diff options
author | Dennis E. Mungai | 2016-05-19 02:00:46 +0300 |
---|---|---|
committer | Dennis E. Mungai | 2016-05-19 02:00:46 +0300 |
commit | 0290484e785f60d4976c749b6bd184af341f05ff (patch) | |
tree | dde652f4b0805acaa3398220a2d07719d0f990c5 | |
parent | 28e10139f165dad1174229fb13193841f97c0389 (diff) | |
download | guix-bioinformatics-gh-e9a93584/15/Brainiarc7/patch-3.tar.gz |
The latest and the greatest cl.scmgh-e9a93584/15/Brainiarc7/patch-3
Key changes:
1. Bumped up Arrayfire, Boost Compute, clFFT and clBLAS.
2. A working version of LLVM 3.8, clang 3.8 and clang-runtime (Thanks, Roel Janssen).
3. WIP: pocl. Last piece of the puzzle.
-rw-r--r-- | gn/packages/arrayfire.scm | 399 |
1 files changed, 322 insertions, 77 deletions
diff --git a/gn/packages/arrayfire.scm b/gn/packages/arrayfire.scm index 361f2f0..6c516b9 100644 --- a/gn/packages/arrayfire.scm +++ b/gn/packages/arrayfire.scm @@ -16,33 +16,35 @@ ;;; 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 (gn packages arrayfire) - #:use-module (guix packages) +(define-module (gn packages cl) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix download) #:use-module (guix git-download) #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) + #:use-module (guix packages) #:use-module (gnu packages) #:use-module (guix utils) #:use-module (gnu packages algebra) #:use-module (gnu packages autotools) #:use-module (gnu packages bootstrap) #:use-module (gnu packages curl) + #:use-module (gnu packages compression) + #:use-module (gnu packages libffi) #:use-module (gnu packages gawk) #:use-module (gnu packages cmake) + #:use-module (gnu packages compression) #:use-module (gnu packages boost) #:use-module (gnu packages glib) #:use-module (gnu packages image) #:use-module (gnu packages video) #:use-module (gnu packages textutils) - ;; #:use-module (gnu packages fftw) - ;; #:use-module (gnu packages fftw-openmpi) - in algebra - ;; #:use-module (gnu packages fftwf) #:use-module (gnu packages gl) + #:use-module (gnu packages llvm) #:use-module (gnu packages gcc) #:use-module (gnu packages gnupg) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages perl) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) #:use-module (gnu packages web) @@ -50,6 +52,7 @@ #:use-module (gnu packages python) #:use-module (gnu packages ruby) #:use-module (gnu packages xorg) + #:use-module (gnu packages xml) #:use-module (gnu packages version-control) #:use-module (gnu packages zip) #:use-module (gnu packages linux)) @@ -57,7 +60,7 @@ (define-public arrayfire (package (name "arrayfire") - (version "3.3.1") + (version "3.3.2") (source (origin (method url-fetch) (uri (string-append "http://arrayfire.com/arrayfire_source/arrayfire-full-" version @@ -65,24 +68,21 @@ (file-name (string-append name "-" version ".tar.bz2")) (sha256 (base32 - "045adww6dqmyz6kkfmq7xawi5v9a894yp5j9pzn6j568gi48pyqc")))) + "0n51pndah1x1kcbcj9x6y8188lf459mi3w3h67kx860ph7r4qk9m")))) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) ("gawk" ,gawk) - ("git" ,git) ("glew" ,glew) ("libtool" ,libtool) ("pkg-config" ,pkg-config))) (inputs `(("boost" ,boost) ("glfw" ,glfw) ("compute" ,compute) - ("curl" ,curl) - ("clBLAS" ,clBLAS) - ("clFFT" ,clFFT) + ("clblas" ,clblas) + ("clfft" ,clfft) ("atlas" ,atlas) ("dbus" ,dbus) ("opencl-headers" ,opencl-headers) - ("ocl-icd" ,ocl-icd) ("enca" ,enca) ("eudev" ,eudev) ("glew" ,glew) @@ -102,22 +102,21 @@ ("fftwf" ,fftwf) ("fftw-openmpi" ,fftw-openmpi) ("glew" ,glew) - ("glu" ,glu) ("openblas" ,openblas) - ("wget" ,wget) - ("cmake" ,cmake))) + ("glu" ,glu))) (build-system cmake-build-system) (arguments - `(#:configure-flags '("-DBUILD_OPENCL=ON" "-DBUILD_CUDA=OFF" "-DBUILD_GRAPHICS=OFF" "-DUSE_SYSTEM_BOOST_COMPUTE=ON" "-DUSE_SYSTEM_CLBLAS=ON" "-DUSE_SYSTEM_CLFFT=ON") + `(#:configure-flags '("-DBUILD_OPENCL=ON" "-DBUILD_CUDA=OFF" "-DBUILD_GRAPHICS=OFF" "-DUSE_SYSTEM_BOOST_COMPUTE=ON" "-DUSE_SYSTEM_CLBLAS=ON" "-DUSE_SYSTEM_CLFFT=ON" "-DBUILD_TEST=ON") #:tests? #t)) (synopsis "ArrayFire: a general purpose GPU library. https://arrayfire.com") - (description "ArrayFire is a high performance software library for parallel computing with an easy-to-use API. Its array based function set makes parallel programming simple.Now on Guix") + (description "ArrayFire is a high performance software library for parallel computing with an easy-to-use API. Its array based function set makes parallel programming simple.") (home-page "http://arrayfire.com/") (license (list license:gpl2 license:gpl2+ - license:gpl3 + license:gpl3 + license:bsd-3 license:gpl3+)))) - + (define-public glfw (package (name "glfw") @@ -158,22 +157,23 @@ (home-page "http://www.glfw.org/") (synopsis "glfw is an Open Source, multi-platform library for creating windows with OpenGL contexts and receiving input and events.") (description "glfw is an Open Source, multi-platform library for creating windows with OpenGL contexts and receiving input and events.") - (license (list license:gpl2)))) - -(define-public clBLAS + (license (list license:gpl2 + license:zlib)))) + +(define-public clblas (package - (name "clBLAS") - (version "v2.10") + (name "clblas") + (version "2.10") (source (origin (method url-fetch) - (uri (string-append "https://github.com/clMathLibraries/clBLAS/archive/" + (uri (string-append "https://github.com/clMathLibraries/clBLAS/archive/v" version ".tar.gz")) (sha256 (base32 "0adlb02lqzrklfybhnv4n0p37mvkvdi3vqiwa05x2mv05ywnr93j")))) (build-system cmake-build-system) (arguments `(#:tests? #f - #:configure-flags '("../clBLAS-2.10/src" "-DBUILD_SHARED_LIBS=ON" "-DCMAKE_BUILD_TYPE=Release" "-DBUILD_TEST=OFF"))) + #:configure-flags '("../clBLAS-2.10/src" "-DBUILD_SHARED_LIBS=ON" "-DCMAKE_BUILD_TYPE=Release" "-DBUILD_TEST=OFF"))) ;;tlpgen requires network access. Disable it. (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) ("cmake" ,cmake) @@ -193,8 +193,8 @@ ("libtiff" ,libtiff) ("mesa-utils" ,mesa-utils) ("openmpi" ,openmpi) - ("ocl-icd" ,ocl-icd) ("opencl-headers" ,opencl-headers) + ("ocd-icd" ,ocl-icd) ("randrproto" ,randrproto) ("libxrandr" ,libxrandr) ("xineramaproto" ,xineramaproto) @@ -204,21 +204,22 @@ (home-page "http://www.glfw.org/") (synopsis "glfw is an Open Source, multi-platform library for creating windows with OpenGL contexts and receiving input and events.") (description "glfw is an Open Source, multi-platform library for creating windows with OpenGL contexts and receiving input and events.") - (license (list license:gpl2)))) - -(define-public clFFT + (license (list license:gpl2 + license:asl2.0)))) + +(define-public clfft (package - (name "clFFT") - (version "v2.10.1") + (name "clfft") + (version "2.12.0") (source (origin (method url-fetch) - (uri (string-append "https://github.com/clMathLibraries/clFFT/archive/" + (uri (string-append "https://github.com/clMathLibraries/clFFT/archive/v" version ".tar.gz")) (sha256 (base32 - "19hrk1lf06kch8x9dpbdj0waycn2mldrmj2y4vzi7zn2gdfw6g73")))) + "004n14q8bp1yvf6hja0nljyv7lnhs3w9ipa461c33znq1jqa28y6")))) (build-system cmake-build-system) - (arguments `(#:configure-flags '("../clFFT-2.10.1/src" "-DBUILD_SHARED_LIBS=ON" "-DCMAKE_BUILD_TYPE=Release") #:tests? #f)) + (arguments `(#:configure-flags '("../clFFT-2.12.0/src" "-DBUILD_SHARED_LIBS=ON" "-DCMAKE_BUILD_TYPE=Release") #:tests? #f)) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) ("cmake" ,cmake) @@ -236,8 +237,8 @@ ("libtiff" ,libtiff) ("mesa-utils" ,mesa-utils) ("openmpi" ,openmpi) - ("ocl-icd" ,ocl-icd) ("opencl-headers" ,opencl-headers) + ("ocd-icd" ,ocl-icd) ("randrproto" ,randrproto) ("libxrandr" ,libxrandr) ("xineramaproto" ,xineramaproto) @@ -247,19 +248,20 @@ (home-page "http://www.glfw.org/") (synopsis "glfw is an Open Source, multi-platform library for creating windows with OpenGL contexts and receiving input and events.") (description "glfw is an Open Source, multi-platform library for creating windows with OpenGL contexts and receiving input and events.") - (license (list license:gpl2)))) - + (license (list license:gpl2 + license:asl2.0)))) + (define-public compute (package (name "compute") - (version "v0.5") + (version "1.61.0") (source (origin (method url-fetch) - (uri (string-append "https://github.com/boostorg/compute/archive/" + (uri (string-append "https://github.com/boostorg/compute/archive/boost-" version ".tar.gz")) (sha256 (base32 - "1r16zd1wdnn9gx278mkvr13k3i79hr35v6vj0fn7v3n92ngwxnhd")))) + "1jkdad65yqqrldi5h3rzph57yl350zn7bl3xv6a923l2p2a6zl2z")))) (build-system cmake-build-system) (arguments `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON" "-DCMAKE_BUILD_TYPE=Release") #:tests? #f)) (native-inputs `(("autoconf" ,autoconf) @@ -281,7 +283,7 @@ ("mesa-utils" ,mesa-utils) ("openmpi" ,openmpi) ("opencl-headers" ,opencl-headers) - ("ocl-icd" ,ocl-icd) + ("ocd-icd" ,ocl-icd) ("randrproto" ,randrproto) ("libxrandr" ,libxrandr) ("xineramaproto" ,xineramaproto) @@ -291,40 +293,9 @@ (home-page "http://boost.org") (synopsis "Peer-reviewed portable C++ source libraries,BoostCompute") (description "Peer-reviewed portable C++ source libraries,BoostCompute") - (license (list license:x11-style)))) - -(define-public ocl-icd - (package - (name "ocl-icd") - (version "2.2.9") - (source (origin - (method url-fetch) - (uri (string-append "https://forge.imag.fr/frs/download.php/716/ocl-icd-" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "1rgaixwnxmrq2aq4kcdvs0yx7i6krakarya9vqs7qwsv5hzc32hc")))) - (inputs `(("zip" ,zip) - ("autoconf" ,autoconf) - ("automake" ,automake) - ("ruby" ,ruby) - ("libtool" ,libtool) - ("opencl-headers" ,opencl-headers) - ("libgcrypt" ,libgcrypt))) - (build-system gnu-build-system) - (arguments - '(#:phases (modify-phases %standard-phases - (add-after 'unpack `bootstrap - (lambda _ - (zero? (system* "autoreconf" "-vfi"))))))) - (home-page "https://forge.imag.fr/projects/ocl-icd/") - (synopsis "OpenCL implementations are provided as ICD (Installable Client Driver).") - (description "OpenCL implementations are provided as ICD (Installable Client Driver). - An OpenCL program can use several ICD thanks to the use of an ICD Loader as provided by this project. - This free ICD Loader can load any (free or non free) ICD") - (license (list license:gpl2 license:ruby)))) - + (license (list license:x11-style + license:boost1.0)))) + (define-public opencl-headers (let ((commit "c1770dc")) (package @@ -359,7 +330,281 @@ (home-page "https://www.khronos.org/registry/cl/") (license (list license:gpl2))))) +(define-public pocl +(let ((commit "5167ffd")) +(package + (name "pocl") + (version (string-append "0.13-" commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pocl/pocl.git") + (commit commit))) + (file-name (string-append name "-" commit)) + (sha256 + (base32 + "09fgby8kwpp2xs2nr6mi05z0yxx6hvqi9scrc4byb8p7v7a7k9gj")))) + (native-inputs `(("autoconf" ,autoconf) + ("automake" ,automake) + ("gawk" ,gawk) + ("glew" ,glew) + ("libtool" ,libtool) + ("pkg-config" ,pkg-config))) + (inputs `(("boost" ,boost) + ("glfw" ,glfw);;compute package deprecated + ("atlas" ,atlas) + ("boost" ,boost) + ("opencl-headers" ,opencl-headers) + ("ocl-icd" ,ocl-icd) + ("enca" ,enca) + ("clang" ,clang-3.8) + ("clang-runtime-3.8" ,clang-runtime-3.8) + ("eudev" ,eudev) + ("glib" ,glib) + ("hwloc" ,hwloc) + ("lapack" ,lapack) + ("scalapack" ,scalapack) + ("libcap" ,libcap) + ("libjpeg" ,libjpeg) + ("libltdl" ,libltdl) + ("libtiff" ,libtiff) + ("libyajl" ,libyajl) + ("llvm" ,llvm-3.8) + ("zlib" ,zlib) + ("mesa-utils" ,mesa-utils) + ("python" ,python-2) + ("perl" ,perl) + ("freeimage" ,freeimage) + ("freeglut" ,freeglut) + ("fftw" ,fftw) + ("fftwf" ,fftwf) + ("fftw-openmpi" ,fftw-openmpi) + ("glew" ,glew) + ("openblas" ,openblas) + ("glu" ,glu))) + (build-system gnu-build-system) + (arguments + '(#:phases (modify-phases %standard-phases + (delete 'tests) + (add-after 'unpack `bootstrap + (lambda _ + (zero? (system* "autoreconf" "-vfi"))))))) + (synopsis "pocl: A portable OpenCL implementation") + (description "pocl is a MIT-licensed open source implementation of the OpenCL standard") + (home-page "http://portablecl.org/") + (license (list license:gpl2 + license:gpl2+ + license:gpl3 + license:bsd-3 + license:gpl3+ + license:x11))))) + +(define-public ocl-icd + (package + (name "ocl-icd") + (version "2.2.9") + (source (origin + (method url-fetch) + (uri (string-append "https://forge.imag.fr/frs/download.php/716/ocl-icd-" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1rgaixwnxmrq2aq4kcdvs0yx7i6krakarya9vqs7qwsv5hzc32hc")))) + (inputs `(("zip" ,zip) + ("autoconf" ,autoconf) + ("automake" ,automake) + ("ruby" ,ruby) + ("libtool" ,libtool) + ("opencl-headers" ,opencl-headers) + ("libgcrypt" ,libgcrypt))) + (build-system