Merge branch 'tom/pinkindexer'

5 files changed, 43 insertions, 23 deletions

diff --git a/src/im-sandbox.c b/src/im-sandbox.c
index da632618..8097c273 100644
--- a/src/im-sandbox.c
+++ b/src/im-sandbox.c
@@ -73,6 +73,12 @@ struct sandbox
 	int n_processed_last_stats;
 	time_t t_last_stats;
 
+	/* Processing timeout in seconds.  After this long without responding
+	 * to a ping, the worker will be killed.  After 3 times this long
+	 * working on one image, even with ping responses, a warning will be
+	 * shown to the user. */
+	int timeout;
+
 	struct index_args *iargs;
 
 	/* Worker processes */
@@ -158,17 +164,18 @@ static void check_hung_workers(struct sandbox *sb)
 			stamp_response(sb, i);
 		}
 
-		if ( tnow - sb->last_response[i] > 240 ) {
-			STATUS("Worker %i did not respond for 4 minutes - "
-			       "sending it SIGKILL.\n", i);
+		if ( tnow - sb->last_response[i] > sb->timeout ) {
+			STATUS("Worker %i did not respond for %i seconds - "
+			       "sending it SIGKILL.\n", i, sb->timeout);
 			kill(sb->pids[i], SIGKILL);
 			stamp_response(sb, i);
 		}
 
-		if ( tnow - sb->shared->time_last_start[i] > 600 ) {
+		if ( tnow - sb->shared->time_last_start[i] > sb->timeout*3 ) {
 			if ( !sb->shared->warned_long_running[i] ) {
 				STATUS("Worker %i has been working on one "
-				       "frame for more than 10 minutes.\n", i);
+				       "frame for more than %i seconds (just "
+				       "for info).\n", i, sb->timeout);
 				STATUS("Event ID is: %s\n",
 				       sb->shared->last_ev[i]);
 				STATUS("Task ID is: %s\n",
@@ -1045,7 +1052,7 @@ char *create_tempdir(const char *temp_location)
 int create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
                    int config_basename, FILE *fh,
                    Stream *stream, const char *tmpdir, int serial_start,
-                   const char *zmq_address, int profile)
+                   const char *zmq_address, int timeout, int profile)
 {
 	int i;
 	struct sandbox *sb;
@@ -1075,6 +1082,7 @@ int create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
 	sb->serial = serial_start;
 	sb->tmpdir = tmpdir;
 	sb->profile = profile;
+	sb->timeout = timeout;
 	if ( zmq_address != NULL ) {
 		sb->zmq = 1;
 		sb->zmq_address = zmq_address;
diff --git a/src/im-sandbox.h b/src/im-sandbox.h
index 2c43a543..3acd62db 100644
--- a/src/im-sandbox.h
+++ b/src/im-sandbox.h
@@ -84,6 +84,6 @@ extern void set_last_task(char *lt, const char *task);
 extern int create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
                           int config_basename, FILE *fh,  Stream *stream,
                           const char *tempdir, int serial_start,
-                          const char *zmq_address, int profile);
+                          const char *zmq_address, int timeout, int profile);
 
 #endif /* IM_SANDBOX_H */
diff --git a/src/indexamajig.c b/src/indexamajig.c
index bb115cc3..e607ec29 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -117,6 +117,7 @@ struct indexamajig_arguments
 	TakeTwoOptions **taketwo_opts_ptr;
 	FelixOptions **felix_opts_ptr;
 	XGandalfOptions **xgandalf_opts_ptr;
+	PinkIndexerOptions **pinkindexer_opts_ptr;
 };
 
 
@@ -139,6 +140,7 @@ static error_t parse_arg(int key, char *arg, struct argp_state *state)
 		state->child_inputs[0] = args->taketwo_opts_ptr;
 		state->child_inputs[1] = args->felix_opts_ptr;
 		state->child_inputs[2] = args->xgandalf_opts_ptr;
+		state->child_inputs[3] = args->pinkindexer_opts_ptr;
 		break;
 
 		case 'h' :
@@ -255,6 +257,7 @@ static error_t parse_arg(int key, char *arg, struct argp_state *state)
 			ERROR("Invalid value for --min-peaks\n");
 			return EINVAL;
 		}
+		(*(args->pinkindexer_opts_ptr))->min_peaks = args->iargs.min_peaks;
 		break;
 
 		case 304 :
@@ -479,10 +482,8 @@ static error_t parse_arg(int key, char *arg, struct argp_state *state)
 		break;
 
 		case 503 :
-		if ( sscanf(arg, "%f", &args->iargs.fix_bandwidth) != 1 ) {
-			ERROR("Invalid value for --fix-bandwidth\n");
-			return EINVAL;
-		}
+		ERROR("The option --fix-bandwidth is no longer used.\n");
+		ERROR("Set the bandwidth in the geometry file instead.\n");
 		break;
 
 		case 504 :
@@ -593,9 +594,11 @@ int main(int argc, char *argv[])
 	int r;
 	struct beam_params beam;
 	char *zmq_address = NULL;
+	int timeout = 240;
 	TakeTwoOptions *taketwo_opts = NULL;
 	FelixOptions *felix_opts = NULL;
 	XGandalfOptions *xgandalf_opts = NULL;
+	PinkIndexerOptions *pinkindexer_opts = NULL;
 
