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gnu: openmpi: Upgrade to 4.0.0. 

* 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.
This commit is contained in:
Eric Bavier 2019-01-31 23:03:35 -06:00
parent 1482531cd7
commit 41313acebf
No known key found for this signature in database
GPG Key ID: FD73CAC719D32566
2 changed files with 20 additions and 16 deletions
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7
gnu/packages/linux.scm
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@ -4717,6 +4717,13 @@ libraries, which are often integrated directly into libfabric.")
(string-append %output "/include"))) (string-append %output "/include")))
(substitute* "Makefile" (substitute* "Makefile"
(("/lib64") "/lib")) (("/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))))) #t)))))
(synopsis "Intel Performance Scaled Messaging (PSM) Libraries") (synopsis "Intel Performance Scaled Messaging (PSM) Libraries")
(description (description

29
gnu/packages/mpi.scm
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@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU ;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014, 2015, 2018 Eric Bavier <bavier@member.fsf.org> ;;; Copyright © 2014, 2015, 2018, 2019 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2014 Ian Denhardt <ian@zenhack.net> ;;; Copyright © 2014 Ian Denhardt <ian@zenhack.net>
;;; Copyright © 2016 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
@ -33,6 +33,7 @@
#:use-module (guix build-system python) #:use-module (guix build-system python)
#:use-module (gnu packages) #:use-module (gnu packages)
#:use-module (gnu packages gcc) #:use-module (gnu packages gcc)
#:use-module (gnu packages libevent)
#:use-module (gnu packages linux) #:use-module (gnu packages linux)
#:use-module (gnu packages pciutils) #:use-module (gnu packages pciutils)
#:use-module (gnu packages xorg) #:use-module (gnu packages xorg)
@ -157,7 +158,7 @@ bind processes, and much more.")
(define-public openmpi (define-public openmpi
(package (package
(name "openmpi") (name "openmpi")
(version "3.0.1") (version "4.0.0")
(source (source
(origin (origin
(method url-fetch) (method url-fetch)
@ -166,12 +167,13 @@ bind processes, and much more.")
"/downloads/openmpi-" version ".tar.bz2")) "/downloads/openmpi-" version ".tar.bz2"))
(sha256 (sha256
(base32 (base32
"0pbqrm5faf57nasy1s81wqivl7zvxmv8lzjh8hvb0f3qxv8m0d36")))) "0srnjwzsmyhka9hhnmqm86qck4w3xwjm8g6sbns58wzbrwv8l2rg"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(inputs (inputs
`(("hwloc" ,hwloc "lib") `(("hwloc" ,hwloc "lib")
("gfortran" ,gfortran) ("gfortran" ,gfortran)
("libfabric" ,libfabric) ("libfabric" ,libfabric)
("libevent" ,libevent)
,@(if (and (not (%current-target-system)) ,@(if (and (not (%current-target-system))
(member (%current-system) (package-supported-systems psm))) (member (%current-system) (package-supported-systems psm)))
`(("psm" ,psm)) `(("psm" ,psm))
@ -191,16 +193,11 @@ bind processes, and much more.")
`(#:configure-flags `("--enable-mpi-ext=affinity" ;cr doesn't work `(#:configure-flags `("--enable-mpi-ext=affinity" ;cr doesn't work
"--enable-memchecker" "--enable-memchecker"
"--with-sge" "--with-sge"
"--with-psm"
;; VampirTrace is obsoleted by scorep and disabling "--with-psm2"
;; it reduces the closure size considerably. "--with-valgrind"
"--disable-vt" "--with-hwloc=external"
"--with-libevent"
,(string-append "--with-valgrind="
(assoc-ref %build-inputs "valgrind"))
,(string-append "--with-hwloc="
(assoc-ref %build-inputs "hwloc"))
;; Enable support for SLURM's Process Manager ;; Enable support for SLURM's Process Manager
;; Interface (PMI). ;; Interface (PMI).
,(string-append "--with-pmi=" ,(string-append "--with-pmi="
@ -219,8 +216,8 @@ bind processes, and much more.")
(("_ABSOLUTE") "")) (("_ABSOLUTE") ""))
;; Avoid valgrind (which pulls in gdb etc.). ;; Avoid valgrind (which pulls in gdb etc.).
(substitute* (substitute*
'("./ompi/mca/io/romio314/src/io_romio314_component.c") '("./ompi/mca/io/romio321/src/io_romio321_component.c")
(("MCA_io_romio314_COMPLETE_CONFIGURE_FLAGS") (("MCA_io_romio321_COMPLETE_CONFIGURE_FLAGS")
"\"[elided to reduce closure]\"")) "\"[elided to reduce closure]\""))
#t)) #t))
(add-before 'build 'scrub-timestamps ;reproducibility (add-before 'build 'scrub-timestamps ;reproducibility
@ -270,7 +267,7 @@ only provides @code{MPI_THREAD_FUNNELED}.")))
(setenv "OMPI_MCA_plm_rsh_agent" (which "false")) (setenv "OMPI_MCA_plm_rsh_agent" (which "false"))
;; Allow oversubscription in case there are less physical cores available ;; Allow oversubscription in case there are less physical cores available
;; in the build environment than the package wants while testing. ;; 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)) #t))
(define-public python-mpi4py (define-public python-mpi4py