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Resent-From: Vinicius Monego Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 01 Jun 2021 22:08:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 48785 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 48785@debbugs.gnu.org Cc: Vinicius Monego Received: via spool by 48785-submit@debbugs.gnu.org id=B48785.162258524213151 (code B ref 48785); Tue, 01 Jun 2021 22:08:02 +0000 Received: (at 48785) by debbugs.gnu.org; 1 Jun 2021 22:07:22 +0000 Received: from localhost ([127.0.0.1]:38121 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1loCXc-0003Pr-HL for submit@debbugs.gnu.org; Tue, 01 Jun 2021 18:07:21 -0400 Received: from mout01.posteo.de ([185.67.36.65]:34521) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1loCXZ-0003PV-Ug for 48785@debbugs.gnu.org; Tue, 01 Jun 2021 18:07:14 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id 0284B240026 for <48785@debbugs.gnu.org>; Wed, 2 Jun 2021 00:07:07 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1622585228; bh=kfPVRjbE42c/fOVdk4jSsXTh9dqDP8JE9rid5U8OSCQ=; h=From:To:Cc:Subject:Date:From; b=ULJpe+H2rwmD+rPAY/MjUskX6dzkeyZUJlgbWinnA6rUv9kydppZTVw4rs0anXzCR +J/pS8XgpVPb9aXkgR1PlUMiaIy1dRks2y0N0NJXPbZxdWqBixxxtk4VNnJuZAdNOY RcRZ2RndFhGAjwUG0S2Q1RdLWt1TXIQqeB7JKm3zqC27NlCYByDo1CmWnGHNnX8aTw HBoU+CRH+SAS0ygi3kzdabkn29X4YnoSkcLm+IStVgtnVDcuGir3604Hsx51wA90Eu 4iEs83auUAQmpU8bABoQaBl6mgsIb7dIiGZXR+u4rMTPvi1+2VKye9LRQCi5R+43pK 7FS0E2cN5wcUw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4FvmV24C1Sz6tmQ; Wed, 2 Jun 2021 00:07:06 +0200 (CEST) From: Vinicius Monego Date: Tue, 1 Jun 2021 22:06:42 +0000 Message-Id: <20210601220643.78439-2-monego@posteo.net> In-Reply-To: <20210601220643.78439-1-monego@posteo.net> References: <20210601220643.78439-1-monego@posteo.net> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Migadu-Flow: FLOW_IN ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1622585289; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-transfer-encoding:content-transfer-encoding:resent-cc: resent-from:resent-sender:resent-message-id:in-reply-to:in-reply-to: references:references:list-id:list-help:list-unsubscribe: list-subscribe:list-post:dkim-signature; bh=lIF4ZVkaPkxLPW6TZA05lbaXG8/mZt9I+ZcGte5yxBU=; b=dFyOFNq+K5MoRlWgFJXzGIJ4XnDPDZVQdDpEidYXVYFiHORTg/tz9mEi/GniBaiddY3gEj B8ofNK12sX/7ECzHnvqSZO+lPyGt0YMVEY+9qcIxs+VsR0bcpTY0jZfzQqdgGkrd9KDLDZ vcC4/DrXVnNW1fykmm/vvIhggy/1QyMHh/1R8fg7J/gSRXPX2yfk6eu9PLvFd8UppyUL0h kOLZ3z0S0Y0tNG1aoKCGQCv2dUEEG9TPIcdP0wFhVWvIRsEjO5X0t1Rp55xeu59drgBVyr 2Vgrzz/kX6xy/DkABkznkLGg8ZB9YWmDrsg6eyfKIqpT6UfzwVlyaXZbjKs2bA== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1622585289; a=rsa-sha256; cv=none; b=EPz5JvkWfdFFHfVut7ZGFyzWc3fPBBQkMzrs3JDrs6Xnodl0+6hc8yourj91erkijbyQTC 3mOU3I/Jnh1gjyhZs1F0MC9ePx3j3yxoG6GeVdIeW42GATcNuRfBbUYx+a/EXOBdvLeOlh lXMczGjbBBHmEv6aw9Lka7h5hcU1qc33jhj7a/TWzKiv+tnYzfeJ2331bvA0VJ6pY5V2gt fubEO92Cs/pAupwqbmGCHmML89Lwj+wbqsIt/iv3OTjVF5Jd95mH9e2579fB7iJDuvs38J Rs/Ddn2HX9NZF91CjsjIaax/R0hppE17/AsQv9eMySS2eQ+vLzpi4O5WKKvwPA== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=posteo.net