 	/* Defaults for "top level" arguments */
 	args.filename = NULL;
@@ -620,6 +623,7 @@ int main(int argc, char *argv[])
 	args.taketwo_opts_ptr = &taketwo_opts;
 	args.felix_opts_ptr = &felix_opts;
 	args.xgandalf_opts_ptr = &xgandalf_opts;
+	args.pinkindexer_opts_ptr = &pinkindexer_opts;
 
 	/* Defaults for process_image arguments */
 	args.iargs.cell = NULL;
@@ -675,7 +679,6 @@ int main(int argc, char *argv[])
 	args.iargs.push_res = -1.0;
 	args.iargs.highres = +INFINITY;
 	args.iargs.fix_profile_r = -1.0;
-	args.iargs.fix_bandwidth = -1.0;
 	args.iargs.fix_divergence = -1.0;
 	args.iargs.no_image_data = 0;
 
@@ -809,6 +812,7 @@ int main(int argc, char *argv[])
 		{&taketwo_argp, 0, NULL, -2},
 		{&felix_argp, 0, NULL, -2},
 		{&xgandalf_argp, 0, NULL, -2},
+		{&pinkIndexer_argp, 0, NULL, -2},
 		{0}
 	};
 
@@ -979,6 +983,8 @@ int main(int argc, char *argv[])
 
 	} else {
 
+		int i, n;
+		const IndexingMethod *methods;
 		IndexingFlags flags = 0;
 
 		if ( args.iargs.cell != NULL ) {
@@ -1005,16 +1011,26 @@ int main(int argc, char *argv[])
 		}
 
 		args.iargs.ipriv = setup_indexing(args.indm_str, args.iargs.cell,
-		                                  args.iargs.det,
+		                                  args.iargs.det, args.iargs.beam,
 		                                  args.iargs.tols, flags,
 		                                  taketwo_opts,
 		                                  xgandalf_opts,
+		                                  pinkindexer_opts,
 		                                  felix_opts);
 		if ( args.iargs.ipriv == NULL ) {
 			ERROR("Failed to set up indexing system\n");
 			return 1;
 		}
 
+		methods = indexing_methods(args.iargs.ipriv, &n);
+		for ( i=0; i<n; i++ ) {
+			if ( methods[i] & INDEXING_PINKINDEXER ) {
+				/* Extend timeout if using pinkIndexer */
+				timeout = 3000;
+				break;
+			}
+		}
+
 	}
 
 	/* Change back to where we were before.  Sandbox code will create
@@ -1056,7 +1072,7 @@ int main(int argc, char *argv[])
 
 	r = create_sandbox(&args.iargs, args.n_proc, args.prefix, args.basename,
 	                   fh, st, tmpdir, args.serial_start, zmq_address,
-	                   args.profile);
+	                   timeout, args.profile);
 
 	free_imagefile_field_list(args.iargs.copyme);
 	cell_free(args.iargs.cell);
diff --git a/src/process_image.c b/src/process_image.c
index 654ffd46..f28952bc 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -226,6 +226,8 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 		                         &imfile) ) return;
 	}
 
+	image.bw = iargs->beam->bandwidth;
+
 	/* Take snapshot of image before applying horrible noise filters */
 	time_accounts_set(taccs, TACC_FILTER);
 	set_last_task(last_task, "image filter");
@@ -369,17 +371,12 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 	} else {
 		image.div = 0.0;
 	}
-	if ( iargs->fix_bandwidth >= 0.0 ) {
-		image.bw = iargs->fix_bandwidth;
-	} else {
-		image.bw = 0.00000001;
-	}
-
-	/* Set beam spectrum for pink beam data */
+	/* Set beam spectrum */
 	if ( iargs->spectrum != NULL ) {
 		image.spectrum = iargs->spectrum;
 	} else {
-		image.spectrum = spectrum_generate_gaussian(image.lambda, image.bw);
+		image.spectrum = spectrum_generate_gaussian(image.lambda,
+		                                            image.bw);
 	}
 
 	if ( image_feature_count(image.features) < iargs->min_peaks ) {
diff --git a/src/process_image.h b/src/process_image.h
index 1b899619..395a54cd 100644
--- a/src/process_image.h
+++ b/src/process_image.h
@@ -107,7 +107,6 @@ struct index_args
 	float push_res;
 	float highres;
 	float fix_profile_r;
-	float fix_bandwidth;
 	float fix_divergence;
 	int overpredict;
 	Spectrum *spectrum;