[mpich-commits] [mpich] MPICH primary repository branch, master, updated. v3.1b1-41-g177120e

mysql vizuser noreply at mpich.org
Fri Sep 20 12:22:45 CDT 2013 

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       via  a460c1eeca56cc4c7f61fddcdb2724bd605fdea2 (commit)
       via  526749d0f10e8c5920836c9191d6a04b74bc167a (commit)
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- Log -----------------------------------------------------------------
http://git.mpich.org/mpich.git/commitdiff/177120ef3171e09c915182061c7d7ec426d46430

commit 177120ef3171e09c915182061c7d7ec426d46430
Author: Pavan Balaji <balaji at mcs.anl.gov>
Date:   Fri Sep 20 12:21:35 2013 -0500

    Update README with hwloc version.
    
    No reviewer.

diff --git a/CHANGES b/CHANGES
index a35ea83..d033542 100644
--- a/CHANGES
+++ b/CHANGES
@@ -21,7 +21,7 @@
 
  # Enable shared library builds by default.
 
- # Upgraded hwloc to 1.7.1.
+ # Upgraded hwloc to 1.7.2.
 
  # Several improvements to the Hydra-SLURM integration.
 

http://git.mpich.org/mpich.git/commitdiff/a460c1eeca56cc4c7f61fddcdb2724bd605fdea2

commit a460c1eeca56cc4c7f61fddcdb2724bd605fdea2
Author: Pavan Balaji <balaji at mcs.anl.gov>
Date:   Sun May 19 00:17:55 2013 -0500

    Hydra-specific patches for hwloc.
    
    Picked up the relevant parts of [2bda6bc7], [49b74176] and [59cbc846].
    
    No reviewer.

diff --git a/src/pm/hydra/tools/topo/hwloc/hwloc/Makefile.am b/src/pm/hydra/tools/topo/hwloc/hwloc/Makefile.am
index a76d42e..5d635d5 100644
--- a/src/pm/hydra/tools/topo/hwloc/hwloc/Makefile.am
+++ b/src/pm/hydra/tools/topo/hwloc/hwloc/Makefile.am
@@ -9,10 +9,10 @@ ACLOCAL_AMFLAGS = -I ./config
 
 SUBDIRS = src include
 if HWLOC_BUILD_STANDALONE
-SUBDIRS += utils tests
+# SUBDIRS += utils tests
 # We need doc/ if HWLOC_BUILD_DOXYGEN, or during make install if HWLOC_INSTALL_DOXYGEN.
 # There's no INSTALL_SUBDIRS, so always enter doc/ and check HWLOC_BUILD/INSTALL_DOXYGEN there
-SUBDIRS += doc
+# SUBDIRS += doc
 endif
 
 # Do not let automake automatically add the non-standalone dirs to the
diff --git a/src/pm/hydra/tools/topo/hwloc/hwloc/autogen.sh b/src/pm/hydra/tools/topo/hwloc/hwloc/autogen.sh
index d69ef09..c73edc2 100755
--- a/src/pm/hydra/tools/topo/hwloc/hwloc/autogen.sh
+++ b/src/pm/hydra/tools/topo/hwloc/hwloc/autogen.sh
@@ -1,2 +1,9 @@
-:
-autoreconf -ivf
+#!/bin/sh
+
+if [ -n "$MPICH_AUTOTOOLS_DIR" ] ; then
+    autoreconf=${MPICH_AUTOTOOLS_DIR}/autoreconf
+else
+    autoreconf=${AUTORECONF:-autoreconf}
+fi
+
+$autoreconf ${autoreconf_args:-"-ivf"}
diff --git a/src/pm/hydra/tools/topo/hwloc/hwloc/config/hwloc.m4 b/src/pm/hydra/tools/topo/hwloc/hwloc/config/hwloc.m4
index 02b1e6f..b9ab48f 100644
--- a/src/pm/hydra/tools/topo/hwloc/hwloc/config/hwloc.m4
+++ b/src/pm/hydra/tools/topo/hwloc/hwloc/config/hwloc.m4
@@ -441,7 +441,25 @@ EOF])
     ])
     AC_CHECK_DECLS([strtoull], [], [], [AC_INCLUDES_DEFAULT])
 
-    AC_CHECK_FUNCS([sysctl sysctlbyname])
+    # Do a full link test instead of just using AC_CHECK_FUNCS, which
+    # just checks to see if the symbol exists or not.  For example,
+    # the prototype of sysctl uses u_int, which on some platforms
+    # (such as FreeBSD) is only defined under __BSD_VISIBLE, __USE_BSD
+    # or other similar definitions.  So while the symbols "sysctl" and
+    # "sysctlbyname" might still be available in libc (which autoconf
+    # checks for), they might not be actually usable.
+    AC_TRY_LINK([
+		#include <stdio.h>
+		#include <sys/sysctl.h>
+		],
+                [return sysctl(NULL,0,NULL,NULL,NULL,0);],
+                AC_DEFINE([HAVE_SYSCTL],[1],[Define to '1' if sysctl is present and usable]))
+    AC_TRY_LINK([
+		#include <stdio.h>
+		#include <sys/sysctl.h>
+		],
+                [return sysctlbyname(NULL,NULL,NULL,NULL,0);],
+                AC_DEFINE([HAVE_SYSCTLBYNAME],[1],[Define to '1' if sysctlbyname is present and usable]))
 
