %d\n",my_ID);
error = 1;
}
bail_out(error);
A_p += offset;
MPI_Win_allocate_shared(size, sizeof(double), rma_winfo, shm_comm,
(void *) &B_p, &shm_win_B);
MPI_Win_shared_query(shm_win_B, MPI_PROC_NULL, &size, &disp_unit, (void *)&B_p);
if (B_p == NULL){
printf(" Error allocating space for transposed matrix by group %d\n",group_ID);
error = 1;
}
bail_out(error);
B_p += offset;
if (Num_groups>1) {
size = Block_size*sizeof(double)*size_mul;
MPI_Win_allocate_shared(size, sizeof(double),rma_winfo, shm_comm,
(void *) &Work_in_p, &shm_win_Work_in);
MPI_Win_shared_query(shm_win_Work_in, MPI_PROC_NULL, &size, &disp_unit,
(void *)&Work_in_p);
if (Work_in_p == NULL){
printf(" Error allocating space for in block by group %d\n",group_ID);
error = 1;
}
bail_out(error);
MPI_Win_allocate_shared(size, sizeof(double), rma_winfo,
shm_comm, (void *) &Work_out_p, &shm_win_Work_out);
MPI_Win_shared_query(shm_win_Work_out, MPI_PROC_NULL, &size, &disp_unit,
(void *)&Work_out_p);
if (Work_out_p == NULL){
printf(" Error allocating space for out block by group %d\n",group_ID);
error = 1;
}
bail_out(error);
}
/* Fill the original column matrix */
istart = 0;
int chunk_size = Block_order/group_size;
if (tiling) {
for (j=shm_ID*chunk_size;j<(shm_ID+1)*chunk_size;j+=Tile_order) {
for (i=0;i<order; i+=Tile_order)
for (jt=j; jt<MIN((shm_ID+1)*chunk_size,j+Tile_order); jt++)
for (it=i; it<MIN(order,i+Tile_order); it++) {
A(it,jt) = (double) (order*(jt+colstart) + it);
B(it,jt) = -1.0;
}
}
}
else {
for (j=shm_ID*chunk_size;j<(shm_ID+1)*chunk_size;j++)
for (i=0;i<order; i++) {
A(i,j) = (double) (order*(j+colstart) + i);
B(i,j) = -1.0;
}
}
/* NEED A STORE FENCE HERE */
MPI_Barrier(shm_comm);
for (iter=0; iter<=iterations; iter++) {
/* start timer after a warmup iteration */
if (iter == 1) {
MPI_Barrier(MPI_COMM_WORLD);
local_trans_time = wtime();
}
/* do the local transpose */
istart = colstart;
if (!tiling) {
for (i=shm_ID*chunk_size; i<(shm_ID+1)*chunk_size; i++) {
for (j=0; j<Block_order; j++)
B(j,i) = A(i,j);
}
}
else {
for (i=shm_ID*chunk_size; i<(shm_ID+1)*chunk_size; i+=Tile_order) {
for (j=0; j<Block_order; j+=Tile_order)
for (it=i; it<MIN(Block_order,i+Tile_order); it++)
for (jt=j; jt<MIN(Block_order,j+Tile_order);jt++) {
B(jt,it) = A(it,jt);
}
}
}
for (phase=1; phase<Num_groups; phase++){
recv_from = ((group_ID + phase )%Num_groups);
send_to = ((group_ID - phase + Num_groups)%Num_groups);
#ifndef SYNCHRONOUS
if (shm_ID==0) {
MPI_Irecv(Work_in_p, Block_size, MPI_DOUBLE,
recv_from*group_size, phase, MPI_COMM_WORLD, &recv_req);
}
#endif
istart = send_to*Block_order;
if (!tiling) {
for (i=shm_ID*chunk_size; i<(shm_ID+1)*chunk_size; i++)
for (j=0; j<Block_order; j++){
Work_out(j,i) = A(i,j);
}
}
else {
for (i=shm_ID*chunk_size; i<(shm_ID+1)*chunk_size; i+=Tile_order)
for (j=0; j<Block_order; j+=Tile_order)
for (it=i; it<MIN(Block_order,i+Tile_order); it++)
for (jt=j; jt<MIN(Block_order,j+Tile_order);jt++) {
Work_out(jt,it) = A(it,jt);
}
}
/* NEED A LOAD/STORE FENCE HERE */
MPI_Barrier(shm_comm);
if (shm_ID==0) {
#ifndef SYNCHRONOUS
MPI_Isend(Work_out_p, Block_size, MPI_DOUBLE, send_to*group_size,
phase, MPI_COMM_WORLD, &send_req);
MPI_Wait(&recv_req, &status);
MPI_Wait(&send_req, &status);
#else
MPI_Sendrecv(Work_out_p, Block_size, MPI_DOUBLE, send_to*group_size,
phase, Work_in_p, Block_size, MPI_DOUBLE,
recv_from*group_size, phase, MPI_COMM_WORLD, &status);
#endif
}
/* NEED A LOAD FENCE HERE */
MPI_Barrier(shm_comm);
istart = recv_from*Block_order;
/* scatter received block to transposed matrix; no need to tile */
for (j=shm_ID*chunk_size; j<(shm_ID+1)*chunk_size; j++)
for (i=0; i<Block_order; i++)
B(i,j) = Work_in(i,j);
} /* end of phase loop */
} /* end of iterations */
local_trans_time = wtime() - local_trans_time;
MPI_Reduce(&local_trans_time, &trans_time, 1, MPI_DOUBLE, MPI_MAX, root,
MPI_COMM_WORLD);
abserr = 0.0;
istart = 0;
/* for (j=shm_ID;j<Block_order;j+=group_size) for (i=0;i<order; i++) { */
for (j=shm_ID*chunk_size; j<(shm_ID+1)*chunk_size; j++)
for (i=0;i<order; i++) {
abserr += ABS(B(i,j) - (double)(order*i + j+colstart));
}
MPI_Reduce(&abserr, &abserr_tot, 1, MPI_DOUBLE, MPI_SUM, root, MPI_COMM_WORLD);
if (my_ID == root) {
if (abserr_tot < epsilon) {
printf("Solution validates\n");
avgtime = trans_time/(double)iterations;
printf("Rate (MB/s): %lf Avg time (s): %lf\n",1.0E-06*bytes/avgtime, avgtime);
#ifdef VERBOSE
printf("Summed errors: %f \n", abserr_tot);
#endif
}
else {
printf("ERROR: Aggregate squared error %e exceeds threshold %e\n", abserr_tot, epsilon);
error = 1;
}
}
bail_out(error);
MPI_Win_free(&shm_win_A);
MPI_Win_free(&shm_win_B);
if (Num_groups>1) {
MPI_Win_free(&shm_win_Work_in);
MPI_Win_free(&shm_win_Work_out);
}
MPI_Info_free(&rma_winfo);
MPI_Finalize();
exit(EXIT_SUCCESS);
} /* end of main */
int main(int argc, char *argv[])
{
bool wantwf, verb;
int ix, iz, is, it, wfit, im, ik, i, j, itau;
int ns, nx, nz, nt, wfnt, rnx, rnz, nzx, rnzx, vnx, ntau, htau, nds;
int scalet, snap, snapshot, fnx, fnz, fnzx, nk, nb;
int rectx, rectz, gpz, n, m, pad1, trunc, spx, spz;
float dt, t0, z0, dz, x0, dx, s0, ds, wfdt, srctrunc;
float dtau, tau0, tau;
char *path1, *path2, number[5], *left, *right;
double tstart, tend;
struct timeval tim;
sf_complex c, **lt, **rt;
sf_complex *ww, **dd;
float ***img1, **img2, ***mig1, **mig2;
float *rr, **ccr, **sill, ***fwf, ***bwf;
sf_complex *cwave, *cwavem, **wave, *curr;
sf_axis at, ax, az, atau;
sf_file Fdat, Fsrc, Fimg1, Fimg2;
sf_file Ffwf, Fbwf, Fvel;
sf_file Fleft, Fright;
int cpuid, numprocs, nth;
float *sendbuf, *recvbuf;
MPI_Comm comm=MPI_COMM_WORLD;
MPI_Init(&argc, &argv);
MPI_Comm_rank(comm, &cpuid);
MPI_Comm_size(comm, &numprocs);
sf_init(argc, argv);
#ifdef _OPENMP
#pragma omp parallel
{
nth=omp_get_num_threads();
}
sf_warning(">>> Using %d threads <<<", nth);
#endif
gettimeofday(&tim, NULL);
tstart=tim.tv_sec+(tim.tv_usec/1000000.0);
if(!sf_getbool("wantwf", &wantwf)) wantwf=false;
if(!sf_getbool("verb", &verb)) verb=false;
if(!sf_getint("pad1", &pad1)) pad1=1;
/* padding factor on the first axis */
if(!sf_getint("nb", &nb)) sf_error("Need nb= ");
if(!sf_getfloat("srctrunc", &srctrunc)) srctrunc=0.4;
if(!sf_getint("rectx", &rectx)) rectx=2;
if(!sf_getint("rectz", &rectz)) rectz=2;
if(!sf_getint("scalet", &scalet)) scalet=1;
if(!sf_getint("snap", &snap)) snap=100;
/* interval of the output wavefield */
if(!sf_getint("snapshot", &snapshot)) snapshot=0;
/* print out the wavefield snapshots of this shot */
if(!sf_getint("nds", &nds)) sf_error("Need nds=!");
/* source and receiver positions */
if(!sf_getint("gpz", &gpz)) sf_error("Need gpz=");
if(!sf_getint("spx", &spx)) sf_error("Need spx=");
if(!sf_getint("spz", &spz)) sf_error("Need spz=");
/* tau parameters */
if(!sf_getint("ntau", &ntau)) sf_error("Need ntau=");
if(!sf_getfloat("dtau", &dtau)) sf_error("Need dtau=");
if(!sf_getfloat("tau0", &tau0)) sf_error("Need tau0=");
/* input/output files */
Fdat=sf_input("in");
Fimg1=sf_output("out");
Fimg2=sf_output("Fimg2");
Fsrc=sf_input("Fsrc");
Fvel=sf_input("Fpadvel");
if(wantwf){
Ffwf=sf_output("Ffwf");
Fbwf=sf_output("Fbwf");
}
at=sf_iaxa(Fsrc, 1); nt=sf_n(at); dt=sf_d(at); t0=sf_o(at);
ax=sf_iaxa(Fvel, 2); vnx=sf_n(ax); x0=sf_o(ax);
az=sf_iaxa(Fvel, 1); rnz=sf_n(az); dz=sf_d(az); z0=sf_o(az);
if(!sf_histint(Fdat, "n2", &rnx)) sf_error("Need n2= in input!");
if(!sf_histfloat(Fdat, "d2", &dx)) sf_error("Need d2= in input!");
if(!sf_histint(Fdat, "n3", &ns)) sf_error("Need n3= in input!");
if(!sf_histfloat(Fdat, "d3", &ds)) sf_error("Need d3= in input!");
if(!sf_histfloat(Fdat, "o3", &s0)) sf_error("Need o3= in input!");
wfnt=(nt-1)/scalet+1;
wfdt=dt*scalet;
/* double check the geometry parameters */
if(nds != (int)(ds/dx)) sf_error("Need ds/dx= %d", nds);
sf_warning("s0=%g, x0+(rnx-1)*dx/2=%g", s0, x0+(rnx-1)*dx/2);
//if(s0 != x0+(rnx-1)*dx/2) sf_error("Wrong origin information!");
if(vnx != nds*(ns-1)+rnx) sf_error("Wrong dimension in x axis!");
/* set up the output files */
atau=sf_iaxa(Fsrc, 1);
sf_setn(atau, ntau);
sf_setd(atau, dtau);
sf_seto(atau, tau0);
sf_setlabel(atau, "Tau");
sf_setunit(atau, "s");
sf_oaxa(Fimg1, az, 1);
sf_oaxa(Fimg1, ax, 2);
sf_oaxa(Fimg1, atau, 3);
sf_oaxa(Fimg2, az, 1);
sf_oaxa(Fimg2, ax, 2);
sf_putint(Fimg2, "n3", 1);
sf_settype(Fimg1, SF_FLOAT);
sf_settype(Fimg2, SF_FLOAT);
if(wantwf){
sf_setn(ax, rnx);
sf_seto(ax, -(rnx-1)*dx/2.0);
sf_oaxa(Ffwf, az, 1);
sf_oaxa(Ffwf, ax, 2);
sf_putint(Ffwf, "n3", (wfnt-1)/snap+1);
sf_putfloat(Ffwf, "d3", snap*wfdt);
sf_putfloat(Ffwf, "o3", t0);
sf_putstring(Ffwf, "label3", "Time");
sf_putstring(Ffwf, "unit3", "s");
sf_settype(Ffwf, SF_FLOAT);
sf_oaxa(Fbwf, az, 1);
sf_oaxa(Fbwf, ax, 2);
sf_putint(Fbwf, "n3", (wfnt-1)/snap+1);
sf_putfloat(Fbwf, "d3", -snap*wfdt);
sf_putfloat(Fbwf, "o3", (wfnt-1)*wfdt);
sf_putstring(Fbwf, "label3", "Time");
sf_putstring(Fbwf, "unit3", "s");
sf_settype(Fbwf, SF_FLOAT);
}
nx=rnx+2*nb; nz=rnz+2*nb;
nzx=nx*nz; rnzx=rnz*rnx;
nk=cfft2_init(pad1, nz, nx, &fnz, &fnx);
fnzx=fnz*fnx;
/* print axies parameters for double check */
sf_warning("cpuid=%d, numprocs=%d", cpuid, numprocs);
sf_warning("nt=%d, dt=%g, scalet=%d, wfnt=%d, wfdt=%g",nt, dt, scalet, wfnt, wfdt);
sf_warning("vnx=%d, nx=%d, dx=%g, nb=%d, rnx=%d", vnx, nx, dx, nb, rnx);
sf_warning("nz=%d, rnz=%d, dz=%g, z0=%g", nz, rnz, dz, z0);
sf_warning("spx=%d, spz=%d, gpz=%d", spx, spz, gpz);
sf_warning("ns=%d, ds=%g, s0=%g", ns, ds, s0);
sf_warning("ntau=%d, dtau=%g, tau0=%g", ntau, dtau, tau0);
sf_warning("nzx=%d, fnzx=%d, nk=%d", nzx, fnzx, nk);
/* allocate storage and read data */
ww=sf_complexalloc(nt);
sf_complexread(ww, nt, Fsrc);
sf_fileclose(Fsrc);
gpz=gpz+nb;
spz=spz+nb;
spx=spx+nb;
trunc=srctrunc/dt+0.5;
dd=sf_complexalloc2(nt, rnx);
rr=sf_floatalloc(nzx);
reflgen(nz, nx, spz, spx, rectz, rectx, 0, rr);
fwf=sf_floatalloc3(rnz, rnx, wfnt);
bwf=sf_floatalloc3(rnz, rnx, wfnt);
img1=sf_floatalloc3(rnz, vnx, ntau);
img2=sf_floatalloc2(rnz, vnx);
mig1=sf_floatalloc3(rnz, rnx, ntau);
mig2=sf_floatalloc2(rnz, rnx);
ccr=sf_floatalloc2(rnz, rnx);
sill=sf_floatalloc2(rnz, rnx);
curr=sf_complexalloc(fnzx);
cwave=sf_complexalloc(nk);
cwavem=sf_complexalloc(nk);
icfft2_allocate(cwavem);
#ifdef _OPENMP
#pragma omp parallel for private(ix, iz, itau)
#endif
for(ix=0; ix<vnx; ix++){
for(iz=0; iz<rnz; iz++){
img2[ix][iz]=0.;
for(itau=0; itau<ntau; itau++){
img1[itau][ix][iz]=0.;
}
}
}
path1=sf_getstring("path1");
path2=sf_getstring("path2");
if(path1==NULL) path1="./mat/left";
if(path2==NULL) path2="./mat/right";
/* shot loop */
for (is=cpuid; is<ns; is+=numprocs){
/* construct the names of left and right matrices */
left=sf_charalloc(strlen(path1));
right=sf_charalloc(strlen(path2));
strcpy(left, path1);
strcpy(right, path2);
sprintf(number, "%d", is+1);
strcat(left, number);
strcat(right, number);
Fleft=sf_input(left);
Fright=sf_input(right);
if(!sf_histint(Fleft, "n1", &n) || n != nzx) sf_error("Need n1=%d in Fleft", nzx);
if(!sf_histint(Fleft, "n2", &m)) sf_error("No n2 in Fleft");
if(!sf_histint(Fright, "n1", &n) || n != m) sf_error("Need n1=%d in Fright", m);
if(!sf_histint(Fright, "n2", &n) || n != nk) sf_error("Need n2=%d in Fright", nk);
/* allocate storage for each shot migration */
lt=sf_complexalloc2(nzx, m);
rt=sf_complexalloc2(m, nk);
sf_complexread(lt[0], nzx*m, Fleft);
sf_complexread(rt[0], m*nk, Fright);
sf_fileclose(Fleft);
sf_fileclose(Fright);
/* read data */
sf_seek(Fdat, is*rnx*nt*sizeof(float complex), SEEK_SET);
sf_complexread(dd[0], rnx*nt, Fdat);
/* initialize curr and imaging variables */
#ifdef _OPENMP
#pragma omp parallel for private(iz)
#endif
for(iz=0; iz<fnzx; iz++){
curr[iz]=sf_cmplx(0.,0.);
}
#ifdef _OPENMP
#pragma omp parallel for private(ix, iz, itau)
#endif
for(ix=0; ix<rnx; ix++){
for(iz=0; iz<rnz; iz++){
mig2[ix][iz]=0.;
ccr[ix][iz]=0.;
sill[ix][iz]=0.;
for(itau=0; itau<ntau; itau++){
mig1[itau][ix][iz]=0.;
}
}
}
/* wave */
wave=sf_complexalloc2(fnzx, m);
/* snapshot */
if(wantwf && is== snapshot) wantwf=true;
else wantwf=false;
wfit=0;
for(it=0; it<nt; it++){
if(verb) sf_warning("Forward propagation it=%d/%d",it+1, nt);
cfft2(curr, cwave);
for(im=0; im<m; im++){
#ifdef _OPENMP
#pragma omp parallel for private(ik)
#endif
for(ik=0; ik<nk; ik++){
#ifdef SF_HAS_COMPLEX_H
cwavem[ik]=cwave[ik]*rt[ik][im];
#else
cwavem[ik]=sf_cmul(cwave[ik],rt[ik][im]);
#endif
}
icfft2(wave[im],cwavem);
}
#ifdef _OPENMP
#pragma omp parallel for private(ix, iz, i, j, im, c) shared(curr, it)
#endif
for(ix=0; ix<nx; ix++){
for(iz=0; iz<nz; iz++){
i=iz+ix*nz;
j=iz+ix*fnz;
if(it<trunc){
#ifdef SF_HAS_COMPLEX_H
c=ww[it]*rr[i];
#else
c=sf_crmul(ww[it],rr[i]);
#endif
}else{
c=sf_cmplx(0.,0.);
}
// c += curr[j];
for(im=0; im<m; im++){
#ifdef SF_HAS_COMPLEX_H
c += lt[im][i]*wave[im][j];
#else
c += sf_cmul(lt[im][i], wave[im][j]);
#endif
}
curr[j]=c;
}
}
if(it%scalet==0){
#ifdef _OPENMP
#pragma omp parallel for private(ix, iz)
#endif
for(ix=0; ix<rnx; ix++){
for(iz=0; iz<rnz; iz++){
fwf[wfit][ix][iz]=crealf(curr[(ix+nb)*fnz+(iz+nb)]);
}
}
wfit++;
}
} //end of it
/* check wfnt */
if(wfit != wfnt) sf_error("At this point, wfit should be equal to wfnt");
/* backward propagation starts from here... */
#ifdef _OPENMP
#pragma omp parallel for private(iz)
#endif
for(iz=0; iz<fnzx; iz++){
