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nested.c
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nested.c
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/* Nested Sampling procedure for Crankite
*
* Skeleton of code from J.Skilling p188 of
* Data Analysis A Bayesian Tutorial D.S.Sivia
*
* Copyright (c) 2007 - 2013 Nikolas Burkoff, Csilla Varnai and David Wild
*
*/
#include<stdlib.h>
#include<stdio.h>
#include<math.h>
#include<string.h>
#include<float.h>
#include<time.h>
#include"error.h"
#include"params.h"
#include"vector.h"
#include"rotation.h"
#include"peptide.h"
#include"vdw.h"
#include"energy.h"
#include"metropolis.h"
#include"probe.h"
#include"nested.h"
#ifdef PARALLEL
#include<mpi.h>
#include"random16.h"
#include"flex.h"
#endif
#include"checkpoint_io.h"
int lowtemp = 0;
#define PLUS(x,y) (x>y ? x + log(1+exp(y-x)) : y + log(1+exp(x-y)))
/* A bit of ordering of the chains wrt. the logL in ascending order.
It takes the first one, and moves it towards the end a bit, or all
the way to the end, if it has the largest logL.
If the first one has the largest logL, it will be moved to the end. */
void heapifyhashout(ChainHash* chainhash ,int length){
int booly = 0;
int k = 1,i;
ChainHash v;
copyhash(&v,&(chainhash[k]));
while((booly == 0) && 2 * k <= length){
i = 2 * k;
if(i < length) //2 children
if(chainhash[i].ll > chainhash[i+1].ll) i += 1;
if(v.ll < chainhash[i].ll) booly = 1;
else{copyhash(&(chainhash[k]),&(chainhash[i])); k = i;}
}
copyhash(&(chainhash[k]),&v);
}
/* A bit of ordering of the chains wrt. the logL in ascending order.
It takes the last one that has probably just been added to the heap,
and moves it down the line a bit, or to the front, if it has the
smallest logL.
If the last one has the smallest logL, it will be moved to the front. */
void heapifyhashin(ChainHash *chainhash, int length){
int current = length;
int booly = 0;
ChainHash v;
while((booly == 0) && current > 1){
int next = current / 2;
if(chainhash[current].ll < chainhash[next].ll){
copyhash(&v,&(chainhash[next]));
copyhash(&(chainhash[next]),&(chainhash[current]));
copyhash(&(chainhash[current]),&v);
current /= 2;
}
else{
booly = 1;
}
}
}
void repairheap(ChainHash* chainhash,int N){
constructhashheap(chainhash, N);
}
void new_amplitude(Chain **cpoints, Biasmap *biasmap, int current_stored, simulation_params *sim_params, void *mpi_comm){
int rank = 0;
int P = 1;
double amptot = 0;
double oldamp = sim_params->amplitude;
Chaint *chaint;
chaint = (Chaint*)malloc(sizeof(Chaint));
chaint->aat = NULL; chaint->ergt = NULL; chaint->xaat = NULL; chaint->xaat_prev = NULL;
double currE;
int copies;
Chain temporary;
temporary.aa = NULL; temporary.xaa = NULL; temporary.erg = NULL; temporary.xaa_prev = NULL;
allocmem_chain(&temporary,(*cpoints)[0].NAA,(*cpoints)[0].Nchains);
//calculate amplitude
#ifdef PARALLEL
MPI_Comm *MPI_COMM = mpi_comm;
MPI_Status status;
MPI_Comm_size(*MPI_COMM, &P);
MPI_Comm_rank(*MPI_COMM, &rank);
if(P == 1){
for(int k = 0; k < 5; k++){
copies = (int)(rand()/(double)RAND_MAX * current_stored) % (current_stored);
sim_params->amplitude = oldamp;
copybetween(&temporary,&((*cpoints)[copies]));
aat_init(&temporary,chaint);
currE = -temporary.ll;
move(&temporary,chaint,biasmap,sim_params->logLstar,&currE,-1, sim_params);
for(int i = 1; (i < sim_params->iter_max || i < 1024); i++){
move(&temporary,chaint,biasmap,sim_params->logLstar,&currE,1, sim_params);
}
amptot += sim_params->amplitude;
}
sim_params->amplitude = amptot / 5;
return;
}
if (rank != 0) { // one chain per processor
#else
for(int k = 0; k < 5; k++){ //5 chains only
#endif
copies = (int)(rand()/(double)RAND_MAX * current_stored) % (current_stored);
//recalculate amplitude on temporary, not changing the actual NS points
copybetween(&temporary,&((*cpoints)[copies]));
aat_init(&temporary,chaint);
#ifndef PARALLEL
sim_params->amplitude = oldamp;
#endif
currE = -temporary.ll;
move(&temporary,chaint,biasmap,sim_params->logLstar,&currE,-1, sim_params);