     case ${target} in
       *-*-mingw*|*-*-cygwin*)
@@ -1232,7 +1250,10 @@ dnl number of arguments (10). Success means the compiler couldn't really check.
 AC_DEFUN([_HWLOC_CHECK_DECL], [
   AC_MSG_CHECKING([whether function $1 is declared])
   AC_REQUIRE([AC_PROG_CC])
-  AC_COMPILE_IFELSE([AC_LANG_PROGRAM([AC_INCLUDES_DEFAULT([$4])],[$1(1,2,3,4,5,6,7,8,9,10);])],
+  AC_COMPILE_IFELSE([AC_LANG_PROGRAM(
+	[AC_INCLUDES_DEFAULT([$4])
+	$1(int,long,int,long,int,long,int,long,int,long);],
+	[$1(1,2,3,4,5,6,7,8,9,10);])],
     [AC_MSG_RESULT([no])
      $3],
     [AC_MSG_RESULT([yes])
diff --git a/src/pm/hydra/tools/topo/hwloc/hwloc/tests/embedded/configure.ac b/src/pm/hydra/tools/topo/hwloc/hwloc/tests/embedded/configure.ac
index d697e58..e7477e9 100644
--- a/src/pm/hydra/tools/topo/hwloc/hwloc/tests/embedded/configure.ac
+++ b/src/pm/hydra/tools/topo/hwloc/hwloc/tests/embedded/configure.ac
@@ -12,6 +12,7 @@ m4_ifdef([AM_SILENT_RULES], [AM_SILENT_RULES([yes])])
 AC_LANG([C])
 
 AC_PROG_CC
+AM_PROG_CC_C_O
 
 cat <<EOF
 

http://git.mpich.org/mpich.git/commitdiff/526749d0f10e8c5920836c9191d6a04b74bc167a

commit 526749d0f10e8c5920836c9191d6a04b74bc167a
Author: Pavan Balaji <balaji at mcs.anl.gov>
Date:   Fri Sep 20 10:37:18 2013 -0500

    Upgrade to hwloc-1.7.2.
    
    No reviewer.

diff --git a/src/pm/hydra/tools/topo/hwloc/hwloc/Makefile.am b/src/pm/hydra/tools/topo/hwloc/hwloc/Makefile.am
index 5d635d5..a76d42e 100644
--- a/src/pm/hydra/tools/topo/hwloc/hwloc/Makefile.am
+++ b/src/pm/hydra/tools/topo/hwloc/hwloc/Makefile.am
@@ -9,10 +9,10 @@ ACLOCAL_AMFLAGS = -I ./config
 
 SUBDIRS = src include
 if HWLOC_BUILD_STANDALONE
-# SUBDIRS += utils tests
+SUBDIRS += utils tests
 # We need doc/ if HWLOC_BUILD_DOXYGEN, or during make install if HWLOC_INSTALL_DOXYGEN.
 # There's no INSTALL_SUBDIRS, so always enter doc/ and check HWLOC_BUILD/INSTALL_DOXYGEN there
-# SUBDIRS += doc
+SUBDIRS += doc
 endif
 
 # Do not let automake automatically add the non-standalone dirs to the
diff --git a/src/pm/hydra/tools/topo/hwloc/hwloc/NEWS b/src/pm/hydra/tools/topo/hwloc/hwloc/NEWS
index bc99c0e..60a762d 100644
--- a/src/pm/hydra/tools/topo/hwloc/hwloc/NEWS
+++ b/src/pm/hydra/tools/topo/hwloc/hwloc/NEWS
@@ -17,6 +17,18 @@ bug fixes (and other actions) for each version of hwloc since version
 in v0.9.1).
 
 
+Version 1.7.2
+-------------
+* Do not create invalid block OS devices on very old Linux kernel such
+  as RHEL4 2.6.9.
+* Fix PCI subvendor/device IDs.
+* Fix the management of Misc objects inserted by parent.
+  Thanks to Jirka Hladky for reporting the problem.
+* Add a Port<n>State into attribute to OpenFabrics OS devices.
+* Add a MICSerialNumber info attribute to Xeon PHI/MIC OS devices.
+* Improve verbose error messages when failing to load from XML.
+
+
 Version 1.7.1
 -------------
 * Fix a failed assertion in the distance grouping code when loading a XML
diff --git a/src/pm/hydra/tools/topo/hwloc/hwloc/VERSION b/src/pm/hydra/tools/topo/hwloc/hwloc/VERSION
index b057041..68cd34e 100644
--- a/src/pm/hydra/tools/topo/hwloc/hwloc/VERSION
+++ b/src/pm/hydra/tools/topo/hwloc/hwloc/VERSION
@@ -7,7 +7,7 @@
 
 major=1
 minor=7
-release=1
+release=2
 
 # greek is used for alpha or beta release tags.  If it is non-empty,
 # it will be appended to the version number.  It does not have to be
@@ -58,4 +58,4 @@ date="Unreleased developer copy"
 # 2. Version numbers are described in the Libtool current:revision:age
 # format.
 
-libhwloc_so_version=8:1:3
+libhwloc_so_version=8:2:3
diff --git a/src/pm/hydra/tools/topo/hwloc/hwloc/autogen.sh b/src/pm/hydra/tools/topo/hwloc/hwloc/autogen.sh
index c73edc2..d69ef09 100755
--- a/src/pm/hydra/tools/topo/hwloc/hwloc/autogen.sh
+++ b/src/pm/hydra/tools/topo/hwloc/hwloc/autogen.sh
@@ -1,9 +1,2 @@
-#!/bin/sh
-
-if [ -n "$MPICH_AUTOTOOLS_DIR" ] ; then
-    autoreconf=${MPICH_AUTOTOOLS_DIR}/autoreconf
-else
-    autoreconf=${AUTORECONF:-autoreconf}
-fi
-
-$autoreconf ${autoreconf_args:-"-ivf"}
+:
+autoreconf -ivf
diff --git a/src/pm/hydra/tools/topo/hwloc/hwloc/config/hwloc.m4 b/src/pm/hydra/tools/topo/hwloc/hwloc/config/hwloc.m4
index b9ab48f..02b1e6f 100644
--- a/src/pm/hydra/tools/topo/hwloc/hwloc/config/hwloc.m4
+++ b/src/pm/hydra/tools/topo/hwloc/hwloc/config/hwloc.m4
@@ -441,25 +441,7 @@ EOF])
     ])
     AC_CHECK_DECLS([strtoull], [], [], [AC_INCLUDES_DEFAULT])
 
