WIP on tidy-up

1 files changed, 181 insertions, 242 deletions

diff --git a/src/indexamajig.c b/src/indexamajig.c
index f4bbb72e..ed84c6a8 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -81,7 +81,7 @@ enum {
 
 
 /* Information about the indexing process which is common to all patterns */
-struct static_index_args
+struct index_args
 {
 	UnitCell *cell;
 	int config_cmfilter;
@@ -110,7 +110,6 @@ struct static_index_args
 	double ir_out;
 
 	/* Output stream */
-	pthread_mutex_t *output_mutex;  /* Protects the output stream */
 	FILE *ofh;
 	const struct copy_hdf5_field *copyme;
 	char *outfile;
@@ -118,36 +117,16 @@ struct static_index_args
 
 
 /* Information about the indexing process for one pattern */
-struct index_args
+struct pattern_args
 {
 	/* "Input" */
 	char *filename;
-	struct static_index_args static_args;
 
 	/* "Output" */
 	int indexable;
 };
 
 
-/* Information needed to choose the next task and dispatch it */
-struct queue_args
-{
-	FILE *fh;
-	char *prefix;
-	int config_basename;
-	struct static_index_args static_args;
-
-	char *use_this_one_instead;
-
-	int n_indexable;
-	int n_processed;
-	int n_indexable_last_stats;
-	int n_processed_last_stats;
-	int t_last_stats;
-	int updateReader;
-};
-
-
 static void show_help(const char *s)
 {
 	printf("Syntax: %s [options]\n\n", s);
@@ -246,16 +225,16 @@ static void show_help(const char *s)
 }
 
 
-// Get next pattern in .lst
-char* get_pattern(FILE *fh) {
-    char *rval;
-    char line[LINE_LENGTH];
-    rval = fgets(line, LINE_LENGTH - 1, fh);
-    if (ferror(fh)) {
-        printf("Read error\n");
-        rval = NULL;
-    }
-    return rval;
+static char *get_pattern(FILE *fh)
+{
+	char *rval;
+	char line[LINE_LENGTH];
+	rval = fgets(line, LINE_LENGTH - 1, fh);
+	if ( ferror(fh) ) {
+		ERROR("Failed to get next filename from list.\n");
+		rval = NULL;
+	}
+	return rval;
 }
 
 
@@ -416,11 +395,11 @@ static void process_image(void *qp, void *pp, int cookie)
 	outfilename = malloc(strlen(outfile) + 1);
 	snprintf(outfilename, LINE_LENGTH - 1, "%s", outfile);
 	if ((fd = open(outfilename, O_WRONLY)) == -1) {
-		perror("Error on opening\n");
+		ERROR("Error on opening\n");
 		exit(1);
 	}
 	if (fcntl(fd, F_SETLKW, &fl) == -1) {
-		perror("Error on setting lock wait\n");
+		ERROR("Error on setting lock wait\n");
 		exit(1);
 	}
 
@@ -428,7 +407,7 @@ static void process_image(void *qp, void *pp, int cookie)
 	FILE *fh;
 	fh = fopen(outfilename, "a");
 	if (fh == NULL) {
-		perror("Error inside lock\n");
+		ERROR("Error inside lock\n");
 	}
 	write_chunk(fh, &image, hdfile, qargs->static_args.stream_flags);
 	fclose(fh);
@@ -436,7 +415,7 @@ static void process_image(void *qp, void *pp, int cookie)
 	/* Unlock stream for other processes */
 	fl.l_type = F_UNLCK; /* set to unlock same region */
 	if (fcntl(fd, F_SETLK, &fl) == -1) {
-		perror("fcntl");
+		ERROR("fcntl");
 		exit(1);
 	}
 	close(fd);
@@ -456,6 +435,36 @@ static void process_image(void *qp, void *pp, int cookie)
 }
 
