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Merge branch 'master' into core-updates-frozen

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Conflicts:
	gnu/packages/algebra.scm
	gnu/packages/games.scm
	gnu/packages/golang.scm
	gnu/packages/kerberos.scm
	gnu/packages/mail.scm
	gnu/packages/python.scm
	gnu/packages/ruby.scm
	gnu/packages/scheme.scm
	gnu/packages/tex.scm
	gnu/packages/tls.scm
	gnu/packages/version-control.scm
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Marius Bakke 2021-08-12 00:30:27 +02:00
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@ -56,6 +56,7 @@
#:use-module (gnu packages check)
#:use-module (gnu packages compression)
#:use-module (gnu packages cmake)
#:use-module (gnu packages cpp)
#:use-module (gnu packages cran)
#:use-module (gnu packages databases)
#:use-module (gnu packages dejagnu)
@ -64,10 +65,12 @@
#:use-module (gnu packages graphviz)
#:use-module (gnu packages gstreamer)
#:use-module (gnu packages image)
#:use-module (gnu packages libffi)
#:use-module (gnu packages linux)
#:use-module (gnu packages llvm)
#:use-module (gnu packages maths)
#:use-module (gnu packages mpi)
#:use-module (gnu packages ninja)
#:use-module (gnu packages ocaml)
#:use-module (gnu packages onc-rpc)
#:use-module (gnu packages parallel)
@ -86,6 +89,7 @@
#:use-module (gnu packages statistics)
#:use-module (gnu packages sqlite)
#:use-module (gnu packages swig)
#:use-module (gnu packages tls)
#:use-module (gnu packages web)
#:use-module (gnu packages xml)
#:use-module (gnu packages xorg)
@ -660,6 +664,50 @@ standard data types.")
;; headers, hence the name change.
(deprecated-package "python-onnx" onnx))
(define-public onnx-optimizer
(package
(name "onnx-optimizer")
;; Note: 0.2.x is *more* recent than 1.5.0.
(version "0.2.6")
(home-page "https://github.com/onnx/optimizer")
(source (origin
(method git-fetch)
(uri (git-reference
(url home-page)
(commit (string-append "v" version))))
(sha256
(base32
"1wkqqdxcxpfbf8zpbdfdd3zz5jkw775g31gyykj11z4y6pp659l6"))
(file-name (git-file-name name version))
(patches (search-patches "onnx-optimizer-system-library.patch"))
(modules '((guix build utils)))
(snippet '(delete-file-recursively "third_party"))))
(build-system python-build-system)
(arguments (package-arguments onnx)) ;reuse build system tweaks
(native-inputs
`(("cmake" ,cmake)
("python-pytest" ,python-pytest)
("python-pytest-runner" ,python-pytest-runner)
("python-nbval" ,python-nbval)
("python-coverage" ,python-coverage)))
(inputs
`(("onnx" ,onnx)
("protobuf" ,protobuf)
("pybind11" ,pybind11)))
(propagated-inputs
`(("python-numpy" ,python-numpy)))
(synopsis "Library to optimize ONNX models")
(description
"This package provides a C++ and Python library for performing arbitrary
optimizations on ONNX models, as well as a growing list of prepackaged
optimization passes.
Not all possible optimizations can be directly implemented on ONNX graphs---
some will need additional backend-specific information---but many can, and the
aim is to provide all such passes along with ONNX so that they can be re-used
with a single function call.")
(license license:expat)))
(define-public rxcpp
(package
(name "rxcpp")
@ -701,23 +749,22 @@ synchronization, thread-safety, concurrent data structures, and non-blocking
I/O.")
(license license:asl2.0)))
(define-public gemmlowp-for-tensorflow
;; The commit hash is taken from "tensorflow/workspace.bzl".