curr[iz]=sf_cmplx(0.,0.);
}
wfit=wfnt-1;
for(it=nt-1; it>=0; it--){
if(verb) sf_warning("Backward propagation it=%d/%d",it+1, nt);
#ifdef _OPENMP
#pragma omp parallel for private(ix)
#endif
for(ix=0; ix<rnx; ix++){
curr[(ix+nb)*fnz+gpz]+=dd[ix][it];
}
cfft2(curr, cwave);
for(im=0; im<m; im++){
#ifdef _OPENMP
#pragma omp parallel for private(ik)
#endif
for(ik=0; ik<nk; ik++){
#ifdef SF_HAS_COMPLEX_H
cwavem[ik]=cwave[ik]*conjf(rt[ik][im]);
#else
cwavem[ik]=sf_cmul(cwave[ik],conjf(rt[ik][im]));
#endif
}
icfft2(wave[im],cwavem);
}
#ifdef _OPENMP
#pragma omp parallel for private(ix, iz, i, j, im, c) shared(curr, it)
#endif
for(ix=0; ix<nx; ix++){
for(iz=0; iz<nz; iz++){
i=iz+ix*nz;
j=iz+ix*fnz;
// c=curr[j];
c=sf_cmplx(0.,0.);
for(im=0; im<m; im++){
#ifdef SF_HAS_COMPLEX_H
c += conjf(lt[im][i])*wave[im][j];
#else
c += sf_cmul(conjf(lt[im][i]), wave[im][j]);
#endif
}
curr[j]=c;
}
}
if(it%scalet==0){
#ifdef _OPENMP
#pragma omp parallel for private(ix, iz)
#endif
for(ix=0; ix<rnx; ix++){
for(iz=0; iz<rnz; iz++){
bwf[wfit][ix][iz]=crealf(curr[(ix+nb)*fnz+(iz+nb)]);
ccr[ix][iz] += fwf[wfit][ix][iz]*bwf[wfit][ix][iz];
sill[ix][iz] += fwf[wfit][ix][iz]*fwf[wfit][ix][iz];
}
}
wfit--;
}
} //end of it
if(wfit != -1) sf_error("Check program! The final wfit should be -1!");
/* free storage */
free(*rt); free(rt);
free(*lt); free(lt);
free(*wave); free(wave);
free(left); free(right);
/* normalized image */
#ifdef _OPENMP
#pragma omp parallel for private(ix, iz)
#endif
for (ix=0; ix<rnx; ix++){
for(iz=0; iz<rnz; iz++){
mig2[ix][iz]=ccr[ix][iz]/(sill[ix][iz]+SF_EPS);
// sill[ix][iz]=0.;
}
}
/* calculate time shift gathers */
for(itau=0; itau<ntau; itau++){
sf_warning("itau/ntau=%d/%d", itau+1, ntau);
tau=itau*dtau+tau0;
htau=tau/wfdt;
for(it=abs(htau); it<wfnt-abs(htau); it++){
#ifdef _OPENMP
#pragma omp parallel for private(ix, iz)
#endif
for(ix=0; ix<rnx; ix++){
for(iz=0; iz<rnz; iz++){
mig1[itau][ix][iz]+=fwf[it+htau][ix][iz]*bwf[it-htau][ix][iz];
// sill[ix][iz]+=fwf[it+htau][ix][iz]*fwf[it+htau][ix][iz];
} // end of iz
} // end of ix
} // end of it
/*
#ifdef _OPENMP
#pragma omp parallel for private(ix, iz)
#endif */
/* source illumination
for(ix=0; ix<rnx; ix++){
for(iz=0; iz<rnz; iz++){
mig1[itau][ix][iz] = mig1[itau][ix][iz]/(sill[ix][iz]+SF_EPS);
}
} */
} //end of itau
/* output wavefield snapshot */
if(wantwf){
for(it=0; it<wfnt; it++){
if(it%snap==0){
sf_floatwrite(fwf[it][0], rnzx, Ffwf);
sf_floatwrite(bwf[wfnt-1-it][0], rnzx, Fbwf);
}
}
sf_fileclose(Ffwf);
sf_fileclose(Fbwf);
}
/* add all the shot images that are on the same node */
#ifdef _OPENMP
#pragma omp parallel for private(itau, ix, iz)
#endif
for(itau=0; itau<ntau; itau++){
for(ix=0; ix<rnx; ix++){
for(iz=0; iz<rnz; iz++){
img1[itau][ix+is*nds][iz] += mig1[itau][ix][iz];
}
}
}
#ifdef _OPENMP
#pragma omp parallel for private(ix, iz)
#endif
for(ix=0; ix<rnx; ix++){
for(iz=0; iz<rnz; iz++){
img2[ix+is*nds][iz] += mig2[ix][iz];
}
}
}
////////////////end of ishot
MPI_Barrier(comm);
cfft2_finalize();
sf_fileclose(Fdat);
free(ww); free(rr);
free(*dd); free(dd);
free(cwave); free(cwavem); free(curr);
free(*ccr); free(ccr);
free(*sill); free(sill);
free(**fwf); free(*fwf); free(fwf);
free(**bwf); free(*bwf); free(bwf);
free(**mig1); free(*mig1); free(mig1);
free(*mig2); free(mig2);
/* sum image */
if(cpuid==0){
sendbuf=(float *)MPI_IN_PLACE;
recvbuf=img1[0][0];
}else{
sendbuf=img1[0][0];
recvbuf=NULL;
}
MPI_Reduce(sendbuf, recvbuf, ntau*vnx*rnz, MPI_FLOAT, MPI_SUM, 0, comm);
if(cpuid==0){
sendbuf=MPI_IN_PLACE;
recvbuf=img2[0];
}else{
sendbuf=img2[0];
recvbuf=NULL;
}
MPI_Reduce(sendbuf, recvbuf, vnx*rnz, MPI_FLOAT, MPI_SUM, 0, comm);
/* output image */
if(cpuid==0){
sf_floatwrite(img1[0][0], ntau*vnx*rnz, Fimg1);
sf_floatwrite(img2[0], vnx*rnz, Fimg2);
}
MPI_Barrier(comm);
sf_fileclose(Fimg1);
sf_fileclose(Fimg2);
free(**img1); free(*img1); free(img1);
free(*img2); free(img2);
gettimeofday(&tim, NULL);
tend=tim.tv_sec+(tim.tv_usec/1000000.0);
sf_warning(">> The computing time is %.3lf minutes <<", (tend-tstart)/60.);
MPI_Finalize();
exit(0);
}
double calc_forces(double* xi_opt, double* forces, int flag)
{
double tmpsum, sum = 0.0;
int first, col, ne, size, i = flag;
double* xi = NULL;
apot_table_t* apt = &g_pot.apot_table;
double charge[g_param.ntypes];
double sum_charges;
double dp_kappa;
#if defined(DIPOLE)
double dp_alpha[g_param.ntypes];
double dp_b[g_calc.paircol];
double dp_c[g_calc.paircol];
#endif // DIPOLE
static double rho_sum_loc, rho_sum;
rho_sum_loc = rho_sum = 0.0;
switch (g_pot.format_type) {
case POTENTIAL_FORMAT_UNKNOWN:
error(1, "Unknown potential format detected! (%s:%d)\n", __FILE__, __LINE__);
case POTENTIAL_FORMAT_ANALYTIC:
xi = g_pot.calc_pot.table;
break;
case POTENTIAL_FORMAT_TABULATED_EQ_DIST:
case POTENTIAL_FORMAT_TABULATED_NON_EQ_DIST:
xi = xi_opt;
break;
case POTENTIAL_FORMAT_KIM:
error(1, "KIM format is not supported by EAM elstat force routine!");
}
#if !defined(MPI)
g_mpi.myconf = g_config.nconf;
#endif // MPI
ne = g_pot.apot_table.total_ne_par;
size = apt->number;
/* This is the start of an infinite loop */
while (1) {
tmpsum = 0.0; /* sum of squares of local process */
rho_sum_loc = 0.0;
#if defined APOT && !defined MPI
if (g_pot.format_type == POTENTIAL_FORMAT_ANALYTIC) {
apot_check_params(xi_opt);
update_calc_table(xi_opt, xi, 0);
}
#endif // APOT && !MPI
#if defined(MPI)
/* exchange potential and flag value */
#if !defined(APOT)
MPI_Bcast(xi, g_pot.calc_pot.len, MPI_DOUBLE, 0, MPI_COMM_WORLD);
#endif // APOT
MPI_Bcast(&flag, 1, MPI_INT, 0, MPI_COMM_WORLD);
if (flag == 1)
break; /* Exception: flag 1 means clean up */
#if defined(APOT)
if (g_mpi.myid == 0)
apot_check_params(xi_opt);
MPI_Bcast(xi_opt, g_calc.ndimtot, MPI_DOUBLE, 0, MPI_COMM_WORLD);
if (g_pot.format_type == POTENTIAL_FORMAT_ANALYTIC)
update_calc_table(xi_opt, xi, 0);
#else /* APOT */
/* if flag==2 then the potential parameters have changed -> sync */
if (flag == 2)
potsync();
#endif // APOT
#endif // MPI
/* local arrays for electrostatic parameters */
sum_charges = 0;
for (i = 0; i < g_param.ntypes - 1; i++) {
if (xi_opt[2 * size + ne + i]) {
charge[i] = xi_opt[2 * size + ne + i];
sum_charges += apt->ratio[i] * charge[i];
} else {
charge[i] = 0.0;
}
}
apt->last_charge = -sum_charges / apt->ratio[g_param.ntypes - 1];
charge[g_param.ntypes - 1] = apt->last_charge;
if (xi_opt[2 * size + ne + g_param.ntypes - 1]) {
dp_kappa = xi_opt[2 * size + ne + g_param.ntypes - 1];
} else {
dp_kappa = 0.0;
}
#if defined(DIPOLE)
for (i = 0; i < g_param.ntypes; i++) {
if (xi_opt[2 * size + ne + g_param.ntypes + i]) {
dp_alpha[i] = xi_opt[2 * size + ne + g_param.ntypes + i];
} else {
dp_alpha[i] = 0.0;
}
}
for (i = 0; i < g_calc.paircol; i++) {
if (xi_opt[2 * size + ne + 2 * g_param.ntypes + i]) {
dp_b[i] = xi_opt[2 * size + ne + 2 * g_param.ntypes + i];
} else {
dp_b[i] = 0.0;
}
if (xi_opt[2 * size + ne + 2 * g_param.ntypes + g_calc.paircol + i]) {
dp_c[i] =
xi_opt[2 * size + ne + 2 * g_param.ntypes + g_calc.paircol + i];
} else {
dp_c[i] = 0.0;
}
}
#endif // DIPOLE
/* init second derivatives for splines */
/* pair potentials & rho */
for (col = 0; col < g_calc.paircol + g_param.ntypes; col++) {
first = g_pot.calc_pot.first[col];
switch (g_pot.format_type) {
case POTENTIAL_FORMAT_UNKNOWN:
error(1, "Unknown potential format detected! (%s:%d)\n", __FILE__,
__LINE__);
case POTENTIAL_FORMAT_ANALYTIC:
case POTENTIAL_FORMAT_TABULATED_EQ_DIST: {
spline_ed(g_pot.calc_pot.step[col], xi + first,
g_pot.calc_pot.last[col] - first + 1, *(xi + first - 2),
0.0, g_pot.calc_pot.d2tab + first);
break;
}
case POTENTIAL_FORMAT_TABULATED_NON_EQ_DIST: {
spline_ne(g_pot.calc_pot.xcoord + first, xi + first,
g_pot.calc_pot.last[col] - first + 1, *(xi + first - 2),
0.0, g_pot.calc_pot.d2tab + first);
}
case POTENTIAL_FORMAT_KIM:
error(1, "KIM format is not supported by EAM elstat force routine!");
}
}
/* F */
for (col = g_calc.paircol + g_param.ntypes;
col < g_calc.paircol + 2 * g_param.ntypes; col++) {
first = g_pot.calc_pot.first[col];
/* gradient at left boundary matched to square root function,
when 0 not in domain(F), else natural spline */
switch (g_pot.format_type) {
case POTENTIAL_FORMAT_UNKNOWN:
error(1, "Unknown potential format detected! (%s:%d)\n", __FILE__,
__LINE__);
case POTENTIAL_FORMAT_ANALYTIC:
case POTENTIAL_FORMAT_TABULATED_EQ_DIST: {
spline_ed(g_pot.calc_pot.step[col], xi + first,
g_pot.calc_pot.last[col] - first + 1, *(xi + first - 2),
*(xi + first - 1), g_pot.calc_pot.d2tab + first);
break;
}
case POTENTIAL_FORMAT_TABULATED_NON_EQ_DIST: {
spline_ne(g_pot.calc_pot.xcoord + first, xi + first,
g_pot.calc_pot.last[col] - first + 1, *(xi + first - 2),
*(xi + first - 1), g_pot.calc_pot.d2tab + first);
}
case POTENTIAL_FORMAT_KIM:
error(1, "KIM format is not supported by EAM elstat force routine!");
}
}
/* region containing loop over configurations */
{
int self;
vector tmp_force;
int h, j, type1, type2, uf;
#if defined(STRESS)
int us = 0;
int stresses = 0;
#endif
int n_i, n_j;
double fnval, grad, fnval_tail, grad_tail, grad_i, grad_j;
#if defined(DIPOLE)
double p_sr_tail = 0.0;
#endif
atom_t* atom;
neigh_t* neigh;
double r;
int col_F;
double eam_force;
double rho_val, rho_grad, rho_grad_j;
/* loop over configurations: M A I N LOOP CONTAINING ALL ATOM-LOOPS */
for (h = g_mpi.firstconf; h < g_mpi.firstconf + g_mpi.myconf; h++) {
uf = g_config.conf_uf[h - g_mpi.firstconf];
#if defined(STRESS)
us = g_config.conf_us[h - g_mpi.firstconf];
#endif // STRESS
/* reset energies and stresses */
forces[g_calc.energy_p + h] = 0.0;
#if defined(STRESS)
stresses = g_calc.stress_p + 6 * h;
for (i = 0; i < 6; i++)
forces[stresses + i] = 0.0;
#endif // STRESS
/* set limiting constraints */
forces[g_calc.limit_p + h] = -g_config.force_0[g_calc.limit_p + h];
#if defined(DIPOLE)
/* reset dipoles and fields: LOOP Z E R O */
for (i = 0; i < g_config.inconf[h]; i++) {
atom =
g_config.conf_atoms + i + g_config.cnfstart[h] - g_mpi.firstatom;
atom->E_stat.x = 0.0;
atom->E_stat.y = 0.0;
atom->E_stat.z = 0.0;
atom->p_sr.x = 0.0;
atom->p_sr.y = 0.0;
atom->p_sr.z = 0.0;
}
#endif // DIPOLE
/* F I R S T LOOP OVER ATOMS: reset forces, dipoles */
for (i = 0; i < g_config.inconf[h]; i++) { /* atoms */
n_i = 3 * (g_config.cnfstart[h] + i);
if (uf) {
forces[n_i + 0] = -g_config.force_0[n_i + 0];
forces[n_i + 1] = -g_config.force_0[n_i + 1];
forces[n_i + 2] = -g_config.force_0[n_i + 2];
} else {
forces[n_i + 0] = 0.0;
forces[n_i + 1] = 0.0;
forces[n_i + 2] = 0.0;
}
/* reset atomic density */
g_config.conf_atoms[g_config.cnfstart[h] - g_mpi.firstatom + i].rho =
0.0;
} /* end F I R S T LOOP */
/* S E C O N D loop: calculate short-range and monopole forces,
calculate static field- and dipole-contributions,
calculate atomic densities */
for (i = 0; i < g_config.inconf[h]; i++) { /* atoms */
atom =
g_config.conf_atoms + i + g_config.cnfstart[h] - g_mpi.firstatom;
type1 = atom->type;
n_i = 3 * (g_config.cnfstart[h] + i);
for (j = 0; j < atom->num_neigh; j++) { /* neighbors */
neigh = atom->neigh + j;
type2 = neigh->type;
col = neigh->col[0];
/* updating tail-functions - only necessary with variing kappa */
if (!apt->sw_kappa)
#if defined(DSF)
elstat_dsf(neigh->r, dp_kappa, &neigh->fnval_el,
&neigh->grad_el, &neigh->ggrad_el);
#else
elstat_shift(neigh->r, dp_kappa, &neigh->fnval_el,
&neigh->grad_el, &neigh->ggrad_el);
#endif // DSF
/* In small cells, an atom might interact with itself */
self = (neigh->nr == i + g_config.cnfstart[h]) ? 1 : 0;
/* calculate short-range forces */
if (neigh->r < g_pot.calc_pot.end[col]) {
if (uf) {
fnval = splint_comb_dir(&g_pot.calc_pot, xi, neigh->slot[0],
neigh->shift[0], neigh->step[0], &grad);
} else {
fnval = splint_dir(&g_pot.calc_pot, xi, neigh->slot[0],
neigh->shift[0], neigh->step[0]);
}
/* avoid double counting if atom is interacting with a copy of
* itself */
if (self) {
fnval *= 0.5;
grad *= 0.5;
}
forces[g_calc.energy_p + h] += fnval;
if (uf) {
tmp_force.x = neigh->dist_r.x * grad;
tmp_force.y = neigh->dist_r.y * grad;
tmp_force.z = neigh->dist_r.z * grad;
forces[n_i + 0] += tmp_force.x;
forces[n_i + 1] += tmp_force.y;
forces[n_i + 2] += tmp_force.z;
/* actio = reactio */
n_j = 3 * neigh->nr;
forces[n_j + 0] -= tmp_force.x;
forces[n_j + 1] -= tmp_force.y;
forces[n_j + 2] -= tmp_force.z;
#if defined(STRESS)
/* calculate pair stresses */
if (us) {
forces[stresses + 0] -= neigh->dist.x * tmp_force.x;
forces[stresses + 1] -= neigh->dist.y * tmp_force.y;
forces[stresses + 2] -= neigh->dist.z * tmp_force.z;
forces[stresses + 3] -= neigh->dist.x * tmp_force.y;
forces[stresses + 4] -= neigh->dist.y * tmp_force.z;
forces[stresses + 5] -= neigh->dist.z * tmp_force.x;
}
#endif // STRESS
}
}
/* calculate monopole forces */
if (neigh->r < g_config.dp_cut &&
(charge[type1] || charge[type2])) {
fnval_tail = neigh->fnval_el;
grad_tail = neigh->grad_el;
grad_i = charge[type2] * grad_tail;
if (type1 == type2) {
grad_j = grad_i;
} else {
grad_j = charge[type1] * grad_tail;
}
fnval = charge[type1] * charge[type2] * fnval_tail;
grad = charge[type1] * grad_i;
if (self) {
grad_i *= 0.5;
grad_j *= 0.5;
fnval *= 0.5;
grad *= 0.5;
}
forces[g_calc.energy_p + h] += fnval;
if (uf) {
tmp_force.x = neigh->dist.x * grad;
tmp_force.y = neigh->dist.y * grad;
