Package: guix-patches;
Reported by: Nicolas Graves <ngraves <at> ngraves.fr>
Date: Fri, 21 Feb 2025 19:54:01 UTC
Severity: normal
Tags: patch
Done: Ludovic Courtès <ludo <at> gnu.org>
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guix-patches <at> gnu.org:bug#76477; Package guix-patches.
(Fri, 21 Feb 2025 19:54:02 GMT) Full text and rfc822 format available.Nicolas Graves <ngraves <at> ngraves.fr>:guix-patches <at> gnu.org.
(Fri, 21 Feb 2025 19:54:02 GMT) Full text and rfc822 format available.Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: guix-patches <at> gnu.org Subject: [PATCH] gnu: faiss: Update to 1.10.0. Date: Fri, 21 Feb 2025 19:24:28 +0100
* gnu/packages/graph.scm (faiss): Update to 1.10.0.
[source]: Adapt snippet. Add patch.
[arguments]: Delete likely uneeded {phases}. Adapt {configure-flags}.
[native-inputs]: Add openmpi.
(python-faiss): Update to 1.10.0.
[build-system]: Switch to cmake-build-system.
[arguments]: Rewrite all arguments.
[inputs]: Improve-style. Switch python for python-wrapper.
[native-inputs]: Add python-scipy.
[propagated-inputs]: Remove python-matplotlib.
* gnu/packages/patches/faiss-tests-CMakeLists-find-googletest.patch:
Add patch.
* gnu/local.mk: Likewise.
* gnu/packages/graph.scm
---
gnu/local.mk | 1 +
gnu/packages/graph.scm | 202 ++++++++----------
...iss-tests-CMakeLists-find-googletest.patch | 53 +++++
3 files changed, 146 insertions(+), 110 deletions(-)
create mode 100644 gnu/packages/patches/faiss-tests-CMakeLists-find-googletest.patch
diff --git a/gnu/local.mk b/gnu/local.mk
index c7f63c458a..464e3896b6 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1258,6 +1258,7 @@ dist_patch_DATA = \
%D%/packages/patches/fail2ban-python310-server-action.patch \
%D%/packages/patches/fail2ban-python310-server-actions.patch \
%D%/packages/patches/fail2ban-python310-server-jails.patch \
+ %D%/packages/patches/faiss-tests-CMakeLists-find-googletest.patch \
%D%/packages/patches/falcosecurity-libs-shared-build.patch \
%D%/packages/patches/farstream-gupnp.patch \
%D%/packages/patches/farstream-make.patch \
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index f29a71c0d7..467a7f661b 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -62,6 +62,7 @@ (define-module (gnu packages graph)
#:use-module (gnu packages linux)
#:use-module (gnu packages machine-learning)
#:use-module (gnu packages maths)
+ #:use-module (gnu packages mpi)
#:use-module (gnu packages multiprecision)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages pkg-config)
@@ -582,85 +583,36 @@ (define-public python-pygsp
(define-public faiss
(package
(name "faiss")
- (version "1.5.0")
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/facebookresearch/faiss")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "0pk15jfa775cy2pqmzq62nhd6zfjxmpvz5h731197c28aq3zw39w"))
- (modules '((guix build utils)))
- (snippet
- '(begin
- (substitute* "utils.cpp"
- (("#include <immintrin.h>")
- "#ifdef __SSE__\n#include <immintrin.h>\n#endif"))
- #t))))
+ (version "1.10.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/facebookresearch/faiss")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1x6z94f6vhh7ppsn7wll46k7i63lzcnc3r3rv5zfarljybqhrsjd"))
+ ;; Including but skipping perf_tests requires to patch
+ ;; perf_tests/CMakeLists.txt. KISS: Remove it instead.
+ (modules '((guix build utils)))
+ (snippet #~(begin
+ (delete-file-recursively "perf_tests")
+ (substitute* "CMakeLists.txt"
+ (("add_subdirectory\\(perf_tests\\)") ""))))
+ (patches
+ (search-patches "faiss-tests-CMakeLists-find-googletest.patch"))))
(build-system cmake-build-system)
(arguments
- `(#:configure-flags
- (list "-DBUILD_WITH_GPU=OFF" ; thanks, but no thanks, CUDA.
- "-DBUILD_TUTORIAL=OFF") ; we don't need those
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'prepare-build
- (lambda _
- (let ((features (list ,@(let ((system (or (%current-target-system)
- (%current-system))))
- (cond
- ((string-prefix? "x86_64" system)
- '("-mavx" "-msse2" "-mpopcnt"))
- ((string-prefix? "i686" system)
- '("-msse2" "-mpopcnt"))
- (else
- '()))))))
- (substitute* "CMakeLists.txt"
- (("-m64") "")
- (("-mpopcnt") "") ; only some architectures
- (("-msse4")
- (string-append
- (string-join features)
- " -I" (getcwd)))
- ;; Build also the shared library
- (("ARCHIVE DESTINATION lib")
- "LIBRARY DESTINATION lib")
- (("add_library.*" m)
- "\
-add_library(objlib OBJECT ${faiss_cpu_headers} ${faiss_cpu_cpp})
-set_property(TARGET objlib PROPERTY POSITION_INDEPENDENT_CODE 1)
-add_library(${faiss_lib}_static STATIC $<TARGET_OBJECTS:objlib>)
-add_library(${faiss_lib} SHARED $<TARGET_OBJECTS:objlib>)
-install(TARGETS ${faiss_lib}_static ARCHIVE DESTINATION lib)
-\n")))
-
- ;; See https://github.com/facebookresearch/faiss/issues/520
- (substitute* "IndexScalarQuantizer.cpp"
- (("#define USE_AVX") ""))
-
- ;; Make header files available for compiling tests.
