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2023-04-07gnu: Purge pre-1.3.0 deprecated packages.Bruno Victal
* gnu/packages/bioinformatics.scm (deeptools): Remove variable. * gnu/packages/efi.scm (efi_analyzer): Ditto. * gnu/packages/guile.scm (guile-2.2/bug-fix, guile-json): Ditto. * gnu/packages/image.scm (libjpeg): Ditto. * gnu/packages/kde.scm (kdevplatform): Ditto * gnu/packages/linphone.scm (linphoneqt): Ditto. * gnu/packages/maths.scm (blis-sandybridge, blis-haswell, blis-knl): Ditto. * gnu/packages/mpi.scm (hwloc-2.0): Ditto. * gnu/packages/music.scm (python-abjad, zlfo): Ditto. * gnu/packages/perl.scm (perl-base, perl-parent): Ditto. * gnu/packages/tryton.scm (python-trytond): Ditto. * gnu/packages/video.scm (gnome-mpv): Ditto. * tests/graph.scm: Use guile-json-1. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-04-07gnu: hwloc: Update to 2.9.1.Philippe SWARTVAGHER
* gnu/packages/mpi.scm (hwloc-2): Update to 2.9.1. Patch to skip tests requiring /sys on non-x86 systems should not be necessary anymore, as https://github.com/open-mpi/hwloc/pull/570 has been merged in this new version. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-02-27gnu: hwloc: Skip failing test on non-x86 systems.Simon South
* gnu/packages/mpi.scm (hwloc-2)[arguments]<#:phases>: Rename "skip-test-that-requires-/sys" phase to "skip-tests-that-require-/sys" and expand to skip additional test requiring /sys on non-x86 systems. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-02-27gnu: hwloc: Remove obsolete comments.Simon South
hwloc 2.x become the default with commit 8ec7ca22d3, "gnu: hwloc: Default to 2.x.". * gnu/packages/mpi.scm (hwloc-1): Remove obsolete comment. (hwloc-2): Remove obsolete comment. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-02-27gnu: Fix openmpi related packages.Christopher Baines
This makes these package definitions compatible with the openmpi package which uses gexps as of f45fc72c282bc14da7212b4acb8fe9707e53aad0. * gnu/packages/mpi.scm (openmpi-c++, java-openmpi, openmpi-thread-multiple)[arguments]: Use gexps.
2023-02-23gnu: openmpi: Use gexps.Ludovic Courtès
* gnu/packages/mpi.scm (openmpi)[arguments]: Use gexps.
2023-01-27gnu: hwloc: Update to 2.9.0.Ludovic Courtès
* gnu/packages/mpi.scm (hwloc-2): Update to 2.9.0. [arguments]: Add 'skip-test-that-requires-/sys' phase. (%openmpi-setup): Set 'HWLOC_SYNTHETIC' environment variable. * gnu/packages/opencl.scm (pocl)[arguments]: In 'set-HOME' phase, also set 'HWLOC_SYNTHETIC'.
2022-11-11gnu: java-openmpi: Remove unused module import.Marius Bakke
* gnu/packages/mpi.scm (java-openmpi)[arguments]: Don't import (guix build syscalls).
2022-10-31gnu: Fix various lint issues in synopsis and descriptions.Vagrant Cascadian
* gnu/packages/android.scm (etc1tool)[synopsis]: Drop trailing period. * gnu/packages/bioinformatics.scm (mudskipper)[synopsis]: Likewise. * gnu/packages/crates-io.scm (rust-async-log-attributes-1)[synopsis]: Likewise. (rust-atomic-polyfill-1)[synopsis]: Likewise. (rust-modifier-0.1)[synopsis]: Likewise. (rust-openssl-macros-0.1)[synopsis]: Likewise. (rust-syn-mid-0.5)[synopsis]: Likewise. (rust-toml-edit-0.14)[synopsis]: Likewise. (rust-valuable-derive-0.1)[synopsis]: Likewise. (rust-inflections-1)[synopsis]: Likewise. * gnu/packages/databases.scm (python-databases)[synopsis]: Likewise. * gnu/packages/games.scm (liquidwar6)[synopsis]: Likewise. * gnu/packages/golang.scm (go-golang.org-x-sync-errgroup)[synopsis]: Likewise. * gnu/packages/guile-xyz.scm (guile-config)[synopsis]: Likewise. * gnu/packages/haskell-web.scm (ghc-hxt-xpath)[synopsis]: Likewise. * gnu/packages/haskell-xyz.scm (ghc-string-qq)[synopsis]: