[PATCH 01/14] gnu: hwloc: Upgrade to 1.10.1.

[ericbavier]

From: Eric Bavier <address@hidden>

* gnu/packages/patches/hwloc-gather-topology-lstopo.patch: New patch.
* gnu/packages/mpi.scm (hwloc): Upgrade to 1.10.1.
  [source]: Use patch.
  [propagated-inputs]: Remove libpci.
  [inputs]: Add libpciaccess.
* gnu-system.am (dist_patch_DATA): Add patch.
---
 gnu-system.am                                      |  1 +
 gnu/packages/mpi.scm                               | 23 ++++++++++------------
 .../patches/hwloc-gather-topology-lstopo.patch     | 13 ++++++++++++
 3 files changed, 24 insertions(+), 13 deletions(-)
 create mode 100644 gnu/packages/patches/hwloc-gather-topology-lstopo.patch

diff --git a/gnu-system.am b/gnu-system.am
index a420d71..2d45e40 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -461,6 +461,7 @@ dist_patch_DATA =                                           
\
   gnu/packages/patches/gtkglext-disable-disable-deprecated.patch \
   gnu/packages/patches/hop-bigloo-4.0b.patch                   \
   gnu/packages/patches/hop-linker-flags.patch                  \
+  gnu/packages/patches/hwloc-gather-topology-lstopo.patch      \
   gnu/packages/patches/hydra-automake-1.15.patch               \
   gnu/packages/patches/hydra-disable-darcs-test.patch          \
   gnu/packages/patches/irrlicht-mesa-10.patch                  \
diff --git a/gnu/packages/mpi.scm b/gnu/packages/mpi.scm
index 8e62da9..0e1016e 100644
--- a/gnu/packages/mpi.scm
+++ b/gnu/packages/mpi.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014 Eric Bavier <address@hidden>
+;;; Copyright © 2014, 2015 Eric Bavier <address@hidden>
 ;;; Copyright © 2014 Ludovic Courtès <address@hidden>
 ;;; Copyright © 2014 Ian Denhardt <address@hidden>
 ;;;
@@ -39,30 +39,29 @@
 (define-public hwloc
   (package
     (name "hwloc")
-    (version "1.9")
+    (version "1.10.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://www.open-mpi.org/software/hwloc/v";
-                                  version "/downloads/hwloc-"
-                                  version ".tar.bz2"))
+                                  (version-major+minor version)
+                                  "/downloads/hwloc-" version ".tar.bz2"))
               (sha256
                (base32
-                "0zjgiili2a8v63s8ly3a8qp8ibxv1jw3zbgm7diic3w1qgqiza14"))))
+                "0jji5rphy05s0lp6bknn8lxwixrq0hy5rjzsqvhjszbkl2li7kim"))
+              (patches (list
+                        (search-patch "hwloc-gather-topology-lstopo.patch")))))
     (build-system gnu-build-system)
-    (arguments
-     ;; Enable libpci support, which effectively makes hwloc GPLv2+.
-     '(#:configure-flags '("--enable-libpci")))
     (inputs
      `(("libx11" ,libx11)
        ("cairo" ,cairo)
        ("ncurses" ,ncurses)
+       ("libpciaccess" ,libpciaccess)
        ("expat" ,expat)))
     (native-inputs
      `(("pkg-config" ,pkg-config)))
     (propagated-inputs
-     ;; 'hwloc.pc' refers to libpci and libnuma, hence the propagation.
-     `(("numactl" ,numactl)
-       ("pciutils" ,pciutils)))
+     ;; 'hwloc.pc' refers to libnuma, hence the propagation.
+     `(("numactl" ,numactl)))
     (home-page "http://www.open-mpi.org/projects/hwloc/";)
     (synopsis "Abstraction of hardware architectures")
     (description
@@ -77,8 +76,6 @@ exploit it accordingly and efficiently.
 hwloc may display the topology in multiple convenient formats.  It also offers
 a powerful programming interface to gather information about the hardware,
 bind processes, and much more.")
-
-    ;; But see above about linking against libpci.
     (license bsd-3)))
 
 (define-public openmpi
diff --git a/gnu/packages/patches/hwloc-gather-topology-lstopo.patch 
b/gnu/packages/patches/hwloc-gather-topology-lstopo.patch
new file mode 100644
index 0000000..06f47ae
--- /dev/null
+++ b/gnu/packages/patches/hwloc-gather-topology-lstopo.patch
@@ -0,0 +1,13 @@
+Derived from upstream commit 0a32f719c.
+
+--- hwloc-1.10.1/tests/linux/Makefile.in       2015-01-26 03:37:52.000000000 
-0600
++++ hwloc-1.10.1/tests/linux/Makefile.in       2015-06-15 11:21:49.824842511 
-0500
+@@ -1633,7 +1633,7 @@
+ 
+ 
+ install-exec-hook:
+-      $(SED) -e 's/HWLOC_top_builddir\/utils/bindir/' -e 
'/HWLOC_top_builddir/d' $(DESTDIR)$(bindir)/hwloc-gather-topology > 
$(DESTDIR)$(bindir)/hwloc-gather-topology.tmp && mv -f 
$(DESTDIR)$(bindir)/hwloc-gather-topology.tmp 
$(DESTDIR)$(bindir)/hwloc-gather-topology
++      $(SED) -e 's/HWLOC_top_builddir\/utils\/lstopo/bindir/' -e 
'/HWLOC_top_builddir/d' $(DESTDIR)$(bindir)/hwloc-gather-topology > 
$(DESTDIR)$(bindir)/hwloc-gather-topology.tmp && mv -f 
$(DESTDIR)$(bindir)/hwloc-gather-topology.tmp 
$(DESTDIR)$(bindir)/hwloc-gather-topology
+       chmod +x $(DESTDIR)$(bindir)/hwloc-gather-topology
+ 
+ # Tell versions [3.59,3.63) of GNU make to not export all variables.
-- 
2.2.1