Merge pull request #1418 from dthain/blue-waters-bugs

Fix misc build issues on Blue Waters.

configure

@@ -36,7 +36,7 @@ fi
 
 # `git archive` (man gitattributes(5)) fills this in, otherwise we do it manually...
 COMMIT='$Format:%H$'
-if [ "$(substr "$COMMIT" 1 1)" = '$' ]; then
+if [ "$(expr substr "$COMMIT" 1 1)" = '$' ]; then
 	if [ "$GIT" = y ]; then
 		COMMIT="$(git rev-parse HEAD)"
 	else
@@ -54,7 +54,7 @@ fi
 
 # The date is the commit date of the commit, or now if the working tree is dirty.
 DATE='$Format:%ci$'
-if [ "$(substr "$DATE" 1 1)" = '$' ]; then
+if [ "$(expr substr "$DATE" 1 1)" = '$' ]; then
 	if [ "$GIT" = y ]; then
 		DATE="$(git log -1 --pretty=format:%ci HEAD)"
 	else
@@ -72,7 +72,7 @@ elif [ -n "$CCTOOLS_BRANCH" ]; then
 	BRANCH="$CCTOOLS_BRANCH"
 else
 	BRANCH='$Format:%d$'
-	if [ "$(substr "$BRANCH" 1 1)" = '$' ]; then
+	if [ "$(expr substr "$BRANCH" 1 1)" = '$' ]; then
 		if [ "$GIT" = y ]; then
 			BRANCH="$(git rev-parse --abbrev-ref HEAD)"
 		else
@@ -95,7 +95,7 @@ else
 	fi
 fi
 
-SOURCE="${BRANCH}:$(substr "$COMMIT" 1 8)${DIRTY}"
+SOURCE="${BRANCH}:$(expr substr "$COMMIT" 1 8)${DIRTY}"
 VERSION="$MAJOR.$MINOR.$MICRO [${SOURCE}]"
 
 # Bourne shell is tricky when you use backtick command substitution backslash
@@ -732,6 +732,10 @@ then
 	then
 		ccflags="${ccflags} -DHAS_MYSQL_MYSQL_H"
 	fi
+
+	# When mysql is enabled, we also need ssl
+	config_openssl_path=auto
+
 else
 	if [ $config_mysql_path = yes ]
 	then

dttools/src/path_disk_size_info.c

@@ -55,7 +55,7 @@ int path_disk_size_info_get_r(const char *path, int64_t max_secs, struct path_di
 
 		if((here->dir = opendir(path))) {
 			here->name = xxstrdup(path);
-			s->current_dirs = list_create(0);
+			s->current_dirs = list_create();
 			s->size_so_far  = 0;
 			s->count_so_far = 1;                     /* count the root directory */
 			list_push_tail(s->current_dirs, here);

dttools/src/rmonitor_poll.c

@@ -454,7 +454,7 @@ int rmonitor_get_mmaps_usage(pid_t pid, struct hash_table *maps)
 		/* add the info to a sorted list per map, by start. Overlaping maps will be merged later. */
 		struct list *infos = hash_table_lookup(maps, info->map_name);
 		if(!infos) {
-			infos = list_create(0);
+			infos = list_create();
 			hash_table_insert(maps, info->map_name, infos);
 		}
 

dttools/src/rmsummary.c

@@ -684,7 +684,7 @@ struct list *rmsummary_parse_file_multiple(const char *filename)
 	struct jx_parser *p = jx_parser_create(0);
 	jx_parser_read_stream(p, stream);
 
-	struct list      *lst = list_create(0);
+	struct list      *lst = list_create();
 	struct rmsummary *s;
 
 	do

makeflow/src/dag.c

@@ -164,7 +164,7 @@ struct list *dag_input_files(struct dag *d)
 	char *filename;
 	struct list *il;
 
-	il = list_create(0);
+	il = list_create();
 
 	hash_table_firstkey(d->files);
 	while((hash_table_nextkey(d->files, &filename, (void **) &f)))

makeflow/src/dag_node.c

@@ -30,8 +30,8 @@ struct dag_node *dag_node_create(struct dag *d, int linenum)
 	n->nodeid = d->nodeid_counter++;
 	n->variables = hash_table_create(0, 0);
 