Likewise. * gnu/packages/machine-learning.scm (python-lap)[synopsis]: Likewise. (python-pyro-api)[synopsis]: Likewise. * gnu/packages/messaging.scm (python-librecaptcha)[synopsis]: Likewise. * gnu/packages/python-check.scm (python-pytest-cram)[synopsis]: Likewise. * gnu/packages/python-web.scm (python-jschema-to-python)[synopsis]: Likewise. (python-sarif-om)[synopsis]: Likewise. (python-socksio)[synopsis]: Likewise. (python-msrest)[synopsis]: Likewise. * gnu/packages/tor.scm (torsocks)[synopsis]: Likewise. * gnu/packages/cran.scm (r-rlist)[synopsis]: Remove leading article. * gnu/packages/crates-io.scm (rust-clippy-lints-0.0.153)[synopsis]: Likewise. (rust-simplelog-0.11)[synopsis]: Likewise. * gnu/packages/samba.scm (wsdd)[synopsis]: Likewise. * gnu/packages/crates-io.scm (rust-spki-0.4)[synopsis]: Remove trailing whitespace. * gnu/packages/golang.scm (go-github-com-mattn-go-zglob)[description]: Remove leading whitespace. * gnu/packages/haskell-check.scm (ghc-crypto-cipher-tests)[description]: Likewise. * gnu/packages/lisp-xyz.scm (sbcl-ctype)[synopsis]: Remove trailing whitespace. * gnu/packages/mpi.scm (openmpi-thread-multiple)[description]: Remove leading whitespace. * gnu/packages/node-xyz.scm (node-string-decoder)[synopsis]: Remove trailing whitespace.
2022-07-12gnu: openmpi: Only build with valgrind on supported systems.Efraim Flashner
* gnu/packages/mpi.scm (openmpi)[inputs]: Wrap valgrind in if-supported macro. [arguments]: Adjust configure-flags based on if valgrind is present.
2022-07-06gnu: hwloc: Update to 2.8.0Philippe SWARTVAGHER
* gnu/packages/mpi.scm (hwloc): Update to 2.8.0 Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-06-05gnu: openmpi: Update to 4.1.4.Tobias Geerinckx-Rice
* gnu/packages/mpi.scm (openmpi): Update to 4.1.4.
2022-04-11gnu: openmpi: Remove trailing #t.Ludovic Courtès
* gnu/packages/mpi.scm (openmpi)[arguments]: Remove trailing #t.
2022-04-11gnu: openmpi: Update to 4.1.3.Ludovic Courtès
* gnu/packages/mpi.scm (openmpi): Update to 4.1.3.
2022-04-11gnu: openmpi: Remove input labels.Ludovic Courtès
* gnu/packages/mpi.scm (openmpi)[inputs]: Remove input labels.
2022-04-11gnu: hwloc: Remove trailing #t.Ludovic Courtès
* gnu/packages/mpi.scm (hwloc-1)[arguments]: Remove trailing #t. (hwloc-2)[arguments]: Likewise.
2022-04-11gnu: hwloc@1: Use 'target-arm32?' in conditional.Ludovic Courtès
Suggested by Maxime Devos. * gnu/packages/mpi.scm (hwloc-1)[inputs]: Use 'target-arm32?' rather than custom code.
2022-04-11gnu: hwloc: Remove input labels.Ludovic Courtès
* gnu/packages/mpi.scm (hwloc-1)[inputs]: Remove labels. (hwloc-2)[inputs]: Use 'modify-inputs'.
2022-04-11gnu: hwloc@1: Update to 1.11.13.Philippe SWARTVAGHER
* gnu/packages/patches/hwloc-1-test-btrfs.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/mpi.scm (hwloc-1): Use it and update to 1.11.13. Co-authored-by: Ludovic Courtès <ludovic.courtes@inria.fr>
2022-03-29gnu: openmpi: Update to 4.1.2Philippe SWARTVAGHER
* gnu/packages/mpi.scm (openmpi): Update to 4.1.2 Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-03-25gnu: hwloc: Update to 2.7.1.Philippe SWARTVAGHER
* gnu/packages/mpi.scm (hwloc-2): Update to 2.7.1. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-01-17gnu: mpich: Remove input labels and trailing #t in phases.Ludovic Courtès
* gnu/packages/mpi.scm (mpich)[inputs]: Remove labels. [arguments]: Remove trailing #t from phases.
2022-01-17gnu: mpich: Allow compilation with GCC 10.Ludovic Courtès
Fixes <https://issues.guix.gnu.org/53320> Reported by Clément Barthelemy <clement.barthelemy@inria.fr>. * gnu/packages/mpi.scm (mpich)[arguments]: Add 'define-gfortran-wrapper' phase.
