;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015, 2018 Eric Bavier <bavier@member.fsf.org>
-;;; Copyright © 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.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 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 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>
;;;
;;; This file is part of GNU Guix.
;;;
(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 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 (gnu packages libevent)
#:use-module (gnu packages linux)
#:use-module (gnu packages pciutils)
#:use-module (gnu packages xorg)
#:use-module (gnu packages xml)
#:use-module (gnu packages perl)
#:use-module (gnu packages ncurses)
+ #:use-module (gnu packages parallel)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages valgrind)
#: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
(name "hwloc")
- (version "1.11.10")
+ (version "1.11.12")
(source (origin
(method url-fetch)
(uri (string-append "https://www.open-mpi.org/software/hwloc/v"
"/downloads/hwloc-" version ".tar.bz2"))
(sha256
(base32
- "1ryibcng40xcq22lsj85fn2vcvrksdx9rr3wwxpq8dw37lw0is1b"))))
+ "0za1b9lvrm3rhn0lrxja5f64r0aq1qs4m0pxn1ji2mbi8ndppyyx"))))
(build-system gnu-build-system)
(outputs '("out" ;'lstopo' & co., depends on Cairo, libx11, etc.
"lib" ;small closure
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-2.0
+(define-public hwloc-2
;; Note: 2.0 isn't the default yet, see above.
(package
- (inherit hwloc)
- (version "2.0.2")
+ (inherit hwloc-1)
+ (version "2.2.0")
(source (origin
(method url-fetch)
(uri (string-append "https://www.open-mpi.org/software/hwloc/v"
"/downloads/hwloc-" version ".tar.bz2"))
(sha256
(base32
- "1phc863d5b2fvwpyyq4mlh4rkjdslh6h0h197zmyk3prwrq7si8l"))))
+ "0li27a3lnmb77qxpijj0kpblz32wmqd3b386sypq8ar7vy9vhw5f"))))
;; 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-public hwloc
+ ;; The latest stable series of hwloc.
+ hwloc-2)
+
(define-public openmpi
(package
(name "openmpi")
- (version "3.0.1")
+ (version "4.0.3")
(source
(origin
(method url-fetch)
(version-major+minor version)
"/downloads/openmpi-" version ".tar.bz2"))
(sha256
- (base32
- "0pbqrm5faf57nasy1s81wqivl7zvxmv8lzjh8hvb0f3qxv8m0d36"))))
+ (base32 "00zxcw99gr5n693cmcmn4f6a47vx1ywna895p0x7p163v37gw0hl"))
+ (patches (search-patches "openmpi-mtl-priorities.patch"))))
(build-system gnu-build-system)
(inputs
- `(("hwloc" ,hwloc "lib")
+ `(("hwloc" ,hwloc-2 "lib")
("gfortran" ,gfortran)
("libfabric" ,libfabric)
+ ("libevent" ,libevent)
+ ("opensm" ,opensm)
,@(if (and (not (%current-target-system))
(member (%current-system) (package-supported-systems psm)))
`(("psm" ,psm))
(member (%current-system) (package-supported-systems psm2)))
`(("psm2" ,psm2))
'())
+ ,@(if (and (not (%current-target-system))
+ (member (%current-system) (package-supported-systems ucx)))
+ `(("ucx" ,ucx))
+ '())
("rdma-core" ,rdma-core)
- ("valgrind" ,valgrind)))
+ ("valgrind" ,valgrind)
+ ("slurm" ,slurm))) ;for PMI support (launching via "srun")
(native-inputs
`(("pkg-config" ,pkg-config)
("perl" ,perl)))
`(#:configure-flags `("--enable-mpi-ext=affinity" ;cr doesn't work
"--enable-memchecker"
"--with-sge"
+ "--with-valgrind"
+ "--with-hwloc=external"
+ "--with-libevent"
- ;; VampirTrace is obsoleted by scorep and disabling
- ;; it reduces the closure size considerably.
- "--disable-vt"
+ ;; InfiniBand support
+ "--enable-openib-control-hdr-padding"
+ "--enable-openib-dynamic-sl"
+ "--enable-openib-udcm"
+ "--enable-openib-rdmacm"
+ "--enable-openib-rdmacm-ibaddr"
- ,(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
+ ;; Interface (PMI).
+ ,(string-append "--with-pmi="
+ (assoc-ref %build-inputs "slurm")))
#:phases (modify-phases %standard-phases
+ ;; opensm is needed for InfiniBand support.
+ (add-after 'unpack 'find-opensm-headers
+ (lambda* (#:key inputs #:allow-other-keys)
+ (setenv "C_INCLUDE_PATH"
+ (string-append (assoc-ref inputs "opensm")
+ "/include/infiniband"))
+ (setenv "CPLUS_INCLUDE_PATH"
+ (string-append (assoc-ref inputs "opensm")
+ "/include/infiniband"))
+ #t))
(add-before 'build 'remove-absolute
(lambda _
;; Remove compiler absolute file names (OPAL_FC_ABSOLUTE
(("_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
(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)
+ (name "java-openmpi")
+ (inputs
+ `(("openmpi" ,openmpi)
+ ,@(package-inputs openmpi)))
+ (native-inputs
+ `(("jdk" ,openjdk11 "jdk")
+ ("zip" ,(@ (gnu packages compression) zip))
+ ,@(package-native-inputs openmpi)))
+ (outputs '("out"))
+ (arguments
+ `(#:modules ((guix build gnu-build-system)
+ ((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)
+ `(cons "--enable-mpi-java" ,flags))
+ ((#:make-flags flags ''())
+ `(append '("-C" "ompi/mpi/java")
+ ,flags))
+ ((#:phases phases)
+ `(modify-phases ,phases
+ ;; We could provide the location of the JDK in the configure
+ ;; flags, but since the configure flags are embedded in the
+ ;; info binaries that would leave a reference to the JDK in
+ ;; the "out" output. To avoid this we set JAVA_HOME.
+ (add-after 'unpack 'set-JAVA_HOME
+ (lambda* (#:key inputs #:allow-other-keys)
+ (setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
+ #t))
+ (add-after 'unpack 'link-with-existing-mpi-libraries
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "ompi/mpi/java/c/Makefile.in"
+ (("\\$\\(top_builddir\\)/ompi/lib@OMPI_LIBMPI_NAME@.la")
+ (string-append (assoc-ref inputs "openmpi") "/lib/libmpi.la")))
+ #t))
+ (add-after 'install 'strip-jar-timestamps
+ (assoc-ref ant:%standard-phases 'strip-jar-timestamps)))))))
+ (synopsis "Java bindings for MPI")))
(define-public openmpi-thread-multiple
(package
(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")
+
+ ;; 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
(name "python-mpi4py")
- (version "3.0.0")
+ (version "3.0.3")
(source
- (origin
- (method url-fetch)
- (uri (pypi-uri "mpi4py" version))
- (sha256
- (base32
- "1mzgd26dfv4vwbci8gq77ss9f0x26i9aqzq9b9vs9ndxhlnv0mxl"))))
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "mpi4py" version))
+ (sha256
+ (base32 "07ssbhssv27rrjx1c5vd3vsr31vay5d8xcf4zh9yblcyidn72b81"))))
(build-system python-build-system)
(arguments
`(#:phases
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"
+ ;; "--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