for(int i = 1; (i < sim_params->iter_max || i < 1024); i++){
move(&temporary,chaint,biasmap,sim_params->logLstar,&currE,1, sim_params);
}
//collect and add up amplitude
#ifdef PARALLEL
//send my new amplitude
MPI_Send(&(sim_params->amplitude),1,MPI_DOUBLE,0,sim_params->iter*6+5,*MPI_COMM);
} else {
for(int k = 1; k < P;k++){
MPI_Recv(&(sim_params->amplitude),1,MPI_DOUBLE,k,sim_params->iter*6+5,*MPI_COMM,&status);
amptot += sim_params->amplitude;
}
sim_params->amplitude = amptot / (P-1);
}
#else
amptot += sim_params->amplitude;
}
sim_params->amplitude = amptot / 5;
//fprintf(stderr,"Amplitude: %f\n",-sim_params->amplitude);
#endif
//broadcast amplitude
#ifdef PARALLEL
//receive the new amplitude from rank 0
MPI_Bcast(&(sim_params->amplitude),1,MPI_DOUBLE,0,*MPI_COMM);
#endif
freemem_chain(&temporary);
freemem_chaint(chaint);
free(chaint);
}
#ifdef PARALLEL
/*set up 2 separate communicators, FLEX_WORLD for
* processors 0,1,...nma_params.number_of_processors >> the master processor and the
* (for now) 1 processor involved in FLEX
* and NS_WORLD for processors
* 0,nma_params.number_of_processors+1,FLEX_params.number_of_processors+2,...P-1
* for the standard NS part
*/
void setup_communicators(MPI_Comm * FLEX_WORLD, MPI_Comm * NS_WORLD, int S, int *P, int *rank,int *SP, int *Srank, int *NSgrouprank, int *FLEXgrouprank, int *in_NS){
MPI_Comm_size(MPI_COMM_WORLD, P);
MPI_Comm_rank(MPI_COMM_WORLD, rank);
if(*P-S < 1){
stop("You must have at least 1 processor running the NS simulation\n");
}
int setup_groups;
MPI_Group NS_GROUP, FLEX_GROUP, ALL_GROUP;
MPI_Comm_group( MPI_COMM_WORLD, &ALL_GROUP );
if(S > 0){
int *FLEX_group_ranks = malloc(sizeof(int)*(S+1));
for(setup_groups = 0; setup_groups <= S; setup_groups++ ){
FLEX_group_ranks[setup_groups] = setup_groups;
}
MPI_Group_incl(ALL_GROUP,S+1,FLEX_group_ranks,&FLEX_GROUP);
MPI_Comm_create(MPI_COMM_WORLD,FLEX_GROUP,FLEX_WORLD);
free(FLEX_group_ranks);
}
int *NS_group_ranks = malloc(sizeof(int)*(*P-S));
NS_group_ranks[0] = 0;
for(setup_groups = 1; setup_groups < *P-S; setup_groups++ ){
NS_group_ranks[setup_groups] = setup_groups+S;
}
MPI_Group_incl(ALL_GROUP,*P-S,NS_group_ranks,&NS_GROUP);
MPI_Comm_create(MPI_COMM_WORLD,NS_GROUP,NS_WORLD);
free(NS_group_ranks);
if(S>0 && *rank <= S){
MPI_Group_rank(FLEX_GROUP,FLEXgrouprank);
MPI_Comm_size(*FLEX_WORLD, SP);
MPI_Comm_rank(*FLEX_WORLD, Srank);
if(*Srank != 0) *in_NS = -1;
}
if(*rank == 0 || *rank > S){
MPI_Group_rank(NS_GROUP,NSgrouprank);
MPI_Comm_size(*NS_WORLD, P);
MPI_Comm_rank(*NS_WORLD, rank);
}
}
void deal_with_flex(int N, int finished,int rank, simulation_params *sim_params, MPI_Comm NS_WORLD, MPI_Comm FLEX_WORLD, ChainHash *chainhash, Chain* temporary,Chain *cpoints){
MPI_Status status;
int flex_status_for_ns;
int one = 1;
if(rank == 0){
int flex_ready = check_flex_ready(sim_params);
if(flex_ready == 1 || sim_params->iter == sim_params->iter_start){
if(flex_ready == 1){
flex_status_for_ns = 1;
MPI_Bcast(&flex_status_for_ns,1,MPI_INT,0,NS_WORLD);
MPI_Send(&(sim_params->logLstar),1,MPI_DOUBLE,one,10,FLEX_WORLD);
int number_to_recv = 0;
MPI_Recv(&number_to_recv,1,MPI_INT,one,11,FLEX_WORLD,&status);
MPI_Bcast(&number_to_recv,1,MPI_INT,0,NS_WORLD);
int receives;
for(receives = 0; receives < number_to_recv; receives++){
mpi_rec_chain(temporary, one, 0, &sim_params->logLstar, 0, FLEX_WORLD);
int overwrite;
overwrite = 1 + ((int)(rand()/(double)RAND_MAX * (N))) % (N);
chainhash[overwrite].ll = temporary->ll;
int where_to_send = chainhash[overwrite].processor;
MPI_Bcast(&where_to_send,1,MPI_INT,0,NS_WORLD);
if(where_to_send == 0){
copybetween(&cpoints[chainhash[overwrite].index],temporary);
}
else{
MPI_Send(&(chainhash[overwrite].index),1,MPI_INT, chainhash[overwrite].processor ,sim_params->iter,NS_WORLD);
mpi_send_chain(temporary,0,where_to_send,&sim_params->logLstar,sim_params->iter,NS_WORLD);
}
}
repairheap(chainhash,N);
}
else{
flex_status_for_ns = 0;
MPI_Bcast(&flex_status_for_ns,1,MPI_INT,0,NS_WORLD);
}