-    # Do a full link test instead of just using AC_CHECK_FUNCS, which
-    # just checks to see if the symbol exists or not.  For example,
-    # the prototype of sysctl uses u_int, which on some platforms
-    # (such as FreeBSD) is only defined under __BSD_VISIBLE, __USE_BSD
-    # or other similar definitions.  So while the symbols "sysctl" and
-    # "sysctlbyname" might still be available in libc (which autoconf
-    # checks for), they might not be actually usable.
-    AC_TRY_LINK([
-		#include <stdio.h>
-		#include <sys/sysctl.h>
-		],
-                [return sysctl(NULL,0,NULL,NULL,NULL,0);],
-                AC_DEFINE([HAVE_SYSCTL],[1],[Define to '1' if sysctl is present and usable]))
-    AC_TRY_LINK([
-		#include <stdio.h>
-		#include <sys/sysctl.h>
-		],
-                [return sysctlbyname(NULL,NULL,NULL,NULL,0);],
-                AC_DEFINE([HAVE_SYSCTLBYNAME],[1],[Define to '1' if sysctlbyname is present and usable]))
+    AC_CHECK_FUNCS([sysctl sysctlbyname])
 
     case ${target} in
       *-*-mingw*|*-*-cygwin*)
@@ -1250,10 +1232,7 @@ dnl number of arguments (10). Success means the compiler couldn't really check.
 AC_DEFUN([_HWLOC_CHECK_DECL], [
   AC_MSG_CHECKING([whether function $1 is declared])
   AC_REQUIRE([AC_PROG_CC])
-  AC_COMPILE_IFELSE([AC_LANG_PROGRAM(
-	[AC_INCLUDES_DEFAULT([$4])
-	$1(int,long,int,long,int,long,int,long,int,long);],
-	[$1(1,2,3,4,5,6,7,8,9,10);])],
+  AC_COMPILE_IFELSE([AC_LANG_PROGRAM([AC_INCLUDES_DEFAULT([$4])],[$1(1,2,3,4,5,6,7,8,9,10);])],
     [AC_MSG_RESULT([no])
      $3],
     [AC_MSG_RESULT([yes])
diff --git a/src/pm/hydra/tools/topo/hwloc/hwloc/doc/Makefile.am b/src/pm/hydra/tools/topo/hwloc/hwloc/doc/Makefile.am
index d756120..4af37db 100644
--- a/src/pm/hydra/tools/topo/hwloc/hwloc/doc/Makefile.am
+++ b/src/pm/hydra/tools/topo/hwloc/hwloc/doc/Makefile.am
@@ -1,5 +1,5 @@
 # Copyright © 2009-2013 Inria.  All rights reserved.
-# Copyright © 2009-2012 Université Bordeaux 1
+# Copyright © 2009-2013 Université Bordeaux 1
 # Copyright © 2009-2010 Cisco Systems, Inc.  All rights reserved.
 # See COPYING in top-level directory.
 
@@ -116,11 +116,8 @@ endif
 # of nested structurre/union declarations.
 #
 
-if HWLOC_BUILD_DOXYGEN
-$(DOX_TAG): $(BUILT_SOURCES) $(dox_inputs) $(PREBUILT_IMAGES)
-	rm -fr $(DOX_DIR)
-	$(DOXYGEN) $(DOX_CONFIG)
-	-$(SED_I) -e 's/__hwloc_restrict/restrict/g' \
+RENAME_SED = \
+	$(SED_I) -e 's/__hwloc_restrict/restrict/g' \
 	          -e 's/\\_\\-\\_\\-hwloc\\_\\-restrict/restrict/g' \
 	          -e 's/__hwloc_attribute_unused//g' \
 	          -e 's/\\_\\-\\_\\-hwloc\\_\\-attribute\\_\\-unused//g' \
@@ -135,7 +132,13 @@ $(DOX_TAG): $(BUILT_SOURCES) $(dox_inputs) $(PREBUILT_IMAGES)
 	          -e 's/HWLOC_DECLSPEC//g' \
 	          -e 's/HWLOC\\_\\-DECLSPEC//g' \
 	          -e 's/__hwloc_inline/inline/g' \
-	          -e 's/\\_\\-\\_\\-hwloc\\_\\-inline/inline/g' \
+	          -e 's/\\_\\-\\_\\-hwloc\\_\\-inline/inline/g'
+
+if HWLOC_BUILD_DOXYGEN
+$(DOX_TAG): $(BUILT_SOURCES) $(dox_inputs) $(PREBUILT_IMAGES)
+	rm -fr $(DOX_DIR)
+	$(DOXYGEN) $(DOX_CONFIG)
+	-$(RENAME_SED) \
 		$(DOX_DIR)/html/*.html $(DOX_DIR)/latex/*.tex $(DOX_DIR)/man/man3/*.3
 	@echo "Work-around spurious leading _ in doxygen filenames..."
 	-(cd $(DOX_DIR)/man/man3 ; \
@@ -149,6 +152,9 @@ $(DOX_TAG): $(BUILT_SOURCES) $(dox_inputs) $(PREBUILT_IMAGES)
 	@mv $(DOX_DIR)/man.tmp $(DOX_MAN_DIR)/man3
 endif
 