- (mkdir-p "faiss")
- (for-each (lambda (file)
- (mkdir-p (string-append "faiss/" (dirname file)))
- (copy-file file (string-append "faiss/" file)))
- (find-files "." "\\.h$"))
- #t))
- (replace 'check
- (lambda _
- (invoke "make" "-C" "tests"
- (format #f "-j~a" (parallel-job-count)))))
- (add-after 'install 'remove-tests
- (lambda* (#:key outputs #:allow-other-keys)
- (delete-file-recursively
- (string-append (assoc-ref outputs "out")
- "/test"))
- #t)))))
+ (list #:configure-flags
+ #~'("-DFAISS_ENABLE_GPU=OFF" ; thanks, but no thanks, CUDA.
+ "-DFAISS_ENABLE_PYTHON=OFF"
+ "-DBUILD_TESTING=ON")))
(inputs
(list openblas))
(native-inputs
- (list googletest))
+ (list googletest openmpi))
(home-page "https://github.com/facebookresearch/faiss")
(synopsis "Efficient similarity search and clustering of dense vectors")
(description "Faiss is a library for efficient similarity search and
@@ -672,45 +624,75 @@ (define-public faiss
(define-public python-faiss
(package (inherit faiss)
(name "python-faiss")
- (build-system python-build-system)
+ (build-system cmake-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'chdir
- (lambda _ (chdir "python") #t))
- (add-after 'chdir 'build-swig
- (lambda* (#:key inputs #:allow-other-keys)
- (with-output-to-file "../makefile.inc"
- (lambda ()
- (let ((python-version ,(version-major+minor (package-version python))))
- (format #t "\
-PYTHONCFLAGS =-I~a/include/python~a/ -I~a/lib/python~a/site-packages/numpy/core/include
-LIBS = -lpython~a -lfaiss
-SHAREDFLAGS = -shared -fopenmp
-CXXFLAGS = -fpermissive -fopenmp -fPIC
-CPUFLAGS = ~{~a ~}~%"
- (assoc-ref inputs "python*") python-version
- (assoc-ref inputs "python-numpy") python-version
- python-version
- (list ,@(let ((system (or (%current-target-system)
- (%current-system))))
- (cond
- ((string-prefix? "x86_64" system)
- '("-mavx" "-msse2" "-mpopcnt"))
- ((string-prefix? "i686" system)
- '("-msse2" "-mpopcnt"))
- (else
- '()))))))))
- (substitute* "Makefile"
- (("../libfaiss.a") ""))
- (invoke "make" "cpu"))))))
+ (list
+ #:imported-modules `(,@%cmake-build-system-modules
+ (guix build gremlin)
+ (guix build python-build-system))
+ #:modules '((guix build cmake-build-system)
+ ((guix build python-build-system) #:prefix python:)
+ (guix build utils)
+ (guix build gremlin)
+ (ice-9 match)
+ (srfi srfi-1)
+ (srfi srfi-26))
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'chdir
+ (lambda _ (chdir "faiss/python")))
+ (add-before 'install 'python-build
+ (lambda _
+ ((assoc-ref python:%standard-phases 'build)
+ #:use-setuptools? #t)))
+ (replace 'install
+ (lambda args
+ (apply
+ (assoc-ref python:%standard-phases 'install)
+ #:use-setuptools? #t
+ #:configure-flags ''()
+ args)
+ (for-each
+ delete-file
+ (find-files #$output
+ "_*faiss_example_external_module\\.(so|py)$"))))
+ ;; Move check phase after 'install.
+ (delete 'check)
+ (add-after 'install 'check
+ (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+ (if tests?
+ (with-directory-excursion "../../tests"
+ (let* ((version #$(version-major+minor
+ (package-version
+ (this-package-input "python-wrapper"))))
+ (destination (string-append "/lib/python" version
+ "/site-packages/")))
+ (setenv
+ "PYTHONPATH"
+ (string-join
+ (filter
+ directory-exists?