header.s=2017 header.b=ULJpe+H2; dmarc=fail reason="SPF not aligned (strict)" header.from=posteo.net (policy=none); spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Spam-Score: 3.67 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=posteo.net header.s=2017 header.b=ULJpe+H2; dmarc=fail reason="SPF not aligned (strict)" header.from=posteo.net (policy=none); spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Queue-Id: 2548D236C2 X-Spam-Score: 3.67 X-Migadu-Scanner: scn1.migadu.com X-TUID: wNQ1V4sw1l3G * gnu/packages/machine-learning.scm (lightgbm): Update to 3.2.1. [source]: Add patches. [native-inputs]: Add googletest, opencl-headers. [inputs]: Add boost, eigen, fast-double-parser, fmt, ocl-icd. [propagated-inputs]: Remove. [arguments]: Add #:tests?, #:test-target. Pass "-DBUILD_CPP_TEST=OFF" and "-DUSE_GPU=ON" to #:configure-flags. Do not replace check phase. * gnu/packages/patches/lightgbm-use-system-libraries.patch, gnu/packages/patches/lightgbm-python-use-system-lib-lightgbm.patch: New files. * gnu/local.mk (dist_PATCH_DATA): Add them. --- gnu/local.mk | 2 + gnu/packages/machine-learning.scm | 57 ++++++++------ ...htgbm-python-use-system-lib-lightgbm.patch | 74 +++++++++++++++++++ .../lightgbm-use-system-libraries.patch | 58 +++++++++++++++ 4 files changed, 167 insertions(+), 24 deletions(-) create mode 100644 gnu/packages/patches/lightgbm-python-use-system-lib-lightgbm.patch create mode 100644 gnu/packages/patches/lightgbm-use-system-libraries.patch diff --git a/gnu/local.mk b/gnu/local.mk index 6a1e459e4e..0016ac12af 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1375,6 +1375,8 @@ dist_patch_DATA = \ %D%/packages/patches/lierolibre-newer-libconfig.patch \ %D%/packages/patches/lierolibre-remove-arch-warning.patch \ %D%/packages/patches/lierolibre-try-building-other-arch.patch \ + %D%/packages/patches/lightgbm-python-use-system-lib-lightgbm.patch \ + %D%/packages/patches/lightgbm-use-system-libraries.patch \ %D%/packages/patches/linbox-fix-pkgconfig.patch \ %D%/packages/patches/linkchecker-tests-require-network.patch \ %D%/packages/patches/linphone-desktop-without-sdk.patch \ diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index ead47a534a..1a3f647dde 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -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) @@ -70,8 +71,10 @@ #:use-module (gnu packages mpi) #:use-module (gnu packages ocaml) #:use-module (gnu packages onc-rpc) + #:use-module (gnu packages opencl) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages pretty-print) #:use-module (gnu packages protobuf) #:use-module (gnu packages python) #:use-module (gnu packages python-build) @@ -1058,33 +1061,39 @@ main intended application of Autograd is gradient-based optimization.") (define-public lightgbm (package (name "lightgbm") - (version "2.0.12") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/Microsoft/LightGBM") - (commit (string-append "v" version)))) - (sha256 - (base32 - "0jlvyn7k81dzrh9ij3zw576wbgiwmmr26rzpdxjn1dbpc3njpvzi")) - (file-name (git-file-name name version)))) + (version "3.2.