+www-doc-sed:
+	-$(RENAME_SED) www.open-mpi.org/html/*.php
+
 #
 # Rules for building the PDF
 #
diff --git a/src/pm/hydra/tools/topo/hwloc/hwloc/doc/hwloc.doxy b/src/pm/hydra/tools/topo/hwloc/hwloc/doc/hwloc.doxy
index d6d5c19..507e962 100644
--- a/src/pm/hydra/tools/topo/hwloc/hwloc/doc/hwloc.doxy
+++ b/src/pm/hydra/tools/topo/hwloc/hwloc/doc/hwloc.doxy
@@ -1647,8 +1647,10 @@ object instead.
 <dt>NVIDIAUUID, NVIDIASerial (NVML GPU OS devices)</dt>
 <dd>The UUID and Serial of NVIDIA GPUs.
 </dd>
-<dt>MICFamily</dt>
-<dd>The family of an Intel Xeon Phi (MIC) coprocessor.
+<dt>MICFamily, MICSKU, MICSerialNumber, MICActiveCores, MICMemorySize</dt>
+<dd>The family, SKU (model), serial number,
+ number of active cores, and memory size (in kB)
+ of an Intel Xeon Phi (MIC) coprocessor.
 </dd>
 <dt>DMIBoardVendor, DMIBoardName, etc. (Machine object)</dt>
 <dd>DMI hardware information such as the motherboard and chassis
@@ -1659,10 +1661,12 @@ as reported by Linux under <tt>/sys/class/dmi/id/</tt>.
 <dd>The MAC address and the port number of a software network
 interface, such as <tt>eth4</tt> on Linux.
 </dd>
-<dt>NodeGUID, SysImageGUID, Port3LID, Port4LMC, Port5GID6
+<dt>NodeGUID, SysImageGUID, Port1State, Port2LID, Port2LMC, Port3GID1
 (OpenFabrics OS devices)</dt>
-<dd>The node GUID and GUID mask, the LID and LID mask count of a given
-port, and a GID of a port.
+<dd>The node GUID and GUID mask,
+the state of a port #1 (value is 4 when active),
+the LID and LID mask count of port #2,
+and GID #1 of port #3.
 </dd>
 </dl>
 
diff --git a/src/pm/hydra/tools/topo/hwloc/hwloc/include/hwloc/rename.h b/src/pm/hydra/tools/topo/hwloc/hwloc/include/hwloc/rename.h
index ddf5731..6aacb8e 100644
--- a/src/pm/hydra/tools/topo/hwloc/hwloc/include/hwloc/rename.h
+++ b/src/pm/hydra/tools/topo/hwloc/hwloc/include/hwloc/rename.h
@@ -528,12 +528,14 @@ extern "C" {
 #define hwloc_set_binding_hooks HWLOC_NAME(set_binding_hooks)
 
 #define hwloc_set_linuxfs_hooks HWLOC_NAME(set_linuxfs_hooks)
+#define hwloc_set_bgq_hooks HWLOC_NAME(set_bgq_hooks)
 #define hwloc_set_solaris_hooks HWLOC_NAME(set_solaris_hooks)
 #define hwloc_set_aix_hooks HWLOC_NAME(set_aix_hooks)
 #define hwloc_set_osf_hooks HWLOC_NAME(set_osf_hooks)
 #define hwloc_set_windows_hooks HWLOC_NAME(set_windows_hooks)
 #define hwloc_set_darwin_hooks HWLOC_NAME(set_darwin_hooks)
 #define hwloc_set_freebsd_hooks HWLOC_NAME(set_freebsd_hooks)
+#define hwloc_set_netbsd_hooks HWLOC_NAME(set_netbsd_hooks)
 #define hwloc_set_hpux_hooks HWLOC_NAME(set_hpux_hooks)
 
 #define hwloc_add_uname_info HWLOC_NAME(add_uname_info)
diff --git a/src/pm/hydra/tools/topo/hwloc/hwloc/src/topology-linux.c b/src/pm/hydra/tools/topo/hwloc/hwloc/src/topology-linux.c
index 1566a2f..3403f51 100644
--- a/src/pm/hydra/tools/topo/hwloc/hwloc/src/topology-linux.c
+++ b/src/pm/hydra/tools/topo/hwloc/hwloc/src/topology-linux.c
@@ -1,7 +1,7 @@
 /*
  * Copyright © 2009 CNRS
  * Copyright © 2009-2013 Inria.  All rights reserved.
- * Copyright © 2009-2012 Université Bordeaux 1
+ * Copyright © 2009-2013 Université Bordeaux 1
  * Copyright © 2009-2011 Cisco Systems, Inc.  All rights reserved.
  * Copyright © 2010 IBM
  * See COPYING in top-level directory.
@@ -272,6 +272,47 @@ hwloc_opendir(const char *p, int d __hwloc_attribute_unused)
 }
 
 
+static int
+hwloc_linux_parse_cpuset_file(FILE *file, hwloc_bitmap_t set)
+{
+  unsigned long start, stop;
+
+  /* reset to zero first */
+  hwloc_bitmap_zero(set);
+
+  while (fscanf(file, "%lu", &start) == 1)
+  {
+    int c = fgetc(file);
+
+    stop = start;
+
+    if (c == '-') {
+      /* Range */
+      if (fscanf(file, "%lu", &stop) != 1) {
+        /* Expected a number here */
+        errno = EINVAL;
+        return -1;
+      }
+      c = fgetc(file);
+    }
+
+    if (c == EOF || c == '\n') {
+      hwloc_bitmap_set_range(set, start, stop);
+      break;
+    }
+
+    if (c != ',') {
+      /* Expected EOF, EOL, or a comma */
+      errno = EINVAL;
+      return -1;
+    }
+
+    hwloc_bitmap_set_range(set, start, stop);
+  }
+
+  return 0;
+}
+
 