 
+static void run_work(const struct index_args *iargs,
+                     int filename_pipe, int results_pipe)
+{
+	int allDone = 0;
+
+	while ( !allDone ) {
+
+		/* read from pipe and return number of bytes read */
+		if ((buff_count=read(fd_pipeOut[batchNum-1][0],&buffR,BUFFER))<0) {
+			ERROR("read1");
+		} else if (buff_count > 0) {
+			/* process image */
+			pargs.filename = buffR;
+			pargs.indexable = 0;
+			process_image(&qargs, &pargs, batchNum);
+			/* request another image */
+			buff_count = sprintf(buffW, "%d\n", pargs.indexable);
+			if(write (fd_pipeIn[batchNum-1][1], buffW, buff_count)<0)
+				ERROR("write P0");
+		} else if (buff_count == 0) {
+			allDone = 1;
+		}
+
+	}
+	/* close my pipes */
+	close(filename_pipe);
+	close(results_pipe);
+}
+
+
 #ifdef HAVE_CLOCK_GETTIME
 
 static time_t get_monotonic_seconds()
@@ -542,7 +551,7 @@ int main(int argc, char *argv[])
 	float tols[4] = {5.0, 5.0, 5.0, 1.5}; /* a,b,c,angles (%,%,%,deg) */
 	int cellr;
 	int peaks;
-	int nProcesses = 1;
+	int n_proc = 1;
 	char *prepare_line;
 	char prepare_filename[LINE_LENGTH];
 	struct queue_args qargs;
@@ -558,6 +567,12 @@ int main(int argc, char *argv[])
 	float ir_inn = 4.0;
 	float ir_mid = 5.0;
 	float ir_out = 7.0;
+	int n_indexable, n_processed, n_indexable_last_stats;
+	int n_processed_last_stats;
+	int t_last_stats;
+	pid_t *pids;
+	int *filename_pipes;
+	int *result_pipes;
 
 	copyme = new_copy_hdf5_field_list();
 	if ( copyme == NULL ) {
@@ -638,7 +653,7 @@ int main(int argc, char *argv[])
 			break;
 
 			case 'j' :
-			nProcesses = atoi(optarg);
+			n_proc = atoi(optarg);
 			break;
 
 			case 'g' :
@@ -909,7 +924,7 @@ int main(int argc, char *argv[])
 		prepare_line = tmp;
 	}
 	snprintf(prepare_filename, LINE_LENGTH-1, "%s%s", prefix, prepare_line);
-	qargs.use_this_one_instead = prepare_line;
+	rewind(fh);
 
 	/* Prepare the indexer */
 	if ( indm != NULL ) {
@@ -925,223 +940,147 @@ int main(int argc, char *argv[])
 
 	gsl_set_error_handler_off();
 