gnu-build-system) + (arguments + '(#:phases (modify-phases %standard-phases + (add-after 'unpack `bootstrap + (lambda _ + (zero? (system* "autoreconf" "-vfi"))))))) + (home-page "https://forge.imag.fr/projects/ocl-icd/") + (synopsis "OpenCL implementations are provided as ICD (Installable Client Driver).") + (description "OpenCL implementations are provided as ICD (Installable Client Driver). + An OpenCL program can use several ICD thanks to the use of an ICD Loader as provided by this project. + This free ICD Loader can load any (free or non free) ICD") + (license (list license:gpl2 + license:ruby)))) + +(define-public llvm + (package + (name "llvm") + (version "3.6.2") + (source + (origin + (method url-fetch) + (uri (string-append "http://llvm.org/releases/" + version "/llvm-" version ".src.tar.xz")) + (sha256 + (base32 + "153vcvj8gvgwakzr4j0kndc0b7wn91c2g1vy2vg24s6spxcc23gn")))) + (build-system cmake-build-system) + (native-inputs + `(("python" ,python-wrapper) + ("perl" ,perl))) + (arguments + `(#:configure-flags '("-DCMAKE_SKIP_BUILD_RPATH=FALSE" + "-DCMAKE_BUILD_WITH_INSTALL_RPATH=FALSE"))) + (home-page "http://www.llvm.org") + (synopsis "Optimizing compiler infrastructure") + (description + "LLVM is a compiler infrastructure designed for compile-time, link-time, +runtime, and idle-time optimization of programs from arbitrary programming +languages. It currently supports compilation of C and C++ programs, using +front-ends derived from GCC 4.0.1. A new front-end for the C family of +languages is in development. The compiler infrastructure includes mirror sets +of programming tools as well as libraries with equivalent functionality.") + (license (list license:ncsa)))) +(define (clang-runtime-from-llvm llvm hash) + (package + (name "clang-runtime") + (version (package-version llvm)) + (source + (origin + (method url-fetch) + (uri (string-append "http://llvm.org/releases/" + version "/compiler-rt-" version ".src.tar.xz")) + (sha256 (base32 hash)))) + (build-system cmake-build-system) + (native-inputs (package-native-inputs llvm)) + (inputs + `(("llvm" ,llvm))) + (arguments + `(;; Don't use '-g' during the build to save space. + #:build-type "Release" + #:tests? #f)) + + (home-page "http://compiler-rt.llvm.org") + (synopsis "Runtime library for Clang/LLVM") + (description + "The \"clang-runtime\" library provides the implementations of run-time +functions for C and C++ programs. It also provides header files that allow C +and C++ source code to interface with the \"sanitization\" passes of the clang +compiler. In LLVM this library is called \"compiler-rt\".") + (license (list license:ncsa)) + + ;; <http://compiler-rt.llvm.org/> doesn't list MIPS as supported. + (supported-systems (delete "mips64el-linux" %supported-systems)))) + +(define (clang-from-llvm llvm clang-runtime hash) + (package + (name "clang") + (version (package-version llvm)) + (source + (origin + (method url-fetch) + (uri (string-append "http://llvm.org/releases/" + version "/cfe-" version ".src.tar.xz")) + (sha256 (base32 hash)))) + ;; Using cmake allows us to treat