 /*****************************
  ******* CpuBind Hooks *******
@@ -353,6 +394,7 @@ hwloc_linux_find_kernel_nr_cpus(hwloc_topology_t topology)
 {
   static int _nr_cpus = -1;
   int nr_cpus = _nr_cpus;
+  FILE *possible;
 
   if (nr_cpus != -1)
     /* already computed */
@@ -365,6 +407,21 @@ hwloc_linux_find_kernel_nr_cpus(hwloc_topology_t topology)
     /* start from scratch, the topology isn't ready yet (complete_cpuset is missing (-1) or empty (0))*/
     nr_cpus = 1;
 
+  possible = fopen("/sys/devices/system/cpu/possible", "r");
+  if (possible) {
+    hwloc_bitmap_t possible_bitmap = hwloc_bitmap_alloc();
+    if (hwloc_linux_parse_cpuset_file(possible, possible_bitmap) == 0) {
+      int max_possible = hwloc_bitmap_last(possible_bitmap);
+
+      hwloc_debug_bitmap("possible CPUs are %s\n", possible_bitmap);
+
+      if (nr_cpus < max_possible + 1)
+        nr_cpus = max_possible + 1;
+    }
+    fclose(possible);
+    hwloc_bitmap_free(possible_bitmap);
+  }
+
   while (1) {
     cpu_set_t *set = CPU_ALLOC(nr_cpus);
     size_t setsize = CPU_ALLOC_SIZE(nr_cpus);
@@ -3542,14 +3599,23 @@ hwloc_linux_class_readdir(struct hwloc_topology *topology, struct hwloc_obj *pci
   DIR *dir;
   struct dirent *dirent;
   hwloc_obj_t obj;
-  int res = 0;
+  int res = 0, err;
 
   if (hwloc_linux_deprecated_classlinks_model == -2)
     hwloc_linux_check_deprecated_classlinks_model();
 
   if (hwloc_linux_deprecated_classlinks_model != 1) {
     /* modern sysfs: <device>/<class>/<name> */
+    struct stat st;
     snprintf(path, sizeof(path), "%s/%s", devicepath, classname);
+
+    /* some very host kernel (2.6.9/RHEL4) have <device>/<class> symlink without any way to find <name>.
+     * make sure <device>/<class> is a directory to avoid this case.
+     */
+    err = lstat(path, &st);
+    if (err < 0 || !S_ISDIR(st.st_mode))
+      goto trydeprecated;
+
     dir = opendir(path);
     if (dir) {
       hwloc_linux_deprecated_classlinks_model = 0;
@@ -3568,6 +3634,7 @@ hwloc_linux_class_readdir(struct hwloc_topology *topology, struct hwloc_obj *pci
     }
   }
 
+trydeprecated:
   if (hwloc_linux_deprecated_classlinks_model != 0) {
     /* deprecated sysfs: <device>/<class>:<name> */
     dir = opendir(devicepath);
@@ -3678,6 +3745,22 @@ hwloc_linux_infiniband_class_fillinfos(struct hwloc_topology *topology __hwloc_a
   }
 
   for(i=1; ; i++) {
+    snprintf(path, sizeof(path), "%s/ports/%u/state", osdevpath, i);
+    fd = fopen(path, "r");
+    if (fd) {
+      char statevalue[2];
+      if (fgets(statevalue, sizeof(statevalue), fd)) {
+	char statename[32];
+	statevalue[1] = '\0'; /* only keep the first byte/digit */
+	snprintf(statename, sizeof(statename), "Port%uState", i);
+	hwloc_obj_add_info(obj, statename, statevalue);
+      }
+      fclose(fd);
+    } else {
+      /* no such port */
+      break;
+    }
+
     snprintf(path, sizeof(path), "%s/ports/%u/lid", osdevpath, i);
     fd = fopen(path, "r");
     if (fd) {
@@ -3691,9 +3774,6 @@ hwloc_linux_infiniband_class_fillinfos(struct hwloc_topology *topology __hwloc_a
 	hwloc_obj_add_info(obj, lidname, lidvalue);
       }
       fclose(fd);
-    } else {
-      /* no such port */
-      break;
     }
 
     snprintf(path, sizeof(path), "%s/ports/%u/lid_mask_count", osdevpath, i);
@@ -3881,6 +3961,19 @@ hwloc_linux_mic_class_fillinfos(struct hwloc_topology *topology __hwloc_attribut
     fclose(fd);
   }
 