tmp_force.z = neigh->dist.z * grad;
forces[n_i + 0] += tmp_force.x;
forces[n_i + 1] += tmp_force.y;
forces[n_i + 2] += tmp_force.z;
/* actio = reactio */
n_j = 3 * neigh->nr;
forces[n_j + 0] -= tmp_force.x;
forces[n_j + 1] -= tmp_force.y;
forces[n_j + 2] -= tmp_force.z;
#if defined(STRESS)
/* calculate coulomb stresses */
if (us) {
forces[stresses + 0] -= neigh->dist.x * tmp_force.x;
forces[stresses + 1] -= neigh->dist.y * tmp_force.y;
forces[stresses + 2] -= neigh->dist.z * tmp_force.z;
forces[stresses + 3] -= neigh->dist.x * tmp_force.y;
forces[stresses + 4] -= neigh->dist.y * tmp_force.z;
forces[stresses + 5] -= neigh->dist.z * tmp_force.x;
}
#endif // STRESS
}
#if defined(DIPOLE)
/* calculate static field-contributions */
atom->E_stat.x += neigh->dist.x * grad_i;
atom->E_stat.y += neigh->dist.y * grad_i;
atom->E_stat.z += neigh->dist.z * grad_i;
g_config.conf_atoms[neigh->nr - g_mpi.firstatom].E_stat.x -=
neigh->dist.x * grad_j;
g_config.conf_atoms[neigh->nr - g_mpi.firstatom].E_stat.y -=
neigh->dist.y * grad_j;
g_config.conf_atoms[neigh->nr - g_mpi.firstatom].E_stat.z -=
neigh->dist.z * grad_j;
/* calculate short-range dipoles */
if (dp_alpha[type1] && dp_b[col] && dp_c[col]) {
p_sr_tail = grad_tail * neigh->r *
shortrange_value(neigh->r, dp_alpha[type1],
dp_b[col], dp_c[col]);
atom->p_sr.x += charge[type2] * neigh->dist_r.x * p_sr_tail;
atom->p_sr.y += charge[type2] * neigh->dist_r.y * p_sr_tail;
atom->p_sr.z += charge[type2] * neigh->dist_r.z * p_sr_tail;
}
if (dp_alpha[type2] && dp_b[col] && dp_c[col] && !self) {
p_sr_tail = grad_tail * neigh->r *
shortrange_value(neigh->r, dp_alpha[type2],
dp_b[col], dp_c[col]);
g_config.conf_atoms[neigh->nr - g_mpi.firstatom].p_sr.x -=
charge[type1] * neigh->dist_r.x * p_sr_tail;
g_config.conf_atoms[neigh->nr - g_mpi.firstatom].p_sr.y -=
charge[type1] * neigh->dist_r.y * p_sr_tail;
g_config.conf_atoms[neigh->nr - g_mpi.firstatom].p_sr.z -=
charge[type1] * neigh->dist_r.z * p_sr_tail;
}
#endif // DIPOLE
}
/* calculate atomic densities */
if (atom->type == neigh->type) {
/* then transfer(a->b)==transfer(b->a) */
if (neigh->r < g_pot.calc_pot.end[neigh->col[1]]) {
rho_val = splint_dir(&g_pot.calc_pot, xi, neigh->slot[1],
neigh->shift[1], neigh->step[1]);
atom->rho += rho_val;
/* avoid double counting if atom is interacting with a
copy of itself */
if (!self) {
g_config.conf_atoms[neigh->nr - g_mpi.firstatom].rho +=
rho_val;
}
}
} else {
/* transfer(a->b)!=transfer(b->a) */
if (neigh->r < g_pot.calc_pot.end[neigh->col[1]]) {
atom->rho += splint_dir(&g_pot.calc_pot, xi, neigh->slot[1],
neigh->shift[1], neigh->step[1]);
}
/* cannot use slot/shift to access splines */
if (neigh->r < g_pot.calc_pot.end[g_calc.paircol + atom->type])
g_config.conf_atoms[neigh->nr - g_mpi.firstatom].rho +=
(*g_splint)(&g_pot.calc_pot, xi,
g_calc.paircol + atom->type, neigh->r);
}
} /* loop over neighbours */
col_F =
g_calc.paircol + g_param.ntypes + atom->type; /* column of F */
if (atom->rho > g_pot.calc_pot.end[col_F]) {
/* then punish target function -> bad potential */
forces[g_calc.limit_p + h] +=
DUMMY_WEIGHT * 10.0 *
dsquare(atom->rho - g_pot.calc_pot.end[col_F]);
atom->rho = g_pot.calc_pot.end[col_F];
}
if (atom->rho < g_pot.calc_pot.begin[col_F]) {
/* then punish target function -> bad potential */
forces[g_calc.limit_p + h] +=
DUMMY_WEIGHT * 10.0 *
dsquare(g_pot.calc_pot.begin[col_F] - atom->rho);
atom->rho = g_pot.calc_pot.begin[col_F];
}
/* embedding energy, embedding gradient */
/* contribution to cohesive energy is F(n) */
#if defined(NORESCALE)
if (atom->rho < g_pot.calc_pot.begin[col_F]) {
/* linear extrapolation left */
rho_val = splint_comb(&calc_pot, xi, col_F,
g_pot.calc_pot.begin[col_F], &atom->gradF);
forces[energy_p + h] +=
rho_val +
(atom->rho - g_pot.calc_pot.begin[col_F]) * atom->gradF;
#if defined(APOT)
forces[limit_p + h] += DUMMY_WEIGHT * 10.0 *
dsquare(calc_pot.begin[col_F] - atom->rho);
#endif // APOT
} else if (atom->rho > g_pot.calc_pot.end[col_F]) {
/* and right */
rho_val = splint_comb(
&calc_pot, xi, col_F,
g_pot.calc_pot.end[col_F] - 0.5 * g_pot.calc_pot.step[col_F],
&atom->gradF);
forces[energy_p + h] +=
rho_val + (atom->rho - g_pot.calc_pot.end[col_F]) * atom->gradF;
#if defined(APOT)
forces[limit_p + h] +=
DUMMY_WEIGHT * 10.0 *
dsquare(atom->rho - g_pot.calc_pot.end[col_F]);
#endif // APOT
}
/* and in-between */
else {
forces[energy_p + h] +=
splint_comb(&calc_pot, xi, col_F, atom->rho, &atom->gradF);
}
#else
forces[g_calc.energy_p + h] += (*g_splint_comb)(
&g_pot.calc_pot, xi, col_F, atom->rho, &atom->gradF);
#endif // NORESCALE
/* sum up rho */
rho_sum_loc += atom->rho;
} /* end S E C O N D loop over atoms */
#if defined(DIPOLE)
/* T H I R D loop: calculate whole dipole moment for every atom */
double rp, dp_sum;
int dp_converged = 0, dp_it = 0;
double max_diff = 10;
while (dp_converged == 0) {
dp_sum = 0;
for (i = 0; i < g_config.inconf[h]; i++) { /* atoms */
atom = g_config.conf_atoms + i + g_config.cnfstart[h] -
g_mpi.firstatom;
type1 = atom->type;
if (dp_alpha[type1]) {
if (dp_it) {
/* note: mixing parameter is different from that on in IMD */
atom->E_tot.x = (1 - g_config.dp_mix) * atom->E_ind.x +
g_config.dp_mix * atom->E_old.x +
atom->E_stat.x;
atom->E_tot.y = (1 - g_config.dp_mix) * atom->E_ind.y +
g_config.dp_mix * atom->E_old.y +
atom->E_stat.y;
atom->E_tot.z = (1 - g_config.dp_mix) * atom->E_ind.z +
g_config.dp_mix * atom->E_old.z +
atom->E_stat.z;
} else {
atom->E_tot.x = atom->E_ind.x + atom->E_stat.x;
atom->E_tot.y = atom->E_ind.y + atom->E_stat.y;
atom->E_tot.z = atom->E_ind.z + atom->E_stat.z;
}
atom->p_ind.x = dp_alpha[type1] * atom->E_tot.x + atom->p_sr.x;
atom->p_ind.y = dp_alpha[type1] * atom->E_tot.y + atom->p_sr.y;
atom->p_ind.z = dp_alpha[type1] * atom->E_tot.z + atom->p_sr.z;
atom->E_old.x = atom->E_ind.x;
atom->E_old.y = atom->E_ind.y;
atom->E_old.z = atom->E_ind.z;
atom->E_ind.x = 0.0;
atom->E_ind.y = 0.0;
atom->E_ind.z = 0.0;
}
}
for (i = 0; i < g_config.inconf[h]; i++) { /* atoms */
atom = g_config.conf_atoms + i + g_config.cnfstart[h] -
g_mpi.firstatom;
type1 = atom->type;
for (j = 0; j < atom->num_neigh; j++) { /* neighbors */
neigh = atom->neigh + j;
type2 = neigh->type;
col = neigh->col[0];
/* In small cells, an atom might interact with itself */
self = (neigh->nr == i + g_config.cnfstart[h]) ? 1 : 0;
if (neigh->r < g_config.dp_cut && dp_alpha[type1] &&
dp_alpha[type2]) {
rp = SPROD(
g_config.conf_atoms[neigh->nr - g_mpi.firstatom].p_ind,
neigh->dist_r);
atom->E_ind.x +=
neigh->grad_el *
(3 * rp * neigh->dist_r.x -
g_config.conf_atoms[neigh->nr - g_mpi.firstatom].p_ind.x);
atom->E_ind.y +=
neigh->grad_el *
(3 * rp * neigh->dist_r.y -
g_config.conf_atoms[neigh->nr - g_mpi.firstatom].p_ind.y);
atom->E_ind.z +=
neigh->grad_el *
(3 * rp * neigh->dist_r.z -
g_config.conf_atoms[neigh->nr - g_mpi.firstatom].p_ind.z);
if (!self) {
rp = SPROD(atom->p_ind, neigh->dist_r);
g_config.conf_atoms[neigh->nr - g_mpi.firstatom].E_ind.x +=
neigh->grad_el *
(3 * rp * neigh->dist_r.x - atom->p_ind.x);
g_config.conf_atoms[neigh->nr - g_mpi.firstatom].E_ind.y +=
neigh->grad_el *
(3 * rp * neigh->dist_r.y - atom->p_ind.y);
g_config.conf_atoms[neigh->nr - g_mpi.firstatom].E_ind.z +=
neigh->grad_el *
(3 * rp * neigh->dist_r.z - atom->p_ind.z);
}
}
}
}
for (i = 0; i < g_config.inconf[h]; i++) { /* atoms */
atom = g_config.conf_atoms + i + g_config.cnfstart[h] -
g_mpi.firstatom;
type1 = atom->type;
if (dp_alpha[type1]) {
dp_sum +=
dsquare(dp_alpha[type1] * (atom->E_old.x - atom->E_ind.x));
dp_sum +=
dsquare(dp_alpha[type1] * (atom->E_old.y - atom->E_ind.y));
dp_sum +=
dsquare(dp_alpha[type1] * (atom->E_old.z - atom->E_ind.z));
}
}
dp_sum /= 3 * g_config.inconf[h];
dp_sum = sqrt(dp_sum);
if (dp_it) {
if ((dp_sum > max_diff) || (dp_it > 50)) {
dp_converged = 1;
for (i = 0; i < g_config.inconf[h]; i++) { /* atoms */
atom = g_config.conf_atoms + i + g_config.cnfstart[h] -
g_mpi.firstatom;
type1 = atom->type;
if (dp_alpha[type1]) {
atom->p_ind.x =
dp_alpha[type1] * atom->E_stat.x + atom->p_sr.x;
atom->p_ind.y =
dp_alpha[type1] * atom->E_stat.y + atom->p_sr.y;
atom->p_ind.z =
dp_alpha[type1] * atom->E_stat.z + atom->p_sr.z;
atom->E_ind.x = atom->E_stat.x;
atom->E_ind.y = atom->E_stat.y;
atom->E_ind.z = atom->E_stat.z;
}
}
}
}
if (dp_sum < g_config.dp_tol)
dp_converged = 1;
dp_it++;
} /* end T H I R D loop over atoms */
/* F O U R T H loop: calculate monopole-dipole and dipole-dipole forces
*/
double rp_i, rp_j, pp_ij, tmp_1, tmp_2;
double grad_1, grad_2, srval, srgrad, srval_tail, srgrad_tail,
fnval_sum, grad_sum;
for (i = 0; i < g_config.inconf[h]; i++) { /* atoms */
atom =
g_config.conf_atoms + i + g_config.cnfstart[h] - g_mpi.firstatom;
type1 = atom->type;
n_i = 3 * (g_config.cnfstart[h] + i);
for (j = 0; j < atom->num_neigh; j++) { /* neighbors */
neigh = atom->neigh + j;
type2 = neigh->type;
col = neigh->col[0];
/* In small cells, an atom might interact with itself */
self = (neigh->nr == i + g_config.cnfstart[h]) ? 1 : 0;
if (neigh->r < g_config.dp_cut &&
(dp_alpha[type1] || dp_alpha[type2])) {
fnval_tail = -neigh->grad_el;
grad_tail = -neigh->ggrad_el;
if (dp_b[col] && dp_c[col]) {
shortrange_term(neigh->r, dp_b[col], dp_c[col], &srval_tail,
&srgrad_tail);
srval = fnval_tail * srval_tail;
srgrad = fnval_tail * srgrad_tail + grad_tail * srval_tail;
}
if (self) {
fnval_tail *= 0.5;
grad_tail *= 0.5;
}
/* monopole-dipole contributions */
if (charge[type1] && dp_alpha[type2]) {
if (dp_b[col] && dp_c[col]) {
fnval_sum = fnval_tail + srval;
grad_sum = grad_tail + srgrad;
} else {
fnval_sum = fnval_tail;
grad_sum = grad_tail;
}
rp_j = SPROD(
g_config.conf_atoms[neigh->nr - g_mpi.firstatom].p_ind,
neigh->dist_r);
fnval = charge[type1] * rp_j * fnval_sum * neigh->r;
grad_1 = charge[type1] * rp_j * grad_sum * neigh->r2;
grad_2 = charge[type1] * fnval_sum;
forces[g_calc.energy_p + h] -= fnval;
if (uf) {
tmp_force.x =
neigh->dist_r.x * grad_1 +
g_config.conf_atoms[neigh->nr - g_mpi.firstatom].p_ind.x *
grad_2;
tmp_force.y =
neigh->dist_r.y * grad_1 +
g_config.conf_atoms[neigh->nr - g_mpi.firstatom].p_ind.y *
grad_2;
tmp_force.z =
neigh->dist_r.z * grad_1 +
g_config.conf_atoms[neigh->nr - g_mpi.firstatom].p_ind.z *
grad_2;
forces[n_i + 0] -= tmp_force.x;
forces[n_i + 1] -= tmp_force.y;
forces[n_i + 2] -= tmp_force.z;
/* actio = reactio */
n_j = 3 * neigh->nr;
forces[n_j + 0] += tmp_force.x;
forces[n_j + 1] += tmp_force.y;
forces[n_j + 2] += tmp_force.z;
#if defined(STRESS)
/* calculate stresses */
if (us) {
forces[stresses + 0] += neigh->dist.x * tmp_force.x;
forces[stresses + 1] += neigh->dist.y * tmp_force.y;
forces[stresses + 2] += neigh->dist.z * tmp_force.z;
forces[stresses + 3] += neigh->dist.x * tmp_force.y;
forces[stresses + 4] += neigh->dist.y * tmp_force.z;
forces[stresses + 5] += neigh->dist.z * tmp_force.x;
}
#endif // STRESS
}
}
/* dipole-monopole contributions */
if (dp_alpha[type2] && charge[type2]) {
if (dp_b[col] && dp_c[col]) {
fnval_sum = fnval_tail + srval;
grad_sum = grad_tail + srgrad;
} else {
fnval_sum = fnval_tail;
grad_sum = grad_tail;
}
rp_i = SPROD(atom->p_ind, neigh->dist_r);
fnval = charge[type2] * rp_i * fnval_sum * neigh->r;
grad_1 = charge[type2] * rp_i * grad_sum * neigh->r2;
grad_2 = charge[type2] * fnval_sum;
forces[g_calc.energy_p + h] += fnval;
if (uf) {
tmp_force.x =
neigh->dist_r.x * grad_1 + atom->p_ind.x * grad_2;
tmp_force.y =
neigh->dist_r.y * grad_1 + atom->p_ind.y * grad_2;
tmp_force.z =
neigh->dist_r.z * grad_1 + atom->p_ind.z * grad_2;
forces[n_i + 0] += tmp_force.x;
forces[n_i + 1] += tmp_force.y;
forces[n_i + 2] += tmp_force.z;
/* actio = reactio */
n_j = 3 * neigh->nr;
forces[n_j + 0] -= tmp_force.x;
forces[n_j + 1] -= tmp_force.y;
forces[n_j + 2] -= tmp_force.z;
#if defined(STRESS)
/* calculate stresses */
if (us) {
forces[stresses + 0] -= neigh->dist.x * tmp_force.x;
forces[stresses + 1] -= neigh->dist.y * tmp_force.y;
forces[stresses + 2] -= neigh->dist.z * tmp_force.z;
forces[stresses + 3] -= neigh->dist.x * tmp_force.y;
forces[stresses + 4] -= neigh->dist.y * tmp_force.z;
forces[stresses + 5] -= neigh->dist.z * tmp_force.x;
}
#endif // STRESS
}
}
/* dipole-dipole contributions */
if (dp_alpha[type1] && dp_alpha[type2]) {
pp_ij = SPROD(
atom->p_ind,
g_config.conf_atoms[neigh->nr - g_mpi.firstatom].p_ind);
tmp_1 = 3 * rp_i * rp_j;
tmp_2 = 3 * fnval_tail / neigh->r2;
fnval = -(tmp_1 - pp_ij) * fnval_tail;
grad_1 = (tmp_1 - pp_ij) * grad_tail;
grad_2 = 2 * rp_i * rp_j;
forces[g_calc.energy_p + h] += fnval;
if (uf) {
tmp_force.x =
grad_1 * neigh->dist.x -
tmp_2 *
(grad_2 * neigh->dist.x -
rp_i * neigh->r *
g_config.conf_atoms[neigh->nr - g_mpi.firstatom]
.p_ind.x -
rp_j * neigh->r * atom->p_ind.x);
tmp_force.y =
grad_1 * neigh->dist.y -
tmp_2 *
(grad_2 * neigh->dist.y -
rp_i * neigh->r *
g_config.conf_atoms[neigh->nr - g_mpi.firstatom]
.p_ind.y -
rp_j * neigh->r * atom->p_ind.y);
tmp_force.z =
grad_1 * neigh->dist.z -
tmp_2 *
(grad_2 * neigh->dist.z -
rp_i * neigh->r *
g_config.conf_atoms[neigh->nr - g_mpi.firstatom]
.p_ind.z -
rp_j * neigh->r * atom->p_ind.z);
forces[n_i + 0] -= tmp_force.x;
forces[n_i + 1] -= tmp_force.y;
forces[n_i + 2] -= tmp_force.z;
/* actio = reactio */
n_j = 3 * neigh->nr;
forces[n_j + 0] += tmp_force.x;
forces[n_j + 1] += tmp_force.y;