(let ((commit "38ebac7b059e84692f53e5938f97a9943c120d98")
(revision "2"))
(define-public gemmlowp
(let ((commit "f9959600daa42992baace8a49544a00a743ce1b6")
(version "0.1")
(revision "1"))
(package
(name "gemmlowp")
(version (git-version "0" revision commit))
(version (git-version version revision commit))
(home-page "https://github.com/google/gemmlowp")
(source (origin
(method url-fetch)
(uri (string-append "https://mirror.bazel.build/"
"github.com/google/gemmlowp/archive/"
commit ".zip"))
(file-name (string-append "gemmlowp-" version ".zip"))
(method git-fetch)
(uri (git-reference (url home-page) (commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"0n56s2g8hrssm4w8qj1v58gfm56a04n9v992ixkmvk6zjiralzxq"))))
(build-system cmake-build-system)
"1hzfhlhzcb827aza6a7drydc67dw5fm3qfqilb9ibskan8dsf0c6"))))
(arguments
`(#:configure-flags
(list ,@(match (%current-system)
@ -737,18 +784,15 @@ I/O.")
(inc (string-append out "/include/")))
(install-file "../build/libeight_bit_int_gemm.so" lib)
(for-each (lambda (dir)
(let ((target (string-append inc "/" dir)))
(mkdir-p target)
(let ((target
(string-append inc "/gemmlowp/" dir)))
(for-each (lambda (h)
(install-file h target))
(find-files (string-append "../" dir)
"\\.h$"))))
'("meta" "profiling" "public" "fixedpoint"
"eight_bit_int_gemm" "internal"))
#t))))))
(native-inputs
`(("unzip" ,unzip)))
(home-page "https://github.com/google/gemmlowp")
"eight_bit_int_gemm" "internal"))))))))
(build-system cmake-build-system)
(synopsis "Small self-contained low-precision GEMM library")
(description
"This is a small self-contained low-precision @dfn{general matrix
@ -758,6 +802,46 @@ at most 8 bits. To avoid overflow, results are internally accumulated on more
than 8 bits, and at the end only some significant 8 bits are kept.")
(license license:asl2.0))))
(define-public gemmlowp-for-tensorflow
;; The commit hash is taken from "tensorflow/workspace.bzl".
(let ((commit "38ebac7b059e84692f53e5938f97a9943c120d98")
(revision "2"))
(package
(inherit gemmlowp)
(version (git-version "0" revision commit))
(source (origin
(method url-fetch)
(uri (string-append "https://mirror.bazel.build/"
"github.com/google/gemmlowp/archive/"
commit ".zip"))
(file-name (string-append "gemmlowp-" version ".zip"))
(sha256
(base32
"0n56s2g8hrssm4w8qj1v58gfm56a04n9v992ixkmvk6zjiralzxq"))))
(arguments
(substitute-keyword-arguments (package-arguments gemmlowp)
((#:phases phases)
`(modify-phases ,phases
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(lib (string-append out "/lib/"))
(inc (string-append out "/include/")))
(install-file "../build/libeight_bit_int_gemm.so" lib)
(for-each (lambda (dir)
;; Note: Install headers straight into
;; $includedir instead of $includedir/gemmlowp.
(let ((target (string-append inc "/" dir)))
(for-each (lambda (h)
(install-file h target))
(find-files (string-append "../" dir)
"\\.h$"))))
'("meta" "profiling" "public" "fixedpoint"
"eight_bit_int_gemm" "internal")))))))))
(native-inputs
`(("unzip" ,unzip)))
(properties '((hidden? . #t))))))
(define-public dlib
(package
(name "dlib")
@ -2030,6 +2114,175 @@ together building blocks and a subclassing API with an imperative style for
advanced research.")
(license license:asl2.0)))
(define-public tensorflow-lite
(package
(name "tensorflow-lite")
(version "2.5.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/tensorflow/tensorflow")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1jdw2i1rq06zqd6aabh7bbm0avsg4pygnfmd7gviv0blhih9054l"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #false ; no "check" target
#:build-type "Release"
#:configure-flags
(list
"-DTFLITE_ENABLE_GPU=OFF"
"-DTFLITE_ENABLE_RUY=OFF"
;; TODO: The build system attempts to build xnnpack from source. We
;; would like to use our xnnpack package here, but this requires more
;; work.
"-DTFLITE_ENABLE_XNNPACK=OFF"
;; Pretend we've already fetched abseil. We won't actually build it
;; but use the existing package.