-	n->source_files = list_create(0);
-	n->target_files = list_create(0);
+	n->source_files = list_create();
+	n->target_files = list_create();
 
 	n->remote_names = itable_create(0);
 	n->remote_names_inv = hash_table_create(0, 0);

makeflow/src/dag_visitors.c

@@ -171,7 +171,7 @@ int dag_to_file_categories(const struct dag *d, FILE * dag_stream, char *(*renam
 		name = n->category->name;
 		ns = hash_table_lookup(nodes_of_category, name);
 		if(!ns) {
-			ns = list_create(0);
+			ns = list_create();
 			hash_table_insert(nodes_of_category, name, (void *) ns);
 		}
 		list_push_tail(ns, n);

makeflow/src/lexer.c

@@ -1243,7 +1243,7 @@ struct lexer *lexer_create(int type, void *data, int line_number, int column_num
 
 	lx->line_number = line_number;
 	lx->column_number = column_number;
-	lx->column_numbers = list_create(0);
+	lx->column_numbers = list_create();
 
 	lx->stream = NULL;
 	lx->buffer = NULL;
@@ -1255,7 +1255,7 @@ struct lexer *lexer_create(int type, void *data, int line_number, int column_num
 	lx->lexeme_size = 0;
 	lx->lexeme_max = BUFFER_CHUNK_SIZE;
 
-	lx->token_queue = list_create(0);
+	lx->token_queue = list_create();
 
 	lx->buffer = calloc(2 * BUFFER_CHUNK_SIZE, sizeof(char));
 	if(!lx->buffer)

makeflow/src/makeflow_wrapper.c

@@ -20,8 +20,8 @@ struct makeflow_wrapper * makeflow_wrapper_create()
 	struct makeflow_wrapper *w = malloc(sizeof(*w));
 	w->command = NULL;
 
-	w->input_files = list_create(0);
-	w->output_files = list_create(0);
+	w->input_files = list_create();
+	w->output_files = list_create();
 
 	w->remote_names = itable_create(0);
 	w->remote_names_inv = hash_table_create(0, 0);

resource_monitor/src/resource_monitor.c

@@ -772,7 +772,7 @@ int64_t peak_cores(int64_t wall_time, int64_t cpu_time) {
 	int64_t max_separation = 60 + 2*interval; /* at least one minute and a complete */
 
 	if(!samples) {
-		samples = list_create(0);
+		samples = list_create();
 
 		struct peak_cores_sample *zero = malloc(sizeof(struct peak_cores_sample));
 		zero->wall_time = 0;
@@ -1822,7 +1822,7 @@ int main(int argc, char **argv) {
 
 	total_bytes_rx = 0;
 	total_bytes_tx = 0;
-	tx_rx_sizes    = list_create(0);
+	tx_rx_sizes    = list_create();
 
     rmsummary_read_env_vars(resources_limits);
 

resource_monitor/src/resource_monitor_cluster.c

@@ -351,7 +351,7 @@ void cluster_collect_summaries_recursive(struct cluster *c, struct list *accum)
 
 struct list *cluster_collect_summaries(struct cluster *c)
 {
-	struct list *summaries = list_create(0);
+	struct list *summaries = list_create();
 
 	cluster_collect_summaries_recursive(c, summaries);
 
@@ -378,7 +378,7 @@ struct cluster *nearest_neighbor_clustering(struct list *initial_clusters, doubl
 	if(list_size(initial_clusters) < 2)
 		return top;
 
-	stack = list_create(0);
+	stack = list_create();
 	list_push_head(stack, top);
 
 	/* Add all of the initial clusters as active clusters. */
@@ -472,7 +472,7 @@ struct list *collect_final_clusters(struct cluster *final, int max_clusters)
 	struct cluster *c, *cmax;
 	double dmax;
 
-	clusters = list_create(0);
+	clusters = list_create();
 	list_push_head(clusters, final);
 
 	/* At each count, we split the cluster with the maximal
@@ -481,7 +481,7 @@ struct list *collect_final_clusters(struct cluster *final, int max_clusters)
 	 * clusters can be split. */
 	for(count = 1; count < max_clusters && count == list_size(clusters); count++)
 	{
-		clusters_next = list_create(0);
+		clusters_next = list_create();
 		list_first_item(clusters);
 
 		cmax = NULL;
@@ -658,7 +658,7 @@ void report_clusters_rules(FILE *freport, struct list *clusters)
 struct list *create_initial_clusters(struct list *summaries)
 {
 	struct rmDsummary *s;
-	struct list *initial_clusters = list_create(0);
+	struct list *initial_clusters = list_create();
 
 	list_first_item(summaries);
 	while( (s = list_next_item(summaries)) )