-	qargs.static_args.cell = cell;
-	qargs.static_args.config_cmfilter = config_cmfilter;
-	qargs.static_args.config_noisefilter = config_noisefilter;
-	qargs.static_args.config_verbose = config_verbose;
-	qargs.static_args.config_satcorr = config_satcorr;
-	qargs.static_args.config_closer = config_closer;
-	qargs.static_args.config_insane = config_insane;
-	qargs.static_args.config_bgsub = config_bgsub;
-	qargs.static_args.cellr = cellr;
-	qargs.static_args.tols[0] = tols[0];
-	qargs.static_args.tols[1] = tols[1];
-	qargs.static_args.tols[2] = tols[2];
-	qargs.static_args.tols[3] = tols[3];
-	qargs.static_args.threshold = threshold;
-	qargs.static_args.min_gradient = min_gradient;
-	qargs.static_args.min_snr = min_snr;
-	qargs.static_args.min_int_snr = min_int_snr;
-	qargs.static_args.det = det;
-	qargs.static_args.indm = indm;
-	qargs.static_args.ipriv = ipriv;
-	qargs.static_args.peaks = peaks;
-	qargs.static_args.ofh = ofh;
-	qargs.static_args.beam = beam;
-	qargs.static_args.element = element;
-	qargs.static_args.stream_flags = stream_flags;
-	qargs.static_args.hdf5_peak_path = hdf5_peak_path;
-	qargs.static_args.copyme = copyme;
-	qargs.static_args.ir_inn = ir_inn;
-	qargs.static_args.ir_mid = ir_mid;
-	qargs.static_args.ir_out = ir_out;
-
-	qargs.fh = fh;
-	qargs.prefix = prefix;
-	qargs.config_basename = config_basename;
-	qargs.n_indexable = 0;
-	qargs.n_processed = 0;
-	qargs.n_indexable_last_stats = 0;
-	qargs.n_processed_last_stats = 0;
-	qargs.updateReader = 0; /* first process updates */
-	qargs.t_last_stats = get_monotonic_seconds();
-
-	/* Read .lst file */
-	register int i;
-	rewind(fh); /* make sure to read from start */
-
-	/* Clear output file content */
-	char *myOutfilename = NULL;
-	chomp(prefix);
-	chomp(outfile);
-	myOutfilename = malloc(strlen(outfile) + 1);
-	snprintf(myOutfilename, LINE_LENGTH - 1, "%s", outfile);
-	FILE *tfh;
-	tfh = fopen(myOutfilename, "a+");
-	if (tfh == NULL) {
-		ERROR("No output filename\n");
-	}
-	fclose(tfh);
-	qargs.static_args.outfile = outfile;
-	int ready_fd;
-	int buff_count;
-	fd_set fdset,tmpset;
-	char buffR[BUFFER], buffW[BUFFER];
-	int fd_pipeIn[nProcesses][2]; /* Process0 In */
-	int fd_pipeOut[nProcesses][2]; /* Process0 Out */
-	unsigned int opts;
-
-	FD_ZERO(&fdset); /* clear the fd_set */
-	/* set pipeIn as non-blocking */
-	for ( i=0; i<nProcesses; i++ ) {
-		opts = fcntl(fd_pipeIn[i][0], F_GETFL);
-		fcntl(fd_pipeIn[i][0], F_SETFL, opts | O_NONBLOCK);
-	}
+	/* Static worker args */
+	iargs.cell = cell;
+	iargs.config_cmfilter = config_cmfilter;
+	iargs.config_noisefilter = config_noisefilter;
+	iargs.config_verbose = config_verbose;
+	iargs.config_satcorr = config_satcorr;
+	iargs.config_closer = config_closer;
+	iargs.config_insane = config_insane;
+	iargs.config_bgsub = config_bgsub;
+	iargs.cellr = cellr;
+	iargs.tols[0] = tols[0];
+	iargs.tols[1] = tols[1];
+	iargs.tols[2] = tols[2];
+	iargs.tols[3] = tols[3];
+	iargs.threshold = threshold;
+	iargs.min_gradient = min_gradient;
+	iargs.min_snr = min_snr;
+	iargs.min_int_snr = min_int_snr;
+	iargs.det = det;
+	iargs.indm = indm;
+	iargs.ipriv = ipriv;
+	iargs.peaks = peaks;
+	iargs.ofh = ofh;
+	iargs.beam = beam;
+	iargs.element = element;
+	iargs.stream_flags = stream_flags;
+	iargs.hdf5_peak_path = hdf5_peak_path;
+	iargs.copyme = copyme;
+	iargs.ir_inn = ir_inn;
+	iargs.ir_mid = ir_mid;
+	iargs.ir_out = ir_out;
+	iargs.outfile = outfile;
+
+	n_indexable = 0;
+	n_processed = 0;
+	n_indexable_last_stats = 0;
+	n_processed_last_stats = 0;
+	t_last_stats = get_monotonic_seconds();
+
+	/* Fork the right number of times */
+	for ( i=0; i<n_proc; i++ ) {
+
+		pid_t p;
+		int filename_pipe[2];
+		int result_pipe[2];
+
+		if ( pipe(filename_pipe) == - 1 ) {
+			ERROR("pipe() failed!\n");
+			return 1;
+		}
 
-	/**** PIPING ****/
-	for ( i=0; i<nProcesses; i++ ) {
-		pipe(fd_pipeIn[i]);
-		pipe(fd_pipeOut[i]);
-	}
+		if ( pipe(results_pipe) == - 1 ) {
+			ERROR("pipe() failed!\n");
+			return 1;
+		}
 