forces[n_j + 2] += tmp_force.z;
#if defined(STRESS)
/* calculate stresses */
if (us) {
forces[stresses + 0] += neigh->dist.x * tmp_force.x;
forces[stresses + 1] += neigh->dist.y * tmp_force.y;
forces[stresses + 2] += neigh->dist.z * tmp_force.z;
forces[stresses + 3] += neigh->dist.x * tmp_force.y;
forces[stresses + 4] += neigh->dist.y * tmp_force.z;
forces[stresses + 5] += neigh->dist.z * tmp_force.x;
}
#endif // STRESS
}
}
}
} /* loop over neighbours */
} /* end F O U R T H loop over atoms */
#endif // DIPOLE
/* F I F T H loop: self energy contributions and sum-up force
* contributions */
double qq;
#if defined(DSF)
double fnval_cut, gtail_cut, ggrad_cut;
elstat_value(g_config.dp_cut, dp_kappa, &fnval_cut, >ail_cut, &ggrad_cut);
#endif // DSF
for (i = 0; i < g_config.inconf[h]; i++) { /* atoms */
atom =
g_config.conf_atoms + i + g_config.cnfstart[h] - g_mpi.firstatom;
type1 = atom->type;
n_i = 3 * (g_config.cnfstart[h] + i);
/* self energy contributions */
if (charge[type1]) {
qq = charge[type1] * charge[type1];
#if defined(DSF)
fnval = qq * ( DP_EPS * dp_kappa / sqrt(M_PI) +
(fnval_cut - gtail_cut * g_config.dp_cut * g_config.dp_cut )*0.5 );
#else
fnval = DP_EPS * dp_kappa * qq / sqrt(M_PI);
#endif // DSF
forces[g_calc.energy_p + h] -= fnval;
}
#if defined(DIPOLE)
double pp;
if (dp_alpha[type1]) {
pp = SPROD(atom->p_ind, atom->p_ind);
fnval = pp / (2 * dp_alpha[type1]);
forces[g_calc.energy_p + h] += fnval;
}
/* alternative dipole self energy including kappa-dependence */
// if (dp_alpha[type1]) {
// pp = SPROD(atom->p_ind, atom->p_ind);
// fnval = kkk * pp / sqrt(M_PI);
// forces[energy_p + h] += fnval;
//}
#endif // DIPOLE
/* sum-up: whole force contributions flow into tmpsum */
/* if (uf) {*/
/*#ifdef FWEIGHT*/
/* Weigh by absolute value of force */
/* forces[k] /= FORCE_EPS + atom->absforce;*/
/* forces[k + 1] /= FORCE_EPS + atom->absforce;*/
/* forces[k + 2] /= FORCE_EPS + atom->absforce;*/
/*#endif |+ FWEIGHT +|*/
/*#ifdef CONTRIB*/
/* if (atom->contrib)*/
/*#endif |+ CONTRIB +|*/
/* tmpsum +=*/
/* conf_weight[h] * (dsquare(forces[k]) +
* dsquare(forces[k + 1]) + dsquare(forces[k + 2]));*/
/* printf("tmpsum = %f (forces)\n",tmpsum);*/
/* }*/
} /* end F I F T H loop over atoms */
/* S I X T H loop: EAM force */
if (uf) { /* only required if we calc forces */
for (i = 0; i < g_config.inconf[h]; i++) {
atom = g_config.conf_atoms + i + g_config.cnfstart[h] -
g_mpi.firstatom;
n_i = 3 * (g_config.cnfstart[h] + i);
for (j = 0; j < atom->num_neigh; j++) {
/* loop over neighbors */
neigh = atom->neigh + j;
/* In small cells, an atom might interact with itself */
self = (neigh->nr == i + g_config.cnfstart[h]) ? 1 : 0;
col_F = g_calc.paircol + g_param.ntypes +
atom->type; /* column of F */
r = neigh->r;
/* are we within reach? */
if ((r < g_pot.calc_pot.end[neigh->col[1]]) ||
(r < g_pot.calc_pot.end[col_F - g_param.ntypes])) {
rho_grad =
(r < g_pot.calc_pot.end[neigh->col[1]])
? splint_grad_dir(&g_pot.calc_pot, xi, neigh->slot[1],
neigh->shift[1], neigh->step[1])
: 0.0;
if (atom->type == neigh->type) /* use actio = reactio */
rho_grad_j = rho_grad;
else
rho_grad_j = (r < g_pot.calc_pot.end[col_F - g_param.ntypes])
? (*g_splint_grad)(&g_pot.calc_pot, xi,
col_F - g_param.ntypes, r)
: 0.0;
/* now we know everything - calculate forces */
eam_force =
(rho_grad * atom->gradF +
rho_grad_j *
g_config.conf_atoms[(neigh->nr) - g_mpi.firstatom]
.gradF);
/* avoid double counting if atom is interacting with a
copy of itself */
if (self)
eam_force *= 0.5;
tmp_force.x = neigh->dist_r.x * eam_force;
tmp_force.y = neigh->dist_r.y * eam_force;
tmp_force.z = neigh->dist_r.z * eam_force;
forces[n_i + 0] += tmp_force.x;
forces[n_i + 1] += tmp_force.y;
forces[n_i + 2] += tmp_force.z;
/* actio = reactio */
n_j = 3 * neigh->nr;
forces[n_j + 0] -= tmp_force.x;
forces[n_j + 1] -= tmp_force.y;
forces[n_j + 2] -= tmp_force.z;
#if defined(STRESS)
/* and stresses */
if (us) {
forces[stresses + 0] -= neigh->dist.x * tmp_force.x;
forces[stresses + 1] -= neigh->dist.y * tmp_force.y;
forces[stresses + 2] -= neigh->dist.z * tmp_force.z;
forces[stresses + 3] -= neigh->dist.x * tmp_force.y;
forces[stresses + 4] -= neigh->dist.y * tmp_force.z;
forces[stresses + 5] -= neigh->dist.z * tmp_force.x;
}
#endif // STRESS
} /* within reach */
} /* loop over neighbours */
#if defined(FWEIGHT)
/* Weigh by absolute value of force */
forces[n_i + 0] /= FORCE_EPS + atom->absforce;
forces[n_i + 1] /= FORCE_EPS + atom->absforce;
forces[n_i + 2] /= FORCE_EPS + atom->absforce;
#endif // FWEIGHT
/* sum up forces */
#if defined(CONTRIB)
if (atom->contrib)
#endif // CONTRIB
tmpsum += g_config.conf_weight[h] *
(dsquare(forces[n_i + 0]) + dsquare(forces[n_i + 1]) +
dsquare(forces[n_i + 2]));
}
}
/* end S I X T H loop over atoms */
/* whole energy contributions flow into tmpsum */
forces[g_calc.energy_p + h] /= (double)g_config.inconf[h];
forces[g_calc.energy_p + h] -= g_config.force_0[g_calc.energy_p + h];
tmpsum += g_config.conf_weight[h] * g_param.eweight *
dsquare(forces[g_calc.energy_p + h]);
#if defined(STRESS)
/* whole stress contributions flow into tmpsum */
if (uf && us) {
for (i = 0; i < 6; i++) {
forces[stresses + i] /= g_config.conf_vol[h - g_mpi.firstconf];
forces[stresses + i] -= g_config.force_0[stresses + i];
tmpsum += g_config.conf_weight[h] * g_param.sweight *
dsquare(forces[stresses + i]);
}
}
#endif // STRESS
/* limiting constraints per configuration */
tmpsum += g_config.conf_weight[h] * dsquare(forces[g_calc.limit_p + h]);
} /* end M A I N loop over configurations */
} /* parallel region */
#if defined(MPI)
/* Reduce rho_sum */
MPI_Reduce(&rho_sum_loc, &rho_sum, 1, MPI_DOUBLE, MPI_SUM, 0,
MPI_COMM_WORLD);
#else /* MPI */
rho_sum = rho_sum_loc;
#endif // MPI
/* dummy constraints (global) */
#if defined(APOT)
/* add punishment for out of bounds (mostly for powell_lsq) */
if (g_mpi.myid == 0) {
tmpsum += apot_punish(xi_opt, forces);
}
#endif // APOT
#if !defined(NOPUNISH)
if (g_mpi.myid == 0) {
int g;
for (g = 0; g < g_param.ntypes; g++) {
#if defined(NORESCALE)
/* clear field */
forces[g_calc.dummy_p + g_param.ntypes + g] = 0.0; /* Free end... */
/* NEW: Constraint on U': U'(1.0)=0.0; */
forces[g_calc.dummy_p + g] =
DUMMY_WEIGHT *
splint_grad(&calc_pot, xi, paircol + g_param.ntypes + g, 1.0);
#else /* NOTHING */
forces[g_calc.dummy_p + g_param.ntypes + g] = 0.0; /* Free end... */
/* constraints on U`(n) */
forces[g_calc.dummy_p + g] =
DUMMY_WEIGHT *
(*g_splint_grad)(
&g_pot.calc_pot, xi, g_calc.paircol + g_param.ntypes + g,
0.5 * (g_pot.calc_pot
.begin[g_calc.paircol + g_param.ntypes + g] +
g_pot.calc_pot
.end[g_calc.paircol + g_param.ntypes + g])) -
g_config.force_0[g_calc.dummy_p + g];
#endif // NORESCALE
tmpsum += dsquare(forces[g_calc.dummy_p + g_param.ntypes + g]);
tmpsum += dsquare(forces[g_calc.dummy_p + g]);
} /* loop over types */
#if defined(NORESCALE)
/* NEW: Constraint on n: <n>=1.0 ONE CONSTRAINT ONLY */
/* Calculate averages */
rho_sum /= (double)natoms;
/* ATTN: if there are invariant potentials, things might be problematic */
forces[dummy_p + g_param.ntypes] = DUMMY_WEIGHT * (rho_sum - 1.0);
tmpsum += dsquare(forces[dummy_p + g_param.ntypes]);
#endif // NORESCALE
}
#endif // NOPUNISH
#if defined(MPI)
/* reduce global sum */
sum = 0.0;
MPI_Reduce(&tmpsum, &sum, 1, MPI_DOUBLE, MPI_SUM, 0, MPI_COMM_WORLD);
/* gather forces, energies, stresses */
if (g_mpi.myid == 0) { /* root node already has data in place */
/* forces */
MPI_Gatherv(MPI_IN_PLACE, g_mpi.myatoms, g_mpi.MPI_VECTOR, forces,
g_mpi.atom_len, g_mpi.atom_dist, g_mpi.MPI_VECTOR, 0,
MPI_COMM_WORLD);
/* energies */
MPI_Gatherv(MPI_IN_PLACE, g_mpi.myconf, MPI_DOUBLE,
forces + g_calc.energy_p, g_mpi.conf_len, g_mpi.conf_dist,
MPI_DOUBLE, 0, MPI_COMM_WORLD);
#if defined(STRESS)
/* stresses */
MPI_Gatherv(MPI_IN_PLACE, g_mpi.myconf, g_mpi.MPI_STENS,
forces + g_calc.stress_p, g_mpi.conf_len, g_mpi.conf_dist,
g_mpi.MPI_STENS, 0, MPI_COMM_WORLD);
#endif // STRESS
#if !defined(NORESCALE)
/* punishment constraints */
MPI_Gatherv(MPI_IN_PLACE, g_mpi.myconf, MPI_DOUBLE,
forces + g_calc.limit_p, g_mpi.conf_len, g_mpi.conf_dist,
MPI_DOUBLE, 0, MPI_COMM_WORLD);
#endif // !NORESCALE
} else {
/* forces */
MPI_Gatherv(forces + g_mpi.firstatom * 3, g_mpi.myatoms, g_mpi.MPI_VECTOR,
forces, g_mpi.atom_len, g_mpi.atom_dist, g_mpi.MPI_VECTOR, 0,
MPI_COMM_WORLD);
/* energies */
MPI_Gatherv(forces + g_calc.energy_p + g_mpi.firstconf, g_mpi.myconf,
MPI_DOUBLE, forces + g_calc.energy_p, g_mpi.conf_len,
g_mpi.conf_dist, MPI_DOUBLE, 0, MPI_COMM_WORLD);
#if defined(STRESS)
/* stresses */
MPI_Gatherv(forces + g_calc.stress_p + 6 * g_mpi.firstconf, g_mpi.myconf,
g_mpi.MPI_STENS, forces + g_calc.stress_p, g_mpi.conf_len,
g_mpi.conf_dist, g_mpi.MPI_STENS, 0, MPI_COMM_WORLD);
#endif // STRESS
#if !defined(NORESCALE)
/* punishment constraints */
MPI_Gatherv(forces + g_calc.limit_p + g_mpi.firstconf, g_mpi.myconf,
MPI_DOUBLE, forces + g_calc.limit_p, g_mpi.conf_len,
g_mpi.conf_dist, MPI_DOUBLE, 0, MPI_COMM_WORLD);
#endif // !NORESCALE
}
/* no need to pick up dummy constraints - they are already @ root */
#else
sum = tmpsum; /* global sum = local sum */
#endif // MPI
/* root process exits this function now */
if (g_mpi.myid == 0) {
g_calc.fcalls++; /* Increase function call counter */
if (isnan(sum)) {
#if defined(DEBUG)
printf("\n--> Force is nan! <--\n\n");
#endif // DEBUG
return 10e10;
} else
return sum;
}
}
/* once a non-root process arrives here, all is done. */
return -1.0;
}
void EXX_Fock_Band(
dcomplex **H,
EXX_t *exx,
dcomplex ****exx_CDM,
int *MP,
double k1,
double k2,
double k3,
int spin
)
{
double *local_H, *mpi_H;
int H_n, nbuf;
int i, j, n, ir, nr, irn, nep;
int iop1, iop2, nb1, nb2, nb3, nb4, nrn;
int ia1, ia2, ia3, ia4, ib1, ib2, ib3, ib4, icell1, icell2;
int ib1_ep, ib2_ep, ib3_ep, ib4_ep;
int nb1_ep, nb2_ep, nb3_ep, nb4_ep;
const int *ep_atom1, *ep_atom2, *ep_cell, *atom_nb;
const int *op_atom1, *op_atom2;
int iep1[8], iep2[8], icell3[8], mul;
double w;
int GA_AN, Anum, GB_AN, Bnum, tnoA, tnoB;
int neri;
double *eri_list;
int *iRm;
double eri;
dcomplex den;
int nproc, myid, iproc;
MPI_Status stat;
int ncd, nshell_ep;
int iRn_x, iRn_y, iRn_z, iRmp_x, iRmp_y, iRmp_z;
double kRn, kRmp, co1, si1, co2, si2;
MPI_Comm comm;
double *k1_list, *k2_list, *k3_list;
int *spin_list;
comm = g_exx_mpicomm;
MPI_Comm_size(comm, &nproc);
MPI_Comm_rank(comm, &myid);
k1_list = (double*)malloc(sizeof(double)*nproc);
k2_list = (double*)malloc(sizeof(double)*nproc);
k3_list = (double*)malloc(sizeof(double)*nproc);
spin_list = (int*)malloc(sizeof(int)*nproc);
/* all-to-all */
MPI_Allgather(&k1, 1, MPI_DOUBLE, k1_list, 1, MPI_DOUBLE, comm);
MPI_Allgather(&k2, 1, MPI_DOUBLE, k2_list, 1, MPI_DOUBLE, comm);
MPI_Allgather(&k3, 1, MPI_DOUBLE, k3_list, 1, MPI_DOUBLE, comm);
MPI_Allgather(&spin, 1, MPI_INT, spin_list, 1, MPI_INT, comm);
op_atom1 = EXX_Array_OP_Atom1(exx);
op_atom2 = EXX_Array_OP_Atom2(exx);
ep_atom1 = EXX_Array_EP_Atom1(exx);
ep_atom2 = EXX_Array_EP_Atom2(exx);
ep_cell = EXX_Array_EP_Cell(exx);
atom_nb = EXX_atom_nb(exx);
nshell_ep = EXX_Number_of_EP_Shells(exx);
ncd = 2*nshell_ep+1;
/* matrix size */
H_n = 0;
for (i=1; i<=atomnum; i++){ H_n += Spe_Total_CNO[WhatSpecies[i]]; }
/* allocation */
nbuf = H_n*H_n*2;
local_H = (double*)malloc(sizeof(double)*nbuf);
mpi_H = (double*)malloc(sizeof(double)*nbuf);
nr = EXX_File_ERI_Read_NRecord(exx);
/* clear buffer */
for (i=0; i<nbuf; i++) { local_H[i] = 0.0; }
for (ir=0; ir<nr; ir++) {
EXX_File_ERI_Read_Data_Head(exx, ir, &iop1, &iop2,
&nb1, &nb2, &nb3, &nb4, &nrn);
neri = nb1*nb2*nb3*nb4*nrn;
eri_list = (double*)malloc(sizeof(double)*neri);
iRm = (int*)malloc(sizeof(int)*nrn); /* Rm */
EXX_File_ERI_Read(exx, ir, eri_list, iRm, iop1, iop2, nrn, neri);
for (iproc=0; iproc<nproc; iproc++) {
/* clear buffer */
for (i=0; i<nbuf; i++) { mpi_H[i] = 0.0; }
k1 = k1_list[iproc];
k2 = k2_list[iproc];
k3 = k3_list[iproc];
spin = spin_list[iproc];
for (irn=0; irn<nrn; irn++) {
EXX_OP2EP_Band(exx, iop1, iop2, iRm[irn],
&iep1[0], &iep2[0], &icell3[0], &mul);
w = 1.0/(double)mul;
for (j=0; j<8; j++) {
ia1 = ep_atom1[iep1[j]]; /* i */
ia2 = ep_atom2[iep1[j]]; /* j */
ia3 = ep_atom1[iep2[j]]; /* k */
ia4 = ep_atom2[iep2[j]]; /* l */
icell1 = ep_cell[iep1[j]]; /* Rn */
icell2 = ep_cell[iep2[j]]; /* Rm' */
nb1_ep = atom_nb[ia1];
nb2_ep = atom_nb[ia2];
nb3_ep = atom_nb[ia3];
nb4_ep = atom_nb[ia4];
GA_AN = ia1+1;
Anum = MP[GA_AN];
GB_AN = ia2+1;
Bnum = MP[GB_AN];
/* phase */
iRn_x = icell1%ncd - nshell_ep;
iRn_y = (icell1/ncd)%ncd - nshell_ep;
iRn_z = (icell1/ncd/ncd)%ncd - nshell_ep;
kRn = k1*(double)iRn_x + k2*(double)iRn_y + k3*(double)iRn_z;
si1 = sin(2.0*PI*kRn);
co1 = cos(2.0*PI*kRn);
iRmp_x = icell2%ncd - nshell_ep;
iRmp_y = (icell2/ncd)%ncd - nshell_ep;
iRmp_z = (icell2/ncd/ncd)%ncd - nshell_ep;
kRmp = k1*(double)iRmp_x + k2*(double)iRmp_y + k3*(double)iRmp_z;
si2 = sin(2.0*PI*kRmp);
co2 = cos(2.0*PI*kRmp);
for (ib1_ep=0; ib1_ep<nb1_ep; ib1_ep++) {
for (ib2_ep=0; ib2_ep<nb2_ep; ib2_ep++) {
for (ib3_ep=0; ib3_ep<nb3_ep; ib3_ep++) {
for (ib4_ep=0; ib4_ep<nb4_ep; ib4_ep++) {
EXX_Basis_Index(ib1_ep, ib2_ep, ib3_ep, ib4_ep,
&ib1, &ib2, &ib3, &ib4, j);
i = (((ib1*nb2+ib2)*nb3+ib3)*nb4+ib4)*nrn+irn;
eri = eri_list[i];