+  snprintf(path, sizeof(path), "%s/serialnumber", osdevpath);
+  fd = fopen(path, "r");
+  if (fd) {
+    char sn[64];
+    if (fgets(sn, sizeof(sn), fd)) {
+      char *eol = strchr(sn, '\n');
+      if (eol)
+        *eol = 0;
+      hwloc_obj_add_info(obj, "MICSerialNumber", sn);
+    }
+    fclose(fd);
+  }
+
   snprintf(path, sizeof(path), "%s/active_cores", osdevpath);
   fd = fopen(path, "r");
   if (fd) {
diff --git a/src/pm/hydra/tools/topo/hwloc/hwloc/src/topology-pci.c b/src/pm/hydra/tools/topo/hwloc/hwloc/src/topology-pci.c
index f70609e..62f88a0 100644
--- a/src/pm/hydra/tools/topo/hwloc/hwloc/src/topology-pci.c
+++ b/src/pm/hydra/tools/topo/hwloc/hwloc/src/topology-pci.c
@@ -503,6 +503,7 @@ hwloc_look_pci(struct hwloc_backend *backend)
     unsigned isbridge;
     unsigned domain;
     unsigned device_class;
+    unsigned short tmp16;
     char name[128];
     unsigned offset;
 #ifdef HWLOC_HAVE_PCI_FIND_CAP
@@ -559,10 +560,6 @@ hwloc_look_pci(struct hwloc_backend *backend)
     obj->attr->pcidev.class_id = device_class;
     HWLOC_BUILD_ASSERT(PCI_REVISION_ID < CONFIG_SPACE_CACHESIZE);
     obj->attr->pcidev.revision = config_space_cache[PCI_REVISION_ID];
-    HWLOC_BUILD_ASSERT(PCI_SUBSYSTEM_VENDOR_ID < CONFIG_SPACE_CACHESIZE);
-    obj->attr->pcidev.subvendor_id = config_space_cache[PCI_SUBSYSTEM_VENDOR_ID];
-    HWLOC_BUILD_ASSERT(PCI_SUBSYSTEM_ID < CONFIG_SPACE_CACHESIZE);
-    obj->attr->pcidev.subdevice_id = config_space_cache[PCI_SUBSYSTEM_ID];
 
     obj->attr->pcidev.linkspeed = 0; /* unknown */
 #ifdef HWLOC_HAVE_PCI_FIND_CAP
@@ -648,6 +645,20 @@ hwloc_look_pci(struct hwloc_backend *backend)
       obj->attr->bridge.downstream.pci.subordinate_bus = config_space_cache[PCI_SUBORDINATE_BUS];
     }
 
+    if (obj->type == HWLOC_OBJ_PCI_DEVICE) {
+      memcpy(&tmp16, &config_space_cache[PCI_SUBSYSTEM_VENDOR_ID], sizeof(tmp16));
+      HWLOC_BUILD_ASSERT(PCI_SUBSYSTEM_VENDOR_ID < CONFIG_SPACE_CACHESIZE);
+      obj->attr->pcidev.subvendor_id = tmp16;
+      memcpy(&tmp16, &config_space_cache[PCI_SUBSYSTEM_ID], sizeof(tmp16));
+      HWLOC_BUILD_ASSERT(PCI_SUBSYSTEM_ID < CONFIG_SPACE_CACHESIZE);
+      obj->attr->pcidev.subdevice_id = tmp16;
+    } else {
+      /* TODO:
+       * bridge must lookup PCI_CAP_ID_SSVID and then look at offset+PCI_SSVID_VENDOR/DEVICE_ID
+       * cardbus must look at PCI_CB_SUBSYSTEM_VENDOR_ID and PCI_CB_SUBSYSTEM_ID
+       */
+    }
+
 /* starting from pciutils 2.2, pci_lookup_name() takes a variable number
  * of arguments, and supports the PCI_LOOKUP_NO_NUMBERS flag.
  */
diff --git a/src/pm/hydra/tools/topo/hwloc/hwloc/src/topology-xml.c b/src/pm/hydra/tools/topo/hwloc/hwloc/src/topology-xml.c
index 2a2c41a..cc6521c 100644
--- a/src/pm/hydra/tools/topo/hwloc/hwloc/src/topology-xml.c
+++ b/src/pm/hydra/tools/topo/hwloc/hwloc/src/topology-xml.c
@@ -706,6 +706,8 @@ hwloc_look_xml(struct hwloc_backend *backend)
  failed:
   if (data->look_failed)
     data->look_failed(data);
+  if (hwloc__xml_verbose())
+    fprintf(stderr, "XML component discovery failed.\n");
  err:
   hwloc_localeswitch_fini();
   return -1;
diff --git a/src/pm/hydra/tools/topo/hwloc/hwloc/src/topology.c b/src/pm/hydra/tools/topo/hwloc/hwloc/src/topology.c
index d09627a..a6fc4f9 100644
--- a/src/pm/hydra/tools/topo/hwloc/hwloc/src/topology.c
+++ b/src/pm/hydra/tools/topo/hwloc/hwloc/src/topology.c
@@ -688,6 +688,7 @@ hwloc___insert_object_by_cpuset(struct hwloc_topology *topology, hwloc_obj_t cur
 	    child->distances_count += obj->distances_count;
 	    child->distances = realloc(child->distances, child->distances_count * sizeof(*child->distances));
 	    memcpy(child->distances + obj->distances_count, obj->distances, obj->distances_count * sizeof(*child->distances));
+	    free(obj->distances);
 	  } else {
 	    child->distances_count = obj->distances_count;
 	    child->distances = obj->distances;
@@ -700,6 +701,7 @@ hwloc___insert_object_by_cpuset(struct hwloc_topology *topology, hwloc_obj_t cur
 	    child->infos_count += obj->infos_count;
 	    child->infos = realloc(child->infos, child->infos_count * sizeof(*child->infos));
 	    memcpy(child->infos + obj->infos_count, obj->infos, obj->infos_count * sizeof(*child->infos));
+	    free(obj->infos);
 	  } else {
 	    child->infos_count = obj->infos_count;
 	    child->infos = obj->infos;
@@ -897,7 +899,7 @@ hwloc_topology_insert_misc_object_by_cpuset(struct hwloc_topology *topology, hwl
 
   if (hwloc_bitmap_iszero(cpuset))
     return NULL;
-  if (!hwloc_bitmap_isincluded(cpuset, hwloc_topology_get_complete_cpuset(topology)))
+  if (!hwloc_bitmap_isincluded(cpuset, hwloc_topology_get_topology_cpuset(topology)))
     return NULL;
 
   obj = hwloc_alloc_setup_object(HWLOC_OBJ_MISC, -1);
@@ -1183,11 +1185,18 @@ add_default_object_sets(hwloc_obj_t obj, int parent_has_sets)
   if (hwloc_obj_type_is_io(obj->type))
     return;
 