"-Dabseil-cpp_POPULATED=TRUE"
;; Don't fetch the sources. We have already built flatbuffers.
"-Dflatbuffers_POPULATED=TRUE"
"-DFFT2D_SOURCE_DIR=/tmp/fft2d"
"-Dneon2sse_SOURCE_DIR=/tmp/neon2sse"
"-Dneon2sse_BINARY_DIR=/tmp/neon2sse-bin"
"-DFARMHASH_SOURCE_DIR=/tmp/farmhash"
"-Dgemmlowp_SOURCE_DIR=/tmp/gemmlowp"
(string-append "-DRUY_SOURCE_DIR="
(assoc-ref %build-inputs "ruy-src")))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'chdir
(lambda _ (chdir "tensorflow/lite")))
(add-after 'chdir 'copy-sources
(lambda* (#:key inputs #:allow-other-keys)
;; Use external cmake finders instead of these stubs that won't
;; find anything but the bundled sources.
(delete-file "tools/cmake/modules/Findabsl.cmake")
(delete-file "tools/cmake/modules/Findeigen.cmake")
(substitute* "CMakeLists.txt"
(("find_package\\(eigen REQUIRED")
"find_package(eigen REQUIRED NAMES Eigen3"))
(substitute* "tools/cmake/modules/Findflatbuffers.cmake"
(("get_target_property.*")
(format #false "set(FLATBUFFERS_INCLUDE_DIRS ~a/include)\n"
(assoc-ref inputs "flatbuffers"))))
;; Don't fetch source code; we already have everything we need.
(substitute* '("tools/cmake/modules/fft2d.cmake"
"tools/cmake/modules/ruy.cmake"
"tools/cmake/modules/farmhash.cmake"
"tools/cmake/modules/neon2sse.cmake"
"tools/cmake/modules/gemmlowp.cmake")
(("OverridableFetchContent_Populate.*") ""))
(mkdir-p "/tmp/farmhash")
(with-directory-excursion "/tmp/farmhash"
(invoke "tar" "--strip-components=1"
"-xf" (assoc-ref inputs "farmhash-src")))
(mkdir-p "/tmp/fft2d")
(with-directory-excursion "/tmp/fft2d"
(invoke "tar" "--strip-components=1"
"-xf" (assoc-ref inputs "fft2d-src")))
(copy-recursively (assoc-ref inputs "neon2sse-src")
"/tmp/neon2sse/")
(copy-recursively (assoc-ref inputs "gemmlowp-src")
"/tmp/gemmlowp/")))
(add-after 'copy-sources 'prepare-shared-library-build
(lambda _ (chdir "c")))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(lib (string-append out "/lib"))
(headers (string-append out "/include/tensorflow/lite")))
(install-file "../build/libtensorflowlite_c.so" lib)
(with-directory-excursion ".."
(for-each
(lambda (file)
(let ((target-dir (string-append headers "/" (dirname file))))
(install-file file target-dir)))
(find-files "." "\\.h$")))))))))
(inputs
`(("abseil-cpp" ,abseil-cpp)
("eigen" ,eigen-for-tensorflow-lite)
("flatbuffers" ,flatbuffers)
("python" ,python)))
(native-inputs
`(("pkg-config" ,pkg-config)
("gemmlowp-src"
;; The commit hash is taken from
;; "tensorflow/lite/tools/cmake/modules/gemmlowp.cmake".