2021-12-17gnu: hwloc: Update to 2.7.0.Philippe SWARTVAGHER
* gnu/packages/mpi.scm (hwloc-2): Update to 2.7.0. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-12-13gnu: Simplify package inputs.Ludovic Courtès
This commit was obtained by running: ./pre-inst-env guix style without any additional argument.
2021-12-05Merge remote-tracking branch 'origin/master' into core-updates-frozenRicardo Wurmus
2021-12-02gnu: Add openmpi-c++.Ricardo Wurmus
* gnu/packages/mpi.scm (openmpi-c++): New variable.
2021-07-24gnu: Use 'search-input-file' when looking for *.so and *.a.Ludovic Courtès
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use 'search-input-file' when looking for *.a and *.so. * gnu/packages/emulators.scm (dolphin-emu): Likewise. * gnu/packages/engineering.scm (lepton-eda): Likewise. (pcb): Likewise. * gnu/packages/golang.scm (go-1.4): Likewise. (go-1.14): Likewise. * gnu/packages/haskell.scm (ghc-7): Likewise. * gnu/packages/irods.scm (irods): Likewise. * gnu/packages/language.scm (python2-tegaki-pygtk): Likewise. * gnu/packages/lisp-xyz.scm (sbcl-lzlib): Likewise. (sbcl-cl-gobject-introspection): Likewise. (sbcl-cl-ana): Likewise. (sbcl-cl-libuv): Likewise. (sbcl-cl-async): Likewise. (sbcl-mcclim): Likewise. (sbcl-zstd): Likewise. (sbcl-cl-opengl): Likewise. (sbcl-lev): Likewise. (sbcl-cl-glfw3): Likewise. * gnu/packages/machine-learning.scm (tensorflow): Likewise. * gnu/packages/messaging.scm (utox): Likewise. * gnu/packages/mpi.scm (java-openmpi): Likewise. * gnu/packages/music.scm (jack-select): Likewise. * gnu/packages/pascal.scm (fpc): Likewise. * gnu/packages/python-crypto.scm (python-libnacl): Likewise. * gnu/packages/python-xyz.scm (python-cairocffi): Likewise. (python-pyev): Likewise. (python-pytidylib): Likewise. * gnu/packages/radio.scm (unixcw): Likewise. * gnu/packages/rust.scm (rust-1.32): Likewise. * gnu/packages/security-token.scm (opensc): Likewise. (python-pyscard): Likewise. * gnu/packages/selinux.scm (python-setools): Likewise. * gnu/packages/spice.scm (libcacard): Likewise. * gnu/packages/telephony.scm (libtgvoip): Likewise.
2021-07-24gnu: Use 'search-input-directory' when looking for C/C++ library headers.Ludovic Courtès
* gnu/packages/arcan.scm (arcan)[arguments]: Use 'search-input-directory' for "include/libdrm" and "include/apr-1". * gnu/packages/bioinformatics.scm (sailfish): Likewise for jellyfish. * gnu/packages/boost.scm (boost-for-irods): Likewise for libcxx headers. * gnu/packages/cedille.scm (cedille): Likewise for IAL headers. * gnu/packages/compression.scm (snappy-with-clang6): Likewise for libcxx headers. * gnu/packages/cups.scm (hplip): Likewise for libusb headers. * gnu/packages/emulators.scm (pcsxr): Likewise for libcdio headers. * gnu/packages/game-development.scm (python2-renpy): Likewise for fribidi headers. * gnu/packages/games.scm (pokerth): Likewise for libircclient. * gnu/packages/guile-xyz.scm (guile-persist): Likewise for Guile. * gnu/packages/hurd.scm (hurd): Likewise for libtirpc. * gnu/packages/irods.scm (irods, irods-client-icommands): Likewise for libcxx, catch2, and nlohmann-json-cpp. * gnu/packages/julia.scm (julia): Use 'search-input-file' for libuv's errno.h. * gnu/packages/kde-pim.scm (kdepim-runtime): Use 'search-input-directory' for "include/KF5". (kmessagelib): Likewise. * gnu/packages/kde.scm (kdeconnect): Likewise. * gnu/packages/llvm.scm (clang-runtime-3.5): Likewise for libtirpc. * gnu/packages/mpi.scm (openmpi): Likewise for "include/infiniband". * gnu/packages/pumpio.scm (pumpa): Use 'search-input-file' for "tidy.h" and "aspell.h". * gnu/packages/radio.scm (dream): Use 'search-input-file' and 'search-input-directory' for pulseaudio, sndfile, etc. * gnu/packages/selinux.scm (policycoreutils): Likewise for PAM and libaudit. * gnu/packages/serialization.scm (avro-cpp-1.9-for-irods): Likewise for libcxx. * gnu/packages/sync.scm (nextcloud-client): Likewise for "include/KF5". * gnu/packages/video.scm (mkvtoolnix): Likewise for "include/gtest". (libopenshot): Likewise for "include/UnitTest++". * gnu/packages/virtualization.scm (criu): Likewise for libnl3 and for protobuf file.
