Bring down upstream hwloc 438d9ed7457888c63d29778bda56cd27c52a8d51 to

work around buggy NUMA node cpusets (i.e., buggy BIOSs).

Thanks to Jeff Becker for reporting the issue.

Submitted by Brice Goglin, reviewed by Jeff Squyres.

cmr=v1.7.4:reviewer=ompi-rm1.7

This commit was SVN r30306.

opal/mca/hwloc/hwloc172/README-ompi.txt

@@ -2,3 +2,5 @@ Applied the following patches from the upstream hwloc 1.7 branch after
 the v1.7.2 release:
 
 5198d4c Only include <malloc.h> if necessary
+438d9ed linux/NUMA: Work around buggy NUMA node cpusets
+

opal/mca/hwloc/hwloc172/hwloc/src/topology-linux.c

@@ -1,6 +1,6 @@
 /*
  * Copyright © 2009 CNRS
- * Copyright © 2009-2013 Inria.  All rights reserved.
+ * Copyright © 2009-2014 Inria.  All rights reserved.
  * Copyright © 2009-2013 Université Bordeaux 1
  * Copyright © 2009-2011 Cisco Systems, Inc.  All rights reserved.
  * Copyright © 2010 IBM
@@ -2676,20 +2676,23 @@ look_sysfsnode(struct hwloc_topology *topology,
 
   {
       hwloc_obj_t * nodes = calloc(nbnodes, sizeof(hwloc_obj_t));
-      float * distances = calloc(nbnodes*nbnodes, sizeof(float));
       unsigned *indexes = calloc(nbnodes, sizeof(unsigned));
+      float * distances;
+      int failednodes = 0;
       unsigned index_;
 
-      if (NULL == indexes || NULL == distances || NULL == nodes) {
+      if (NULL == nodes || NULL == indexes) {
           free(nodes);
           free(indexes);
-          free(distances);
           hwloc_bitmap_free(nodeset);
+          nbnodes = 0;
           goto out;
       }
 
-      /* Get node indexes now. We need them in order since Linux groups
-       * sparse distances but keep them in order in the sysfs distance files.
+      /* Unsparsify node indexes.
+       * We'll need them later because Linux groups sparse distances
+       * and keeps them in order in the sysfs distance files.
+       * It'll simplify things in the meantime.
        */
       index_ = 0;
       hwloc_bitmap_foreach_begin (osnode, nodeset) {
@@ -2699,14 +2702,14 @@ look_sysfsnode(struct hwloc_topology *topology,
       hwloc_bitmap_free(nodeset);
 
 #ifdef HWLOC_DEBUG
-      hwloc_debug("%s", "numa distance indexes: ");
+      hwloc_debug("%s", "NUMA indexes: ");
       for (index_ = 0; index_ < nbnodes; index_++) {
 	hwloc_debug(" %u", indexes[index_]);
       }
       hwloc_debug("%s", "\n");
 #endif
 
-      /* Get actual distances now */
+      /* Create NUMA objects */
       for (index_ = 0; index_ < nbnodes; index_++) {
           char nodepath[SYSFS_NUMA_NODE_PATH_LEN];
           hwloc_bitmap_t cpuset;
@@ -2716,8 +2719,11 @@ look_sysfsnode(struct hwloc_topology *topology,
 
           sprintf(nodepath, "%s/node%u/cpumap", path, osnode);
           cpuset = hwloc_parse_cpumap(nodepath, data->root_fd);
-          if (!cpuset)
-              continue;
+          if (!cpuset) {
+	    /* This NUMA object won't be inserted, we'll ignore distances */
+	    failednodes++;
+	    continue;
+	  }
 
           node = hwloc_alloc_setup_object(HWLOC_OBJ_NODE, osnode);
           node->cpuset = cpuset;
@@ -2729,9 +2735,36 @@ look_sysfsnode(struct hwloc_topology *topology,
           hwloc_debug_1arg_bitmap("os node %u has cpuset %s\n",
                                   osnode, node->cpuset);
           res_obj = hwloc_insert_object_by_cpuset(topology, node);
-          assert(node == res_obj); /* if we got merged, somebody else added NODEs earlier, things went wrong?! */
+	  if (node == res_obj) {
+	    nodes[index_] = node;
+	  } else {
+	    /* We got merged somehow, could be a buggy BIOS reporting wrong NUMA node cpuset.
+	     * This object disappeared, we'll ignore distances */
+	    failednodes++;
+	  }
+      }
 
-          nodes[index_] = node;
+      if (failednodes) {
+	/* failed to read/create some nodes, don't bother reading/fixing
+	 * a distance matrix that would likely be wrong anyway.
+	 */
+	nbnodes -= failednodes;
+	distances = NULL;
+      } else {
+	distances = calloc(nbnodes*nbnodes, sizeof(float));
+      }
+
+      if (NULL == distances) {
+          free(nodes);
+          free(indexes);
+          goto out;
+      }
+
+      /* Get actual distances now */
+      for (index_ = 0; index_ < nbnodes; index_++) {
+          char nodepath[SYSFS_NUMA_NODE_PATH_LEN];
+
+	  osnode = indexes[index_];
 
 	  /* Linux nodeX/distance file contains distance from X to other localities (from ACPI SLIT table or so),
 	   * store them in slots X*N...X*N+N-1 */