den.r = exx_CDM[spin][iep2[j]][ib3_ep][ib4_ep].r;
den.i = exx_CDM[spin][iep2[j]][ib3_ep][ib4_ep].i;
i = (Anum+ib1_ep-1)*H_n + (Bnum+ib2_ep-1);
mpi_H[2*i+0] += -w*eri*(co1*den.r - si1*den.i); /* real */
mpi_H[2*i+1] += -w*eri*(co1*den.i + si1*den.r); /* imag */
}
}
}
}
} /* loop of j */
} /* loop of irn */
/* reduce to the iproc-th proc */
MPI_Reduce(mpi_H, mpi_H, nbuf, MPI_DOUBLE, MPI_SUM, iproc, comm);
if (myid==iproc) {
for (i=0; i<nbuf; i++) { local_H[i] = mpi_H[i]; }
}
} /* loop of iproc */
free(eri_list);
free(iRm);
} /* loop of irn */
#if 1
for (GA_AN=1; GA_AN<=atomnum; GA_AN++) {
tnoA = Spe_Total_CNO[WhatSpecies[GA_AN]];
Anum = MP[GA_AN];
for (GB_AN=1; GB_AN<=atomnum; GB_AN++) {
tnoB = Spe_Total_CNO[WhatSpecies[GB_AN]];
Bnum = MP[GB_AN];
for (ib1=0; ib1<tnoA; ib1++) {
for (ib2=0; ib2<tnoB; ib2++) {
i = (Anum+ib1-1)*H_n + (Bnum+ib2-1);
H[Anum+ib1][Bnum+ib2].r += local_H[2*i+0];
H[Anum+ib1][Bnum+ib2].i += local_H[2*i+1];
}
}
}
}
#endif
/* free*/
free(local_H);
free(mpi_H);
}
void step3_gpu(int *n) {
int nprocs, procid;
MPI_Comm_rank(MPI_COMM_WORLD, &procid);
MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
/* Create Cartesian Communicator */
int c_dims[2]={0};
MPI_Comm c_comm;
accfft_create_comm(MPI_COMM_WORLD,c_dims,&c_comm);
Complexf *data, *data_cpu;
Complexf *data_hat;
double f_time=0*MPI_Wtime(),i_time=0, setup_time=0;
int alloc_max=0;
int isize[3],osize[3],istart[3],ostart[3];
/* Get the local pencil size and the allocation size */
alloc_max=accfft_local_size_dft_c2c_gpuf(n,isize,istart,osize,ostart,c_comm);
#ifdef INPLACE
data_cpu=(Complexf*)malloc(alloc_max);
cudaMalloc((void**) &data, alloc_max);
#else
data_cpu=(Complexf*)malloc(isize[0]*isize[1]*isize[2]*2*sizeof(float));
cudaMalloc((void**) &data,isize[0]*isize[1]*isize[2]*2*sizeof(float));
cudaMalloc((void**) &data_hat, alloc_max);
#endif
//accfft_init(nthreads);
setup_time=-MPI_Wtime();
/* Create FFT plan */
#ifdef INPLACE
accfft_plan_gpuf * plan=accfft_plan_dft_3d_c2c_gpuf(n,data,data,c_comm,ACCFFT_MEASURE);
#else
accfft_plan_gpuf * plan=accfft_plan_dft_3d_c2c_gpuf(n,data,data_hat,c_comm,ACCFFT_MEASURE);
#endif
setup_time+=MPI_Wtime();
/* Warmup Runs */
#ifdef INPLACE
accfft_execute_c2c_gpuf(plan,ACCFFT_FORWARD,data,data);
accfft_execute_c2c_gpuf(plan,ACCFFT_FORWARD,data,data);
#else
accfft_execute_c2c_gpuf(plan,ACCFFT_FORWARD,data,data_hat);
accfft_execute_c2c_gpuf(plan,ACCFFT_FORWARD,data,data_hat);
#endif
/* Initialize data */
initialize(data_cpu,n,c_comm);
#ifdef INPLACE
cudaMemcpy(data, data_cpu,alloc_max, cudaMemcpyHostToDevice);
#else
cudaMemcpy(data, data_cpu,isize[0]*isize[1]*isize[2]*2*sizeof(float), cudaMemcpyHostToDevice);
#endif
MPI_Barrier(c_comm);
/* Perform forward FFT */
f_time-=MPI_Wtime();
#ifdef INPLACE
accfft_execute_c2c_gpuf(plan,ACCFFT_FORWARD,data,data);
#else
accfft_execute_c2c_gpuf(plan,ACCFFT_FORWARD,data,data_hat);
#endif
f_time+=MPI_Wtime();
MPI_Barrier(c_comm);
#ifndef INPLACE
Complexf *data2_cpu, *data2;
cudaMalloc((void**) &data2, isize[0]*isize[1]*isize[2]*2*sizeof(float));
data2_cpu=(Complexf*) malloc(isize[0]*isize[1]*isize[2]*2*sizeof(float));
#endif
/* Perform backward FFT */
i_time-=MPI_Wtime();
#ifdef INPLACE
accfft_execute_c2c_gpuf(plan,ACCFFT_BACKWARD,data,data);
#else
accfft_execute_c2c_gpuf(plan,ACCFFT_BACKWARD,data_hat,data2);
#endif
i_time+=MPI_Wtime();
/* copy back results on CPU and check error*/
#ifdef INPLACE
cudaMemcpy(data_cpu, data, alloc_max, cudaMemcpyDeviceToHost);
check_err(data_cpu,n,c_comm);
#else
cudaMemcpy(data2_cpu, data2, isize[0]*isize[1]*isize[2]*2*sizeof(float), cudaMemcpyDeviceToHost);
check_err(data2_cpu,n,c_comm);
#endif
/* Compute some timings statistics */
double g_f_time, g_i_time, g_setup_time;
MPI_Reduce(&f_time,&g_f_time,1, MPI_DOUBLE, MPI_MAX,0, MPI_COMM_WORLD);
MPI_Reduce(&i_time,&g_i_time,1, MPI_DOUBLE, MPI_MAX,0, MPI_COMM_WORLD);
MPI_Reduce(&setup_time,&g_setup_time,1, MPI_DOUBLE, MPI_MAX,0, MPI_COMM_WORLD);
#ifdef INPLACE
PCOUT<<"GPU Timing for Inplace FFT of size "<<n[0]<<"*"<<n[1]<<"*"<<n[2]<<std::endl;
#else
PCOUT<<"GPU Timing for Outplace FFT of size "<<n[0]<<"*"<<n[1]<<"*"<<n[2]<<std::endl;
#endif
PCOUT<<"Setup \t"<<g_setup_time<<std::endl;
PCOUT<<"FFT \t"<<g_f_time<<std::endl;
PCOUT<<"IFFT \t"<<g_i_time<<std::endl;
MPI_Barrier(c_comm);
cudaDeviceSynchronize();
free(data_cpu);
cudaFree(data);
#ifndef INPLACE
cudaFree(data_hat);
free(data2_cpu);
cudaFree(data2);
#endif
accfft_destroy_plan_gpu(plan);
accfft_cleanup_gpuf();
MPI_Comm_free(&c_comm);
return ;
} // end step3_gpu
/*
* This test looks at the handling of logical and for types that are not
* integers or are not required integers (e.g., long long). MPICH allows
* these as well. A strict MPI test should not include this test.
*/
int main( int argc, char *argv[] )
{
int errs = 0;
int rc;
int rank, size;
MPI_Comm comm;
char cinbuf[3], coutbuf[3];
signed char scinbuf[3], scoutbuf[3];
unsigned char ucinbuf[3], ucoutbuf[3];
short sinbuf[3], soutbuf[3];
unsigned short usinbuf[3], usoutbuf[3];
long linbuf[3], loutbuf[3];
unsigned long ulinbuf[3], uloutbuf[3];
unsigned uinbuf[3], uoutbuf[3];
int iinbuf[3], ioutbuf[3];
MTest_Init( &argc, &argv );
comm = MPI_COMM_WORLD;
/* Set errors return so that we can provide better information
should a routine reject one of the operand/datatype pairs */
MPI_Errhandler_set( comm, MPI_ERRORS_RETURN );
MPI_Comm_rank( comm, &rank );
MPI_Comm_size( comm, &size );
#ifndef USE_STRICT_MPI
/* char */
MTestPrintfMsg( 10, "Reduce of MPI_CHAR\n" );
cinbuf[0] = 0xff;
cinbuf[1] = 0;
cinbuf[2] = (rank > 0) ? 0x3c : 0xc3;
coutbuf[0] = 0xf;
coutbuf[1] = 1;
coutbuf[2] = 1;
rc = MPI_Reduce( cinbuf, coutbuf, 3, MPI_CHAR, MPI_BXOR, 0, comm );
if (rc) {
MTestPrintErrorMsg( "MPI_BXOR and MPI_CHAR", rc );
errs++;
}
else {
if (rank == 0) {
if (coutbuf[0] != ((size % 2) ? (char)0xff : (char)0) ) {
errs++;
fprintf( stderr, "char BXOR(1) test failed\n" );
}
if (coutbuf[1]) {
errs++;
fprintf( stderr, "char BXOR(0) test failed\n" );
}
if (coutbuf[2] != ((size % 2) ? (char)0xc3 : (char)0xff)) {
errs++;
fprintf( stderr, "char BXOR(>) test failed\n" );
}
}
}
#endif /* USE_STRICT_MPI */
/* signed char */
MTestPrintfMsg( 10, "Reduce of MPI_SIGNED_CHAR\n" );
scinbuf[0] = 0xff;
scinbuf[1] = 0;
scinbuf[2] = (rank > 0) ? 0x3c : 0xc3;
scoutbuf[0] = 0xf;
scoutbuf[1] = 1;
scoutbuf[2] = 1;
rc = MPI_Reduce( scinbuf, scoutbuf, 3, MPI_SIGNED_CHAR, MPI_BXOR, 0, comm );
if (rc) {
MTestPrintErrorMsg( "MPI_BXOR and MPI_SIGNED_CHAR", rc );
errs++;
}
else {
if (rank == 0) {
if (scoutbuf[0] != ((size % 2) ? (signed char)0xff : (signed char)0) ) {
errs++;
fprintf( stderr, "signed char BXOR(1) test failed\n" );
}
if (scoutbuf[1]) {
errs++;
fprintf( stderr, "signed char BXOR(0) test failed\n" );
}
if (scoutbuf[2] != ((size % 2) ? (signed char)0xc3 : (signed char)0xff)) {
errs++;
fprintf( stderr, "signed char BXOR(>) test failed\n" );
}
}
}
/* unsigned char */
MTestPrintfMsg( 10, "Reduce of MPI_UNSIGNED_CHAR\n" );
ucinbuf[0] = 0xff;
ucinbuf[1] = 0;
ucinbuf[2] = (rank > 0) ? 0x3c : 0xc3;
ucoutbuf[0] = 0;
ucoutbuf[1] = 1;
ucoutbuf[2] = 1;
rc = MPI_Reduce( ucinbuf, ucoutbuf, 3, MPI_UNSIGNED_CHAR, MPI_BXOR, 0, comm );
if (rc) {
MTestPrintErrorMsg( "MPI_BXOR and MPI_UNSIGNED_CHAR", rc );
errs++;
}
else {
if (rank == 0) {
if (ucoutbuf[0] != ((size % 2) ? 0xff : 0)) {
errs++;
fprintf( stderr, "unsigned char BXOR(1) test failed\n" );
}
if (ucoutbuf[1]) {
errs++;
fprintf( stderr, "unsigned char BXOR(0) test failed\n" );
}
if (ucoutbuf[2] != ((size % 2) ? (unsigned char)0xc3 : (unsigned char)0xff)) {
errs++;
fprintf( stderr, "unsigned char BXOR(>) test failed\n" );
}
}
}
/* bytes */
MTestPrintfMsg( 10, "Reduce of MPI_BYTE\n" );
cinbuf[0] = 0xff;
cinbuf[1] = 0;
cinbuf[2] = (rank > 0) ? 0x3c : 0xc3;
coutbuf[0] = 0;
coutbuf[1] = 1;
coutbuf[2] = 1;
rc = MPI_Reduce( cinbuf, coutbuf, 3, MPI_BYTE, MPI_BXOR, 0, comm );
if (rc) {
MTestPrintErrorMsg( "MPI_BXOR and MPI_BYTE", rc );
errs++;
}
else {
if (rank == 0) {
if (coutbuf[0] != ((size % 2) ? (char)0xff : 0)) {
errs++;
fprintf( stderr, "byte BXOR(1) test failed\n" );
}
if (coutbuf[1]) {
errs++;
fprintf( stderr, "byte BXOR(0) test failed\n" );
}
if (coutbuf[2] != ((size % 2) ? (char)0xc3 : (char)0xff)) {
errs++;
fprintf( stderr, "byte BXOR(>) test failed\n" );
}
}
}
/* short */
MTestPrintfMsg( 10, "Reduce of MPI_SHORT\n" );
sinbuf[0] = 0xffff;
sinbuf[1] = 0;
sinbuf[2] = (rank > 0) ? 0x3c3c : 0xc3c3;
soutbuf[0] = 0;
soutbuf[1] = 1;
soutbuf[2] = 1;
rc = MPI_Reduce( sinbuf, soutbuf, 3, MPI_SHORT, MPI_BXOR, 0, comm );
if (rc) {
MTestPrintErrorMsg( "MPI_BXOR and MPI_SHORT", rc );
errs++;
}
else {
if (rank == 0) {
if (soutbuf[0] != ((size % 2) ? (short)0xffff : 0)) {
errs++;
fprintf( stderr, "short BXOR(1) test failed\n" );
}
if (soutbuf[1]) {
errs++;
fprintf( stderr, "short BXOR(0) test failed\n" );
}
if (soutbuf[2] != ((size % 2) ? (short)0xc3c3 : (short)0xffff)) {
errs++;
fprintf( stderr, "short BXOR(>) test failed\n" );
}
}
}
/* unsigned short */
MTestPrintfMsg( 10, "Reduce of MPI_UNSIGNED_SHORT\n" );
usinbuf[0] = 0xffff;
usinbuf[1] = 0;
usinbuf[2] = (rank > 0) ? 0x3c3c : 0xc3c3;
usoutbuf[0] = 0;
usoutbuf[1] = 1;
usoutbuf[2] = 1;
rc = MPI_Reduce( usinbuf, usoutbuf, 3, MPI_UNSIGNED_SHORT, MPI_BXOR, 0, comm );
if (rc) {
MTestPrintErrorMsg( "MPI_BXOR and MPI_UNSIGNED_SHORT", rc );
errs++;
}
else {
if (rank == 0) {
if (usoutbuf[0] != ((size % 2) ? 0xffff : 0)) {
errs++;
fprintf( stderr, "short BXOR(1) test failed\n" );
}
if (usoutbuf[1]) {
errs++;
fprintf( stderr, "short BXOR(0) test failed\n" );
}
if (usoutbuf[2] != ((size % 2) ? 0xc3c3 : 0xffff)) {
errs++;
fprintf( stderr, "short BXOR(>) test failed\n" );
}
}
}
/* unsigned */
MTestPrintfMsg( 10, "Reduce of MPI_UNSIGNED\n" );
uinbuf[0] = 0xffffffff;
uinbuf[1] = 0;
uinbuf[2] = (rank > 0) ? 0x3c3c3c3c : 0xc3c3c3c3;
uoutbuf[0] = 0;
uoutbuf[1] = 1;
uoutbuf[2] = 1;
rc = MPI_Reduce( uinbuf, uoutbuf, 3, MPI_UNSIGNED, MPI_BXOR, 0, comm );
if (rc) {
MTestPrintErrorMsg( "MPI_BXOR and MPI_UNSIGNED", rc );
errs++;
}
else {
if (rank == 0) {
if (uoutbuf[0] != ((size % 2) ? 0xffffffff : 0)) {
errs++;
fprintf( stderr, "unsigned BXOR(1) test failed\n" );
}
if (uoutbuf[1]) {
errs++;
fprintf( stderr, "unsigned BXOR(0) test failed\n" );
}
if (uoutbuf[2] != ((size % 2) ? 0xc3c3c3c3 : 0xffffffff)) {
errs++;
fprintf( stderr, "unsigned BXOR(>) test failed\n" );
}
}
}
/* int */
MTestPrintfMsg( 10, "Reduce of MPI_INT\n" );
iinbuf[0] = 0xffffffff;
iinbuf[1] = 0;
iinbuf[2] = (rank > 0) ? 0x3c3c3c3c : 0xc3c3c3c3;
ioutbuf[0] = 0;
ioutbuf[1] = 1;
ioutbuf[2] = 1;
rc = MPI_Reduce( iinbuf, ioutbuf, 3, MPI_INT, MPI_BXOR, 0, comm );
if (rc) {
MTestPrintErrorMsg( "MPI_BXOR and MPI_INT", rc );
errs++;
}
else {
if (rank == 0) {
if (ioutbuf[0] != ((size % 2) ? 0xffffffff : 0)) {
errs++;
fprintf( stderr, "int BXOR(1) test failed\n" );
}
if (ioutbuf[1]) {
errs++;
fprintf( stderr, "int BXOR(0) test failed\n" );
}
if (ioutbuf[2] != ((size % 2) ? 0xc3c3c3c3 : 0xffffffff)) {
errs++;
fprintf( stderr, "int BXOR(>) test failed\n" );
}
}
}
/* long */
MTestPrintfMsg( 10, "Reduce of MPI_LONG\n" );
linbuf[0] = 0xffffffff;
linbuf[1] = 0;
linbuf[2] = (rank > 0) ? 0x3c3c3c3c : 0xc3c3c3c3;
loutbuf[0] = 0;
loutbuf[1] = 1;
loutbuf[2] = 1;
rc = MPI_Reduce( linbuf, loutbuf, 3, MPI_LONG, MPI_BXOR, 0, comm );
if (rc) {
MTestPrintErrorMsg( "MPI_BXOR and MPI_LONG", rc );
errs++;
}
else {
if (rank == 0) {
if (loutbuf[0] != ((size % 2) ? 0xffffffff : 0)) {
errs++;
fprintf( stderr, "long BXOR(1) test failed\n" );
}
if (loutbuf[1]) {
errs++;
fprintf( stderr, "long BXOR(0) test failed\n" );
}
if (loutbuf[2] != ((size % 2) ? 0xc3c3c3c3 : 0xffffffff)) {
errs++;
fprintf( stderr, "long BXOR(>) test failed\n" );
}
}
}
/* unsigned long */
MTestPrintfMsg( 10, "Reduce of MPI_UNSIGNED_LONG\n" );
ulinbuf[0] = 0xffffffff;
ulinbuf[1] = 0;
ulinbuf[2] = (rank > 0) ? 0x3c3c3c3c : 0xc3c3c3c3;
uloutbuf[0] = 0;
uloutbuf[1] = 1;
uloutbuf[2] = 1;
rc = MPI_Reduce( ulinbuf, uloutbuf, 3, MPI_UNSIGNED_LONG, MPI_BXOR, 0, comm );
if (rc) {
MTestPrintErrorMsg( "MPI_BXOR and MPI_UNSIGNED_LONG", rc );
errs++;
}
else {
if (rank == 0) {
if (uloutbuf[0] != ((size % 2) ? 0xffffffff : 0)) {
errs++;
fprintf( stderr, "unsigned long BXOR(1) test failed\n" );
}
if (uloutbuf[1]) {
errs++;
fprintf( stderr, "unsigned long BXOR(0) test failed\n" );
}
if (uloutbuf[2] != ((size % 2) ? 0xc3c3c3c3 : 0xffffffff)) {
errs++;
fprintf( stderr, "unsigned long BXOR(>) test failed\n" );
}
}
}
#ifdef HAVE_LONG_LONG
{
long long llinbuf[3], lloutbuf[3];
/* long long */
llinbuf[0] = 0xffffffff;
llinbuf[1] = 0;
llinbuf[2] = (rank > 0) ? 0x3c3c3c3c : 0xc3c3c3c3;
lloutbuf[0] = 0;
lloutbuf[1] = 1;
lloutbuf[2] = 1;
if (MPI_LONG_LONG != MPI_DATATYPE_NULL) {
MTestPrintfMsg( 10, "Reduce of MPI_LONG_LONG\n" );
rc = MPI_Reduce( llinbuf, lloutbuf, 3, MPI_LONG_LONG, MPI_BXOR, 0, comm );
if (rc) {
MTestPrintErrorMsg( "MPI_BXOR and MPI_LONG_LONG", rc );
errs++;
}
else {
if (rank == 0) {
if (lloutbuf[0] != ((size % 2) ? 0xffffffff : 0)) {
errs++;
fprintf( stderr, "long long BXOR(1) test failed\n" );
}
if (lloutbuf[1]) {
errs++;
fprintf( stderr, "long long BXOR(0) test failed\n" );
}
if (lloutbuf[2] != ((size % 2) ? 0xc3c3c3c3 : 0xffffffff)) {
errs++;
fprintf( stderr, "long long BXOR(>) test failed\n" );
}
}
}
}
}
#endif