2021-06-14gnu: hwloc: Update to 2.5.0.Ludovic Courtès
* gnu/packages/mpi.scm (hwloc-2): Update to 2.5.0.
2021-05-02gnu: openmpi: Update to 4.1.1.Tobias Geerinckx-Rice
* gnu/packages/mpi.scm (openmpi): Update to 4.1.1.
2021-03-19gnu: openmpi: Update to 4.1.0.Ludovic Courtès
* gnu/packages/mpi.scm (openmpi): Update to 4.1.0.
2021-03-19gnu: openmpi: Add 'release-monitoring-url' property.Ludovic Courtès
* gnu/packages/mpi.scm (openmpi)[properties]: New field.
2021-03-17gnu: hwloc: Add 'release-monitoring-url' property.Ludovic Courtès
* gnu/packages/mpi.scm (hwloc-1)[properties]: New field.
2021-03-17gnu: Use PACKAGE/INHERIT in more places.Mark H Weaver
* gnu/packages/algebra.scm (fftwf, fftw-openmpi), gnu/packages/audio.scm (ztoolkit-rsvg), gnu/packages/bioinformatics.scm (python2-dendropy), gnu/packages/boost.scm (boost-with-python2), gnu/packages/check.scm (python2-mock, python2-pytest-mock), gnu/packages/cups.scm (hplip-minimal), gnu/packages/freedesktop.scm (libinput-minimal), gnu/packages/gettext.scm (gnu-gettext), gnu/packages/glib.scm (python2-pygobject), gnu/packages/gnome.scm (gdl-minimal, libsoup-minimal, python2-pyatspi), gnu/packages/groff.scm (groff-minimal), gnu/packages/jami.scm (ffmpeg-jami), gnu/packages/libcanberra.scm (libcanberra/gtk+-2), gnu/packages/lirc.scm (python2-lirc), gnu/packages/llvm.scm (clang-runtime-3.5), gnu/packages/mpi.scm (java-openmpi, openmpi-thread-multiple), gnu/packages/node.scm (libnode), gnu/packages/onc-rpc.scm (libtirpc/hurd), gnu/packages/python-compression.scm (bitshuffle-for-snappy), gnu/packages/python-crypto.scm (python2-pycrypto, python2-cryptography) (python2-cryptography, python2-m2crypto), gnu/packages/python-web.scm (python2-html2text, python2-tornado) (python2-terminado, python2-ndg-httpsclient, python2-websocket-client) (python2-rauth, python2-url, python2-s3transfer), gnu/packages/python-xyz.scm (python2-psutil, python2-serpent) (python2-humanfriendly, python2-empy, python2-parse-type, python2-polib) (python2-jsonschema, python2-pystache, python2-cython, python2-numpydoc) (python2-ipyparallel, python2-traitlets, python2-dbus) (python2-beautifulsoup4, python2-pep517, python2-flake8, python2-llfuse) (python2-tlsh, python-file, python2-notebook, python-jupyter-console-minimal) (python2-contextlib2, python2-promise, python2-anyjson, python2-amqp) (python2-kombu, python2-billiard, python2-celery, python2-whoosh) (python2-jellyfish, python-rope, ptpython-2, python2-binaryornot) (python2-setproctitle, python2-argcomplete, python2-xopen, python2-isort) (python2-radon, python2-rfc6555, python2-activepapers, python2-send2trash) (python2-cloudpickle, python2-reparser), gnu/packages/python.scm (python2-called-python), gnu/packages/qt.scm (python2-sip, python-pyqt-without-qtwebkit, python2-pyqt) (python-qscintilla, python-pyqt+qscintilla), gnu/packages/scanner.scm (sane-backends), gnu/packages/sdl.scm (guile3.0-sdl2), gnu/packages/selinux.scm (checkpolicy, libselinux, libsemanage, secilc) (python-sepolgen, policycoreutils), gnu/packages/serialization.scm (lua5.1-libmpack, lua5.2-libmpack), gnu/packages/simulation.scm (fenics), gnu/packages/statistics.scm (python2-statsmodels), gnu/packages/texinfo.scm (info-reader), gnu/packages/wxwidgets.scm (wxwidgets-gtk2, wxwidgets-gtk2-3.1), gnu/packages/xml.scm (xmlsec-nss), gnu/packages/xorg.scm (uim-gtk, uim-qt), guix/build-system/python.scm (package-with-explicit-python) (strip-python2-variant): Use PACKAGE/INHERIT.