-	int max_fd = 0;
-	for ( i=0; i<nProcesses; i++ ) {
-		FD_SET(fd_pipeIn[i][0], &fdset);
-		if (fd_pipeIn[i][0] > max_fd) { /* find max_fd */
-			max_fd = fd_pipeIn[i][0];
+		p = fork();
+		if ( p == -1 ) {
+			ERROR("fork() failed!\n");
+			return 1;
 		}
-	}
-	max_fd = max_fd+1;
-	/* copy file set to tmpset */
-	memcpy((void *) &tmpset,(void *) &fdset, sizeof(fd_set));
-
-	/**** FORKING ****/
-	int power = 10; /* 2^power must be larger than nProcesses */
-	int pid[power];
-	double num = 0;
-	int batchNum = 0;
-	/* Fork 2^power times */
-	for ( i=0; i<power; i++ ) {
-		pid[i] = fork();
-	}
-	/* Assign id */
-	for ( i=0; i<power; i++ ) {
-		if (pid[i] == 0) { /* keep parents and kill off children */
-			num += pow(2, i);
+
+		if ( p == 0 ) {
+			/* Child process gets the 'read' end of the filename
+			 * pipe, and the 'write' end of the result pipe. */
+			close(filename_pipe[1]);
+			close(result_pipe[0]);
+			run_work(&iargs, filename_pipe[0], result_pipe[1]);
+			exit(0);
 		}
+
+		/* Parent process gets the 'write' end of the filename pipe
+		 * and the 'read' end of the result pipe. */
+		pid[i] = p;
+		close(filename_pipe[0]);
+		close(result_pipe[1]);
+		filename_pipes[i] = filename_pipe[1];
+		result_pipes[i] = result_pipe[0];
+
 	}
-	/* Kill if batchNum too high */
-	if (num >= nProcesses + 1) {
-		exit(0); /* kill */
-	}
-	batchNum = (int) num;
 
