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2014-05-27gnu: librsync: Fix source uri...Eric Bavier
2014-05-27gnu: Add duplicity....Eric Bavier
2014-05-27gnu: Add python-mock....Eric Bavier
2014-05-27gnu: Add python-lockfile....Eric Bavier
2014-05-26services: Add D-Bus and Avahi....Ludovic Courtès
2014-05-26gnu: Add Transmission....Ludovic Courtès
2014-05-26gnu: Add gsegrafix and dependent libraries....John Darrington
2014-05-26gnu: Add mcrypt, libmcrypt, and libmhash....Eric Bavier
2014-05-25gnu: Add librsync....Eric Bavier
2014-05-26gnu: Add inotify-tools....Ludovic Courtès
2014-05-24services: nscd: Provide an 'activate' script to make /var/run/nscd....Ludovic Courtès
2014-05-24services: Support per-service activation scripts....Ludovic Courtès
2014-05-24system: Separate the activation script from the boot script....Ludovic Courtès
2014-05-24gnu: Add lzop....Eric Bavier
2014-05-23vm: Disable QEMU networking in the disk image initrd....Ludovic Courtès
2014-05-22vm: Add 'system-disk-image'....Ludovic Courtès
2014-05-22vm: Use a para-virtualized disk when creating an image....Ludovic Courtès
2014-05-22vm: Make the image format a parameter....Ludovic Courtès
2014-05-22gnu: imagemagick: Upgrade to 6.8.9-0....Andreas Enge
2014-05-22gnu: perl-io-tty: Upgrade to 1.11....Andreas Enge
2014-05-21gnu: Add wpa_supplicant....Ludovic Courtès
2014-05-20Add (gnu system file-systems)....Ludovic Courtès
2014-05-20gnu: Add ccache....Eric Bavier
2014-05-20gnu: Edit synopses of petsc packages....Eric Bavier
2014-05-20gnu: offlineimap: fix license....Eric Bavier
2014-05-20gnu: Add mu....Eric Bavier
2014-05-20gnu: Add offlineimap...Eric Bavier
2014-05-19gnu: Add Linux kbd....Ludovic Courtès
2014-05-19vm: Make the device name a parameter....Ludovic Courtès
2014-05-19gnu: Add superlu-dist package....Eric Bavier
2014-05-19gnu: Add pt-scotch package....Eric Bavier
2014-05-19gnu: Add scotch package....Eric Bavier
2014-05-18system: Add 'grub-configuration' record....Ludovic Courtès
2014-05-18gnu: openmpi: Add memchecker support....Eric Bavier
2014-05-18system: Make /run/current-system at activation time....Ludovic Courtès
2014-05-17gnu: soprano: Add input redland....Andreas Enge
2014-05-17gnu: Add redland....Andreas Enge
2014-05-17gnu: rasqal: Propagate input raptor2....Andreas Enge
2014-05-17gnu: Add rasqal....Andreas Enge
2014-05-16gnu: Add libuv....Ludovic Courtès
2014-05-15system: Add (guix build install) module....Ludovic Courtès
2014-05-15vm: Support initialization of the store DB when the store is shared....Ludovic Courtès
2014-05-14system: Provide declarations for the 'fusectl' and 'binfmt_misc' file systems....Ludovic Courtès
2014-05-14vm: Keep acceptable file systems from the original OS....Ludovic Courtès
2014-05-14gnu: xterm: Upgrade to 304....Ludovic Courtès
2014-05-14system: When unionfs-fuse is used for /, don't kill it when halting....Ludovic Courtès
2014-05-14gnu: libsm: Propagate input libice....Andreas Enge
2014-05-14gnu: qt-4: Upgrade to 4.8.6....Andreas Enge
2014-05-14gnu: qt-4: Enable session management by adding libsm as an input....Andreas Enge
2014-05-14vm: Pass '-serial stdio' in the run-vm.sh....Ludovic Courtès
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names (OPAL_FC_ABSOLUTE ;; etc.) to reduce the closure size. See ;; <https://lists.gnu.org/archive/html/guix-devel/2017-07/msg00388.html> ;; and ;; <https://www.mail-archive.com/users@lists.open-mpi.org//msg31397.html>. (substitute* '("orte/tools/orte-info/param.c" "oshmem/tools/oshmem_info/param.c" "ompi/tools/ompi_info/param.c") (("_ABSOLUTE") "")) ;; Avoid valgrind (which pulls in gdb etc.). (substitute* '("./ompi/mca/io/romio321/src/io_romio321_component.c") (("MCA_io_romio321_COMPLETE_CONFIGURE_FLAGS") "\"[elided to reduce closure]\"")))) (add-before 'build 'scrub-timestamps ;reproducibility (lambda _ (substitute* '("ompi/tools/ompi_info/param.c" "orte/tools/orte-info/param.c" "oshmem/tools/oshmem_info/param.c") ((".*(Built|Configured) on.*") "")))) (add-after 'install 'remove-logs ;reproducibility (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) (for-each delete-file (find-files out "config.log")))))))) (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 maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available. Open MPI offers advantages for system and software vendors, application developers and computer science researchers.") ;; See file://LICENSE (license license:bsd-2))) (define-public openmpi openmpi-4) (define-public openmpi-5 (package (inherit openmpi) (version "5.0.3") (source (origin (method url-fetch) (uri (string-append "https://www.open-mpi.org/software/ompi/v" (version-major+minor version) "/downloads/openmpi-" version ".tar.bz2")) (sha256 (base32 "02x9xmpggw77mdpikjjx83j6i4v3gkqbncda73lk5axk0vr841cr")))) (inputs (modify-inputs (package-inputs openmpi) ;; As of Open MPI 5.0.X, PMIx is used to communicate ;; with SLURM, so SLURM'S PMI is no longer needed. (delete "slurm") (append ucx) ;for Infiniband support (append openpmix) ;for PMI support (launching via "srun") (append prrte))) ;for PMI support (launching via "srun") (native-inputs (modify-inputs (package-native-inputs openmpi) (append