llvm as an external library. There + ;; doesn't seem to be any way to do this with clang's autotools-based + ;; build system. + (build-system cmake-build-system) + (native-inputs (package-native-inputs llvm)) + (inputs + `(("libxml2" ,libxml2) + ("gcc-lib" ,gcc "lib") + ,@(package-inputs llvm))) + (propagated-inputs + `(("llvm" ,llvm) + ("clang-runtime" ,clang-runtime))) + (arguments + `(#:configure-flags + (list "-DCLANG_INCLUDE_TESTS=True" + + ;; Find libgcc_s, crtbegin.o, and crtend.o. + (string-append "-DGCC_INSTALL_PREFIX=" + (assoc-ref %build-inputs "gcc-lib")) + + ;; Use a sane default include directory. + (string-append "-DC_INCLUDE_DIRS=" + (assoc-ref %build-inputs "libc") + "/include")) + + ;; Don't use '-g' during the build to save space. + #:build-type "Release" + + #:phases (modify-phases %standard-phases + (add-after + 'unpack 'set-glibc-file-names + (lambda* (#:key inputs #:allow-other-keys) + (let ((libc (assoc-ref inputs "libc")) + (compiler-rt (assoc-ref inputs "clang-runtime"))) + (substitute* "lib/Driver/Tools.cpp" + ;; Patch the 'getLinuxDynamicLinker' function to that + ;; it uses the right dynamic linker file name. + (("/lib64/ld-linux-x86-64.so.2") + (string-append libc + ,(glibc-dynamic-linker))) + + ;; Link to libclang_rt files from clang-runtime. + (("TC\\.getDriver\\(\\)\\.ResourceDir") + (string-append "\"" compiler-rt "\""))))))))) + + ;; Clang supports the same environment variables as GCC. + (native-search-paths + (list (search-path-specification + (variable "CPATH") + (files '("include"))) + (search-path-specification + (variable "LIBRARY_PATH") + (files '("lib" "lib64"))))) + + (home-page "http://clang.llvm.org") + (synopsis "C language family frontend for LLVM") + (description + "Clang is a compiler front end for the C, C++, Objective-C and +Objective-C++ programming languages. It uses LLVM as its back end. The Clang +project includes the Clang front end, the Clang static analyzer, and several +code analysis tools.") + (license (list license:ncsa)))) + +(define-public clang-runtime + (clang-runtime-from-llvm + llvm + "11qx8d3pbfqjaj2x207pvlvzihbs1z2xbw4crpz7aid6h1yz6bqg")) + +(define-public clang + (clang-from-llvm llvm clang-runtime + "1wwr8s6lzr324hv4s1k6na4j5zv6n9kdhi14s4kb9b13d93814df")) - +(define-public llvm-3.8 + (package (inherit llvm) + (version "3.8.0") + (source + (origin + (method url-fetch) + (uri (string-append "http://llvm.org/releases/" + version "/llvm-" version ".src.tar.xz")) + (sha256 + (base32 + "0ikfq0gxac8xpvxj23l4hk8f12ydx48fljgrz1gl9xp0ks704nsm")))) + (native-inputs + `(("python" ,python-wrapper) + ("perl" ,perl) + ("libffi" ,libffi) + ("zlib" ,zlib))) + (arguments + `(#:configure-flags '("-DCMAKE_SKIP_BUILD_RPATH=FALSE" + "-DCMAKE_BUILD_WITH_INSTALL_RPATH=FALSE" + "-DLLVM_ENABLE_PIC=ON" + ;"-DLLVM_ENABLE_RTTI=ON" + "-DLLVM_ENABLE_WERROR=OFF" + ;;"-DLLVM_REQUIRES_RTTI=ON" + ))))) + +(define-public clang-runtime-3.8 + (clang-runtime-from-llvm + llvm-3.8 + "1c2nkp9563873ffz22qmhc0wakgj428pch8rmhym8agjamz3ily8")) +(define-public clang-3.8 + (clang-from-llvm llvm-3.8 clang-runtime-3.8 + "1ybcac8hlr9vl3wg8s4v6cp0c0qgqnwprsv85lihbkq3vqv94504")) |