;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015 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 Paul Garlick <pgarlick@tourbillion-technology.com>
+;;; Copyright © 2019 Ricardo Wurmus <rekado@elephly.net>
;;;
;;; This file is part of GNU Guix.
;;;
#:use-module (guix download)
#:use-module (guix utils)
#:use-module (guix build-system gnu)
+ #:use-module (guix build-system python)
#:use-module (gnu packages)
+ #: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)
;; to migrate to 2.0.
(package
(name "hwloc")
- (version "1.11.9")
+ (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
- "0r2im1s5lp7zjwqalcqcnlxx0dsky1bnx5waf2r3rmj888c36hrr"))))
+ "0za1b9lvrm3rhn0lrxja5f64r0aq1qs4m0pxn1ji2mbi8ndppyyx"))))
(build-system gnu-build-system)
(outputs '("out" ;'lstopo' & co., depends on Cairo, libx11, etc.
"lib" ;small closure
`(#:configure-flags '("--localstatedir=/var")
#:phases
(modify-phases %standard-phases
+ (add-before 'check 'skip-linux-libnuma-test
+ (lambda _
+ ;; Arrange to skip 'tests/linux-libnuma', which fails on some
+ ;; machines: <https://github.com/open-mpi/hwloc/issues/213>.
+ (substitute* "tests/linux-libnuma.c"
+ (("numa_available\\(\\)")
+ "-1"))
+ #t))
(add-after 'install 'refine-libnuma
;; Give -L arguments for libraries to avoid propagation
(lambda* (#:key inputs outputs #:allow-other-keys)
;; Note: 2.0 isn't the default yet, see above.
(package
(inherit hwloc)
- (version "2.0.0")
+ (version "2.0.3")
(source (origin
(method url-fetch)
(uri (string-append "https://www.open-mpi.org/software/hwloc/v"
"/downloads/hwloc-" version ".tar.bz2"))
(sha256
(base32
- "021765f9y6pxcxrvfpzzwaig16ypfbph5xjpkd29qkhzs9r6zrcr"))
- (patches (search-patches "hwloc-tests-without-sysfs.patch"))))
+ "09f7ajak8wv5issr0hw72vs3jkldc7crcc7z5fd34sspkvrsm4z3"))))
;; libnuma is no longer needed.
- (inputs (alist-delete "numactl" (package-inputs hwloc)))))
+ (inputs (alist-delete "numactl" (package-inputs hwloc)))
+ (arguments
+ (substitute-keyword-arguments (package-arguments hwloc)
+ ((#:phases phases)
+ `(modify-phases ,phases
+ (replace 'skip-linux-libnuma-test
+ (lambda _
+ ;; Arrange to skip 'tests/hwloc/linux-libnuma', which fails on
+ ;; some machines: <https://github.com/open-mpi/hwloc/issues/213>.
+ (substitute* "tests/hwloc/linux-libnuma.c"
+ (("numa_available\\(\\)")
+ "-1"))
+ #t))))))))
(define-public openmpi
(package
(name "openmpi")
- (version "1.10.7")
+ (version "4.0.0")
(source
(origin
(method url-fetch)
"/downloads/openmpi-" version ".tar.bz2"))
(sha256
(base32
- "142s1vny9gllkq336yafxayjgcirj2jv0ddabj879jgya7hyr2d0"))))
+ "0srnjwzsmyhka9hhnmqm86qck4w3xwjm8g6sbns58wzbrwv8l2rg"))))
(build-system gnu-build-system)
(inputs
`(("hwloc" ,hwloc "lib")
("gfortran" ,gfortran)
("libfabric" ,libfabric)
- ,@(match (%current-system)
- ((member (package-supported-systems psm))
- `(("psm" ,psm)))
- (_ `()))
+ ("libevent" ,libevent)
+ ("opensm" ,opensm)
+ ,@(if (and (not (%current-target-system))
+ (member (%current-system) (package-supported-systems psm)))
+ `(("psm" ,psm))
+ '())
+ ,@(if (and (not (%current-target-system))
+ (member (%current-system) (package-supported-systems psm2)))
+ `(("psm2" ,psm2))
+ '())
("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/:"
+ (getenv "C_INCLUDE_PATH")))
+ (setenv "CPLUS_INCLUDE_PATH"
+ (string-append (assoc-ref inputs "opensm")
+ "/include/infiniband/:"
+ (getenv "CPLUS_INCLUDE_PATH")))
+ #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/romio/src/io_romio_component.c")
- (("MCA_io_romio_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
;; See file://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
(inherit openmpi)
work correctly with all transports (such as @code{openib}), and the
performance is generally worse than the vanilla @code{openmpi} package, which
only provides @code{MPI_THREAD_FUNNELED}.")))
+
+;;; Build phase to be used for packages that execute MPI code.
+(define-public %openmpi-setup
+ '(lambda _
+ ;; By default, running the test suite would fail because 'ssh' could not
+ ;; be found in $PATH. Define this variable to placate Open MPI without
+ ;; adding a dependency on OpenSSH (the agent isn't used anyway.)
+ (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_mapping_policy" "core:OVERSUBSCRIBE")
+ #t))
+
+(define-public python-mpi4py
+ (package
+ (name "python-mpi4py")
+ (version "3.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "mpi4py" version))
+ (sha256
+ (base32
+ "0ld8rjmsjr0dklvj2g1gr3ax32sdq0xjxyh0cspknc1i36waajb5"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'build 'mpi-setup
+ ,%openmpi-setup)
+ (add-before 'check 'pre-check
+ (lambda _
+ ;; Skip BaseTestSpawn class (causes error 'ompi_dpm_dyn_init()
+ ;; failed --> Returned "Unreachable"' in chroot environment).
+ (substitute* "test/test_spawn.py"
+ (("unittest.skipMPI\\('openmpi\\(<3.0.0\\)'\\)")
+ "unittest.skipMPI('openmpi')"))
+ #t)))))
+ (inputs
+ `(("openmpi" ,openmpi)))
+ (home-page "https://bitbucket.org/mpi4py/mpi4py/")
+ (synopsis "Python bindings for the Message Passing Interface standard")
+ (description "MPI for Python (mpi4py) provides bindings of the Message
+Passing Interface (MPI) standard for the Python programming language, allowing
+any Python program to exploit multiple processors.
+
+mpi4py is constructed on top of the MPI-1/MPI-2 specification and provides an
+object oriented interface which closely follows MPI-2 C++ bindings. It
+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)))
HCoop / jackhill / guix / guix.git / blobdiff