python))) (outputs '("out" "debug")) (arguments (substitute-keyword-arguments (package-arguments openmpi) ((#:configure-flags _) #~(list "--enable-mpi-ext=affinity" ;cr doesn't work "--with-sge" #$@(if (package? (this-package-input "valgrind")) #~("--enable-memchecker" "--with-valgrind") #~("--without-valgrind")) "--with-hwloc=external" "--with-libevent" ;; This replaces --enable-mpirun-prefix-by-default wich is deprecated ;; since 5.x. "--enable-prte-prefix-by-default" ;; Enable support for the 'Process Management Interface for Exascale' ;; (PMIx) used e.g. by Slurm for the management communication and ;; coordination of MPI processes. (string-append "--with-pmix=" #$(this-package-input "openpmix")) (string-append "--with-prrte=" #$(this-package-input "prrte")) ;; Since 5.x, Infiniband support is provided by ucx. ;; See https://docs.open-mpi.org/en/main/release-notes/networks.html#miscellaneous-network-notes (string-append "--with-ucx=" #$(this-package-input "ucx")))) ((#:phases phases) #~(modify-phases #$phases (delete 'remove-absolute) (delete 'scrub-timestamps))))))) (define-public openmpi-c++ (package/inherit openmpi (name "openmpi-c++") (outputs '("out")) (arguments (substitute-keyword-arguments (package-arguments openmpi) ((#:configure-flags flags) #~(cons "--enable-mpi-cxx" #$flags)))) (synopsis "C++ bindings for MPI"))) ;; 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 (cons* #:modules '((guix build gnu-build-system) ((guix build ant-build-system) #:prefix ant:) (guix build utils)) #:imported-modules `((guix build ant-build-system) ,@%default-gnu-imported-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") (search-input-file inputs "/lib/libmpi.la"))))) (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 (name "openmpi-thread-multiple") (arguments (substitute-keyword-arguments (package-arguments openmpi) ((#:configure-flags flags) #~(cons "--enable-mpi-thread-multiple" #$flags)))) (description "This version of Open@tie{}MPI has an implementation of @code{MPI_Init_thread} that provides @code{MPI_THREAD_MULTIPLE}. This won't 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") ;; 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") ;; Starting from 2.9.0, hwloc fails when /sys is unavailable: ;; ;; [hwloc/linux] failed to find sysfs cpu topology directory, aborting linux discovery. ;; ;; This in turn breaks Open MPI users. To work around it, define a fake ;; topology with 4 cores. That silently disables CPU binding, though ;; 'get_cpubind' will report there's no binding. (setenv "HWLOC_SYNTHETIC" "4") #t)) (define-public python-mpi4py (package (name "python-mpi4py") (version "3.1.4") (source (origin (method url-fetch) (uri (pypi-uri "mpi4py" version)) (sha256 (base32 "101lz7bnm9l17nrkbg6497kxscyh53aah7qd2b820ck2php8z18p")))) (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 (list openmpi)) (properties '((updater-extra-inputs . ("openmpi")))) (home-page "https://github.com/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 license:bsd-3))) (define-public mpich (package (name "mpich") (version "4.2.2") (source (origin (method url-fetch) (uri (string-append "http://www.mpich.org/static/downloads/" version "/mpich-" version ".tar.gz")) (sha256 (base32 "0h8xg1wi2d88hnfmj3xydf1hj78r7fh05jljhk5jgxmbmsrmngw8")))) (build-system gnu-build-system) (inputs `(,zlib (,hwloc-2 "lib") ,slurm ,@(if (and (not (%current-target-system)) (member (%current-system) (package-supported-systems ucx))) (list ucx) '()))) (native-inputs (list perl which gfortran python-minimal)) (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"))))) (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@ (.*)$" _ before after) (string-append "pmpi_convenience_libs = " before " " after))))) (add-before 'configure 'define-gfortran-wrapper (lambda* (#:key inputs #:allow-other-keys) ;; 'configure' checks whether the Fortran compiler ;; allows argument type mismatch. Since gfortran >= 10 ;; does not, provide a wrapper that passes ;; '-fallow-argument-mismatch' to get the desired ;; behavior. (mkdir-p ".gfortran-wrapper/bin") (call-with-output-file ".gfortran-wrapper/bin/gfortran" (lambda (port) (display (string-append "#!" (which "sh") "\n") port) (display (string-append "exec \"" (which "gfortran") "\" -fallow-argument-mismatch" " \"$@\"\n") port) (chmod port #o755))) (setenv "PATH" (string-append (getcwd) "/" ".gfortran-wrapper/bin:" (getenv "PATH")))))))) (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))) (define-public mpich-ofi (package/inherit mpich (name "mpich-ofi") (inputs (modify-inputs (package-inputs mpich) (delete ucx) (append libfabric) (append rdma-core) (append psm2))) (arguments (substitute-keyword-arguments (package-arguments mpich) ((#:configure-flags flags) #~(list "--disable-silent-rules" ;let's see what's happening "--enable-debuginfo" "--with-device=ch4:ofi" (string-append "--with-hwloc-prefix=" #$(this-package-input "hwloc")) (string-append "--with-libfabric=" #$(this-package-input "libfabric")))) ((#:phases phases '%standard-phases) phases))) (synopsis "Implementation of the Message Passing Interface (MPI) for OmniPath")))
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