-	/**** PLUMBING ****/
-	if (batchNum == qargs.updateReader) {
-		for ( i=0; i<nProcesses; i++ ) {
-			close(fd_pipeIn[i][1]); /* close all write pipes In */
-			close(fd_pipeOut[i][0]); /* close all read pipes Out */
-		}
-	} else {
-		for ( i=0; i<nProcesses; i++ ) {
-			if (i == batchNum - 1) { /* batchNum = 1,2,3 ... */
-				close(fd_pipeIn[i][0]); /* close read pipe In */
-				close(fd_pipeOut[i][1]); /* close write pipe Out */
-			} else {
-				close(fd_pipeIn[i][0]); // close remaining pipes In
-				close(fd_pipeIn[i][1]);
-				close(fd_pipeOut[i][0]); // close remaining pipes Out
-				close(fd_pipeOut[i][1]);
-			}
-		}
+	/* Send first image to all children */
+	char *nextImage = NULL;
+	for ( i=0; i<nProcesses; i++ ) {
+		nextImage = get_pattern(fh);
+		buff_count = sprintf(buffW, "%s",nextImage);
+		write (fd_pipeOut[i][1], buffW, buff_count);
 	}
-	/**** INDEXING ****/
-	double tStart, tEnd;
-	tStart = get_monotonic_seconds();
-	int allDone = 0;
-	if (batchNum == qargs.updateReader){
-		char *nextImage = NULL;
-		for ( i=0; i<nProcesses; i++ ) { /* Send out image to all processes*/
-			nextImage = get_pattern(fh);
-			buff_count = sprintf(buffW, "%s",nextImage);
-			write (fd_pipeOut[i][1], buffW, buff_count);
-		}
-		int nFinished = 0;
-		while (!allDone) {
-			/* select from file set for reading */
-			if ((ready_fd = select(max_fd,&fdset,NULL,NULL,NULL)) < 0)
-				perror("select");
-			if (ready_fd > 0) {
-				for ( i=0; i<nProcesses; i++ ) {
-					/* is in file set that raised flag? */
-					if (FD_ISSET(fd_pipeIn[i][0],&fdset)) {
-						/* read from pipe and return number of bytes read */
-						if ((buff_count=read(fd_pipeIn[i][0],&buffR,BUFFER))<0) {
-							perror("read");
+	int nFinished = 0;
+	while (!allDone) {
+		/* select from file set for reading */
+		if ((ready_fd = select(max_fd,&fdset,NULL,NULL,NULL)) < 0)
+			ERROR("select");
+		if (ready_fd > 0) {
+			for ( i=0; i<nProcesses; i++ ) {
+				/* is in file set that raised flag? */
+				if (FD_ISSET(fd_pipeIn[i][0],&fdset)) {
+					/* read from pipe and return number of bytes read */
+					if ((buff_count=read(fd_pipeIn[i][0],&buffR,BUFFER))<0) {
+						ERROR("read");
+					} else {
+						qargs.n_indexable += atoi(buffR);
+						qargs.n_processed++;
+						/* write to pipe */
+						if ((nextImage = get_pattern(fh)) == NULL){
+							nFinished++; /* no more images */
+							if ( nFinished == nProcesses )
+								allDone = 1; /* EXIT */
 						} else {
-							qargs.n_indexable += atoi(buffR);
-							qargs.n_processed++;
-							/* write to pipe */
-							if ((nextImage = get_pattern(fh)) == NULL){
-								nFinished++; /* no more images */
-								if ( nFinished == nProcesses )
-									allDone = 1; /* EXIT */
-							} else {
-								/* send out image */
-								buff_count = sprintf(buffW, "%s",nextImage);
-								if (write (fd_pipeOut[i][1], buffW, buff_count)<0)
-									perror("write pipe");
-							}
+							/* send out image */
+							buff_count = sprintf(buffW, "%s",nextImage);
+							if (write (fd_pipeOut[i][1], buffW, buff_count)<0)
+								ERROR("write pipe");
 						}
 					}
 				}
 			}
-			/* file set is modified, so copy original from tmpset */
-			memcpy((void *) &fdset,(void *) &tmpset, sizeof(fd_set));
-
-			/* Update to screen */
-			double tNow = get_monotonic_seconds();
-			if ( tNow >= qargs.t_last_stats+STATS_EVERY_N_SECONDS ) {
-					STATUS("%i out of %i indexed so far,"
-				    " %i out of %i since the last message.\n\n",
-				    qargs.n_indexable, qargs.n_processed,
-				    qargs.n_indexable - qargs.n_indexable_last_stats,
-				    qargs.n_processed - qargs.n_processed_last_stats);
-
-					qargs.n_indexable_last_stats = qargs.n_indexable;
-					qargs.n_processed_last_stats = qargs.n_processed;
-					qargs.t_last_stats = tNow;
-			}
 		}
-		/* close my pipes */
-		for ( i=0; i<nProcesses; i++ ) {
-			close(fd_pipeIn[i][0]);
-			close(fd_pipeOut[i][1]);
+		/* file set is modified, so copy original from tmpset */
+		memcpy((void *) &fdset,(void *) &tmpset, sizeof(fd_set));
+
+		/* Update to screen */
+		double tNow = get_monotonic_seconds();
+		if ( tNow >= qargs.t_last_stats+STATS_EVERY_N_SECONDS ) {
+				STATUS("%i out of %i indexed so far,"
+			    " %i out of %i since the last message.\n\n",
+			    qargs.n_indexable, qargs.n_processed,
+			    qargs.n_indexable - qargs.n_indexable_last_stats,
+			    qargs.n_processed - qargs.n_processed_last_stats);
+
+				qargs.n_indexable_last_stats = qargs.n_indexable;
+				qargs.n_processed_last_stats = qargs.n_processed;
+				qargs.t_last_stats = tNow;
 		}
-		tEnd = get_monotonic_seconds();
-		printf("Compute Time: %.2fs\n", tEnd - tStart);
-	} else {
-		while(!allDone){
-			/* read from pipe and return number of bytes read */
-			if ((buff_count=read(fd_pipeOut[batchNum-1][0],&buffR,BUFFER))<0) {
-				perror("read1");
-			} else if (buff_count > 0) {
-				/* process image */
-				pargs.filename = buffR;
-				pargs.indexable = 0;
-				process_image(&qargs, &pargs, batchNum);
-				/* request another image */
-				buff_count = sprintf(buffW, "%d\n", pargs.indexable);
-				if(write (fd_pipeIn[batchNum-1][1], buffW, buff_count)<0)
-					perror("write P0");
-			} else if (buff_count == 0) {
-				allDone = 1; /* EXIT */
-			}
-		}
-		/* close my pipes */
-		close(fd_pipeIn[batchNum-1][1]);
-		close(fd_pipeOut[batchNum-1][0]);
 	}
+	/* close my pipes */
+	for ( i=0; i<nProcesses; i++ ) {
+		close(fd_pipeIn[i][0]);
+		close(fd_pipeOut[i][1]);
+	}
+	tEnd = get_monotonic_seconds();
 
 	cleanup_indexing(ipriv);