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Accepting request 857142 from science

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OBS-URL: https://build.opensuse.org/request/show/857142
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/eigen3?expand=0&rev=23
This commit is contained in:
Dominique Leuenberger 2020-12-23 13:19:50 +00:00 committed by Git OBS Bridge
commit 622d3cb5a9
9 changed files with 323 additions and 75 deletions
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64
Remove-error-counting-in-OpenMP-parallelize_gemm.patch
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@ -1,64 +0,0 @@
From ef3cc72cb65e2d500459c178c63e349bacfa834f Mon Sep 17 00:00:00 2001
From: Luke Peterson <hazelnusse@gmail.com>
Date: Thu, 8 Oct 2020 12:16:53 -0700
Subject: [PATCH] Remove error counting in OpenMP parallelize_gemm
This resolves a compilation error associated with
Eigen::eigen_assert_exception. It also eliminates the counting of
exceptions that may occur in the OpenMP parallel section. If an
unhandled exception occurs in this section, the behavior is non-conforming
according to the OpenMP specification.
---
Eigen/src/Core/products/Parallelizer.h | 14 +++++---------
test/CMakeLists.txt | 2 +-
2 files changed, 6 insertions(+), 10 deletions(-)
diff --git a/Eigen/src/Core/products/Parallelizer.h b/Eigen/src/Core/products/Parallelizer.h
index 67b2442b5..a3cc05b77 100644
--- a/Eigen/src/Core/products/Parallelizer.h
+++ b/Eigen/src/Core/products/Parallelizer.h
@@ -132,8 +132,7 @@ void parallelize_gemm(const Functor& func, Index rows, Index cols, Index depth,
ei_declare_aligned_stack_constructed_variable(GemmParallelInfo<Index>,info,threads,0);
- int errorCount = 0;
- #pragma omp parallel num_threads(threads) reduction(+: errorCount)
+ #pragma omp parallel num_threads(threads)
{
Index i = omp_get_thread_num();
// Note that the actual number of threads might be lower than the number of request ones.
@@ -152,14 +151,11 @@ void parallelize_gemm(const Functor& func, Index rows, Index cols, Index depth,
info[i].lhs_start = r0;
info[i].lhs_length = actualBlockRows;
- EIGEN_TRY {
- if(transpose) func(c0, actualBlockCols, 0, rows, info);
- else func(0, rows, c0, actualBlockCols, info);
- } EIGEN_CATCH(...) {
- ++errorCount;
- }
+ if(transpose)
+ func(c0, actualBlockCols, 0, rows, info);
+ else
+ func(0, rows, c0, actualBlockCols, info);
}
- if (errorCount) EIGEN_THROW_X(Eigen::eigen_assert_exception());
#endif
}
diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
index 0747aa6cb..b02577780 100644
--- a/test/CMakeLists.txt
+++ b/test/CMakeLists.txt
@@ -163,7 +163,7 @@ ei_add_test(constructor)
ei_add_test(linearstructure)
ei_add_test(integer_types)
ei_add_test(unalignedcount)
-if(NOT EIGEN_TEST_NO_EXCEPTIONS)
+if(NOT EIGEN_TEST_NO_EXCEPTIONS AND NOT EIGEN_TEST_OPENMP)
ei_add_test(exceptions)
endif()
ei_add_test(redux)
--
GitLab

3
eigen-3.3.8.tar.bz2
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@ -1,3 +0,0 @@
version https://git-lfs.github.com/spec/v1
oid sha256:0215c6593c4ee9f1f7f28238c4e8995584ebf3b556e9dbf933d84feb98d5b9ef
size 1667794

3
eigen-3.3.9.tar.bz2 Normal file
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@ -0,0 +1,3 @@
version https://git-lfs.github.com/spec/v1
oid sha256:0fa5cafe78f66d2b501b43016858070d52ba47bd9b1016b0165a7b8e04675677
size 1667231