int tosend = 1;//1 + ((int)(rand()/(double)RAND_MAX * (N))) % (N);
int where_from = chainhash[tosend].processor;
MPI_Bcast(&where_from,1,MPI_INT,0,NS_WORLD);
if(where_from == 0){
copybetween(temporary,&cpoints[chainhash[tosend].index]);
}
else{
MPI_Send(&(chainhash[tosend].index),1,MPI_INT, chainhash[tosend].processor ,sim_params->iter,NS_WORLD);
mpi_rec_chain(temporary, chainhash[tosend].processor, 0, &sim_params->logLstar, sim_params->iter, NS_WORLD);
}
//chain sent to FLEX
mpi_send_chain(temporary,0,one,&sim_params->logLstar,1,FLEX_WORLD);
}
else{
flex_status_for_ns = -1; //done
MPI_Bcast(&flex_status_for_ns,1,MPI_INT,0,NS_WORLD);
}
}
else{ //not rank 0
MPI_Bcast(&flex_status_for_ns,1,MPI_INT,0,NS_WORLD);
if(flex_status_for_ns == 1){
int number_to_recv = 0;
MPI_Bcast(&number_to_recv,1,MPI_INT,0,NS_WORLD);
int receives;
for(receives = 0; receives < number_to_recv; receives++){
int want_it;
MPI_Bcast(&want_it,1,MPI_INT,0,NS_WORLD);
if(want_it == rank){
int which_index;
MPI_Recv(&(which_index),1,MPI_INT,0,sim_params->iter,NS_WORLD,&status);
mpi_rec_chain(&(cpoints[which_index]), 0, rank, &sim_params->logLstar , sim_params->iter,NS_WORLD);
}
}
}
if(flex_status_for_ns >= 0){
int where_from;
MPI_Bcast(&where_from,1,MPI_INT,0,NS_WORLD);
if(where_from == rank){
int which_index;
MPI_Recv(&which_index,1,MPI_INT, 0 ,sim_params->iter,NS_WORLD,&status);
mpi_send_chain(&cpoints[which_index],rank,0,&sim_params->logLstar,sim_params->iter,NS_WORLD);
}
}
}
if(finished == 0 && rank == 0){
char filename[DEFAULT_SHORT_STRING_LENGTH];
//strcpy(filename,sim_params->flex_params.output_path);
strcpy(filename,"finished");
FILE *fptr = fopen(filename,"w");
fclose(fptr);
}
}
#endif
void check_to_output_checkpoint_file(Chain* cpoints, int current_stored, int N, simulation_params *sim_params, int rank, void*comm_pointer){
//if outputting checkpoint file
// The output printing has to happen before updating the logX, weight, logZ etc., otherwise
// a) the logZ will contain the highest energy configuration's weight twice
// b) logX will have been advanced using the old run's alpha and we cannot correct for it any more (matters if P changes)
// This means we print the previous logX, logZ, logL*, H and amplitude
if(sim_params->checkpoint == 1){
sim_params->N = N;
if(sim_params->iter != sim_params->iter_start) {
//fprintf(stderr,"trying to print checkpoint\n");
output_checkpoint_file(cpoints, current_stored, sim_params,comm_pointer);
}
if (rank == 0) {
if( sim_params->iter % sim_params->num_NS_per_checkpoint == 0 ){
char *out = (char*)malloc(sizeof(char)*1010);
if(sim_params->outfile_name != NULL){
sprintf(out,"%s_%d",sim_params->outfile_name,sim_params->checkpoint_counter);
if (sim_params->outfile) fclose(sim_params->outfile);
sim_params->outfile = fopen(out, "w");
}
free(out);
}
}
}
}
void find_worst(simulation_params *sim_params, ChainHash *chainhash, int *heaplength, int N, int P ){
/*find P worst samples in positions, N,N-1,N-2,... */
for(int k = 0; k < P; k++){
copyhash(&(chainhash[0]),&(chainhash[1]));
copyhash(&(chainhash[1]),&(chainhash[*heaplength]));
copyhash(&(chainhash[*heaplength]),&(chainhash[0]));
(*heaplength)--;
heapifyhashout(chainhash,*heaplength);
}
sim_params->logLstar = chainhash[N-P+1].ll;
}
void update_NS_parameters(simulation_params *sim_params, int *converged, double *logZnew, double *lweight){
/*update weight = width * likelihood */
*lweight = sim_params->log_DeltaX + sim_params->logLstar*sim_params->thermobeta;
//fprintf(stderr,"LWJ %f %d\n",sim_params->log_DeltaX,sim_params->iter);
sim_params->logX = sim_params->logX_start + sim_params->Delta_logX*(sim_params->iter-sim_params->iter_start+1);
/* update evidence and information */
*logZnew = PLUS(sim_params->logZ,*lweight);
sim_params->H = exp(*lweight - *logZnew) * sim_params->logLstar * sim_params->thermobeta + exp(sim_params->logZ-*logZnew)*(sim_params->H+sim_params->logZ) - *logZnew;
/* control */
if(sim_params->checkpoint == 1 && sim_params->iter % sim_params->num_NS_per_checkpoint == 0 && sim_params->iter != sim_params->iter_start) {