-  if (parent_has_sets || obj->cpuset) {
-    /* if the parent has non-NULL sets, or if the object has non-NULL cpusets,
-     * it must have non-NULL nodesets
-     */
+  if (parent_has_sets && obj->type != HWLOC_OBJ_MISC) {
+    /* non-MISC object must have cpuset if parent has one. */
     assert(obj->cpuset);
+  }
+
+  /* other sets must be consistent with main cpuset:
+   * check cpusets and add nodesets if needed.
+   *
+   * MISC may have no sets at all (if added by parent), or usual ones (if added by cpuset),
+   * but that's not easy to detect, so just make sure sets are consistent as usual.
+   */
+  if (obj->cpuset) {
     assert(obj->online_cpuset);
     assert(obj->complete_cpuset);
     assert(obj->allowed_cpuset);
@@ -1198,9 +1207,9 @@ add_default_object_sets(hwloc_obj_t obj, int parent_has_sets)
     if (!obj->allowed_nodeset)
       obj->allowed_nodeset = hwloc_bitmap_alloc_full();
   } else {
-    /* parent has no sets and object has NULL cpusets,
-     * it must have NULL nodesets
-     */
+    assert(!obj->online_cpuset);
+    assert(!obj->complete_cpuset);
+    assert(!obj->allowed_cpuset);
     assert(!obj->nodeset);
     assert(!obj->complete_nodeset);
     assert(!obj->allowed_nodeset);
@@ -1239,6 +1248,9 @@ propagate_nodeset(hwloc_obj_t obj, hwloc_obj_t sys)
     /* don't propagate nodesets in I/O objects, keep them NULL */
     if (hwloc_obj_type_is_io(child->type))
       return;
+    /* don't propagate nodesets in Misc inserted by parent (no nodeset if no cpuset) */
+    if (child->type == HWLOC_OBJ_MISC && !child->cpuset)
+      return;
 
     /* Propagate singleton nodesets down */
     if (parent_weight == 1) {
@@ -1450,7 +1462,7 @@ remove_empty(hwloc_topology_t topology, hwloc_obj_t *pobj)
 
   if (obj->type != HWLOC_OBJ_NODE
       && !obj->first_child /* only remove if all children were removed above, so that we don't remove parents of NUMAnode */
-      && !hwloc_obj_type_is_io(obj->type)
+      && !hwloc_obj_type_is_io(obj->type) && obj->type != HWLOC_OBJ_MISC
       && obj->cpuset /* don't remove if no cpuset at all, there's likely a good reason why it's different from having an empty cpuset */
       && hwloc_bitmap_iszero(obj->cpuset)) {
     /* Remove empty children */
@@ -2195,7 +2207,7 @@ next_cpubackend:
   }
 
   if (!discoveries) {
-    hwloc_debug("%s", "No CPU backend enabled\n");
+    hwloc_debug("%s", "No CPU backend enabled or no discovery succeeded\n");
     errno = EINVAL;
     return -1;
   }
diff --git a/src/pm/hydra/tools/topo/hwloc/hwloc/tests/embedded/configure.ac b/src/pm/hydra/tools/topo/hwloc/hwloc/tests/embedded/configure.ac
index c0d6ba1..d697e58 100644
--- a/src/pm/hydra/tools/topo/hwloc/hwloc/tests/embedded/configure.ac
+++ b/src/pm/hydra/tools/topo/hwloc/hwloc/tests/embedded/configure.ac
@@ -9,11 +9,9 @@ AC_CANONICAL_TARGET
 AM_INIT_AUTOMAKE([1.10 dist-bzip2 foreign subdir-objects tar-ustar -Wall -Werror])
 m4_ifdef([AM_SILENT_RULES], [AM_SILENT_RULES([yes])])
 
-
 AC_LANG([C])
 
 AC_PROG_CC
-AM_PROG_CC_C_O
 
 cat <<EOF
 
diff --git a/src/pm/hydra/tools/topo/hwloc/hwloc/tests/hwloc_insert_misc.c b/src/pm/hydra/tools/topo/hwloc/hwloc/tests/hwloc_insert_misc.c
index 95365af..74180c1 100644
--- a/src/pm/hydra/tools/topo/hwloc/hwloc/tests/hwloc_insert_misc.c
+++ b/src/pm/hydra/tools/topo/hwloc/hwloc/tests/hwloc_insert_misc.c
@@ -23,8 +23,9 @@ int main(void)
   hwloc_topology_load(topology);
   hwloc_topology_check(topology);
   cpuset = hwloc_bitmap_alloc();
-  hwloc_bitmap_set(cpuset, 0);
+  hwloc_bitmap_set(cpuset, hwloc_bitmap_first(hwloc_topology_get_topology_cpuset(topology)));
   obj = hwloc_topology_insert_misc_object_by_cpuset(topology, cpuset, "test");
+  assert(obj);
   hwloc_bitmap_free(cpuset);
   hwloc_topology_insert_misc_object_by_parent(topology, obj, "test2");
   hwloc_topology_check(topology);
diff --git a/src/pm/hydra/tools/topo/hwloc/hwloc/tests/linux/hwloc-gather-topology.in b/src/pm/hydra/tools/topo/hwloc/hwloc/tests/linux/hwloc-gather-topology.in
index 54f5295..969eda7 100755
--- a/src/pm/hydra/tools/topo/hwloc/hwloc/tests/linux/hwloc-gather-topology.in
+++ b/src/pm/hydra/tools/topo/hwloc/hwloc/tests/linux/hwloc-gather-topology.in
@@ -34,6 +34,10 @@ usage()
    echo "  $0 /tmp/\$(uname -n)"
 }
 
