;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
;;; Copyright © 2017, 2020, 2021 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2017 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2021 Ryan Sundberg <ryan@arctype.co>
;;; Copyright © 2022 Marius Bakke <marius@gnu.org>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

(define-module (gnu packages jemalloc)
  #:use-module (srfi srfi-1)
  #:use-module (srfi srfi-26)
  #:use-module (ice-9 match)
  #:use-module ((guix licenses) #:select (bsd-2))
  #:use-module (guix packages)
  #:use-module (guix gexp)
  #:use-module (guix download)
  #:use-module (guix utils)
  #:use-module (gnu packages)
  #:use-module (gnu packages perl)
  #:use-module (guix build-system gnu))

(define-public jemalloc
  (package
    (name "jemalloc")
    (version "5.3.0")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://github.com/jemalloc/jemalloc/releases/download/"
                    version "/jemalloc-" version ".tar.bz2"))
              (sha256
               (base32
                "1apyxjd1ixy4g8xkr61p0ny8jiz8vyv1j0k4nxqkxpqrf4g2vf1d"))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'delete-thp-test
            ;; This test does not check if transparent huge pages are supported
            ;; on the system before running the test.
            (lambda _
              (substitute* "Makefile.in"
                (("\\$\\(srcroot\\)test/unit/pages.c \\\\") "\\")))))
      #:configure-flags
      ;; Disable the thread local storage model in jemalloc 5 to prevent
      ;; shared libraries linked to libjemalloc from crashing on dlopen()
      ;; https://github.com/jemalloc/jemalloc/issues/937
      #~'("--disable-initial-exec-tls"
          #$@(match (%current-system)
               ("aarch64-linux"
                (list "--with-lg-page=14"))
               ("powerpc-linux"
                (list "CPPFLAGS=-maltivec"))
               (_
                '())))))
    (inputs (list perl))
    ;; Install the scripts to a separate output to avoid referencing Perl and
    ;; Bash in the default output, saving ~75 MiB on the closure.
    (outputs '("out" "bin"))
    (home-page "https://jemalloc.net/")
    (synopsis "General-purpose scalable concurrent malloc implementation")
    (description
     "This library providing a malloc(3) implementation that emphasizes
fragmentation avoidance and scalable concurrency support.")
    (license bsd-2)))
a51znf7vm2nyh89yqpizcll9q66")))) (patch-flags '("-p2")) (sha256 (base32 "13iviiwk1srpw9dmiwabkxv56v0pl0zggjp8zxy1419k5zzfsy34")))) (build-system gnu-build-system) (inputs (append (list icu4c zlib) (if (%current-target-system) '() (list python-minimal-wrapper)))) (native-inputs (list perl tcsh)) (arguments (list #:imported-modules `((guix build python-build-system) ,@%default-gnu-imported-modules) #:modules `(((guix build python-build-system) #:select (python-version)) ,@%default-gnu-modules) #:tests? #f #:configure-flags #~(let ((icu (dirname (dirname (search-input-file %build-inputs "bin/uconv"))))) (list ;; Auto-detection looks for ICU only in traditional ;; install locations. (string-append "--with-icu=" icu) ;; Ditto for Python. #$@(if (%current-target-system) #~() #~((let ((python (dirname (dirname (search-input-file %build-inputs "bin/python"))))) (string-append "--with-python-root=" python) (string-append "--with-python=" python "/bin/python") (string-append "--with-python-version=" (python-version python))))) "--with-toolset=gcc")) #:make-flags #~(list "threading=multi" "link=shared" ;; Set the RUNPATH to $libdir so that the libs find each other. (string-append "linkflags=-Wl,-rpath=" #$output "/lib") #$@(if (%current-target-system) #~("--user-config=user-config.jam" ;; Python is not supported when cross-compiling. "--without-python" "binary-format=elf" "target-os=linux" #$@(cond ((string-prefix? "arm" (%current-target-system)) #~("abi=aapcs" "address-model=32" "architecture=arm")) ((string-prefix? "aarch64" (%current-target-system)) #~("abi=aapcs" "address-model=64" "architecture=arm")) (else #~()))) #~())) #:phases #~(modify-phases %standard-phases (add-after 'unpack 'patch-shells (lambda _ (substitute* '("libs/config/configure" "libs/spirit/classic/phoenix/test/runtest.sh" "tools/build/src/engine/execunix.cpp") (("/bin/sh") (which "sh"))))) (delete 'bootstrap) (replace 'configure (lambda* (#:key (configure-flags ''()) #:allow-other-keys) (setenv "SHELL" (which "sh")) (setenv "CONFIG_SHELL" (which "sh")) #$@(if (%current-target-system) #~((call-with-output-file "user-config.jam" (lambda (port) (format