MPI_Errhandler_set( comm, MPI_ERRORS_ARE_FATAL );
MTest_Finalize( errs );
MPI_Finalize();
return 0;
}
int main(int argc, char *argv[])
{
int rank;
int size;
int i;
int status;
MPI_Init(&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &size);
unsigned long long* sb = (unsigned long long *) xbt_malloc(size * sizeof(unsigned long long));
unsigned long long* rb = (unsigned long long *) xbt_malloc(size * sizeof(unsigned long long));
for (i = 0; i < size; ++i) {
sb[i] = rank*size + i;
rb[i] = 0;
}
printf("[%d] sndbuf=[", rank);
for (i = 0; i < size; i++)
printf("%llu ", sb[i]);
printf("]\n");
int root=0;
status = MPI_Reduce(sb, rb, size, MPI_UNSIGNED_LONG_LONG, MPI_SUM, root, MPI_COMM_WORLD);
MPI_Barrier(MPI_COMM_WORLD);
if (rank == root) {
printf("[%d] rcvbuf=[", rank);
for (i = 0; i < size; i++)
printf("%llu ", rb[i]);
printf("]\n");
if (status != MPI_SUCCESS) {
printf("all_to_all returned %d\n", status);
fflush(stdout);
}
}
printf("[%d] second sndbuf=[", rank);
for (i = 0; i < 1; i++)
printf("%llu ", sb[i]);
printf("]\n");
root=size-1;
status = MPI_Reduce(sb, rb, 1, MPI_UNSIGNED_LONG_LONG, MPI_PROD, root, MPI_COMM_WORLD);
MPI_Barrier(MPI_COMM_WORLD);
if (rank == root) {
printf("[%d] rcvbuf=[", rank);
for (i = 0; i < 1; i++)
printf("%llu ", rb[i]);
printf("]\n");
if (status != MPI_SUCCESS) {
printf("all_to_all returned %d\n", status);
fflush(stdout);
}
}
free(sb);
free(rb);
MPI_Finalize();
return (EXIT_SUCCESS);
}
void pion_norm(const int traj, const int id) {
int i, j, z, zz, z0;
double *Cpp;
double res = 0.;
double pionnorm;
double atime, etime;
float tmp;
#ifdef MPI
double mpi_res = 0.;
#endif
FILE *ofs, *ofs2;
char *filename, *filename2, *sourcefilename;
char buf[100];
char buf2[100];
char buf3[100];
filename=buf;
filename2=buf2;
sourcefilename=buf3;
sprintf(filename,"pionnormcorrelator_finiteT.%.6d",traj);
sprintf(filename2,"%s", "pion_norm.data");
/* generate random source point */
if(ranlxs_init == 0) {
rlxs_init(1, 123456);
}
ranlxs(&tmp, 1);
z0 = (int)(measurement_list[id].max_source_slice*tmp);
#ifdef MPI
MPI_Bcast(&z0, 1, MPI_INT, 0, MPI_COMM_WORLD);
#endif
#ifdef MPI
atime = MPI_Wtime();
#else
atime = (double)clock()/(double)(CLOCKS_PER_SEC);
#endif
Cpp = (double*) calloc(g_nproc_z*LZ, sizeof(double));
printf("Doing finite Temperature online measurement\n");
/* stochastic source in z-slice */
source_generation_pion_zdir(g_spinor_field[0], g_spinor_field[1],
z0, 0, traj);
/* invert on the stochastic source */
invert_eo(g_spinor_field[2], g_spinor_field[3],
g_spinor_field[0], g_spinor_field[1],
1.e-14, measurement_list[id].max_iter, CG, 1, 0, 1, 0, NULL, -1);
/* now we bring it to normal format */
/* here we use implicitly DUM_MATRIX and DUM_MATRIX+1 */
convert_eo_to_lexic(g_spinor_field[DUM_MATRIX], g_spinor_field[2], g_spinor_field[3]);
/* now we sums only over local space for every z */
for(z = 0; z < LZ; z++) {
res = 0.;
/* sum here over all points in one z-slice
we have to look up g_ipt*/
j = g_ipt[0][0][0][z];
for(i = 0; i < T*LX*LY ; i++) {
res += _spinor_prod_re(g_spinor_field[DUM_MATRIX][j], g_spinor_field[DUM_MATRIX][j]);
j += LZ; /* jump LZ sites in array, z ist fastest index */
}
#if defined MPI
MPI_Reduce(&res, &mpi_res, 1, MPI_DOUBLE, MPI_SUM, 0, g_mpi_z_slices);
res = mpi_res;
#endif
Cpp[z+g_proc_coords[3]*LZ] = +res/(g_nproc_x*LX)/(g_nproc_y*LY)/(g_nproc_t*T)*2.;
}
#ifdef MPI
/* some gymnastics needed in case of parallelisation */
if(g_mpi_z_rank == 0) {
MPI_Gather(&Cpp[g_proc_coords[3]*LZ], LZ, MPI_DOUBLE, Cpp, LZ, MPI_DOUBLE, 0, g_mpi_ST_slices);
}
#endif
/* and write everything into a file */
if(g_mpi_z_rank == 0 && g_proc_coords[3] == 0) {
ofs = fopen(filename, "w");
fprintf( ofs, "1 1 0 %e %e\n", Cpp[z0], 0.);
for(z = 1; z < g_nproc_z*LZ/2; z++) {
zz = (z0+z)%(g_nproc_z*LZ);
fprintf( ofs, "1 1 %d %e ", z, Cpp[zz]);
zz = (z0+g_nproc_z*LZ-z)%(g_nproc_z*LZ);
fprintf( ofs, "%e\n", Cpp[zz]);
}
zz = (z0+g_nproc_z*LZ/2)%(g_nproc_z*LZ);
fprintf( ofs, "1 1 %d %e %e\n", z, Cpp[zz], 0.);
fclose(ofs);
/* sum over all Cpp to get pionnorm*/
ofs2 = fopen(filename2, "a");
pionnorm = 0.;
for(z=0; z<g_nproc_z*LZ; z++){
pionnorm += Cpp[z];
}
/* normalize */
pionnorm = pionnorm/(g_nproc_z*LZ);
fprintf(ofs2,"%d\t %.16e\n",traj,pionnorm);
fclose(ofs2);
}
free(Cpp);
#ifdef MPI
etime = MPI_Wtime();
#else
etime = (double)clock()/(double)(CLOCKS_PER_SEC);
#endif
if(g_proc_id == 0 && g_debug_level > 0) {
printf("PIONNORM : measurement done int t/s = %1.4e\n", etime - atime);
}
return;
}
void compute_error_p3dfft(double * A,int* n)
{
double pi=4*atan(1.0);
long long int size=n[0];
size*=n[1]; size*=n[2];
int istart[3],iend[3],isize[3];
int xx=0.,yy=0.,zz=0.;
//double an,aa;
Cp3dfft_get_dims(istart,iend,isize,1);
int num_th= omp_get_max_threads();
double diff_th[num_th],norm_th[num_th];
for (int i=0;i<num_th;i++){
diff_th[i]=0.;norm_th[i]=0.;
}
int procid;
MPI_Comm_rank(MPI_COMM_WORLD,&procid);
//First Determine the constant difference between analytic and numerical solutions
#pragma omp parallel
{
long int ptr;
double X,Y,Z;
double analytic_solution,diff=0.0;
int thid=omp_get_thread_num();
// double aa=0.,an=0.;
#pragma omp for
for (int k=0; k<isize[2]; k++){
for (int j=0; j<isize[1]; j++){
for (int i=0; i<isize[0]; i++){
X=2*pi/n[0]*(istart[0]-1+i);
Y=2*pi/n[1]*(istart[1]-1+j);
Z=2*pi/n[2]*(istart[2]-1+k);
ptr=i+isize[0]*j+isize[0]*isize[1]*k;
analytic_solution=testcase(X,Y,Z);
diff=std::abs(A[ptr]/size-analytic_solution);
diff_th[thid]+=diff;
norm_th[thid]+=analytic_solution;
//std::cout<<"x,y,z= "<<X<<Y<<Z<<" diff= "<<diff<<" analytic= "<<analytic_solution<<" numerical= "<<A[ptr]/size<<std::endl;
}
}
}
}
double DIFF=0.,NORM=0.;
for (int i=0; i<num_th;i++){
DIFF+=diff_th[i];
NORM+=norm_th[i];
}
double gerr=0,gnorm=0;
MPI_Reduce(&DIFF,&gerr,1, MPI_DOUBLE, MPI_SUM,0, MPI_COMM_WORLD);
MPI_Reduce(&NORM,&gnorm,1, MPI_DOUBLE, MPI_SUM,0, MPI_COMM_WORLD);
PCOUT<<"The L1 error between iFF(a)-a is == "<<gerr<<std::endl;
PCOUT<<"The Rel. L1 error between iFF(a)-a is == "<<gerr/gnorm<<std::endl;
if(gerr/gnorm>1e-10){
PCOUT<<"\033[1;31m ERROR!!! FFT not computed correctly!\033[0m"<<std::endl;
}
else{
PCOUT<<"\033[1;36m FFT computed correctly!\033[0m"<<std::endl;
}
}
void reb_output_timing(struct reb_simulation* r, const double tmax){
const int N = r->N;
#ifdef MPI
int N_tot = 0;
MPI_Reduce(&N, &N_tot, 1, MPI_INT, MPI_SUM, 0, MPI_COMM_WORLD);
if (r->mpi_id!=0) return;
#else
int N_tot = N;
#endif
struct timeval tim;
gettimeofday(&tim, NULL);
double temp = tim.tv_sec+(tim.tv_usec/1000000.0);
if (r->output_timing_last==-1){
r->output_timing_last = temp;
}else{
printf("\r");
#ifdef PROFILING
fputs("\033[A\033[2K",stdout);
for (int i=0;i<=PROFILING_CAT_NUM;i++){
fputs("\033[A\033[2K",stdout);
}
#endif // PROFILING
}
printf("N_tot= %- 9d ",N_tot);
if (r->integrator==REB_INTEGRATOR_SEI){
printf("t= %- 9f [orb] ",r->t*r->ri_sei.OMEGA/2./M_PI);
}else{
printf("t= %- 9f ",r->t);
}
printf("dt= %- 9f ",r->dt);
if (r->integrator==REB_INTEGRATOR_HYBRID){
printf("INT= %- 1d ",r->ri_hybrid.mode);
}
printf("cpu= %- 9f [s] ",temp-r->output_timing_last);
if (tmax>0){
printf("t/tmax= %5.2f%%",r->t/tmax*100.0);
}
#ifdef PROFILING
if (profiling_timing_initial==0){
struct timeval tim;
gettimeofday(&tim, NULL);
profiling_timing_initial = tim.tv_sec+(tim.tv_usec/1000000.0);
}
printf("\nCATEGORY TIME \n");
double _sum = 0;
for (int i=0;i<=PROFILING_CAT_NUM;i++){
switch (i){
case PROFILING_CAT_INTEGRATOR:
printf("Integrator ");
break;
case PROFILING_CAT_BOUNDARY:
printf("Boundary check ");
break;
case PROFILING_CAT_GRAVITY:
printf("Gravity/Forces ");
break;
case PROFILING_CAT_COLLISION:
printf("Collisions ");
break;
#ifdef OPENGL
case PROFILING_CAT_VISUALIZATION:
printf("Visualization ");
break;
#endif // OPENGL
case PROFILING_CAT_NUM:
printf("Other ");
break;
}
if (i==PROFILING_CAT_NUM){
printf("%5.2f%%",(1.-_sum/(profiling_time_final - profiling_timing_initial))*100.);
}else{
printf("%5.2f%%\n",profiling_time_sum[i]/(profiling_time_final - profiling_timing_initial)*100.);
_sum += profiling_time_sum[i];
}
}
#endif // PROFILING
fflush(stdout);
r->output_timing_last = temp;
}
int main (int argc, char * argv[]) {
int rank,size;
MPI_Init(&argc,&argv);
MPI_Comm_size(MPI_COMM_WORLD,&size);
MPI_Comm_rank(MPI_COMM_WORLD,&rank);
int X,Y,x,y,X_ext,i;
double **A, **localA;
X=atoi(argv[1]);
Y=X;
//Extend dimension X with ghost cells if X%size!=0
if (X%size!=0)
X_ext=X+size-X%size;
else
X_ext=X;
if (rank==0) {
//Allocate and init matrix A
A=malloc2D(X_ext,Y);
init2D(A,X,Y);
}
//Local dimensions x,y
x=X_ext/size;
y=Y;
//Allocate local matrix and scatter global matrix
localA=malloc2D(x,y);
double * idx;
for (i=0;i<x;i++) {
if (rank==0)
idx=&A[i*size][0];
MPI_Scatter(idx,Y,MPI_DOUBLE,&localA[i][0],y,MPI_DOUBLE,0,MPI_COMM_WORLD);
}
if (rank==0)
free2D(A,X_ext,Y);
//Timers
struct timeval ts,tf,comps,compf,comms,commf;
double total_time,computation_time,communication_time;
MPI_Barrier(MPI_COMM_WORLD);
gettimeofday(&ts,NULL);
/******************************************************************************
The matrix A is distributed in a round-robin fashion to the local matrices localA
You have to use point-to-point communication routines.
Don't forget the timers for computation and communication!
******************************************************************************/
int line_index, line_owner;
int k, start;
double *k_row, *temp;
MPI_Status status;
temp = malloc(y * sizeof(*temp));
// k_row = malloc(y * sizeof(*k_row));
/* omoia me to allo cyclic, vriskoume ton line_owner */
for (k=0; k<y-1; k++){
line_owner = k % size;
line_index = k / size;
if (rank <= line_owner)
start = k / size + 1;
else
start = k / size;
if (rank == line_owner)
k_row = localA[line_index];
else
k_row = temp;
/* set communication timer */
gettimeofday(&comms, NULL);
/* COMM */
// if (rank != line_owner){
// if (rank == 0)
// MPI_Recv( k_row, y, MPI_DOUBLE, size-1, MPI_ANY_SOURCE, MPI_COMM_WORLD, &status);
// else
// MPI_Recv( k_row, y, MPI_DOUBLE, rank-1, MPI_ANY_SOURCE, MPI_COMM_WORLD, &status);
// }
//
// /* autos pou einai prin ton line_owner den prepei na steilei */
// if (rank != line_owner -1){
// /* o teleutaios prepei na steilei ston prwto, ektos an o prwtos einai o line_owner */
// if (rank == size-1) {
// if (line_owner != 0)
// MPI_Send( k_row, y, MPI_DOUBLE, 0, rank, MPI_COMM_WORLD);
// }
// else
// MPI_Send(k_row, y, MPI_DOUBLE, rank+1, rank, MPI_COMM_WORLD);
// }
/* o line_owner stelnei se olous (ektos tou eautou tou) kai oloi oi alloi kanoun
* receive */
if (rank == line_owner){
for (i=0; i<size; i++)
if (i != line_owner)
MPI_Send( k_row, y, MPI_DOUBLE, i, line_owner, MPI_COMM_WORLD);
}
else
MPI_Recv(k_row, y, MPI_DOUBLE, line_owner, line_owner, MPI_COMM_WORLD, &status);
/* stop communication timer */
gettimeofday(&commf, NULL);
communication_time += commf.tv_sec - comms.tv_sec + (commf.tv_usec - comms.tv_usec)*0.000001;
/* set computation timer */
gettimeofday(&comps, NULL);
/* Compute */
go_to_work( localA, k_row, x, y, rank, start, k );
/* stop computation timer */
gettimeofday(&compf, NULL);
computation_time += compf.tv_sec - comps.tv_sec + (compf.tv_usec - comps.tv_usec)*0.000001;
}
gettimeofday(&tf,NULL);
total_time=tf.tv_sec-ts.tv_sec+(tf.tv_usec-ts.tv_usec)*0.000001;
//Gather local matrices back to the global matrix
if (rank==0)
A=malloc2D(X_ext,Y);
for (i=0;i<x;i++) {
if (rank==0)
idx=&A[i*size][0];
MPI_Gather(&localA[i][0],y,MPI_DOUBLE,idx,Y,MPI_DOUBLE,0,MPI_COMM_WORLD);
}
double avg_total,avg_comp,avg_comm,max_total,max_comp,max_comm;
MPI_Reduce(&total_time,&max_total,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD);
MPI_Reduce(&computation_time,&max_comp,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD);
MPI_Reduce(&communication_time,&max_comm,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD);
MPI_Reduce(&total_time,&avg_total,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD);
MPI_Reduce(&computation_time,&avg_comp,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD);
MPI_Reduce(&communication_time,&avg_comm,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD);
avg_total/=size;
avg_comp/=size;
avg_comm/=size;
if (rank==0) {
printf("LU-Cyclic-p2p\tSize\t%d\tProcesses\t%d\n",X,size);
printf("Max times:\tTotal\t%lf\tComp\t%lf\tComm\t%lf\n",max_total,max_comp,max_comm);
printf("Avg times:\tTotal\t%lf\tComp\t%lf\tComm\t%lf\n",avg_total,avg_comp,avg_comm);
}
//Print triangular matrix U to file
if (rank==0) {
char * filename="output_cyclic_p2p";
print2DFile(A,X,Y,filename);
}
MPI_Finalize();
return 0;
}
int main( int argc, char *argv[])
{
int n, myid, numprocs, i, j;
double PI25DT = 3.141592653589793238462643;
double mypi, pi, h, sum, x;
double startwtime = 0.0, endwtime;
int namelen;
int event1a, event1b, event2a, event2b,
event3a, event3b, event4a, event4b;
char processor_name[MPI_MAX_PROCESSOR_NAME];
MPI_Init(&argc,&argv);
MPI_Pcontrol( 0 );
MPI_Comm_size(MPI_COMM_WORLD,&numprocs);
MPI_Comm_rank(MPI_COMM_WORLD,&myid);
MPI_Get_processor_name(processor_name,&namelen);
fprintf(stderr,"Process %d running on %s\n", myid, processor_name);
/*
MPE_Init_log() & MPE_Finish_log() are NOT needed when
liblmpe.a is linked with this program. In that case,
MPI_Init() would have called MPE_Init_log() already.
