;;; GNU Guix --- Functional package management for GNU
;;; 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, 2020, 2021 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2014 Ian Denhardt <ian@zenhack.net>
;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2017 Dave Love <fx@gnu.org>
;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Paul Garlick <pgarlick@tourbillion-technology.com>
;;; Copyright © 2019 Ricardo Wurmus <rekado@elephly.net>
;;;
(define-module (gnu packages mpi)
#:use-module (guix packages)
- #:use-module ((guix licenses)
- #:hide (expat))
+ #:use-module ((guix licenses) #:prefix license:)
#:use-module (guix download)
- #:use-module (guix git-download)
#:use-module (guix utils)
#:use-module (guix deprecation)
#:use-module (guix build-system gnu)
#:use-module (guix build-system python)
#:use-module (gnu packages)
+ #:use-module (gnu packages base)
+ #:use-module (gnu packages compression)
#:use-module (gnu packages fabric-management)
#:use-module (gnu packages gcc)
#:use-module (gnu packages java)
#:use-module (srfi srfi-1)
#:use-module (ice-9 match))
-(define-public hwloc
+(define-public hwloc-1
;; Note: For now we keep 1.x as the default because many packages have yet
;; to migrate to 2.0.
(package
(build-system gnu-build-system)
(outputs '("out" ;'lstopo' & co., depends on Cairo, libx11, etc.
"lib" ;small closure
+ "doc" ;400+ section 3 man pages
"debug"))
(inputs
`(("libx11" ,libx11)
(substitute* (string-append lib "/lib/pkgconfig/hwloc.pc")
(("^.*prefix=.*$")
""))
+ #t)))
+ (add-after 'install 'move-man3-pages
+ (lambda* (#:key outputs #:allow-other-keys)
+ ;; Move section 3 man pages to the "doc" output.
+ (let ((out (assoc-ref outputs "out"))
+ (doc (assoc-ref outputs "doc")))
+ (copy-recursively (string-append out "/share/man/man3")
+ (string-append doc "/share/man/man3"))
+ (delete-file-recursively (string-append out "/share/man/man3"))
#t))))))
(home-page "https://www.open-mpi.org/projects/hwloc/")
(synopsis "Abstraction of hardware architectures")
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.")
- (license bsd-3)))
+ (license license:bsd-3)))
(define-public hwloc-2
- ;; Note: 2.0 isn't the default yet, see above.
+ ;; Note: 2.x isn't the default yet, see above.
(package
- (inherit hwloc)
- (version "2.1.0")
+ (inherit hwloc-1)
+ (version "2.4.1")
(source (origin
(method url-fetch)
- (uri (string-append "https://www.open-mpi.org/software/hwloc/v"
+ (uri (string-append "https://download.open-mpi.org/release/hwloc/v"
(version-major+minor version)
- "/downloads/hwloc-" version ".tar.bz2"))
+ "/hwloc-" version ".tar.bz2"))
(sha256
(base32
- "0qh8s7pphz0m5cwb7liqmc17xzfs23xhz5wn24r6ikvjyx99fhhr"))))
+ "0qyywmyns2jf3is3axrwmffvdd7ji7liy5axp650q4i6kzk2291r"))))
;; libnuma is no longer needed.
- (inputs (alist-delete "numactl" (package-inputs hwloc)))
+ (inputs (alist-delete "numactl" (package-inputs hwloc-1)))
(arguments
- (substitute-keyword-arguments (package-arguments hwloc)
+ (substitute-keyword-arguments (package-arguments hwloc-1)
((#:phases phases)
`(modify-phases ,phases
(replace 'skip-linux-libnuma-test
(substitute* "tests/hwloc/linux-libnuma.c"
(("numa_available\\(\\)")
"-1"))
+ #t))
+ (add-before 'check 'skip-test-that-fails-on-qemu
+ (lambda _
+ ;; Skip test that fails on emulated hardware due to QEMU bug:
+ ;; <https://bugs.gnu.org/40342>.