fprintf(stderr,"%d %lf %lf %lf %lf %lf\n", sim_params->iter, sim_params->logX, sim_params->logLstar,sim_params->logZ,sim_params->H,sim_params->amplitude);
}
/*Check if converged */
if(sim_params->lowtemp == 1 && fabs(*logZnew - sim_params->logZ) < 1e-8) *converged = 0;
sim_params->logZ = *logZnew;
}
#ifdef PARALLEL
void MC_first(ChainHash *ChainHash,Chain *cpoints, Chaint* chaint, int current_stored, Biasmap *biasmap,simulation_params *sim_params, int rank, int N,int P, MPI_Comm *NSWORLD){
int i;
MPI_Status status;
double *newls = (double*)malloc(sizeof(double)*(1+N/P));
for(i = 0; i < current_stored; i++){
int iter;
double currE = -cpoints[i].ll;
for(iter= 0; iter < sim_params->number_initial_MC; iter++){
move(&(cpoints[i]),chaint,biasmap,0,&currE,0,sim_params);
}
cpoints[i].ll = -currE;
newls[i] = cpoints[i].ll;
}
if(rank == 0){
fprintf(stderr,"Beware: %d initial MC moves before NS started\n",sim_params->number_initial_MC);
for(i = 0; i < current_stored; i++){
ChainHash[1+i*P].ll = newls[i];
}
int proc;
if(P > 1){
for(proc = 1; proc < P; proc++){
MPI_Recv(newls,1+N/P,MPI_DOUBLE,proc,proc,*NSWORLD,&status);
for(i = 0; i < N/P+1; i++){
if(1+i*P+proc <= N) ChainHash[1+i*P+proc].ll = newls[i];
}
}
}
}
else{
MPI_Send(newls,1+N/P,MPI_DOUBLE,0,rank,*NSWORLD);
}
free(newls);
}
#ifndef FAST
void collect_chains(ChainHash *chainhash,Chain *cpoints, Chain*chaincopies, simulation_params *sim_params, int rank, int P, int N,MPI_Comm *NS_WORLD,Instructions *instructions){
//first collect the P chains which will be the start of the MMC
int copies, got_all;
MPI_Status status;
int minus1 = -1;
//collect the chains
if (rank == 0) {
//random number generation would fail if N==P
if (N==P) stop("number of processors = number of active points. All chains would be scrapped at each MC step.");
if (N<P) stop("number of processors > number of active points. All chains would be scrapped at each MC step.");
//first collect the P chains which will be the start of the MMC
int * start_chains = (int*)malloc(sizeof(int)*P);
for(int k = 0; k < P; k++){
copies = 1 + ((int)(rand()/(double)RAND_MAX * (N-P))) % (N-P);
start_chains[k] = copies;
}
for(int k = 0; k < P; k++){
if(chainhash[start_chains[k]].processor == 0){
copybetween(&(chaincopies[k]),&(cpoints[chainhash[start_chains[k]].index]));
}
else{
MPI_Send(&(chainhash[start_chains[k]].index),1,MPI_INT,chainhash[start_chains[k]].processor,sim_params->iter,*NS_WORLD);
mpi_rec_chain(&(chaincopies[k]), chainhash[start_chains[k]].processor, 0,&sim_params->logLstar , sim_params->iter,*NS_WORLD);
}
}
//let all processors know we're done
for(int i = 1; i < P; i++){
MPI_Send(&minus1,1,MPI_INT,i,sim_params->iter,*NS_WORLD);
}
//then send one to each processor
for(int k = 1; k < P; k++){
mpi_send_chain(&(chaincopies[k]), 0, k,&sim_params->logLstar,sim_params->iter,*NS_WORLD);
}
free(start_chains);
} //end rank 0
else{
//processor 0 is asking for a random P cpoints spread throughout all processors
//send any it wants
got_all = 0;
while(got_all != -1){
MPI_Recv(&got_all,1,MPI_INT,0,sim_params->iter,*NS_WORLD,&status);
if(got_all != -1) mpi_send_chain(&(cpoints[got_all]), rank,0, &sim_params->logLstar , sim_params->iter,*NS_WORLD);
}
//receive the chain I'm expected to MC
mpi_rec_chain(&chaincopies[0],0,rank,&sim_params->logLstar,sim_params->iter,*NS_WORLD);
}
}
void return_and_reheap_chains(ChainHash *chainhash,Chain *cpoints, Chain*chaincopies, simulation_params *sim_params, int rank, int P, int *heaplength, MPI_Comm *NS_WORLD, Instructions *instructions){
//recieve the P chains on the master processor
int minus1 = -1;
int got_all;
MPI_Status status;
if (rank == 0) {
for(int k = 1; k < P; k++){
mpi_rec_chain(&(chaincopies[k]), k, 0,&sim_params->logLstar,sim_params->iter,*NS_WORLD);
}
}
else {
mpi_send_chain(&chaincopies[0],rank,0,&sim_params->logLstar,sim_params->iter,*NS_WORLD);
}
if (rank == 0) {
//put them back in heap and send them to overwrite the worst ones