,(let ((commit "fda83bdc38b118cc6b56753bd540caa49e570745"))
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/google/gemmlowp")
(commit commit)))
(file-name (git-file-name "gemmlowp" (string-take commit 8)))
(sha256
(base32
"1sbp8kmr2azwlvfbzryy1frxi99jhsh1nc93bdbxdf8zdgpv0kxl")))))
("neon2sse-src"
,(let ((commit "a1652fd5253afbf3e39357b012974f93511f6108"))
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/intel/ARM_NEON_2_x86_SSE")
(commit commit)))
(file-name (git-file-name "neon2sse" (string-take commit 8)))
(sha256
(base32
"1q8gkxag9wlnwdwad2pclsrkwzrdjy94hyrkayrsvxyj7szb5y8i")))))
("farmhash-src"
,(let ((commit "816a4ae622e964763ca0862d9dbd19324a1eaf45"))
(origin
(method url-fetch)
(uri (string-append
"https://mirror.bazel.build/github.com/google/farmhash/archive/"
commit ".tar.gz"))
(file-name (git-file-name "farmhash" (string-take commit 8)))
(sha256
(base32
"185b2xdxl4d4cnsnv6abg8s22gxvx8673jq2yaq85bz4cdy58q35")))))
("fft2d-src"
,(origin
(method url-fetch)
(uri (string-append "https://storage.googleapis.com/"
"mirror.tensorflow.org/"
"www.kurims.kyoto-u.ac.jp/~ooura/fft2d.tgz"))
(file-name "fft2d.tar.gz")
(sha256
(base32
"1jfflzi74fag9z4qmgwvp90aif4dpbr1657izmxlgvf4hy8fk9xd"))))
("ruy-src"
,(let ((commit "9c56af3fce210a8a103eda19bd6f47c08a9e3d90"))
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/google/ruy")
(commit commit)
(recursive? #true)))
(file-name (git-file-name "ruy" (string-take commit 8)))
(sha256
(base32
"1cfd5gk6kaj8kbl3h98gx1ap8czd59y6p8qq8nr28fklpyzf5cis")))))))
(home-page "https://tensorflow.org")
(synopsis "Machine learning framework")
(description
"TensorFlow is a flexible platform for building and training machine
learning models. This package provides the \"lite\" variant for mobile
devices.")
(license license:asl2.0)))
(define-public python-iml
(package
(name "python-iml")
@ -2194,8 +2447,8 @@ that:
(define-public gloo
(let ((version "0.0.0") ; no proper version tag
(commit "ca528e32fea9ca8f2b16053cff17160290fc84ce")
(revision "0"))
(commit "c22a5cfba94edf8ea4f53a174d38aa0c629d070f")
(revision "1"))
(package
(name "gloo")
(version (git-version version revision commit))
@ -2208,18 +2461,20 @@ that:
(file-name (git-file-name name version))
(sha256
(base32
"1q9f80zy75f6njrzrqkmhc0g3qxs4gskr7ns2jdqanxa2ww7a99w"))))
"1crmqgybzkgkpbmcx16912gsl5qsj49swa0ikx6mhqgph0chrh11"))))
(build-system cmake-build-system)
(native-inputs
`(("googletest" ,googletest)))
(inputs
`(("openssl" ,openssl)))
(arguments
`(#:configure-flags '("-DBUILD_TEST=1")
#:phases
(modify-phases %standard-phases
(replace 'check
(lambda _
(invoke "make" "gloo_test")
#t)))))
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "make" "gloo_test")))))))
(synopsis "Collective communications library")
(description
"Gloo is a collective communications library. It comes with a
@ -2265,7 +2520,7 @@ general non-linear dimension reduction.")
(package
(name "xnnpack")
(version (git-version version revision commit))
(home-page "https://github.com/google/XNNPACK")
(home-page "https://github.com/google/XNNPACK") ;fork of QNNPACK
(source (origin
(method git-fetch)
(uri (git-reference (url home-page) (commit commit)))
@ -2305,3 +2560,134 @@ high-level machine learning frameworks, such as TensorFlow Lite,
TensorFlow.js, PyTorch, and MediaPipe.")
(license license:bsd-3))))
(define-public python-pytorch
(package
(name "python-pytorch")
(version "1.9.0")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/pytorch/pytorch")
(commit (string-append "v" version))
(recursive? #t)))
(file-name (git-file-name name version))
(sha256
(base32
"0cznsh68hwk5761gv7iijb4g6jgjpvs3bbixwpzzmkbkbn2q96c1"))
(patches (search-patches "python-pytorch-system-libraries.patch"
"python-pytorch-runpath.patch"))
(modules '((guix build utils)))
(snippet
'(begin
;; XXX: Let's be clear: this package is a bundling fest. We
;; delete as much as we can, but there's still a lot left.
(for-each (lambda (directory)
(delete-file-recursively
(string-append "third_party/" directory)))
'("benchmark" "cpuinfo" "eigen"
;; FIXME: QNNPACK (of which XNNPACK is a fork)
;; needs these.