+ (substitute* "tests/hwloc/hwloc_get_last_cpu_location.c"
+ (("hwloc_topology_init" all)
+ (string-append "exit (77);\n" all)))
#t))))))))
-(define-deprecated hwloc-2.0 'hwloc-2
+(define-deprecated hwloc-2.0 hwloc-2)
+
+(define-public hwloc
+ ;; The latest stable series of hwloc.
hwloc-2)
(define-public openmpi
(package
(name "openmpi")
- (version "4.0.2")
+ (version "4.0.5")
(source
(origin
(method url-fetch)
(version-major+minor version)
"/downloads/openmpi-" version ".tar.bz2"))
(sha256
- (base32 "0ms0zvyxyy3pnx9qwib6zaljyp2b3ixny64xvq3czv3jpr8zf2wh"))
- (patches (search-patches "openmpi-psm2-priority.patch"))))
+ (base32 "02f0r9d3xgs08svkmj8v7lzviyxqnkk4yd3z0wql550xnriki3y5"))
+ (patches (search-patches "openmpi-mtl-priorities.patch"))))
(build-system gnu-build-system)
(inputs
`(("hwloc" ,hwloc-2 "lib")
"--with-hwloc=external"
"--with-libevent"
- ;; Make sure ./configure fails if one of these is
- ;; missing.
- "--with-ucx"
- "--with-psm"
- "--with-psm2"
+ ;; Help 'orterun' and 'mpirun' find their tools
+ ;; under $prefix by default.
+ "--enable-mpirun-prefix-by-default"
;; InfiniBand support
"--enable-openib-control-hdr-padding"
(let ((out (assoc-ref outputs "out")))
(for-each delete-file (find-files out "config.log"))
#t))))))
- (home-page "http://www.open-mpi.org")
+ (home-page "https://www.open-mpi.org")
(synopsis "MPI-3 implementation")
(description
"The Open MPI Project is an MPI-3 implementation that is developed and
best MPI library available. Open MPI offers advantages for system and
software vendors, application developers and computer science researchers.")
;; See file://LICENSE
- (license bsd-2)))
+ (license license:bsd-2)))
;; TODO: javadoc files contain timestamps.
(define-public java-openmpi
- (package (inherit openmpi)
+ (package/inherit openmpi
(name "java-openmpi")
(inputs
`(("openmpi" ,openmpi)
(synopsis "Java bindings for MPI")))
(define-public openmpi-thread-multiple
- (package
- (inherit openmpi)
+ (package/inherit openmpi
(name "openmpi-thread-multiple")
(arguments
(substitute-keyword-arguments (package-arguments openmpi)
;; 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_mapping_policy" "core:OVERSUBSCRIBE")
- #t))
-
-(define-public intel-mpi-benchmarks
- (package
- (name "intel-mpi-benchmarks")
- (version "2019.3")
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/intel/mpi-benchmarks.git")
- (commit (string-append "IMB-v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "0si5xi6ilhd3w0gbsg124589pvp094hvf366rvjjb9pi7pdk5p4i"))))
- (build-system gnu-build-system)
- (arguments
- '(#:phases (modify-phases %standard-phases
- (delete 'configure)
- (delete 'check)
- (replace 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (define (benchmark? file stat)
- (and (string-prefix? "IMB-" (basename file))
- (executable-file? file)))
-
- (let* ((out (assoc-ref outputs "out"))
- (bin (string-append out "/bin")))
- (for-each (lambda (file)
- (install-file file bin))
- (find-files "." benchmark?))
- #t))))
- ;; The makefile doesn't express all the dependencies, it seems.
- #:parallel-build? #t
-
- #:make-flags (list (string-append "CC="
- (assoc-ref %build-inputs "openmpi")
- "/bin/mpicc")
- (string-append "CXX="
- (assoc-ref %build-inputs "openmpi")
- "/bin/mpicxx"))))
- (inputs
- `(("openmpi" ,openmpi)))
- (home-page "https://github.com/intel/mpi-benchmarks")
- (synopsis "Benchmarks for the Message Passing Interface (MPI)")
- (description
- "Intel MPI Benchmarks (IMB) provides a set of elementary benchmarks that
-conform with versions 1, 2, and 3 of the Message Passing Interface (MPI).")