*/
/*
MPE_Init_log();
*/
/* Get event ID from MPE, user should NOT assign event ID */
event1a = MPE_Log_get_event_number();
event1b = MPE_Log_get_event_number();
event2a = MPE_Log_get_event_number();
event2b = MPE_Log_get_event_number();
event3a = MPE_Log_get_event_number();
event3b = MPE_Log_get_event_number();
event4a = MPE_Log_get_event_number();
event4b = MPE_Log_get_event_number();
if (myid == 0) {
MPE_Describe_state(event1a, event1b, "Broadcast", "red");
MPE_Describe_state(event2a, event2b, "Compute", "blue");
MPE_Describe_state(event3a, event3b, "Reduce", "green");
MPE_Describe_state(event4a, event4b, "Sync", "orange");
}
if (myid == 0) {
n = 1000000;
startwtime = MPI_Wtime();
}
MPI_Barrier(MPI_COMM_WORLD);
MPI_Pcontrol( 1 );
/*
MPE_Start_log();
*/
for (j = 0; j < 5; j++) {
MPE_Log_event(event1a, 0, NULL);
MPI_Bcast(&n, 1, MPI_INT, 0, MPI_COMM_WORLD);
MPE_Log_event(event1b, 0, NULL);
MPE_Log_event(event4a, 0, NULL);
MPI_Barrier(MPI_COMM_WORLD);
MPE_Log_event(event4b, 0, NULL);
MPE_Log_event(event2a, 0, NULL);
h = 1.0 / (double) n;
sum = 0.0;
for (i = myid + 1; i <= n; i += numprocs) {
x = h * ((double)i - 0.5);
sum += f(x);
}
mypi = h * sum;
MPE_Log_event(event2b, 0, NULL);
MPE_Log_event(event3a, 0, NULL);
MPI_Reduce(&mypi, &pi, 1, MPI_DOUBLE, MPI_SUM, 0, MPI_COMM_WORLD);
MPE_Log_event(event3b, 0, NULL);
}
/*
MPE_Finish_log("cpilog");
*/
if (myid == 0) {
endwtime = MPI_Wtime();
printf("pi is approximately %.16f, Error is %.16f\n",
pi, fabs(pi - PI25DT));
printf("wall clock time = %f\n", endwtime-startwtime);
}
MPI_Finalize();
return(0);
}
int main(int argc, char ** argv) {
int Num_procs; // number of ranks
int Num_procsx,
Num_procsy; // number of ranks in each coord direction
int args_used = 1; // keeps track of # consumed arguments
int my_ID; // MPI rank
int my_IDx, my_IDy; // coordinates of rank in rank grid
int root = 0; // master rank
uint64_t L; // dimension of grid in cells
uint64_t iterations ; // total number of simulation steps
uint64_t n; // total number of particles requested in the simulation
uint64_t actual_particles, // actual number of particles owned by my rank
total_particles; // total number of generated particles
char *init_mode; // particle initialization mode (char)
double rho ; // attenuation factor for geometric particle distribution
uint64_t k, m; // determine initial horizontal and vertical velocity of
// particles-- (2*k)+1 cells per time step
double *grid; // the grid is represented as an array of charges
uint64_t iter, i; // dummies
double fx, fy, ax, ay; // particle forces and accelerations
int error=0; // used for graceful exit after error
uint64_t correctness=0; // boolean indicating correct particle displacements
uint64_t istart, jstart, iend, jend, particles_size, particles_count;
bbox_t grid_patch, // whole grid
init_patch, // subset of grid used for localized initialization
my_tile; // subset of grid owner by my rank
particle_t *particles, *p; // array of particles owned by my rank
uint64_t *cur_counts; //
uint64_t ptr_my; //
uint64_t owner; // owner (rank) of a particular particle
double pic_time, local_pic_time, avg_time;
uint64_t my_checksum = 0, tot_checksum = 0, correctness_checksum = 0;
uint64_t width, height; // minimum dimensions of grid tile owned by my rank
int particle_mode; // type of initialization
double alpha, beta; // negative slope and offset for linear initialization
int nbr[8]; // topological neighbor ranks
int icrit, jcrit; // global grid indices where tile size drops to minimum
find_owner_type find_owner;
int ileftover, jleftover;// excess grid points divided among "fat" tiles
uint64_t to_send[8], to_recv[8];//
int procsize; // number of ranks per OS process
MPI_Status status[16];
MPI_Request requests[16];
/* Initialize the MPI environment */
MPI_Init(&argc,&argv);
MPI_Comm_rank(MPI_COMM_WORLD, &my_ID);
MPI_Comm_size(MPI_COMM_WORLD, &Num_procs);
/* FIXME: This can be further improved */
/* Create MPI data type for particle_t */
MPI_Datatype PARTICLE;
MPI_Type_contiguous(sizeof(particle_t)/sizeof(double), MPI_DOUBLE, &PARTICLE);
MPI_Type_commit( &PARTICLE );
if (my_ID==root) {
printf("Parallel Research Kernels version %s\n", PRKVERSION);
printf("FG_MPI Particle-in-Cell execution on 2D grid\n");
if (argc<6) {
printf("Usage: %s <#simulation steps> <grid size> <#particles> <k (particle charge semi-increment)> ", argv[0]);
printf("<m (vertical particle velocity)>\n");
printf(" <init mode> <init parameters>]\n");
printf(" init mode \"GEOMETRIC\" parameters: <attenuation factor>\n");
printf(" \"SINUSOIDAL\" parameters: none\n");
printf(" \"LINEAR\" parameters: <negative slope> <constant offset>\n");
printf(" \"PATCH\" parameters: <xleft> <xright> <ybottom> <ytop>\n");
error = 1;
goto ENDOFTESTS;
}
iterations = atol(*++argv); args_used++;
if (iterations<1) {
printf("ERROR: Number of time steps must be positive: %llu\n", iterations);
error = 1;
goto ENDOFTESTS;
}
L = atol(*++argv); args_used++;
if (L<1 || L%2) {
printf("ERROR: Number of grid cells must be positive and even: %llu\n", L);
error = 1;
goto ENDOFTESTS;
}
n = atol(*++argv); args_used++;
if (n<1) {
printf("ERROR: Number of particles must be positive: %llu\n", n);
error = 1;
goto ENDOFTESTS;
}
particle_mode = UNDEFINED;
k = atoi(*++argv); args_used++;
if (k<0) {
printf("ERROR: Particle semi-charge must be non-negative: %llu\n", k);
error = 1;
goto ENDOFTESTS;
}
m = atoi(*++argv); args_used++;
init_mode = *++argv; args_used++;
ENDOFTESTS:;
} // done with standard initialization parameters
bail_out(error);
MPI_Bcast(&iterations, 1, MPI_UINT64_T, root, MPI_COMM_WORLD);
MPI_Bcast(&L, 1, MPI_UINT64_T, root, MPI_COMM_WORLD);
MPI_Bcast(&n, 1, MPI_UINT64_T, root, MPI_COMM_WORLD);
MPI_Bcast(&k, 1, MPI_UINT64_T, root, MPI_COMM_WORLD);
MPI_Bcast(&m, 1, MPI_UINT64_T, root, MPI_COMM_WORLD);
grid_patch = (bbox_t){0, L+1, 0, L+1};
if (my_ID==root) { // process initialization parameters
/* Initialize particles with geometric distribution */
if (strcmp(init_mode, "GEOMETRIC") == 0) {
if (argc<args_used+1) {
printf("ERROR: Not enough arguments for GEOMETRIC\n");
error = 1;
goto ENDOFTESTS2;
}
particle_mode = GEOMETRIC;
rho = atof(*++argv); args_used++;
}
/* Initialize with a sinusoidal particle distribution (single period) */
if (strcmp(init_mode, "SINUSOIDAL") == 0) {
particle_mode = SINUSOIDAL;
}
/* Initialize particles with linear distribution */
/* The linear function is f(x) = -alpha * x + beta , x in [0,1]*/
if (strcmp(init_mode, "LINEAR") == 0) {
if (argc<args_used+2) {
printf("ERROR: Not enough arguments for LINEAR initialization\n");
error = 1;
goto ENDOFTESTS2;
exit(EXIT_FAILURE);
}
particle_mode = LINEAR;
alpha = atof(*++argv); args_used++;
beta = atof(*++argv); args_used++;
if (beta <0 || beta<alpha) {
printf("ERROR: linear profile gives negative particle density\n");
error = 1;
goto ENDOFTESTS2;
}
}
/* Initialize particles uniformly within a "patch" */
if (strcmp(init_mode, "PATCH") == 0) {
if (argc<args_used+4) {
printf("ERROR: Not enough arguments for PATCH initialization\n");
error = 1;
goto ENDOFTESTS2;
}
particle_mode = PATCH;
init_patch.left = atoi(*++argv); args_used++;
init_patch.right = atoi(*++argv); args_used++;
init_patch.bottom = atoi(*++argv); args_used++;
init_patch.top = atoi(*++argv); args_used++;
if (bad_patch(&init_patch, &grid_patch)) {
printf("ERROR: inconsistent initial patch\n");
error = 1;
goto ENDOFTESTS2;
}
}
ENDOFTESTS2:;
} //done with processing initializaton parameters, now broadcast
bail_out(error);
MPI_Bcast(&particle_mode, 1, MPI_INT, root, MPI_COMM_WORLD);
switch (particle_mode) {
case GEOMETRIC: MPI_Bcast(&rho, 1, MPI_DOUBLE, root, MPI_COMM_WORLD);
break;
case SINUSOIDAL: break;
case LINEAR: MPI_Bcast(&alpha, 1, MPI_DOUBLE, root, MPI_COMM_WORLD);
MPI_Bcast(&beta, 1, MPI_DOUBLE, root, MPI_COMM_WORLD);
break;
case PATCH: MPI_Bcast(&init_patch.left, 1, MPI_INT64_T, root, MPI_COMM_WORLD);
MPI_Bcast(&init_patch.right, 1, MPI_INT64_T, root, MPI_COMM_WORLD);
MPI_Bcast(&init_patch.bottom, 1, MPI_INT64_T, root, MPI_COMM_WORLD);
MPI_Bcast(&init_patch.top, 1, MPI_INT64_T, root, MPI_COMM_WORLD);
break;
}
/* determine best way to create a 2D grid of ranks (closest to square, for
best surface/volume ratio); we do this brute force for now */
for (Num_procsx=(int) (sqrt(Num_procs+1)); Num_procsx>0; Num_procsx--) {
if (!(Num_procs%Num_procsx)) {
Num_procsy = Num_procs/Num_procsx;
break;
}
}
my_IDx = my_ID%Num_procsx;
my_IDy = my_ID/Num_procsx;
if (my_ID == root) {
MPIX_Get_collocated_size(&procsize);
printf("Number of ranks = %llu\n", Num_procs);
printf("Number of ranks/process = %d\n", procsize);
printf("Load balancing = None\n");
printf("Grid size = %llu\n", L);
printf("Tiles in x/y-direction = %d/%d\n", Num_procsx, Num_procsy);
printf("Number of particles requested = %llu\n", n);
printf("Number of time steps = %llu\n", iterations);
printf("Initialization mode = %s\n", init_mode);
switch(particle_mode) {
case GEOMETRIC: printf(" Attenuation factor = %lf\n", rho); break;
case SINUSOIDAL: break;
case LINEAR: printf(" Negative slope = %lf\n", alpha);
printf(" Offset = %lf\n", beta); break;
case PATCH: printf(" Bounding box = %llu, %llu, %llu, %llu\n",
init_patch.left, init_patch.right,
init_patch.bottom, init_patch.top); break;
default: printf("ERROR: Unsupported particle initializating mode\n");
error = 1;
}
printf("Particle charge semi-increment (k) = %llu\n", k);
printf("Vertical velocity (m) = %llu\n", m);
}
bail_out(error);
/* The processes collectively create the underlying grid following a 2D block decomposition;
unlike in the stencil code, successive blocks share an overlap vertex */
width = L/Num_procsx;
if (width < 2*k) {
if (my_ID==0) printf("k-value too large: %llu, must be no greater than %llu\n", k, width/2);
bail_out(1);
}
ileftover = L%Num_procsx;
if (my_IDx<ileftover) {
istart = (width+1) * my_IDx;
iend = istart + width + 1;
}
else {
istart = (width+1) * ileftover + width * (my_IDx-ileftover);
iend = istart + width;
}
icrit = (width+1) * ileftover;
height = L/Num_procsy;
if (height < m) {
if (my_ID==0) printf("m-value too large: %llu, must be no greater than %llu\n", m, height);
bail_out(1);
}
jleftover = L%Num_procsy;
if (my_IDy<jleftover) {
jstart = (height+1) * my_IDy;
jend = jstart + height + 1;
}
else {
jstart = (height+1) * jleftover + height * (my_IDy-jleftover);
jend = jstart + height;
}
jcrit = (height+1) * jleftover;
/* if the problem can be divided evenly among ranks, use the simple owner finding function */
if (icrit==0 && jcrit==0) {
find_owner = find_owner_simple;
if (my_ID==root) printf("Rank search mode used = simple\n");
}
else {
find_owner = find_owner_general;
if (my_ID==root) printf("Rank search mode used = general\n");
}
/* define bounding box for tile owned by my rank for convenience */
my_tile = (bbox_t){istart,iend,jstart,jend};
/* Find neighbors. Indexing: left=0, right=1, bottom=2, top=3,
bottom-left=4, bottom-right=5, top-left=6, top-right=7 */
/* These are IDs in the global communicator */
nbr[0] = (my_IDx == 0 ) ? my_ID + Num_procsx - 1 : my_ID - 1;
nbr[1] = (my_IDx == Num_procsx-1) ? my_ID - Num_procsx + 1 : my_ID + 1;
nbr[2] = (my_IDy == Num_procsy-1) ? my_ID + Num_procsx - Num_procs : my_ID + Num_procsx;
nbr[3] = (my_IDy == 0 ) ? my_ID - Num_procsx + Num_procs : my_ID - Num_procsx;
nbr[4] = (my_IDy == Num_procsy-1) ? nbr[0] + Num_procsx - Num_procs : nbr[0] + Num_procsx;
nbr[5] = (my_IDy == Num_procsy-1) ? nbr[1] + Num_procsx - Num_procs : nbr[1] + Num_procsx;
nbr[6] = (my_IDy == 0 ) ? nbr[0] - Num_procsx + Num_procs : nbr[0] - Num_procsx;
nbr[7] = (my_IDy == 0 ) ? nbr[1] - Num_procsx + Num_procs : nbr[1] - Num_procsx;
grid = initializeGrid(my_tile);
switch(particle_mode){
case GEOMETRIC:
particles = initializeGeometric(n, L, rho, my_tile, k, m,
&particles_count, &particles_size);
break;
case LINEAR:
particles = initializeLinear(n, L, alpha, beta, my_tile, k, m,
&particles_count, &particles_size);
break;
case SINUSOIDAL:
particles = initializeSinusoidal(n, L, my_tile, k, m,
&particles_count, &particles_size);
break;
case PATCH:
particles = initializePatch(n, L, init_patch, my_tile, k, m,
&particles_count, &particles_size);
}
if (!particles) {
printf("ERROR: Rank %d could not allocate space for %llu particles\n", my_ID, particles_size);
error=1;
}
bail_out(error);
#if VERBOSE
for (i=0; i<Num_procs; i++) {
MPI_Barrier(MPI_COMM_WORLD);
if (i == my_ID) printf("Rank %d has %llu particles\n", my_ID, particles_count);
}
#endif
if (my_ID==root) {
MPI_Reduce(&particles_count, &total_particles, 1, MPI_UINT64_T, MPI_SUM, root, MPI_COMM_WORLD);
printf("Number of particles placed = %llu\n", total_particles);
}
else {
MPI_Reduce(&particles_count, &total_particles, 1, MPI_UINT64_T, MPI_SUM, root, MPI_COMM_WORLD);
}
/* Allocate space for communication buffers. Adjust appropriately as the simulation proceeds */
uint64_t sendbuf_size[8], recvbuf_size[8];
particle_t *sendbuf[8], *recvbuf[8];
error=0;
for (i=0; i<8; i++) {
sendbuf_size[i] = MAX(1,n/(MEMORYSLACK*Num_procs));
recvbuf_size[i] = MAX(1,n/(MEMORYSLACK*Num_procs));
sendbuf[i] = (particle_t*) prk_malloc(sendbuf_size[i] * sizeof(particle_t));
recvbuf[i] = (particle_t*) prk_malloc(recvbuf_size[i] * sizeof(particle_t));
if (!sendbuf[i] || !recvbuf[i]) error++;
}
if (error) printf("Rank %d could not allocate communication buffers\n", my_ID);
bail_out(error);
/* Run the simulation */
for (iter=0; iter<=iterations; iter++) {
/* start timer after a warmup iteration */
if (iter == 1) {
MPI_Barrier(MPI_COMM_WORLD);
local_pic_time = wtime();
}
ptr_my = 0;
for (i=0; i<8; i++) to_send[i]=0;
/* Process own particles */
p = particles;
for (i=0; i < particles_count; i++) {
fx = 0.0;
fy = 0.0;
computeTotalForce(p[i], my_tile, grid, &fx, &fy);
ax = fx * MASS_INV;
ay = fy * MASS_INV;
/* Update particle positions, taking into account periodic boundaries */
p[i].x = fmod(p[i].x + p[i].v_x*DT + 0.5*ax*DT*DT + L, L);
p[i].y = fmod(p[i].y + p[i].v_y*DT + 0.5*ay*DT*DT + L, L);
/* Update velocities */
p[i].v_x += ax * DT;
p[i].v_y += ay * DT;
/* Check if particle stayed in same subdomain or moved to another */
owner = find_owner(p[i], width, height, Num_procsx, icrit, jcrit, ileftover, jleftover);
if (owner==my_ID) {
add_particle_to_buffer(p[i], &p, &ptr_my, &particles_size);
/* Add particle to the appropriate communication buffer */
} else if (owner == nbr[0]) {
add_particle_to_buffer(p[i], &sendbuf[0], &to_send[0], &sendbuf_size[0]);
} else if (owner == nbr[1]) {
add_particle_to_buffer(p[i], &sendbuf[1], &to_send[1], &sendbuf_size[1]);
} else if (owner == nbr[2]) {
add_particle_to_buffer(p[i], &sendbuf[2], &to_send[2], &sendbuf_size[2]);
} else if (owner == nbr[3]) {
add_particle_to_buffer(p[i], &sendbuf[3], &to_send[3], &sendbuf_size[3]);
} else if (owner == nbr[4]) {
add_particle_to_buffer(p[i], &sendbuf[4], &to_send[4], &sendbuf_size[4]);
} else if (owner == nbr[5]) {
add_particle_to_buffer(p[i], &sendbuf[5], &to_send[5], &sendbuf_size[5]);
} else if (owner == nbr[6]) {
add_particle_to_buffer(p[i], &sendbuf[6], &to_send[6], &sendbuf_size[6]);
} else if (owner == nbr[7]) {
add_particle_to_buffer(p[i], &sendbuf[7], &to_send[7], &sendbuf_size[7]);
} else {
printf("Could not find neighbor owner of particle %llu in tile %llu\n",
i, owner);
MPI_Abort(MPI_COMM_WORLD, EXIT_FAILURE);
}
}
/* Communicate the number of particles to be sent/received */
for (i=0; i<8; i++) {
MPI_Isend(&to_send[i], 1, MPI_UINT64_T, nbr[i], 0, MPI_COMM_WORLD, &requests[i]);
MPI_Irecv(&to_recv[i], 1, MPI_UINT64_T, nbr[i], 0, MPI_COMM_WORLD, &requests[8+i]);
}
MPI_Waitall(16, requests, status);
/* Resize receive buffers if need be */
for (i=0; i<8; i++) {
resize_buffer(&recvbuf[i], &recvbuf_size[i], to_recv[i]);
}
/* Communicate the particles */
for (i=0; i<8; i++) {
MPI_Isend(sendbuf[i], to_send[i], PARTICLE, nbr[i], 0, MPI_COMM_WORLD, &requests[i]);
MPI_Irecv(recvbuf[i], to_recv[i], PARTICLE, nbr[i], 0, MPI_COMM_WORLD, &requests[8+i]);
}
MPI_Waitall(16, requests, status);
/* Attach received particles to particles buffer */
for (i=0; i<4; i++) {
attach_received_particles(&particles, &ptr_my, &particles_size, recvbuf[2*i], to_recv[2*i],
recvbuf[2*i+1], to_recv[2*i+1]);
}
particles_count = ptr_my;
}
local_pic_time = MPI_Wtime() - local_pic_time;
MPI_Reduce(&local_pic_time, &pic_time, 1, MPI_DOUBLE, MPI_MAX, root,
MPI_COMM_WORLD);
/* Run the verification test */
/* First verify own particles */
for (i=0; i < particles_count; i++) {
correctness += verifyParticle(particles[i], (double)L, iterations);
my_checksum += (uint64_t)particles[i].ID;
}
/* Gather total checksum of particles */
MPI_Reduce(&my_checksum, &tot_checksum, 1, MPI_UINT64_T, MPI_SUM, root, MPI_COMM_WORLD);
/* Gather total checksum of correctness flags */
MPI_Reduce(&correctness, &correctness_checksum, 1, MPI_UINT64_T, MPI_SUM, root, MPI_COMM_WORLD);
if ( my_ID == root) {
if (correctness_checksum != total_particles ) {
printf("ERROR: there are %llu miscalculated locations\n", total_particles-correctness_checksum);
}
else {
if (tot_checksum != (total_particles*(total_particles+1))/2) {
printf("ERROR: Particle checksum incorrect\n");
}
else {
avg_time = total_particles*iterations/pic_time;
printf("Solution validates\n");
printf("Rate (Mparticles_moved/s): %lf\n", 1.0e-6*avg_time);
}
}
}
#if VERBOSE
for (i=0; i<Num_procs; i++) {
MPI_Barrier(MPI_COMM_WORLD);
if (i == my_ID) printf("Rank %d has %llu particles\n", my_ID, particles_count);
}
#endif
MPI_Finalize();
return 0;
}
/*
* This test looks at the handling of char and types that are not required
* integers (e.g., long long). MPICH allows
* these as well. A strict MPI test should not include this test.
