Merge remote-tracking branch 'origin/master' into core-updates

 Conflicts:
	doc/guix.texi
	gnu/local.mk
	gnu/packages/admin.scm
	gnu/packages/base.scm
	gnu/packages/chromium.scm
	gnu/packages/compression.scm
	gnu/packages/databases.scm
	gnu/packages/diffoscope.scm
	gnu/packages/freedesktop.scm
	gnu/packages/gnome.scm
	gnu/packages/gnupg.scm
	gnu/packages/guile.scm
	gnu/packages/inkscape.scm
	gnu/packages/llvm.scm
	gnu/packages/openldap.scm
	gnu/packages/pciutils.scm
	gnu/packages/ruby.scm
	gnu/packages/samba.scm
	gnu/packages/sqlite.scm
	gnu/packages/statistics.scm
	gnu/packages/syndication.scm
	gnu/packages/tex.scm
	gnu/packages/tls.scm
	gnu/packages/version-control.scm
	gnu/packages/xml.scm
	guix/build-system/copy.scm
	guix/scripts/home.scm

1 files changed, 17 insertions, 5 deletions

diff --git a/gnu/packages/mpi.scm b/gnu/packages/mpi.scm
index ebf9238906..70b14c30b3 100644
--- a/gnu/packages/mpi.scm
+++ b/gnu/packages/mpi.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014, 2015, 2018, 2019 Eric Bavier <[email protected]>
-;;; Copyright © 2014-2022 Ludovic Courtès <[email protected]>
+;;; Copyright © 2014-2023 Ludovic Courtès <[email protected]>
 ;;; Copyright © 2014 Ian Denhardt <[email protected]>
 ;;; Copyright © 2016 Andreas Enge <[email protected]>
 ;;; Copyright © 2017 Dave Love <[email protected]>
@@ -143,7 +143,7 @@ bind processes, and much more.")
   ;; Note: 2.x isn't the default yet, see above.
   (package
     (inherit hwloc-1)
-    (version "2.8.0")
+    (version "2.9.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://download.open-mpi.org/release/hwloc/v"
@@ -151,7 +151,7 @@ bind processes, and much more.")
                                   "/hwloc-" version ".tar.bz2"))
               (sha256
                (base32
-                "1ha23yqfx9kfxm5fcj9m0fnyf0r2k6p4k88xxqishclcsky752il"))))
+                "11v8hnl6fdsdbm3wnz5gg88f2ghixjyl7jlfmywj293ab5iyjw10"))))
 
     ;; libnuma is no longer needed.
     (inputs (modify-inputs (package-inputs hwloc-1)
@@ -167,6 +167,10 @@ bind processes, and much more.")
                (substitute* "tests/hwloc/linux-libnuma.c"
                  (("numa_available\\(\\)")
                   "-1"))))
+           (add-before 'check 'skip-test-that-requires-/sys
+             (lambda _
+               ;; 'test-gather-topology.sh' requires /sys as of 2.9.0; skip it.
+               (setenv "HWLOC_TEST_GATHER_TOPOLOGY" "0")))
            (add-before 'check 'skip-test-that-fails-on-qemu
              (lambda _
                ;; Skip test that fails on emulated hardware due to QEMU bug:
@@ -325,7 +329,6 @@ software vendors, application developers and computer science researchers.")
                   ((guix build ant-build-system) #:prefix ant:)
                   (guix build utils))
        #:imported-modules ((guix build ant-build-system)
-                           (guix build syscalls)
                            ,@%gnu-build-system-modules)
        ,@(substitute-keyword-arguments (package-arguments openmpi)
            ((#:configure-flags flags)
@@ -359,7 +362,7 @@ software vendors, application developers and computer science researchers.")
      (substitute-keyword-arguments (package-arguments openmpi)
        ((#:configure-flags flags)
         `(cons "--enable-mpi-thread-multiple" ,flags))))
-    (description " This version of Open@tie{}MPI has an implementation of
+    (description "This version of Open@tie{}MPI has an implementation of
 @code{MPI_Init_thread} that provides @code{MPI_THREAD_MULTIPLE}.  This won't
 work correctly with all transports (such as @code{openib}), and the
 performance is generally worse than the vanilla @code{openmpi} package, which
@@ -384,6 +387,15 @@ only provides @code{MPI_THREAD_FUNNELED}.")))
      ;; compare stdout, such as that of 'hdf5-parallel-openmpi'.  Thus, tell
      ;; UCX to not emit those warnings.
      (setenv "UCX_LOG_LEVEL" "error")
+
+     ;; Starting from 2.9.0, hwloc fails when /sys is unavailable:
+     ;;
+     ;;  [hwloc/linux] failed to find sysfs cpu topology directory, aborting linux discovery.
+     ;;
+     ;; This in turn breaks Open MPI users.  To work around it, define a fake
+     ;; topology with 4 cores.  That silently disables CPU binding, though
+     ;; 'get_cpubind' will report there's no binding.
+     (setenv "HWLOC_SYNTHETIC" "4")
      #t))
 
 (define-public python-mpi4py