Subject: [PATCH] gnu: openmpi: Upgrade to 4.0.0.
From: [email-masked]
To: [email-masked]
Cc: Eric Bavier <[email-masked]>
Date: Fri, 8 Feb 2019 09:06:22 -0600
List-Id: <debbugs-submit.debbugs.gnu.org>

From: Eric Bavier <[email-masked]>

* gnu/packages/linux.scm (psm)[arguments]: Add 'patch-sysmacros phase to fix
"undefined reference to `minor'" errors while linking against
libinfinipath.so.
* gnu/packages/mpi.scm (openmpi): Upgrade to 4.0.0.
[inputs]: Add libevent.
[arguments]: Simplify configure-flags.  Use system libevent.  Adjust romio
version strings.
(%openmpi-setup): Use OMPI_MCA_rmaps_base_mapping_policy for oversubscription.
---
 gnu/packages/linux.scm |  7 +++++++
 gnu/packages/mpi.scm   | 29 +++++++++++++----------------
 2 files changed, 20 insertions(+), 16 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index b1dfb7f701..66a1ad4508 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -4717,6 +4717,13 @@ libraries, which are often integrated directly into libfabric.")
                          (string-append %output "/include")))
                       (substitute* "Makefile"
                         (("/lib64") "/lib"))
+                      #t))
+                  (add-after 'unpack 'patch-sysmacros
+                    (lambda _
+                      (substitute* "ipath/ipath_proto.c"
+                        (("#include <sys/poll.h>" m)
+                         (string-append m "\n"
+                                        "#include <sys/sysmacros.h>")))
                       #t)))))
     (synopsis "Intel Performance Scaled Messaging (PSM) Libraries")
     (description
diff --git a/gnu/packages/mpi.scm b/gnu/packages/mpi.scm
index 1f69a04bc9..0a43c55b7a 100644
--- a/gnu/packages/mpi.scm
+++ b/gnu/packages/mpi.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015, 2018 Eric Bavier <[email-masked]>
+;;; Copyright © 2014, 2015, 2018, 2019 Eric Bavier <[email-masked]>
 ;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <[email-masked]>
 ;;; Copyright © 2014 Ian Denhardt <[email-masked]>
 ;;; Copyright © 2016 Andreas Enge <[email-masked]>
@@ -33,6 +33,7 @@
   #:use-module (guix build-system python)
   #:use-module (gnu packages)
   #:use-module (gnu packages gcc)
+  #:use-module (gnu packages libevent)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages pciutils)
   #:use-module (gnu packages xorg)
@@ -157,7 +158,7 @@ bind processes, and much more.")
 (define-public openmpi
   (package
     (name "openmpi")
-    (version "3.0.1")
+    (version "4.0.0")
     (source
      (origin
       (method url-fetch)
@@ -166,12 +167,13 @@ bind processes, and much more.")
                           "/downloads/openmpi-" version ".tar.bz2"))
       (sha256
        (base32
-        "0pbqrm5faf57nasy1s81wqivl7zvxmv8lzjh8hvb0f3qxv8m0d36"))))
+        "0srnjwzsmyhka9hhnmqm86qck4w3xwjm8g6sbns58wzbrwv8l2rg"))))
     (build-system gnu-build-system)
     (inputs
      `(("hwloc" ,hwloc "lib")
        ("gfortran" ,gfortran)
        ("libfabric" ,libfabric)
+       ("libevent" ,libevent)
        ,@(if (and (not (%current-target-system))
                   (member (%current-system) (package-supported-systems psm)))
              `(("psm" ,psm))
@@ -191,16 +193,11 @@ bind processes, and much more.")
      `(#:configure-flags `("--enable-mpi-ext=affinity" ;cr doesn't work
                            "--enable-memchecker"
                            "--with-sge"
-
-                           ;; VampirTrace is obsoleted by scorep and disabling
-                           ;; it reduces the closure size considerably.
-                           "--disable-vt"
-
-                           ,(string-append "--with-valgrind="
-                                           (assoc-ref %build-inputs "valgrind"))
-                           ,(string-append "--with-hwloc="
-                                           (assoc-ref %build-inputs "hwloc"))
-
+                           "--with-psm"
+                           "--with-psm2"
+                           "--with-valgrind"
+                           "--with-hwloc=external"
+                           "--with-libevent"
                            ;; Enable support for SLURM's Process Manager
                            ;; Interface (PMI).
                            ,(string-append "--with-pmi="
@@ -219,8 +216,8 @@ bind processes, and much more.")
                         (("_ABSOLUTE") ""))
                       ;; Avoid valgrind (which pulls in gdb etc.).
                       (substitute*
-                          '("./ompi/mca/io/romio314/src/io_romio314_component.c")
-                        (("MCA_io_romio314_COMPLETE_CONFIGURE_FLAGS")
+                          '("./ompi/mca/io/romio321/src/io_romio321_component.c")
+                        (("MCA_io_romio321_COMPLETE_CONFIGURE_FLAGS")
                          "\"[elided to reduce closure]\""))
                       #t))
                   (add-before 'build 'scrub-timestamps ;reproducibility
@@ -270,7 +267,7 @@ only provides @code{MPI_THREAD_FUNNELED}.")))
      (setenv "OMPI_MCA_plm_rsh_agent" (which "false"))
      ;; Allow oversubscription in case there are less physical cores available
      ;; in the build environment than the package wants while testing.
-     (setenv "OMPI_MCA_rmaps_base_oversubscribe" "yes")
+     (setenv "OMPI_MCA_rmaps_base_mapping_policy" "core:OVERSUBSCRIBE")
      #t))

 (define-public python-mpi4py
--
2.20.1