*
* The rule on max loc is that if there is a tie in the value, the minimum
* rank is used (see 4.9.3 in the MPI-1 standard)
*/
int main( int argc, char *argv[] )
{
int errs = 0;
int rank, size;
MPI_Comm comm;
MTest_Init( &argc, &argv );
comm = MPI_COMM_WORLD;
MPI_Comm_rank( comm, &rank );
MPI_Comm_size( comm, &size );
/* 2 int */
{
struct twoint { int val; int loc; } cinbuf[3], coutbuf[3];
cinbuf[0].val = 1;
cinbuf[0].loc = rank;
cinbuf[1].val = 0;
cinbuf[1].loc = rank;
cinbuf[2].val = rank;
cinbuf[2].loc = rank;
coutbuf[0].val = 0;
coutbuf[0].loc = -1;
coutbuf[1].val = 1;
coutbuf[1].loc = -1;
coutbuf[2].val = 1;
coutbuf[2].loc = -1;
MPI_Reduce( cinbuf, coutbuf, 3, MPI_2INT, MPI_MAXLOC, 0, comm );
if (rank == 0) {
if (coutbuf[0].val != 1 || coutbuf[0].loc != 0) {
errs++;
fprintf( stderr, "2int MAXLOC(1) test failed\n" );
}
if (coutbuf[1].val != 0) {
errs++;
fprintf( stderr, "2int MAXLOC(0) test failed, value = %d, should be zero\n", coutbuf[1].val );
}
if (coutbuf[1].loc != 0) {
errs++;
fprintf( stderr, "2int MAXLOC(0) test failed, location of max = %d, should be zero\n", coutbuf[1].loc );
}
if (coutbuf[2].val != size-1 || coutbuf[2].loc != size-1) {
errs++;
fprintf( stderr, "2int MAXLOC(>) test failed\n" );
}
}
}
/* float int */
{
struct floatint { float val; int loc; } cinbuf[3], coutbuf[3];
cinbuf[0].val = 1;
cinbuf[0].loc = rank;
cinbuf[1].val = 0;
cinbuf[1].loc = rank;
cinbuf[2].val = (float)rank;
cinbuf[2].loc = rank;
coutbuf[0].val = 0;
coutbuf[0].loc = -1;
coutbuf[1].val = 1;
coutbuf[1].loc = -1;
coutbuf[2].val = 1;
coutbuf[2].loc = -1;
MPI_Reduce( cinbuf, coutbuf, 3, MPI_FLOAT_INT, MPI_MAXLOC, 0, comm );
if (rank == 0) {
if (coutbuf[0].val != 1 || coutbuf[0].loc != 0) {
errs++;
fprintf( stderr, "float-int MAXLOC(1) test failed\n" );
}
if (coutbuf[1].val != 0) {
errs++;
fprintf( stderr, "float-int MAXLOC(0) test failed, value = %f, should be zero\n", coutbuf[1].val );
}
if (coutbuf[1].loc != 0) {
errs++;
fprintf( stderr, "float-int MAXLOC(0) test failed, location of max = %d, should be zero\n", coutbuf[1].loc );
}
if (coutbuf[2].val != size-1 || coutbuf[2].loc != size-1) {
errs++;
fprintf( stderr, "float-int MAXLOC(>) test failed\n" );
}
}
}
/* long int */
{
struct longint { long val; int loc; } cinbuf[3], coutbuf[3];
cinbuf[0].val = 1;
cinbuf[0].loc = rank;
cinbuf[1].val = 0;
cinbuf[1].loc = rank;
cinbuf[2].val = rank;
cinbuf[2].loc = rank;
coutbuf[0].val = 0;
coutbuf[0].loc = -1;
coutbuf[1].val = 1;
coutbuf[1].loc = -1;
coutbuf[2].val = 1;
coutbuf[2].loc = -1;
MPI_Reduce( cinbuf, coutbuf, 3, MPI_LONG_INT, MPI_MAXLOC, 0, comm );
if (rank == 0) {
if (coutbuf[0].val != 1 || coutbuf[0].loc != 0) {
errs++;
fprintf( stderr, "long-int MAXLOC(1) test failed\n" );
}
if (coutbuf[1].val != 0) {
errs++;
fprintf( stderr, "long-int MAXLOC(0) test failed, value = %ld, should be zero\n", coutbuf[1].val );
}
if (coutbuf[1].loc != 0) {
errs++;
fprintf( stderr, "long-int MAXLOC(0) test failed, location of max = %d, should be zero\n", coutbuf[1].loc );
}
if (coutbuf[2].val != size-1 || coutbuf[2].loc != size-1) {
errs++;
fprintf( stderr, "long-int MAXLOC(>) test failed\n" );
}
}
}
/* short int */
{
struct shortint { short val; int loc; } cinbuf[3], coutbuf[3];
cinbuf[0].val = 1;
cinbuf[0].loc = rank;
cinbuf[1].val = 0;
cinbuf[1].loc = rank;
cinbuf[2].val = rank;
cinbuf[2].loc = rank;
coutbuf[0].val = 0;
coutbuf[0].loc = -1;
coutbuf[1].val = 1;
coutbuf[1].loc = -1;
coutbuf[2].val = 1;
coutbuf[2].loc = -1;
MPI_Reduce( cinbuf, coutbuf, 3, MPI_SHORT_INT, MPI_MAXLOC, 0, comm );
if (rank == 0) {
if (coutbuf[0].val != 1 || coutbuf[0].loc != 0) {
errs++;
fprintf( stderr, "short-int MAXLOC(1) test failed\n" );
}
if (coutbuf[1].val != 0) {
errs++;
fprintf( stderr, "short-int MAXLOC(0) test failed, value = %d, should be zero\n", coutbuf[1].val );
}
if (coutbuf[1].loc != 0) {
errs++;
fprintf( stderr, "short-int MAXLOC(0) test failed, location of max = %d, should be zero\n", coutbuf[1].loc );
}
if (coutbuf[2].val != size-1) {
errs++;
fprintf( stderr, "short-int MAXLOC(>) test failed, value = %d, should be %d\n", coutbuf[2].val, size-1 );
}
if (coutbuf[2].loc != size -1) {
errs++;
fprintf( stderr, "short-int MAXLOC(>) test failed, location of max = %d, should be %d\n", coutbuf[2].loc, size-1 );
}
}
}
/* double int */
{
struct doubleint { double val; int loc; } cinbuf[3], coutbuf[3];
cinbuf[0].val = 1;
cinbuf[0].loc = rank;
cinbuf[1].val = 0;
cinbuf[1].loc = rank;
cinbuf[2].val = rank;
cinbuf[2].loc = rank;
coutbuf[0].val = 0;
coutbuf[0].loc = -1;
coutbuf[1].val = 1;
coutbuf[1].loc = -1;
coutbuf[2].val = 1;
coutbuf[2].loc = -1;
MPI_Reduce( cinbuf, coutbuf, 3, MPI_DOUBLE_INT, MPI_MAXLOC, 0, comm );
if (rank == 0) {
if (coutbuf[0].val != 1 || coutbuf[0].loc != 0) {
errs++;
fprintf( stderr, "double-int MAXLOC(1) test failed\n" );
}
if (coutbuf[1].val != 0) {
errs++;
fprintf( stderr, "double-int MAXLOC(0) test failed, value = %lf, should be zero\n", coutbuf[1].val );
}
if (coutbuf[1].loc != 0) {
errs++;
fprintf( stderr, "double-int MAXLOC(0) test failed, location of max = %d, should be zero\n", coutbuf[1].loc );
}
if (coutbuf[2].val != size-1 || coutbuf[2].loc != size-1) {
errs++;
fprintf( stderr, "double-int MAXLOC(>) test failed\n" );
}
}
}
#ifdef HAVE_LONG_DOUBLE
/* long double int */
{
struct longdoubleint { long double val; int loc; } cinbuf[3], coutbuf[3];
/* avoid valgrind warnings about padding bytes in the long double */
memset(&cinbuf[0], 0, sizeof(cinbuf));
memset(&coutbuf[0], 0, sizeof(coutbuf));
cinbuf[0].val = 1;
cinbuf[0].loc = rank;
cinbuf[1].val = 0;
cinbuf[1].loc = rank;
cinbuf[2].val = rank;
cinbuf[2].loc = rank;
coutbuf[0].val = 0;
coutbuf[0].loc = -1;
coutbuf[1].val = 1;
coutbuf[1].loc = -1;
coutbuf[2].val = 1;
coutbuf[2].loc = -1;
if (MPI_LONG_DOUBLE != MPI_DATATYPE_NULL) {
MPI_Reduce( cinbuf, coutbuf, 3, MPI_LONG_DOUBLE_INT, MPI_MAXLOC,
0, comm );
if (rank == 0) {
if (coutbuf[0].val != 1 || coutbuf[0].loc != 0) {
errs++;
fprintf( stderr, "long double-int MAXLOC(1) test failed\n" );
}
if (coutbuf[1].val != 0) {
errs++;
fprintf( stderr, "long double-int MAXLOC(0) test failed, value = %lf, should be zero\n", (double)coutbuf[1].val );
}
if (coutbuf[1].loc != 0) {
errs++;
fprintf( stderr, "long double-int MAXLOC(0) test failed, location of max = %d, should be zero\n", coutbuf[1].loc );
}
if (coutbuf[2].val != size-1) {
errs++;
fprintf( stderr, "long double-int MAXLOC(>) test failed, value = %lf, should be %d\n", (double)coutbuf[2].val, size-1 );
}
if (coutbuf[2].loc != size-1) {
errs++;
fprintf( stderr, "long double-int MAXLOC(>) test failed, location of max = %d, should be %d\n", coutbuf[2].loc, size-1 );
}
}
}
}
#endif
MTest_Finalize( errs );
MPI_Finalize();
return 0;
}
/*------------------------------------------------*/
int main (int argc, char **argv)
{
int cols, rows, iter, particles, x, y;
int *pic;
PartStr *p, *changes, *totalChanges;
int rank, num, i, numChanges, numTotalChanges;
int *changesPerNode, *buffDispl;
MPI_Init (&argc, &argv);
MPI_Comm_rank (MPI_COMM_WORLD, &rank);
MPI_Comm_size (MPI_COMM_WORLD, &num);
if (argc < 2) // use default values if user does not specify anything
{
cols = PIC_SIZE + 2;
rows = PIC_SIZE + 2;
iter = MAX_ITER;
particles = PARTICLES;
}
else
{
cols = atoi (argv[1]) + 2;
rows = atoi (argv[2]) + 2;
particles = atoi (argv[3]);
iter = atoi (argv[4]);
}
// initialize the random number generator
srand(rank);
// srand(time(0)); // this should be used instead if the program runs on multiple hosts
int particlesPerNode = particles / num;
if (rank == num - 1)
particlesPerNode = particles - particlesPerNode * (num - 1); // in case particles cannot be split evenly
// printf("%i has %i\n", rank, particlesPerNode);
pic = (int *) malloc (sizeof (int) * cols * rows);
p = (PartStr *) malloc (sizeof (PartStr) * particlesPerNode);
changes = (PartStr *) malloc (sizeof (PartStr) * particlesPerNode);
totalChanges = (PartStr *) malloc (sizeof (PartStr) * particlesPerNode);
changesPerNode = (int *) malloc (sizeof (int) * num);
buffDispl = (int *) malloc (sizeof (int) * num);
assert (pic != 0 && p != 0 && changes != 0 && totalChanges != 0
&& changesPerNode != 0);
// MPI user type declaration
int lengths[2] = { 1, 1 };
MPI_Datatype types[2] = { MPI_INT, MPI_INT };
MPI_Aint add1, add2;
MPI_Aint displ[2];
MPI_Datatype Point;
MPI_Address (p, &add1);
MPI_Address (&(p[0].y), &add2);
displ[0] = 0;
displ[1] = add2 - add1;
MPI_Type_struct (2, lengths, displ, types, &Point);
MPI_Type_commit (&Point);
dla_init_plist (pic, rows, cols, p, particlesPerNode, 1);
while (--iter)
{
dla_evolve_plist (pic, rows, cols, p, &particlesPerNode, changes, &numChanges);
// printf("%i changed %i on iter %i : ",rank, numChanges, iter);
// for(i=0;i<numChanges;i++) printf("(%i, %i) ", changes[i].x, changes[i].y);
// printf("\n");
//exchange information with other nodes
MPI_Allgather (&numChanges, 1, MPI_INT, changesPerNode, 1, MPI_INT, MPI_COMM_WORLD);
//calculate offsets
numTotalChanges = 0;
for (i = 0; i < num; i++)
{
buffDispl[i] = numTotalChanges;
numTotalChanges += changesPerNode[i];
}
// if(rank==0)
// {
// for(i=0;i<num;i++)
// printf("%i tries to send %i\n",i,changesPerNode[i]);
// printf("-----------\n");
// }
if(numTotalChanges >0)
{
MPI_Allgatherv (changes, numChanges, Point,
totalChanges, changesPerNode, buffDispl, Point,
MPI_COMM_WORLD);
apply_changes (pic, rows, cols, totalChanges, numTotalChanges);
// if(rank==0)
// {
// printf("Total changes %i : ", numTotalChanges);
// for(i=0;i<numTotalChanges;i++) printf("(%i, %i) ", totalChanges[i].x, totalChanges[i].y);
//
// printf("\n");
// printf("-----------\n");
// }
}
}
/* Print to stdout a PBM picture of the simulation space */
if (rank == 0)
{
printf ("P1\n%i %i\n", cols - 2, rows - 2);
for (y = 1; y < rows - 1; y++)
{
for (x = 1; x < cols - 1; x++)
{
if (pic[y * cols + x] < 0)
printf ("1 ");
else
printf ("0 ");
}
printf ("\n");
}
}
MPI_Reduce(&particlesPerNode, &particles, 1, MPI_INT, MPI_SUM, 0, MPI_COMM_WORLD);
if(rank==0) fprintf(stderr, "Remaining particles %i\n", particles);
free (pic);
free (p);
free (changes);
free (changesPerNode);
free (buffDispl);
MPI_Finalize ();
return 0;
}
void
PStatPrint(superlu_options_t *options, SuperLUStat_t *stat, gridinfo_t *grid)
{
double *utime = stat->utime;
flops_t *ops = stat->ops;
int_t iam = grid->iam;
flops_t flopcnt, factflop, solveflop;
if ( options->PrintStat == NO ) return;
if ( !iam && options->Fact != FACTORED ) {
printf("**************************************************\n");
printf("**** Time (seconds) ****\n");
if ( options->Equil != NO )
printf("\tEQUIL time %8.2f\n", utime[EQUIL]);
if ( options->RowPerm != NOROWPERM )
printf("\tROWPERM time %8.2f\n", utime[ROWPERM]);
if ( options->ColPerm != NATURAL )
printf("\tCOLPERM time %8.2f\n", utime[COLPERM]);
printf("\tSYMBFACT time %8.2f\n", utime[SYMBFAC]);
printf("\tDISTRIBUTE time %8.2f\n", utime[DIST]);
}
MPI_Reduce(&ops[FACT], &flopcnt, 1, MPI_FLOAT, MPI_SUM,
0, grid->comm);
factflop = flopcnt;
if ( !iam && options->Fact != FACTORED ) {
printf("\tFACTOR time %8.2f\n", utime[FACT]);
if ( utime[FACT] != 0.0 )
printf("\tFactor flops\t%e\tMflops \t%8.2f\n",
flopcnt,
flopcnt*1e-6/utime[FACT]);
}
MPI_Reduce(&ops[SOLVE], &flopcnt, 1, MPI_FLOAT, MPI_SUM,
0, grid->comm);
solveflop = flopcnt;
if ( !iam ) {
printf("\tSOLVE time %8.2f\n", utime[SOLVE]);
if ( utime[SOLVE] != 0.0 )
printf("\tSolve flops\t%e\tMflops \t%8.2f\n",
flopcnt,
flopcnt*1e-6/utime[SOLVE]);
if ( options->IterRefine != NOREFINE ) {
printf("\tREFINEMENT time %8.2f\tSteps%8d\n\n",
utime[REFINE], stat->RefineSteps);
}
printf("**************************************************\n");
}
#if ( PROFlevel>=1 )
fflush(stdout);
MPI_Barrier( grid->comm );
{
int_t i, P = grid->nprow*grid->npcol;
flops_t b, maxflop;
if ( !iam ) printf("\n.. FACT time breakdown:\tcomm\ttotal\n");
for (i = 0; i < P; ++i) {
if ( iam == i) {
printf("\t\t(%d)%8.2f%8.2f\n", iam, utime[COMM], utime[FACT]);
fflush(stdout);
}
MPI_Barrier( grid->comm );
}
if ( !iam ) printf("\n.. FACT ops distribution:\n");
for (i = 0; i < P; ++i) {
if ( iam == i ) {
printf("\t\t(%d)\t%e\n", iam, ops[FACT]);
fflush(stdout);
}
MPI_Barrier( grid->comm );
}
MPI_Reduce(&ops[FACT], &maxflop, 1, MPI_FLOAT, MPI_MAX, 0, grid->comm);
if ( !iam ) {
b = factflop/P/maxflop;
printf("\tFACT load balance: %.2f\n", b);
}
if ( !iam ) printf("\n.. SOLVE ops distribution:\n");
for (i = 0; i < P; ++i) {
if ( iam == i ) {
printf("\t\t%d\t%e\n", iam, ops[SOLVE]);
fflush(stdout);
}
MPI_Barrier( grid->comm );
}
MPI_Reduce(&ops[SOLVE], &maxflop, 1, MPI_FLOAT, MPI_MAX, 0,grid->comm);
if ( !iam ) {
b = solveflop/P/maxflop;
printf("\tSOLVE load balance: %.2f\n", b);
}
}
#endif
/* if ( !iam ) fflush(stdout); CRASH THE SYSTEM pierre. */
}