for(int k = 0; k < P; k++){
(*heaplength)++;
chainhash[*heaplength].ll = chaincopies[k].ll;
if(chainhash[*heaplength].processor == 0){
copybetween(&cpoints[chainhash[*heaplength].index],&chaincopies[k]);
}
else{
MPI_Send(&(chainhash[*heaplength].index),1,MPI_INT, chainhash[*heaplength].processor ,sim_params->iter,*NS_WORLD);
mpi_send_chain(&(chaincopies[k]),0, chainhash[*heaplength].processor,&sim_params->logLstar,sim_params->iter,*NS_WORLD);
}
heapifyhashin(chainhash,*heaplength);
}
//tell processors we've given out all chains
for(int i = 1; i < P; i++){
MPI_Send(&minus1,1,MPI_INT,i,sim_params->iter,*NS_WORLD);
}
}
else {
//get given any of the new points to replace the worst P points in the collective cpoints arrays
got_all = 0;
while(got_all != -1){
MPI_Recv(&got_all,1,MPI_INT, 0 ,sim_params->iter,*NS_WORLD,&status);
if(got_all != -1) mpi_rec_chain(&(cpoints[got_all]),0,rank,&sim_params->logLstar,sim_params->iter,*NS_WORLD);
}
}
}
#else
void initialize_instruction_set(Instructions * instruction, int P){
instruction->length = 6*P+1;
instruction->current_position = -1;
instruction->instructions = (int*)malloc(sizeof(int)*instruction->length);
}
void finalize_instruction_set(Instructions * instruction){
free(instruction->instructions);
}
void carry_out_first_instructions(ChainHash *chainhash,Chain *cpoints, Chain*chaincopies, simulation_params *sim_params, int rank, int P, int N,MPI_Comm *NS_WORLD,Instructions *instructions){
instructions[0].current_position = -3;
int instruct; int proc;
int index;
do{
instructions[0].current_position+=3;
instruct = instructions[0].instructions[instructions[0].current_position];
proc = instructions[0].instructions[instructions[0].current_position+1];
index = instructions[0].instructions[instructions[0].current_position+2];
if(instruct == 1 ){ //send
mpi_send_chain(&(cpoints[index]), rank, proc,&sim_params->logLstar,sim_params->iter,*NS_WORLD);
}
else if(instruct == -1){ //receive
mpi_rec_chain(&(chaincopies[0]), proc,rank,&sim_params->logLstar , sim_params->iter,*NS_WORLD);
}
}while(instruct != 0);
if(index != -1){
copybetween(&(chaincopies[0]),&(cpoints[index]));
}
instructions[0].current_position+=3;
}
void carry_out_last_instructions(ChainHash *chainhash,Chain *cpoints, Chain*chaincopies, simulation_params *sim_params, int rank, int P, int N,MPI_Comm *NS_WORLD,Instructions *instructions){
instructions[0].current_position-=3;
int instruct; int proc;
int index;
do{
instructions[0].current_position+=3;
instruct = instructions[0].instructions[instructions[0].current_position];
proc = instructions[0].instructions[instructions[0].current_position+1];
index = instructions[0].instructions[instructions[0].current_position+2];
if(instruct == 1 ){ //send
mpi_send_chain(&(chaincopies[0]), rank, proc,&sim_params->logLstar,sim_params->iter,*NS_WORLD);
}
else if(instruct == -1){ //receive
mpi_rec_chain(&(cpoints[index]), proc,rank,&sim_params->logLstar , sim_params->iter,*NS_WORLD);
}
}while(instruct != 0);
if(index != -1){
copybetween(&(cpoints[index]),&(chaincopies[0]));
}
}
void output_instructions(Instructions *instructions, int rank){
fprintf(stderr, "Rank %d Number Instructions %d:\n",rank,instructions->current_position/3);
for(int i = 0; i < instructions->current_position/3; i++){
fprintf(stderr, "%d %d %d\n",instructions->instructions[3*i],instructions->instructions[3*i+1],instructions->instructions[3*i+2]);
}
}
void send_and_receive_instructions( Instructions * instructions, int rank, int P, MPI_Comm *NS_WORLD){
if(rank == 0){
//output_instructions(&(instructions[0]),0);
for(int k = 1; k < P; k++){
//output_instructions(&(instructions[k]),k);
MPI_Send(&(instructions[k].current_position),1,MPI_INT,k,25,*NS_WORLD);
MPI_Send(instructions[k].instructions,instructions[k].current_position,MPI_INT,k,50,*NS_WORLD);
}
}
else{
MPI_Status status;
MPI_Recv(&(instructions[0].current_position),1,MPI_INT,0,25,*NS_WORLD,&status);
MPI_Recv(instructions[0].instructions,instructions[0].current_position,MPI_INT,0,50,*NS_WORLD,&status);