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Microsoft/LightGBM") + (commit (string-append "v" version)))) + (patches + (search-patches "lightgbm-use-system-libraries.patch" + "lightgbm-python-use-system-lib-lightgbm.patch")) + (sha256 + (base32 "1fchiiwl3pz1kpi0kbfanif6c6b688wmmjjbqz4ff4djc6g2sg7z")) + (file-name (git-file-name name version)))) (native-inputs - `(("python-pytest" ,python-pytest) - ("python-nose" ,python-nose))) + `(("googletest" ,googletest) + ("opencl-headers" ,opencl-headers))) (inputs - `(("openmpi" ,openmpi))) - (propagated-inputs - `(("python-numpy" ,python-numpy) - ("python-scipy" ,python-scipy))) + `(("boost" ,boost) + ("eigen" ,eigen) + ("fast-double-parser" ,fast-double-parser) + ("fmt" ,fmt) + ("ocl-icd" ,ocl-icd) + ("openmpi" ,openmpi))) (arguments - `(#:configure-flags - '("-DUSE_MPI=ON") - #:phases - (modify-phases %standard-phases - (replace 'check - (lambda _ - (with-directory-excursion "../source" - (invoke "pytest" "tests/c_api_test/test_.py"))))))) + `(;; FIXME: With 'find_package(GTest CONFIG)' (default), googletest + ;; is not found by CMake. If we replace CONFIG with REQUIRED, the + ;; test files fail to link with googletest in the build phase. + #:tests? #f + #:test-target "testlightgbm" + #:configure-flags + (list "-DBUILD_CPP_TEST=OFF" + "-DUSE_GPU=ON" ;using OpenCL + "-DUSE_MPI=ON"))) (build-system cmake-build-system) (home-page "https://github.com/Microsoft/LightGBM") (synopsis "Gradient boosting framework based on decision tree algorithms") diff --git a/gnu/packages/patches/lightgbm-python-use-system-lib-lightgbm.patch b/gnu/packages/patches/lightgbm-python-use-system-lib-lightgbm.patch new file mode 100644 index 0000000000..69cb721daa --- /dev/null +++ b/gnu/packages/patches/lightgbm-python-use-system-lib-lightgbm.patch @@ -0,0 +1,74 @@ +From c73be84d8ec6ac71dfdaa71b7943ae344f5d7cde Mon Sep 17 00:00:00 2001 +From: Vinicius Monego +Date: Tue, 1 Jun 2021 00:24:38 -0300 +Subject: [PATCH] Use system lib_lightgbm. + +--- + python-package/lightgbm/libpath.py | 4 ++++ + python-package/setup.py | 12 ++++++++---- + 2 files changed, 12 insertions(+), 4 deletions(-) + +diff --git a/python-package/lightgbm/libpath.py b/python-package/lightgbm/libpath.py +index 6533792..27af2b9 100644 +--- a/python-package/lightgbm/libpath.py ++++ b/python-package/lightgbm/libpath.py +@@ -17,8 +17,12 @@ def find_lib_path() -> List[str]: + # we don't need lib_lightgbm while building docs + return [] + ++ # This variable will be set during substitution. ++ lib_lightgbm_path = '' ++ + curr_path = os.path.dirname(os.path.abspath(os.path.expanduser(__file__))) + dll_path = [curr_path, ++ lib_lightgbm_path, + os.path.join(curr_path, '../../'), + os.path.join(curr_path, 'compile'), + os.path.join(curr_path, '../compile'), +diff --git a/python-package/setup.py b/python-package/setup.py +index ee98b1a..2f7ce38 100644 +--- a/python-package/setup.py ++++ b/python-package/setup.py +@@ -231,7 +231,7 @@ class CustomInstall(install): + self.opencl_library = None + self.mpi = 0 + self.hdfs = 0 +- self.precompile = 0 ++ self.precompile = 1 + self.nomp = 0 + self.bit32 = 0 + +@@ -274,7 +274,7 @@ class CustomBdistWheel(bdist_wheel): + self.opencl_library = None + self.mpi = 0 + self.hdfs = 0 +- self.precompile = 0 ++ self.precompile = 1 + self.nomp = 0 + self.bit32 = 0 + +@@ -324,7 +324,10 @@ if __name__ == "__main__": + copy_file(os.path.join(CURRENT_DIR, os.path.pardir, 'VERSION.txt'), + os.path.join(CURRENT_DIR, 'lightgbm', 'VERSION.txt'), + verbose=0) # type:ignore +- version = open(os.path.join(CURRENT_DIR, 'lightgbm', 'VERSION.txt'), encoding='utf-8').read().strip() ++ ++ # This variable will be set during substitution. ++ version = '' ++ + readme = open(os.path.join(CURRENT_DIR, 'README.rst'), encoding='utf-8').read() + + sys.path.insert(0, CURRENT_DIR) +@@ -355,7 +358,8 @@ if __name__ == "__main__": + zip_safe=False, + cmdclass={ + 'install': CustomInstall, +- 'install_lib': CustomInstallLib, ++ # Lib will be loaded from the lightgbm package. ++ # 'install_lib': CustomInstallLib, + 'bdist_wheel': CustomBdistWheel, + 'sdist': CustomSdist, + }, +-- +2.31.1 + diff --git a/gnu/packages/patches/lightgbm-use-system-libraries.patch b/gnu/packages/patches/lightgbm-use-system-libraries.patch new file mode 100644 index 0000000000..115ca02775 --- /dev/null +++ b/gnu/packages/patches/lightgbm-use-system-libraries.patch @@ -0,0 +1,58 @@ +From 894648291b9629d51785e4fd1cae820d2858e039 Mon Sep 17 00:00:00 2001 +From: Vinicius Monego +Date: Mon, 31 May 2021 21:23:52 -0300 +Subject: [PATCH] Use system libraries. + +--- + CMakeLists.txt | 11 ++++++++--- + include/LightGBM/utils/common.h | 4 ++-- + 2 files changed, 10 insertions(+), 5 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index b845f36..560e477 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -93,9 +93,6 @@ if(USE_SWIG) + endif() + endif(USE_SWIG) + +-SET(EIGEN_DIR "${PROJECT_SOURCE_DIR}/external_libs/eigen") +-include_directories(${EIGEN_DIR}) +- + # See https://gitlab.com/libeigen/eigen/-/blob/master/COPYING.README + ADD_DEFINITIONS(-DEIGEN_MPL2_ONLY) + +@@ -399,6 +396,14 @@ if(USE_SWIG) + endif() + endif(USE_SWIG) + ++find_package (Eigen3 3.3 REQUIRED NO_MODULE) ++TARGET_LINK_LIBRARIES (lightgbm Eigen3::Eigen) ++TARGET_LINK_LIBRARIES (_lightgbm Eigen3::Eigen) ++ ++find_package(fmt) ++TARGET_LINK_LIBRARIES(lightgbm fmt::fmt) ++TARGET_LINK_LIBRARIES(_lightgbm fmt::fmt) ++ + if(USE_MPI) + TARGET_LINK_LIBRARIES(lightgbm ${MPI_CXX_LIBRARIES}) + TARGET_LINK_LIBRARIES(_lightgbm ${MPI_CXX_LIBRARIES}) +diff --git a/include/LightGBM/utils/common.h b/include/LightGBM/utils/common.h +index 4357357..00101a5 100644 +--- a/include/LightGBM/utils/common.h ++++ b/include/LightGBM/utils/common.h +@@ -32,9 +32,9 @@ + + #if (!((defined(sun) || defined(__sun)) && (defined(__SVR4) || defined(__svr4__)))) + #define FMT_HEADER_ONLY +-#include "../../../external_libs/fmt/include/fmt/format.h" ++#include "fmt/format.h" + #endif +-#include "../../../external_libs/fast_double_parser/include/fast_double_parser.h" ++#include "fast_double_parser.h" + + #ifdef _MSC_VER + #include +-- +2.31.1 + -- 2.31.1