2021-03-10gnu: hwloc: Update to 2.4.1.Ludovic Courtès
* gnu/packages/mpi.scm (hwloc-2): Update to 2.4.1. Adjust URL.
2020-11-26gnu: hwloc: Add "doc" output.Ludovic Courtès
* gnu/packages/mpi.scm (hwloc-1)[outputs]: Add "doc". [arguments]: Add 'move-man3-pages' phase.
2020-11-02gnu: mpich: Configure to use ucx.Ludovic Courtès
Suggested by Maurice Brémond <Maurice.Bremond@inria.fr>. Fixes bug when running test suites involving MPICH: <https://issues.guix.gnu.org/39588#15>. * gnu/packages/mpi.scm (mpich)[arguments]: Pass "--with-device=ch4:ucx".
2020-09-24gnu: openmpi: Have 'mpirun' look for executables under $prefix.Ludovic Courtès
* gnu/packages/mpi.scm (openmpi)[arguments]: Add "--enable-mpirun-prefix-by-default" to #:configure-flags.
2020-09-17gnu: openmpi: Update to 4.0.5.Greg Hogan
* gnu/packages/mpi.scm (openmpi): Update to 4.0.5. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2020-03-31gnu: hwloc@2: Update to 2.2.0.Ludovic Courtès
* gnu/packages/mpi.scm (hwloc-2): Update to 2.2.0.
2020-03-31gnu: hwloc@2: Skip test that fails on emulated hardware.Ludovic Courtès
Works around <https://bugs.gnu.org/40342>. * gnu/packages/mpi.scm (hwloc-2)[arguments]: Add 'skip-test-that-fails-on-qemu' phase.
2020-03-10gnu: openmpi: Use HTTPS home page.Tobias Geerinckx-Rice
* gnu/packages/mpi.scm (openmpi)[home-page]: Use HTTPS.
2020-03-10gnu: openmpi: Update to 4.0.3.Tobias Geerinckx-Rice
* gnu/packages/mpi.scm (openmpi): Update to 4.0.3.
2020-02-17gnu: mpi.scm: Use 'license:' prefix.Efraim Flashner
* gnu/packages/mpi.scm: Import (guix licenses) with the 'license:' prefix.
2020-02-17gnu: Add MPICH.Maurice Brémond
* gnu/packages/mpi.scm (mpich): New variable. Co-authored-by: Ludovic Courtès <ludovic.courtes@inria.fr>
2020-01-12gnu: Use the two-element 'define-deprecated' form where applicable.Ludovic Courtès
* gnu/packages/guile.scm (guile-json): Use the two-element 'define-deprecated' form. * gnu/packages/kde.scm (kdevplatform): Likewise. * gnu/packages/mpi.scm (hwloc-2.0): Likewise. * gnu/packages/qt.scm (qt): Likewise.
2019-12-20gnu: intel-mpi-benchmarks: Merge with "imb-openmpi".Ludovic Courtès
* gnu/packages/mpi.scm (intel-mpi-benchmarks): Remove. * gnu/packages/benchmark.scm (imb): Rename to... (intel-mpi-benchmarks): ... this. Change 'name'. Update to 2019.3. [arguments]: Remove 'build phase. Rewrite 'install phase. Pass #:parallel-build? and #:make-flags. (intel-mpi-benchmarks/openmpi): New variable. (imb-openmpi): Rewrite in terms of 'deprecated-package'.
2019-11-29gnu: openmpi: Increase priority of the PSM component.Ludovic Courtès
* gnu/packages/patches/openmpi-psm2-priority.patch: Rename to... * gnu/packages/patches/openmpi-mtl-priorities.patch: ... this. Add hunk to change the priority of PSM. * gnu/packages/mpi.scm (openmpi)[source]: Adjust accordingly. * gnu/local.mk (dist_patch_DATA): Likewise.
2019-11-19gnu: hwloc: Adjust references to 'hwloc'.Ludovic Courtès
This is a followup to 8ec7ca22d363b80b173ce87c5f39d5ca9686d248, which led to a stack overflow (cyclic graph) when attempting to build HWLOC-2. * gnu/packages/mpi.scm (hwloc-2): Refer to HWLOC-1 instead of HWLOC.
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