GNU bug report logs - #34388
[PATCH] gnu: openmpi: Upgrade to 4.0.0.

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: ericbavier <at> centurylink.net
To: guix-patches <at> gnu.org
Cc: Eric Bavier <bavier <at> member.fsf.org>
Subject: [PATCH] gnu: openmpi: Upgrade to 4.0.0.
Date: Fri,  8 Feb 2019 09:06:22 -0600

From: Eric Bavier <bavier <at> member.fsf.org>

* 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 <bavier <at> member.fsf.org>
+;;; Copyright © 2014, 2015, 2018, 2019 Eric Bavier <bavier <at> member.fsf.org>
 ;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo <at> gnu.org>
 ;;; Copyright © 2014 Ian Denhardt <ian <at> zenhack.net>
 ;;; Copyright © 2016 Andreas Enge <andreas <at> enge.fr>
@@ -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

Message #8 received at 34388 <at> debbugs.gnu.org (full text, mbox):

From: Eric Bavier <ericbavier <at> centurylink.net>
To: Ricardo Wurmus <rekado <at> elephly.net>
Cc: 34388 <at> debbugs.gnu.org, Eric Bavier <bavier <at> member.fsf.org>
Subject: Re: [bug#34388] [PATCH] gnu: openmpi: Upgrade to 4.0.0.
Date: Fri, 8 Feb 2019 22:31:21 -0600

[Message part 1 (text/plain, inline)]

On Fri, 08 Feb 2019 19:31:49 +0100
Ricardo Wurmus <rekado <at> elephly.net> wrote:

> Hi Eric,
> 
> ericbavier <at> centurylink.net writes:
> 
> > From: Eric Bavier <bavier <at> member.fsf.org>
> >
> > * 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.  
> 
> Thank you, this looks good to me!

Thanks for reviewing and providing the nice starting patch.

> 
> (After this has been pushed to the “master” branch I would like to add
> support for Infiniband with a few minor changes.)

Great, I thought I'd leave that to you.

`~Eric

[Message part 2 (application/pgp-signature, inline)]

Message #13 received at 34388-done <at> debbugs.gnu.org (full text, mbox):

From: Eric Bavier <ericbavier <at> centurylink.net>
To: Ricardo Wurmus <rekado <at> elephly.net>
Cc: 34388-done <at> debbugs.gnu.org
Subject: Re: [bug#34388] [PATCH] gnu: openmpi: Upgrade to 4.0.0.
Date: Sat, 9 Feb 2019 00:55:15 -0600

[Message part 1 (text/plain, inline)]

On Fri, 8 Feb 2019 22:31:21 -0600
Eric Bavier <ericbavier <at> centurylink.net> wrote:

> On Fri, 08 Feb 2019 19:31:49 +0100
> Ricardo Wurmus <rekado <at> elephly.net> wrote:
> 
> > Hi Eric,
> > 
> > ericbavier <at> centurylink.net writes:
> >   
> > > From: Eric Bavier <bavier <at> member.fsf.org>
> > >
> > > * 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.    
> > 
> > Thank you, this looks good to me!  
> 
> Thanks for reviewing and providing the nice starting patch.

Pushed to master in 41313acebf39e04c9ddd0857b8cd8b69991c88c3

`~Eric

[Message part 2 (application/pgp-signature, inline)]

Message #16 received at 34388 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: ericbavier <at> centurylink.net
Cc: 34388 <at> debbugs.gnu.org, Eric Bavier <bavier <at> member.fsf.org>
Subject: Re: [bug#34388] [PATCH] gnu: openmpi: Upgrade to 4.0.0.
Date: Fri, 08 Feb 2019 19:31:49 +0100

Hi Eric,

ericbavier <at> centurylink.net writes:

> From: Eric Bavier <bavier <at> member.fsf.org>
>
> * 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.

Thank you, this looks good to me!

(After this has been pushed to the “master” branch I would like to add
support for Infiniband with a few minor changes.)

--
Ricardo

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