port "using gcc : cross : ~a-c++ ;" #$(%current-target-system))))) #~()) (apply invoke "./bootstrap.sh" (string-append "--prefix=" #$output) configure-flags))) (replace 'build (lambda* (#:key make-flags #:allow-other-keys) (apply invoke "./b2" (format #f "-j~a" (parallel-job-count)) make-flags))) (replace 'install (lambda* (#:key make-flags #:allow-other-keys) (apply invoke "./b2" "install" make-flags))) #$@(if (%current-target-system) #~() #~((add-after 'install 'provide-libboost_python (lambda* (#:key make-flags inputs outputs #:allow-other-keys) (let* ((static? (member "link=static" make-flags)) (libext (if static? ".a" ".so")) (python (dirname (dirname (search-input-file inputs "bin/python")))) (python-version (python-version python)) (libboost_pythonNN (string-append "libboost_python" (string-join (string-split python-version #\.) "") libext))) (with-directory-excursion (string-append #$output "/lib") (symlink libboost_pythonNN (string-append "libboost_python" libext)) ;; Some packages only look for the major version. (symlink libboost_pythonNN (string-append "libboost_python" (string-take python-version 1) libext))))))))))) (home-page "https://www.boost.org") (synopsis "Peer-reviewed portable C++ source libraries") (description "A collection of libraries intended to be widely useful, and usable across a broad spectrum of applications.") (license (license:x11-style "https://www.boost.org/LICENSE_1_0.txt" "Some components have other similar licences.")))) (define-public boost-for-source-highlight (hidden-package (package (inherit boost) (name "boost") (version "1.83.0") (source (origin (method url-fetch) (uri (string-append "https://boostorg.jfrog.io/artifactory/main/release/" version "/source/boost_" (version-with-underscores version) ".tar.bz2")) (patches (list (boost-patch "0001-unordered-fix-copy-assign.patch" version "09j61m5xh7099k5na9i43x5rra51znf7vm2nyh89yqpizcll9q66"))) (patch-flags '("-p2")) (sha256 (base32 "13iviiwk1srpw9dmiwabkxv56v0pl0zggjp8zxy1419k5zzfsy34"))))))) ;; Sadly, this is needed for irods. It won't link with 1.69 or later. (define-public boost-for-irods (package (inherit boost) (name "boost-for-irods") (version "1.68.0") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/boost/boost/" version "/boost_" (string-map (lambda (x) (if (eq? x #\.) #\_ x)) version) ".tar.bz2")) (sha256 (base32 "1dyqsr9yb01y0nnjdq9b8q5s2kvhxbayk34832k5cpzn7jy30qbz")))) (build-system gnu-build-system) (properties `((hidden? . #true))) (inputs `(("icu4c" ,icu4c) ("libcxx" ,libcxx+libcxxabi-6) ("libcxxabi" ,libcxxabi-6) ("zlib" ,zlib))) (native-inputs (list clang-6 perl tcsh)) (arguments `(#:tests? #f #:make-flags (list "threading=multi" "link=shared" "cxxflags=-stdlib=libc++" "--without-python" ;; Set the RUNPATH to $libdir so that the libs find each other. (string-append "linkflags=-stdlib=libc++ -Wl,-rpath=" (assoc-ref %outputs "out") "/lib")) #:phases (modify-phases %standard-phases (delete 'bootstrap) (add-after 'set-paths 'adjust-CPLUS_INCLUDE_PATH (lambda* (#:key native-inputs inputs #:allow-other-keys) (let ((gcc (assoc-ref (or native-inputs inputs) "gcc"))) (setenv "CPLUS_INCLUDE_PATH" (string-join (cons (search-input-directory inputs "/include/c++/v1") ;; Hide GCC's C++ headers so that they do not interfere with ;; the Clang headers. (delete (string-append gcc "/include/c++") (string-split (getenv "CPLUS_INCLUDE_PATH") #\:))) ":")) (format #true "environment variable `CPLUS_INCLUDE_PATH' changed to ~a~%" (getenv "CPLUS_INCLUDE_PATH"))))) (replace 'configure (lambda* (#:key inputs outputs #:allow-other-keys) (let ((icu (assoc-ref inputs "icu4c")) (out (assoc-ref outputs "out")) (sh (search-input-file inputs "/bin/sh"))) (substitute* '("libs/config/configure" "libs/spirit/classic/phoenix/test/runtest.sh" "tools/build/src/engine/execunix.c" "tools/build/src/engine/Jambase" "tools/build/src/engine/jambase.c") (("/bin/sh") sh)) (setenv "SHELL" (which "sh")) (setenv "CONFIG_SHELL" (which "sh")) (invoke "./bootstrap.sh" (string-append "--prefix=" out) ;; Auto-detection looks for ICU only in traditional ;; install locations. (string-append "--with-icu=" icu) "--with-toolset=clang")))) (replace 'build (lambda* (#:key make-flags #:allow-other-keys) (apply invoke "./b2" (format #f "-j~a" (parallel-job-count)) make-flags))) (replace 'install (lambda* (#:key make-flags #:allow-other-keys) (apply invoke "./b2" "install" make-flags)))))))) (define-public boost-with-python3 (deprecated-package "boost-with-python3" boost)) (define-public boost-static (package (inherit boost) (name "boost-static") (arguments (substitute-keyword-arguments (package-arguments boost) ((#:make-flags flags) #~(cons "link=static" (delete "link=shared" #$flags))))))) (define-public boost-for-mysql ;; Older version for MySQL 5.7.23. (package (inherit boost) (version "1.59.0") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/boost/boost/" version "/boost_" (string-map (lambda (x) (if (eq? x #\.) #\_ x)) version) ".tar.bz2")) (sha256 (base32 "1jj1aai5rdmd72g90a3pd8sw9vi32zad46xv5av8fhnr48ir6ykj")))) (arguments (substitute-keyword-arguments (package-arguments boost) ((#:configure-flags _ #~'()) #~(let ((icu (dirname (dirname (search-input-file %build-inputs "bin/uconv"))))) (list ;; Auto-detection looks for ICU only in traditional ;; install locations. (string-append "--with-icu=" icu) "--with-toolset=gcc"))) ((#:phases phases) #~(modify-phases #$phases (replace 'patch-shells (lambda _ (substitute* (append (find-files "tools/build/src/engine/" "execunix\\.c.*") '("libs/config/configure" "libs/spirit/classic/phoenix/test/runtest.sh" "tools/build/doc/bjam.qbk" "tools/build/src/engine/Jambase")) (("/bin/sh") (which "sh"))))) (delete 'provide-libboost_python))) ((#:make-flags make-flags) #~(cons* "--without-python" #$make-flags)))) (inputs (modify-inputs (package-inputs boost) (delete "python-minimal-wrapper"))) (properties '((hidden? . #t))))) (define-public boost-sync (let ((commit "e690de2d30e2f1649ff500c9a6f3539814994b1c") (version "1.55") (revision "2")) (package (name "boost-sync") (version (git-version version revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/boostorg/sync") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "0473hb15affjq2804xa99ikk4y1gzi46rygd9zhncl28ib7mnn26")))) (build-system trivial-build-system) (arguments `(#:modules ((guix build utils)) #:builder (begin (use-modules (guix build utils)) (let ((source (assoc-ref %build-inputs "source"))) (copy-recursively (string-append source "/include") (string-append %output "/include")))))) (home-page "https://github.com/boostorg/sync") (synopsis "Boost.Sync library") (description "The Boost.Sync library provides mutexes, semaphores, locks and events and other thread related facilities. Boost.Sync originated from Boost.Thread.") (license (license:x11-style "https://www.boost.org/LICENSE_1_0.txt"))))) (define-public boost-signals2 (package (name "boost-signals2") (version (package-version boost)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/boostorg/signals2") (commit (string-append "boost-" version)))) (file-name (git-file-name name version)) (sha256 (base32 "1prhj98jgvkj2m3ia5lcgxnl1a4h13cyzqd55skjn983rivi6090")))) (build-system trivial-build-system) (arguments `(#:modules ((guix build utils)) #:builder (begin (use-modules (guix build utils)) (let ((source (assoc-ref %build-inputs "source"))) (copy-recursively (string-append source "/include") (string-append %output "/include")))))) (home-page "https://github.com/boostorg/signals2") (synopsis "Boost.Signals2 library") (description "The Boost.Signals2 library is an implementation of a managed signals and slots system.") (license (license:x11-style "https://www.boost.org/LICENSE_1_0.txt")))) (define-public boost-mpi (package (inherit boost) (name "boost-mpi") (inputs (modify-inputs (package-inputs boost) (append openmpi))) (arguments (substitute-keyword-arguments (package-arguments boost) ((#:phases phases) #~(modify-phases #$phases (add-after 'configure 'update-jam (lambda* (#:key inputs outputs #:allow-other-keys) (let ((output-port (open-file "project-config.jam" "a"))) (display "using mpi ;" output-port) (newline output-port) (close output-port)))))))) (home-page "https://www.boost.org") (synopsis "Message Passing Interface (MPI) library for C++"))) (define-public mdds (package (name "mdds") (version "2.1.1") (source (origin (method git-fetch) (uri (git-reference (url "https://gitlab.com/mdds/mdds") (commit version))) (file-name (git-file-name name version)) (sha256 (base32 "0866020brc1kmiryh7dmhjamnywlsd56ks649hy87283k0p7d3bb")))) (build-system gnu-build-system) (native-inputs (list autoconf automake)) (propagated-inputs (list boost)) ; inclusion of header files (home-page "https://gitlab.com/mdds/mdds") (synopsis "Multi-dimensional C++ data structures and indexing algorithms") (description "Mdds (multi-dimensional data structure) provides a collection of multi-dimensional data structures and indexing algorithms for C++. It includes flat segment trees, segment trees, rectangle sets, point quad trees, multi-type vectors and multi-type matrices.") (license license:expat)))