- (license
- (fsf-free "https://directory.fsf.org/wiki/License:CPL-1.0"
- "https://www.gnu.org/licenses/license-list.html#CommonPublicLicense10"))))
+ ;; UCX sometimes outputs uninteresting warnings such as:
+ ;;
+ ;; mpool.c:38 UCX WARN object 0x7ffff44fffc0 was not returned to mpool ucp_am_bufs
+ ;;
+ ;; These in turn leads to failures of test suites that capture and
+ ;; compare stdout, such as that of 'hdf5-parallel-openmpi'. Thus, tell
+ ;; UCX to not emit those warnings.
+ (setenv "UCX_LOG_LEVEL" "error")
+ #t))
(define-public python-mpi4py
(package
supports point-to-point and collective communications of any picklable Python
object as well as optimized communications of Python objects (such as NumPy
arrays) that expose a buffer interface.")
- (license bsd-3)))
+ (license license:bsd-3)))
+
+(define-public mpich
+ (package
+ (name "mpich")
+ (version "3.3.2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "http://www.mpich.org/static/downloads/"
+ version "/mpich-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1farz5zfx4cd0c3a0wb9pgfypzw0xxql1j1294z1sxslga1ziyjb"))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("zlib" ,zlib)
+ ("hwloc" ,hwloc-2 "lib")
+ ("slurm" ,slurm)
+ ,@(if (and (not (%current-target-system))
+ (member (%current-system) (package-supported-systems ucx)))
+ `(("ucx" ,ucx))
+ '())))
+ (native-inputs
+ `(("perl" ,perl)
+ ("which" ,which)
+ ("gfortran" ,gfortran)))
+ (outputs '("out" "debug"))
+ (arguments
+ `(#:configure-flags
+ (list "--disable-silent-rules" ;let's see what's happening
+ "--enable-debuginfo"
+
+ ;; Default to "ch4", as will be the case in 3.4. It also works
+ ;; around issues when running test suites of packages that use
+ ;; MPICH: <https://issues.guix.gnu.org/39588#15>.
+ "--with-device=ch4:ucx" ; --with-device=ch4:ofi segfaults in tests
+
+ (string-append "--with-hwloc-prefix="
+ (assoc-ref %build-inputs "hwloc"))
+
+ ,@(if (assoc "ucx" (package-inputs this-package))
+ `((string-append "--with-ucx="
+ (assoc-ref %build-inputs "ucx")))
+ '()))
+
+ #:phases (modify-phases %standard-phases
+ (add-after 'unpack 'patch-sources
+ (lambda _
+ (substitute* "./maint/gen_subcfg_m4"
+ (("/usr/bin/env") (which "env")))
+ (substitute* "src/glue/romio/all_romio_symbols"
+ (("/usr/bin/env") (which "env")))
+ (substitute* (find-files "." "buildiface")
+ (("/usr/bin/env") (which "env")))
+ (substitute* "maint/extracterrmsgs"
+ (("/usr/bin/env") (which "env")))
+ (substitute* (find-files "." "f77tof90")
+ (("/usr/bin/env") (which "env")))
+ (substitute* (find-files "." "\\.sh$")
+ (("/bin/sh") (which "sh")))
+ #t))
+ (add-before 'configure 'fix-makefile
+ (lambda _
+ ;; Remove "@hwloclib@" from 'pmpi_convenience_libs'.
+ ;; This fixes "No rule to make target '-lhwloc', needed
+ ;; by 'lib/libmpi.la'".
+ (substitute* "Makefile.in"
+ (("^pmpi_convenience_libs = (.*) @hwloclib@ (.*)$" _
+ before after)
+ (string-append "pmpi_convenience_libs = "
+ before " " after)))
+ #t)))))
+ (home-page "https://www.mpich.org/")
+ (synopsis "Implementation of the Message Passing Interface (MPI)")
+ (description
+ "MPICH is a high-performance and portable implementation of the Message
+Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3). MPICH provides an
+MPI implementation that efficiently supports different computation and
+communication platforms including commodity clusters, high-speed networks (10
+Gigabit Ethernet, InfiniBand, Myrinet, Quadrics), and proprietary high-end
+computing systems (Blue Gene, Cray). It enables research in MPI through a
+modular framework for other derived implementations.")
+ (license license:bsd-2)))
HCoop / jackhill / guix / guix.git / blobdiff