immutables - A mirror of https://github.com/MagicStack/immutables with Debian packaging in additional branches

Age	Commit message (Expand)	Author
2018-03-31	immutables v0.2v0.2	Elvis Pranskevichus
2018-03-30	Do not use f-strings for Python 3.5 compatibility	Elvis Pranskevichus
2018-03-30	Initial commit	Yury Selivanov

(gnu packages linux) #:use-module (gnu packages pciutils) #:use-module (gnu packages python) #:use-module (gnu packages xorg) #:use-module (gnu packages gtk) #: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 python) #:use-module (gnu packages valgrind) #:use-module (srfi srfi-1) #:use-module (ice-9 match)) (define-public hwloc-1 (package (name "hwloc") (version "1.11.13") (source (origin (method url-fetch) (uri (string-append "https://www.open-mpi.org/software/hwloc/v" (version-major+minor version) "/downloads/hwloc-" version ".tar.bz2")) (sha256 (base32 "1j69p8a1pjpbpwn4w7l4dfxmaxxqikchjzqw1ncw05zmcmvlnjd4")) (patches (search-patches "hwloc-1-test-btrfs.patch")))) (properties ;; Tell the 'generic-html' updater to monitor this URL for updates. `((release-monitoring-url . "https://www-lb.open-mpi.org/software/hwloc/current"))) (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 (append (if (%current-target-system) '() ;fewer dependencies when cross-compiling (list libx11 cairo ncurses expat)) (if (target-arm32?) '() (list numactl)))) (propagated-inputs ;; hwloc.pc lists it in 'Requires.private'. (list libpciaccess)) (native-inputs (list pkg-config)) (arguments `(#: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")))) (add-after 'install 'refine-libnuma ;; Give -L arguments for libraries to avoid propagation (lambda* (#:key inputs outputs #:allow-other-keys) (let ((out (assoc-ref outputs "lib")) (numa (assoc-ref inputs "numactl"))) (substitute* (map (lambda (f) (string-append out "/" f)) '("lib/pkgconfig/hwloc.pc" "lib/libhwloc.la")) (("-lnuma" lib) (string-append "-L" numa "/lib " lib)))))) (add-after 'install 'avoid-circular-references (lambda* (#:key outputs #:allow-other-keys) (let ((lib (assoc-ref outputs "lib"))) ;; Suppress the 'prefix=' and 'exec_prefix=' lines so that the ;; "lib" output doesn't refer to "out". (substitute* (string-append lib "/lib/pkgconfig/hwloc.pc") (("^.*prefix=.*$") ""))))) (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")))))))) (home-page "https://www.open-mpi.org/projects/hwloc/") (synopsis "Abstraction of hardware architectures") (description "hwloc provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various attributes such as cache and memory information. It primarily aims at helping high-performance computing applications with gathering information about the hardware so as to exploit it accordingly and efficiently. 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 license:bsd-3))) (define-public hwloc-2 (package (inherit hwloc-1) (version "2.11.1") (source (origin (method url-fetch) (uri (string-append "https://download.open-mpi.org/release/hwloc/v" (version-major+minor version) "/hwloc-" version ".tar.bz2")) (sha256 (base32 "1ikhg35pll9zs628n2nii3ranz9j850hykqqcrgy2p12mpzzpk84")))) (native-inputs (modify-inputs (package-native-inputs hwloc-1) (append bash))) ;for completion tests (inputs (modify-inputs (package-inputs hwloc-1) (delete "numactl"))) ;libnuma is no longer needed. (arguments (substitute-keyword-arguments (package-arguments hwloc-1) ((#: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")))) (add-before 'check 'skip-tests-that-require-/sys (lambda _ ;; 'test-gather-topology.sh' requires /sys as of 2.9.0; skip it. (setenv "HWLOC_TEST_GATHER_TOPOLOGY" "0"))) (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))))))))))) (define-public hwloc ;; The latest stable series of hwloc. hwloc-2) (define-public openmpi-4 (package (name "openmpi") (version "4.1.6") (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 "05g4245v0pdqcyjmgn50519ry5v5q8ig26iinmiynvaihm29jh7p")) (patches (search-patches "openmpi-mtl-priorities.patch")))) (properties ;; Tell the 'generic-html' updater to monitor this URL for updates. `((release-monitoring-url . "https://www.open-mpi.org/software/ompi/current"))) (build-system gnu-build-system) (inputs (let ((if-supported (lambda (package) (if (and (not (%current-target-system)) (member (%current-system) (package-supported-systems package))) (list package) '())))) (append (list `(,hwloc-2 "lib") gfortran libfabric libevent opensm) (if-supported psm) (if-supported psm2) (if-supported ucx) (if-supported valgrind) (list rdma-core slurm)))) ;for PMI support (launching via "srun") (native-inputs (list pkg-config perl)) (outputs '("out" "debug")) (arguments (list #:configure-flags #~`("--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" ;; Help 'orterun' and 'mpirun' find their tools ;; under $prefix by default. "--enable-mpirun-prefix-by-default" ;; InfiniBand support "--enable-openib-control-hdr-padding" "--enable-openib-dynamic-sl" "--enable-openib-udcm" "--enable-openib-rdmacm" "--enable-openib-rdmacm-ibaddr" ;; Enable support for the 'Process Management ;; Interface for Exascale' (PMIx) used e.g. by ;; Slurm for the management communication and ;; coordination of MPI processes. "--with-pmix=internal" ;; Enable support for SLURM's Process Manager ;; Interface (PMI). ,(string-append "--with-pmi=" #$(this-package-input "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" (search-input-directory inputs "/include/infiniband")) (setenv "CPLUS_INCLUDE_PATH" (search-input-directory inputs "/include/infiniband")))) (add-before 'build 'remove-absolute (lambda _ ;; Remove compiler absolute file 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")))