;; "FP16" "FXdiv" "gemmlowp" "psimd"
"gloo" "googletest" "ios-cmake"
"onnx" "protobuf" "pthreadpool"
"pybind11" "python-enum" "python-peachpy"
"python-six" "tbb" "XNNPACK" "zstd"))
;; Adjust references to the onnx-optimizer headers.
(substitute* "caffe2/onnx/backend.cc"
(("onnx/optimizer/")
"onnxoptimizer/"))))))
(build-system python-build-system)
(arguments
'(#:phases (modify-phases %standard-phases
(add-before 'build 'use-system-libraries
(lambda* (#:key outputs #:allow-other-keys)
;; Tell 'setup.py' to let 'CMakeLists.txt' know that we
;; want to use "system libraries" instead of the bundled
;; ones.
(setenv "USE_SYSTEM_LIBS" "1")
;; XXX: Disable that for simplicity for now.
(setenv "USE_FBGEMM" "0")))
(add-before 'build 'make-things-writable
(lambda _
;; The 'build_caffe2' function in
;; 'tools/build_pytorch_libs.py', called from the
;; top-level 'setup.py', needs write access to this
;; directory.
(for-each make-file-writable
(find-files "caffe2/proto" "."
#:directories? #t))))
(replace 'check
(lambda* (#:key inputs outputs tests? #:allow-other-keys)
;; Run the test suite following the instructions in
;; 'CONTRIBUTING.md'. XXX: Unfortunately this doesn't
;; work, unless you set PYTHONPATH presumably.
(when tests?
(let ((python-site (site-packages inputs outputs)))
(setenv "PYTHONPATH"
(string-append python-site ":"
(getenv "PYTHONPATH")))
(invoke "python" "test/run_test.py")))))
(add-after 'install 'remove-test-executables
(lambda* (#:key inputs outputs #:allow-other-keys)
;; Remove test executables, but keep other executables
;; such as 'torch_shm_manager' and and .so files such as
;; 'libtorch_global_deps.so'.
(let ((python-site (site-packages inputs outputs)))
(for-each delete-file
(find-files python-site
"(^test_cpp_rpc|_test)$"))))))
;; XXX: Tests attempt to download data such as
;; <https://raw.githubusercontent.com/pytorch/test-infra/master/stats/slow-tests.json>.
#:tests? #f))
(native-inputs
`(("cmake" ,cmake)
("ninja" ,ninja)))
(inputs
`(("eigen" ,eigen)
;; ("fmt" ,fmt)
("fp16" ,fp16)
("gemmlowp" ,gemmlowp)
("googletest" ,googletest)
("googlebenchmark" ,googlebenchmark)
("gloo" ,gloo)
("openblas" ,openblas)
("openmpi" ,openmpi)
("pthreadpool" ,pthreadpool)
("protobuf" ,protobuf)
("pybind11" ,pybind11)
("sleef" ,sleef)
("xnnpack" ,xnnpack)
("zstd" ,zstd)))
(propagated-inputs
`(("python-astunparse" ,python-astunparse)
("python-numpy" ,python-numpy)
("python-pyyaml" ,python-pyyaml)
("python-cffi" ,python-cffi)
("python-peachpy" ,python-peachpy)
("python-typing-extensions" ,python-typing-extensions)
("python-future" ,python-future)
("python-six" ,python-six)
("python-requests" ,python-requests)
("onnx" ,onnx) ;propagated for its Python modules
("onnx-optimizer" ,onnx-optimizer)
("cpuinfo" ,cpuinfo)))
(home-page "https://pytorch.org/")
(synopsis "Python library for tensor computation and deep neural networks")
(description
"PyTorch is a Python package that provides two high-level features:
@itemize
@item tensor computation (like NumPy) with strong GPU acceleration;
@item deep neural networks (DNNs) built on a tape-based autograd system.
@end itemize
You can reuse Python packages such as NumPy, SciPy, and Cython to extend
PyTorch when needed.
Note: currently this package does not provide GPU support.")
(license license:bsd-3)))