132
eigen3-failtests-handling.patch Normal file
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@ -0,0 +1,132 @@
From 72c0bbe2bd1c49c75b6efdb81d0558f8b62578d1 Mon Sep 17 00:00:00 2001
From: Gael Guennebaud <g.gael@free.fr>
Date: Wed, 12 Dec 2018 15:48:36 +0100
Subject: [PATCH] Simplify handling of tests that must fail to compile. Each
test is now a normal ctest target, and build properties (compiler+flags) are
preserved (instead of starting a new build-dir from scratch).
---
CMakeLists.txt | 5 +----
cmake/EigenTesting.cmake | 45 ++++++++++++++++++----------------------
failtest/CMakeLists.txt | 10 ---------
test/CMakeLists.txt | 5 -----
4 files changed, 21 insertions(+), 44 deletions(-)
Index: eigen-3.3.8/CMakeLists.txt
===================================================================
--- eigen-3.3.8.orig/CMakeLists.txt
+++ eigen-3.3.8/CMakeLists.txt
@@ -497,10 +497,7 @@ message(STATUS "")
message(STATUS "Configured Eigen ${EIGEN_VERSION_NUMBER}")
message(STATUS "")
-option(EIGEN_FAILTEST "Enable failtests." OFF)
-if(EIGEN_FAILTEST)
- add_subdirectory(failtest)
-endif()
+add_subdirectory(failtest)
string(TOLOWER "${CMAKE_GENERATOR}" cmake_generator_tolower)
if(cmake_generator_tolower MATCHES "makefile")
Index: eigen-3.3.8/cmake/EigenTesting.cmake
===================================================================
--- eigen-3.3.8.orig/cmake/EigenTesting.cmake
+++ eigen-3.3.8/cmake/EigenTesting.cmake
@@ -320,37 +320,32 @@ endmacro(ei_add_test_sycl)
# note that the test runner for these is CMake itself, when passed -DEIGEN_FAILTEST=ON
# so here we're just running CMake commands immediately, we're not adding any targets.
macro(ei_add_failtest testname)
- get_property(EIGEN_FAILTEST_FAILURE_COUNT GLOBAL PROPERTY EIGEN_FAILTEST_FAILURE_COUNT)
- get_property(EIGEN_FAILTEST_COUNT GLOBAL PROPERTY EIGEN_FAILTEST_COUNT)
- message(STATUS "Checking failtest: ${testname}")
- set(filename "${testname}.cpp")
- file(READ "${filename}" test_source)
-
- try_compile(succeeds_when_it_should_fail
- "${CMAKE_CURRENT_BINARY_DIR}"
- "${CMAKE_CURRENT_SOURCE_DIR}/${filename}"
- COMPILE_DEFINITIONS "-DEIGEN_SHOULD_FAIL_TO_BUILD")
- if (succeeds_when_it_should_fail)
- message(STATUS "FAILED: ${testname} build succeeded when it should have failed")
- endif()
-
- try_compile(succeeds_when_it_should_succeed
- "${CMAKE_CURRENT_BINARY_DIR}"
- "${CMAKE_CURRENT_SOURCE_DIR}/${filename}"
- COMPILE_DEFINITIONS)
- if (NOT succeeds_when_it_should_succeed)
- message(STATUS "FAILED: ${testname} build failed when it should have succeeded")
- endif()
-
- if (succeeds_when_it_should_fail OR NOT succeeds_when_it_should_succeed)
- math(EXPR EIGEN_FAILTEST_FAILURE_COUNT ${EIGEN_FAILTEST_FAILURE_COUNT}+1)
- endif()
+ set(test_target_ok ${testname}_ok)
+ set(test_target_ko ${testname}_ko)
- math(EXPR EIGEN_FAILTEST_COUNT ${EIGEN_FAILTEST_COUNT}+1)
+ # Add executables
+ add_executable(${test_target_ok} ${testname}.cpp)
+ add_executable(${test_target_ko} ${testname}.cpp)
+
+ # Remove them from the normal build process
+ set_target_properties(${test_target_ok} ${test_target_ko} PROPERTIES
+ EXCLUDE_FROM_ALL TRUE
+ EXCLUDE_FROM_DEFAULT_BUILD TRUE)
+
+ # Configure the failing test
+ target_compile_definitions(${test_target_ko} PRIVATE EIGEN_SHOULD_FAIL_TO_BUILD)
+
+ # Add the tests to ctest.
+ add_test(NAME ${test_target_ok}
+ COMMAND ${CMAKE_COMMAND} --build . --target ${test_target_ok} --config $<CONFIGURATION>
+ WORKING_DIRECTORY ${CMAKE_BINARY_DIR})
+ add_test(NAME ${test_target_ko}
+ COMMAND ${CMAKE_COMMAND} --build . --target ${test_target_ko} --config $<CONFIGURATION>
+ WORKING_DIRECTORY ${CMAKE_BINARY_DIR})
- set_property(GLOBAL PROPERTY EIGEN_FAILTEST_FAILURE_COUNT ${EIGEN_FAILTEST_FAILURE_COUNT})
- set_property(GLOBAL PROPERTY EIGEN_FAILTEST_COUNT ${EIGEN_FAILTEST_COUNT})
+ # Expect the second test to fail
+ set_tests_properties(${test_target_ko} PROPERTIES WILL_FAIL TRUE)
endmacro(ei_add_failtest)
# print a summary of the different options
Index: eigen-3.3.8/failtest/CMakeLists.txt
===================================================================
--- eigen-3.3.8.orig/failtest/CMakeLists.txt
+++ eigen-3.3.8/failtest/CMakeLists.txt
@@ -1,4 +1,3 @@
-message(STATUS "Running the failtests")
ei_add_failtest("failtest_sanity_check")
@@ -64,12 +63,3 @@ ei_add_failtest("bdcsvd_int")
ei_add_failtest("eigensolver_int")
ei_add_failtest("eigensolver_cplx")
-if (EIGEN_FAILTEST_FAILURE_COUNT)
- message(FATAL_ERROR
- "${EIGEN_FAILTEST_FAILURE_COUNT} out of ${EIGEN_FAILTEST_COUNT} failtests FAILED. "
- "To debug these failures, manually compile these programs in ${CMAKE_CURRENT_SOURCE_DIR}, "
- "with and without #define EIGEN_SHOULD_FAIL_TO_BUILD.")
-else()
- message(STATUS "Failtest SUCCESS: all ${EIGEN_FAILTEST_COUNT} failtests passed.")
- message(STATUS "")
-endif()
Index: eigen-3.3.8/test/CMakeLists.txt
===================================================================
--- eigen-3.3.8.orig/test/CMakeLists.txt
+++ eigen-3.3.8/test/CMakeLists.txt
@@ -380,10 +380,6 @@ endif(CUDA_FOUND)
endif(EIGEN_TEST_CUDA)
-
-file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/failtests)
-add_test(NAME failtests WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/failtests COMMAND ${CMAKE_COMMAND} ${Eigen_SOURCE_DIR} -G "${CMAKE_GENERATOR}" -DEIGEN_FAILTEST=ON)
-
option(EIGEN_TEST_BUILD_DOCUMENTATION "Test building the doxygen documentation" OFF)
IF(EIGEN_TEST_BUILD_DOCUMENTATION)
add_dependencies(buildtests doc)