+if test $# -lt 1 ; then
+  usage
+  exit 1
+fi
 name="$1"; shift
 if [ -z "$name" -o x`echo $name | cut -c1` = x- ] ; then
   [ x$name != x -a x$name != x-h -a x$name != x--help ] && echo "Unrecognized option: $name"
diff --git a/src/pm/hydra/tools/topo/hwloc/hwloc/utils/hwloc-annotate.1in b/src/pm/hydra/tools/topo/hwloc/hwloc/utils/hwloc-annotate.1in
index a2195d7..72bb583 100644
--- a/src/pm/hydra/tools/topo/hwloc/hwloc/utils/hwloc-annotate.1in
+++ b/src/pm/hydra/tools/topo/hwloc/hwloc/utils/hwloc-annotate.1in
@@ -84,12 +84,12 @@ hwloc-annotate's operation is best described through several examples.
 .PP
 Add an info attribute to all Core objects:
 
-    $ hwloc-annotate input.xml output.xml Core:all infoname infovalue
+    $ hwloc-annotate input.xml output.xml Core:all info infoname infovalue
 
 Add an info attribute to the root object of the topology
 and modify the input XML directly:
 
-    $ hwloc-annotate file.xml file.xml root infoname infovalue
+    $ hwloc-annotate file.xml file.xml root info infoname infovalue
 
 .
 .\" **************************
diff --git a/src/pm/hydra/tools/topo/hwloc/hwloc/utils/hwloc-info.1in b/src/pm/hydra/tools/topo/hwloc/hwloc/utils/hwloc-info.1in
index 8bfe806..75ada8a 100644
--- a/src/pm/hydra/tools/topo/hwloc/hwloc/utils/hwloc-info.1in
+++ b/src/pm/hydra/tools/topo/hwloc/hwloc/utils/hwloc-info.1in
@@ -16,7 +16,7 @@ hwloc-info \- Show some information about some objects or about a topology
 .B hwloc-info
 [ \fIoptions \fR]...
 \fI<object>\fR...
-.
+.PP
 .B hwloc-info
 [ \fIoptions \fR]...
 .
diff --git a/src/pm/hydra/tools/topo/hwloc/hwloc/utils/lstopo.1in b/src/pm/hydra/tools/topo/hwloc/hwloc/utils/lstopo.1in
index f089597..549a53a 100644
--- a/src/pm/hydra/tools/topo/hwloc/hwloc/utils/lstopo.1in
+++ b/src/pm/hydra/tools/topo/hwloc/hwloc/utils/lstopo.1in
@@ -351,6 +351,8 @@ in the particular case of NUMA nodes, the layout is always a flat
 rectangle, to avoid letting the user believe any particular NUMA
 topology (lstopo is not able to render that yet).
 .
+The layout of a level may be changed with \-\-vert and \-\-horiz.
+.
 .\" **************************
 .\"    Examples Section
 .\" **************************
diff --git a/src/pm/hydra/tools/topo/hwloc/hwloc/utils/lstopo.c b/src/pm/hydra/tools/topo/hwloc/hwloc/utils/lstopo.c
index 7c2d6d6..16d5b1f 100644
--- a/src/pm/hydra/tools/topo/hwloc/hwloc/utils/lstopo.c
+++ b/src/pm/hydra/tools/topo/hwloc/hwloc/utils/lstopo.c
@@ -557,8 +557,10 @@ main (int argc, char *argv[])
   }
 
   err = hwloc_topology_load (topology);
-  if (err)
+  if (err) {
+    fprintf(stderr, "hwloc_topology_load() failed (%s).\n", strerror(errno));
     return EXIT_FAILURE;
+  }
 
   if (top)
     add_process_objects(topology);

-----------------------------------------------------------------------

Summary of changes:
 CHANGES                                            |    2 +-
 src/pm/hydra/tools/topo/hwloc/hwloc/NEWS           |   12 +++
 src/pm/hydra/tools/topo/hwloc/hwloc/VERSION        |    4 +-
 .../hydra/tools/topo/hwloc/hwloc/doc/Makefile.am   |   20 +++--
 src/pm/hydra/tools/topo/hwloc/hwloc/doc/hwloc.doxy |   14 ++-
 .../tools/topo/hwloc/hwloc/include/hwloc/rename.h  |    2 +
 .../tools/topo/hwloc/hwloc/src/topology-linux.c    |  103 +++++++++++++++++++-
 .../tools/topo/hwloc/hwloc/src/topology-pci.c      |   19 +++-
 .../tools/topo/hwloc/hwloc/src/topology-xml.c      |    2 +
 src/pm/hydra/tools/topo/hwloc/hwloc/src/topology.c |   32 ++++--
 .../topo/hwloc/hwloc/tests/embedded/configure.ac   |    1 -
 .../topo/hwloc/hwloc/tests/hwloc_insert_misc.c     |    3 +-
 .../hwloc/tests/linux/hwloc-gather-topology.in     |    4 +
 .../topo/hwloc/hwloc/utils/hwloc-annotate.1in      |    4 +-
 .../tools/topo/hwloc/hwloc/utils/hwloc-info.1in    |    2 +-
 .../hydra/tools/topo/hwloc/hwloc/utils/lstopo.1in  |    2 +
 src/pm/hydra/tools/topo/hwloc/hwloc/utils/lstopo.c |    4 +-
 17 files changed, 190 insertions(+), 40 deletions(-)


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