+ (map (match-lambda
+ ((name . directory)
+ (string-append directory destination)))
+ (append outputs inputs)))
+ ":")))
+ (for-each
+ (lambda (file)
+ (invoke "python" file))
+ (remove (cut member <> '(;; External module removed
+ "./external_module_test.py"
+ ;; Avoid torch dependency
+ "./torch_test_contrib.py"
+ "./torch_test_neural_net.py"))
+ (find-files "." "\\.py$"))))
+ (format #t "test suite not run~%")))))))
+ (native-inputs
+ (list python-scipy))
(inputs
- `(("faiss" ,faiss)
- ("openblas" ,openblas)
- ("python*" ,python)
- ("swig" ,swig)))
+ (list faiss openblas python-wrapper swig))
(propagated-inputs
- (list python-matplotlib python-numpy))
+ (list python-numpy))
(description "Faiss is a library for efficient similarity search and
clustering of dense vectors. This package provides Python bindings to the
Faiss library.")))
diff --git a/gnu/packages/patches/faiss-tests-CMakeLists-find-googletest.patch b/gnu/packages/patches/faiss-tests-CMakeLists-find-googletest.patch
new file mode 100644
index 0000000000..5183bac08a
--- /dev/null
+++ b/gnu/packages/patches/faiss-tests-CMakeLists-find-googletest.patch
@@ -0,0 +1,53 @@
+From 9f845321de3bdd2b840c42b977c1c092ac553cc2 Mon Sep 17 00:00:00 2001
+From: Nicolas Graves <ngraves <at> ngraves.fr>
+Date: Fri, 21 Feb 2025 12:05:59 +0100
+Subject: [PATCH] tests/CMakeLists.txt: Find googletest package from inputs
+
+---
+ tests/CMakeLists.txt | 29 +----------------------------
+ 1 file changed, 1 insertion(+), 28 deletions(-)
+
+diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
+index dfab76e0..16a51b0b 100644
+--- a/tests/CMakeLists.txt
++++ b/tests/CMakeLists.txt
+@@ -48,35 +48,8 @@ if (FAISS_ENABLE_PYTHON)
+ target_link_libraries(faiss_test PUBLIC faiss_example_external_module)
+ endif()
+
+-include(FetchContent)
+-FetchContent_Declare(
+- googletest
+- GIT_REPOSITORY https://github.com/google/googletest.git
+- GIT_TAG 58d77fa8070e8cec2dc1ed015d66b454c8d78850 # release-1.12.1
+- OVERRIDE_FIND_PACKAGE)
+-set(BUILD_GMOCK CACHE BOOL OFF)
+-set(INSTALL_GTEST CACHE BOOL OFF)
+-FetchContent_MakeAvailable(googletest)
+-
+-if(NOT EXISTS ${CMAKE_FIND_PACKAGE_REDIRECTS_DIR}/gtest-config.cmake
+- AND NOT EXISTS ${CMAKE_FIND_PACKAGE_REDIRECTS_DIR}/GTestConfig.cmake)
+- file(
+- WRITE ${CMAKE_FIND_PACKAGE_REDIRECTS_DIR}/gtest-config.cmake
+- [=[
+-include(CMakeFindDependencyMacro)
+-find_dependency(googletest)
+-if(NOT TARGET GTest::GTest)
+- add_library(GTest::GTest INTERFACE IMPORTED)
+- target_link_libraries(GTest::GTest INTERFACE GTest::gtest)
+-endif()
+-if(NOT TARGET GTest::Main)
+- add_library(GTest::Main INTERFACE IMPORTED)
+- target_link_libraries(GTest::Main INTERFACE GTest::gtest_main)
+-endif()
+-]=])
+-endif()
+-
+ find_package(OpenMP REQUIRED)
++find_package(GTest REQUIRED)
+ find_package(GTest CONFIG REQUIRED)
+
+ target_link_libraries(faiss_test PRIVATE
+--
+2.48.1
+
--
2.48.1
--
Best regards,
Nicolas Graves
Ludovic Courtès <ludo <at> gnu.org>:Nicolas Graves <ngraves <at> ngraves.fr>:Message #10 received at 76477-done <at> debbugs.gnu.org (full text, mbox):
From: Ludovic Courtès <ludo <at> gnu.org> To: Nicolas Graves <ngraves <at> ngraves.fr> Cc: 76477-done <at> debbugs.gnu.org Subject: Re: [bug#76477] [PATCH] gnu: faiss: Update to 1.10.0. Date: Sun, 09 Mar 2025 23:30:13 +0100
Nicolas Graves <ngraves <at> ngraves.fr> skribis:
> * gnu/packages/graph.scm (faiss): Update to 1.10.0.
> [source]: Adapt snippet. Add patch.
> [arguments]: Delete likely uneeded {phases}. Adapt {configure-flags}.
> [native-inputs]: Add openmpi.
> (python-faiss): Update to 1.10.0.
> [build-system]: Switch to cmake-build-system.
> [arguments]: Rewrite all arguments.
> [inputs]: Improve-style. Switch python for python-wrapper.
> [native-inputs]: Add python-scipy.
> [propagated-inputs]: Remove python-matplotlib.
>
> * gnu/packages/patches/faiss-tests-CMakeLists-find-googletest.patch:
> Add patch.
> * gnu/local.mk: Likewise.
>
> * gnu/packages/graph.scm
Applied, thanks!
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