}
}
void collect_chains(ChainHash *chainhash,Chain *cpoints, Chain*chaincopies, simulation_params *sim_params, int rank, int P, int N,MPI_Comm *NS_WORLD,Instructions *instructions){
MPI_Bcast(&(sim_params->logLstar),1,MPI_DOUBLE,0,*NS_WORLD);
if (rank == 0) {
int *procs = malloc(sizeof(int)*P);
for(int k = 0; k < P; k++){
procs[k] = -1;
instructions[k].current_position = 0;
}
int *leftovers = malloc(sizeof(int)*(P*2));
int number_leftovers = 0;
int copies;
for(int k = 0; k < P; k++){
copies = 1 + ((int)(rand()/(double)RAND_MAX * (N-P))) % (N-P);
int which_proc = chainhash[copies].processor;
int which_index = chainhash[copies].index;
if(procs[which_proc] == -1){
procs[which_proc] = which_index;
}
else{
leftovers[number_leftovers*2] = which_proc;
leftovers[number_leftovers*2+1] = which_index;
number_leftovers++;
}
}
// static int number_chain = 0;
// number_chain += number_leftovers;
for(int k = 0; k < P; k++){
if(procs[k] == -1){
instructions[k].instructions[instructions[k].current_position] = -1;
instructions[k].instructions[instructions[k].current_position+1] = leftovers[(number_leftovers-1)*2];
instructions[k].instructions[instructions[k].current_position+2] = leftovers[(number_leftovers-1)*2+1];
instructions[k].current_position+=3;
instructions[leftovers[(number_leftovers-1)*2]].instructions[instructions[leftovers[(number_leftovers-1)*2]].current_position] = +1;
instructions[leftovers[(number_leftovers-1)*2]].instructions[instructions[leftovers[(number_leftovers-1)*2]].current_position+1] = k;
instructions[leftovers[(number_leftovers-1)*2]].instructions[instructions[leftovers[(number_leftovers-1)*2]].current_position+2] = leftovers[(number_leftovers-1)*2+1];
instructions[leftovers[(number_leftovers-1)*2]].current_position+=3;
number_leftovers--;
}
}
for(int k = 0; k < P; k++){
instructions[k].instructions[instructions[k].current_position] = 0;
instructions[k].instructions[instructions[k].current_position+1] = 0;
instructions[k].instructions[instructions[k].current_position+2] = procs[k];
instructions[k].current_position+=3;
}
//now sort out after MC move instructions
for(int k = 0; k < P; k++)procs[k] = -1;
number_leftovers = 0;
for(int k = 0; k < P; k++){
copies = N-k;
int which_proc = chainhash[copies].processor;
int which_index = chainhash[copies].index;
if(procs[which_proc] == -1){
procs[which_proc] = which_index;
}
else{
leftovers[number_leftovers*2] = which_proc;
leftovers[number_leftovers*2+1] = which_index;
number_leftovers++;
}
}
// number_chain += number_leftovers;
//fprintf(stderr,"NUMBER CHAINS %d\n",number_chain);
for(int k = 0; k < P; k++){
if(procs[k] == -1){
instructions[k].instructions[instructions[k].current_position] = 1;
instructions[k].instructions[instructions[k].current_position+1] = leftovers[(number_leftovers-1)*2];
instructions[k].instructions[instructions[k].current_position+2] = leftovers[(number_leftovers-1)*2+1];
instructions[k].current_position+=3;
instructions[leftovers[(number_leftovers-1)*2]].instructions[instructions[leftovers[(number_leftovers-1)*2]].current_position] = -1;
instructions[leftovers[(number_leftovers-1)*2]].instructions[instructions[leftovers[(number_leftovers-1)*2]].current_position+1] = k;
instructions[leftovers[(number_leftovers-1)*2]].instructions[instructions[leftovers[(number_leftovers-1)*2]].current_position+2] = leftovers[(number_leftovers-1)*2+1];
instructions[leftovers[(number_leftovers-1)*2]].current_position+=3;
number_leftovers--;
}
}
for(int k = 0; k < P; k++){
instructions[k].instructions[instructions[k].current_position] = 0;
instructions[k].instructions[instructions[k].current_position+1] = 0;
instructions[k].instructions[instructions[k].current_position+2] = procs[k];
instructions[k].current_position+=3;
}
free(procs);
free(leftovers);
}
send_and_receive_instructions(instructions,rank,P,NS_WORLD);
carry_out_first_instructions(chainhash,cpoints, chaincopies, sim_params, rank, P, N,NS_WORLD,instructions);
}
void return_and_reheap_chains(ChainHash *chainhash,Chain *cpoints, Chain*chaincopies, simulation_params *sim_params, int rank, int P, int *heaplength, MPI_Comm *NS_WORLD, Instructions *instructions){
carry_out_last_instructions(chainhash,cpoints, chaincopies, sim_params, rank, P, *heaplength,NS_WORLD,instructions);
if (rank == 0) {
MPI_Status status;
for(int k = 0; k < P; k++){
(*heaplength)++;
if(k == 0){
chainhash[*heaplength].ll = chaincopies[0].ll;
instructions[k].current_position+=2;
}
else{
instructions[k].current_position--;
MPI_Recv(&(chainhash[*heaplength].ll),1,MPI_DOUBLE,k,75,*NS_WORLD,&status);
}
//fprintf(stderr,"KK %d %d %d\n",k,instructions[k].current_position,instructions[k].instructions[instructions[k].current_position]); fflush(stderr);
if(instructions[k].instructions[instructions[k].current_position] == -1){
instructions[k].current_position -=3;
chainhash[*heaplength].processor = instructions[k].instructions[instructions[k].current_position-1];
}
else{
chainhash[*heaplength].processor = k;
}
chainhash[*heaplength].index = instructions[k].instructions[instructions[k].current_position];
heapifyhashin(chainhash,*heaplength);
}
}
else{
MPI_Send(&(chaincopies[0].ll),1,MPI_DOUBLE,0,75,*NS_WORLD);
}
}
#endif
#endif
/* Output NS point (in a serial run), or
collect the NS point through MPI and output it on the master node. */
void output_NS_point(ChainHash *chainhash, Chain *cpoints, Biasmap *biasmap, simulation_params *sim_params, int N,void*mpi_comm) {
Chain *chain_to_output = NULL;
int P = 1;
//get the chain to be output
#ifdef PARALLEL
MPI_Comm *MPI_COMM = mpi_comm;
int rank = 0;
MPI_Status status;
MPI_Comm_size(*MPI_COMM, &P);
MPI_Comm_rank(*MPI_COMM, &rank);
Chain temporary; //if the chain needs collecting from another processor
if (rank == 0) {
temporary.aa = NULL; temporary.xaa = NULL; temporary.erg = NULL; temporary.xaa_prev = NULL;
allocmem_chain(&temporary,cpoints[0].NAA,cpoints[0].Nchains);
//We need to update AA.id and AA.num, because those are not sent through MPI.
for (int i=0; i< sim_params->NAA; i++) {
temporary.aa[i].id = sim_params->seq[i];
temporary.aa[i].num = i;
}
//Need to actually get the chain first!
MPI_Bcast(&chainhash[N-P+1].processor,1,MPI_INT,0,*MPI_COMM);
if(chainhash[N-P+1].processor != 0){
MPI_Send(&chainhash[N-P+1].index,1,MPI_INT,chainhash[N-P+1].processor,sim_params->iter,*MPI_COMM );
mpi_rec_chain(&temporary, chainhash[N-P+1].processor, 0, &sim_params->logLstar,sim_params->iter,*MPI_COMM);
chain_to_output = &temporary;
}
else{
chain_to_output = &(cpoints[chainhash[N-P+1].index]);
}
}
else {
int whichP, whichindex;
//if it's my chain processor 0 wants then send it
MPI_Bcast(&whichP,1,MPI_INT,0,*MPI_COMM);
if(whichP == rank){
MPI_Recv(&whichindex,1,MPI_INT,0,sim_params->iter,*MPI_COMM,&status );
mpi_send_chain( &(cpoints[whichindex]), rank,0, &sim_params->logLstar,sim_params->iter,*MPI_COMM);
}
}
#else
chain_to_output = &(cpoints[chainhash[N-P+1].index]);
// chain_to_output = &(cpoints[chainhash[1].index]);
#endif
//do the tests on it
#ifdef PARALLEL
if (rank == 0) {
#endif
tests(chain_to_output,biasmap,sim_params->tmask, sim_params, 0x11, NULL);
// if((sim_params->tmask >> 15) & 0x1)fprintf(sim_params->outfile,"log(X): %f \t log(Evidence) estimate: %f\n",sim_params->logfactor*(sim_params->iter+1),sim_params->logZ);
if((sim_params->tmask >> 15) & 0x1)fprintf(sim_params->outfile,"log(X): %f \t log(Evidence) estimate: %f\n",sim_params->logX,sim_params->logZ);
if((sim_params->tmask >> 16) & 0x1)fprintf(sim_params->outfile,"Information estimate: %f\n",sim_params->H);
// fprintf(stderr,"%f ",sim_params->logfactor * (sim_params->iter+1));
// fprintf(stderr,"bad %f ",sim_params->Delta_logX * (sim_params->iter+1));
// fprintf(stderr,",%f + %f * (%d - %d + 1) = %f, ",sim_params->logX_start,sim_params->Delta_logX,sim_params->iter,sim_params->iter_start,sim_params->logX);
fprintf(stderr,"%f ",sim_params->logX);
#ifdef PARALLEL
freemem_chain(&temporary);
}
#endif
}
/* Nested Sampling routine.
Eventually, we want to remove the reading in routine from here and put it into main. */
void nestedsampling(int thinning, int maxiter, simulation_params *sim_params){
//set P and rank for serial job
int P = 1; //number of processors used for NS
int rank = 0; //master process
void *comm_pointer = NULL;
//NS points and their chaint-s
Chain* cpoints = NULL;
Chaint *chaint= (Chaint*)malloc(sizeof(Chaint));
chaint->aat = NULL; chaint->ergt = NULL; chaint->xaat = NULL; chaint->xaat_prev = NULL;
//biasmap
Biasmap *biasmap = (Biasmap*)malloc(sizeof(Biasmap));
biasmap->distb = NULL;
//temporary chain for reading in
Chain* temporary = NULL;
temporary = (Chain *)malloc(sizeof(Chain));
temporary->aa = NULL; temporary->xaa = NULL; temporary->erg = NULL; temporary->xaa_prev = NULL;
//number of chains
int N = 0;
//number of chains stored on this processor
int current_stored = 0;
time_t timer1 = 0;
time_t timer2 = 0;
#ifdef PARALLEL
timer1 = MPI_Wtime();
#else
timer1 = time(NULL);
#endif
#ifdef PARALLEL
MPI_Comm FLEX_WORLD, NS_WORLD;
int S = sim_params->flex_params.number_of_processors;
int SP,Srank, NSgrouprank,FLEXgrouprank;
/*If only reading in from checkpoint file then do not use FLEX processor, even if it was asked for*/
if(sim_params->num_NS_per_checkpoint == -1 && S != 0){
S=0;
fprintf(stderr,"Note, ignoring FLEX options as -C -1,FILENAME is used!\n");
}
int in_NS = 1;
setup_communicators(&FLEX_WORLD,&NS_WORLD,S,&P,&rank,&SP,&Srank,&NSgrouprank,&FLEXgrouprank,&in_NS);
/* P and rank now refer to the rank and number of processors in NS_WORLD and
* SP and srank refer to the rank and number of processors in FLEX_WORLD*/
if(rank == 0){
fprintf(stderr,"Nested Sampling using %d processors + %d FLEX processors\n",P,S);
}
if(in_NS == -1){
ns_for_flex_processor(FLEX_WORLD,FLEXgrouprank,biasmap,sim_params);
return;
}
else{
comm_pointer = (void*)(&NS_WORLD);
}
//parallel variable changes
maxiter /= P;
maxiter++;
thinning /= P;
if(thinning == 0) thinning = 1;
#endif
Instructions *instructions=NULL;
int copies = 0;
//in case restarting from checkpoint
int only_output_checkpoint = 0;
if(sim_params->num_NS_per_checkpoint == -1)
only_output_checkpoint = 1;
else sim_params->num_NS_per_checkpoint /= P;
if(sim_params->num_NS_per_checkpoint == 0) sim_params->num_NS_per_checkpoint = 1;
//initialising Nested Sampling variables
sim_params->iter_start = 0; //this is to make sure we restart after checkpoint at correct place
sim_params->iter = 0;
sim_params->H = 0.0; //information estimate
sim_params->logZ = -DBL_MAX; //evidence or partition function estimate
sim_params->amplitude = -M_PI; //MCMC crankshaft amplitude
sim_params->alpha = 1; //shrinkage ratio of X, the available prior space ratio
sim_params->logX = 0; //log of the available prior space ratio estimate
sim_params->logX_start = 0; //log of the available prior space ratio estimate -- this is important if we restart the simulation
sim_params->Delta_logX = 0; //step length along the logX axis: logX_{i-1} - logX_i = log alpha
sim_params->log_DeltaX = 0; //current width of the prior space weight: log( X_{i-1} - X_i ) = i * log(1 - alpha)
//local Nested Sampling variables
double currE, logZnew, lweight;
//the array where the chains are stored
//this stores the processor, index and ll of cpoints arrays from ALL processors
ChainHash* chainhash = NULL; //only used by master processor of parallel
//this is used to bring in and send out the P chains at each NS interation and for new sample point generation by MCMC
Chain* chaincopies = NULL;
//read in chains from either PDB file or checkpoint file
if(sim_params->restart_from_checkpoint == 1){
//note if only outputting from checkpoint then the tests are performed in here and no chains are stored or sent
current_stored = read_in_from_checkpoint(sim_params, &biasmap, temporary, &cpoints, &chaint, &chainhash, rank, P,comm_pointer,only_output_checkpoint);
} else {
//this will also map and initialise the chains
time_t timer_init1 = 0, timer_init2 = 0;
#ifdef PARALLEL
timer_init1 = MPI_Wtime();