18
eigen3-fix-forward_adolc-unit-test.patch Normal file
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@ -0,0 +1,18 @@
Index: eigen-3.3.8/unsupported/test/forward_adolc.cpp
===================================================================
--- eigen-3.3.8.orig/unsupported/test/forward_adolc.cpp
+++ eigen-3.3.8/unsupported/test/forward_adolc.cpp
@@ -7,12 +7,12 @@
// Public License v. 2.0. If a copy of the MPL was not distributed
// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
-#include "main.h"
#include <Eigen/Dense>
#define NUMBER_DIRECTIONS 16
#include <unsupported/Eigen/AdolcForward>
+#include "main.h"
template<typename Vector>
EIGEN_DONT_INLINE typename Vector::Scalar foo(const Vector& p)
{

13
eigen3-googlehash-detection.patch Normal file
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@ -0,0 +1,13 @@
Index: eigen-3.3.8/cmake/FindGoogleHash.cmake
===================================================================
--- eigen-3.3.8.orig/cmake/FindGoogleHash.cmake
+++ eigen-3.3.8/cmake/FindGoogleHash.cmake
@@ -12,6 +12,8 @@ find_path(GOOGLEHASH_INCLUDES
if(GOOGLEHASH_INCLUDES)
# let's make sure it compiles with the current compiler
+ # C++11 is needed for googlehash
+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
file(WRITE ${CMAKE_BINARY_DIR}/googlehash_test.cpp
"#include <google/sparse_hash_map>\n#include <google/dense_hash_map>\nint main(int argc, char** argv) { google::dense_hash_map<int,float> a; google::sparse_hash_map<int,float> b; return 0;}\n")
try_compile(GOOGLEHASH_COMPILE ${CMAKE_BINARY_DIR} ${CMAKE_BINARY_DIR}/googlehash_test.cpp OUTPUT_VARIABLE GOOGLEHASH_COMPILE_RESULT)

66
eigen3-make-sparseqr-unit-test-stable.patch Normal file
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@ -0,0 +1,66 @@
From 3b5deeb546d4017b24846f5b0dc3296a50a039fe Mon Sep 17 00:00:00 2001
From: Gael Guennebaud <g.gael@free.fr>
Date: Tue, 19 Feb 2019 22:57:51 +0100
Subject: [PATCH] bug #899: make sparseqr unit test more stable by 1) trying
with larger threshold and 2) relax rank computation for rank-deficient
problems.
---
test/sparseqr.cpp | 31 ++++++++++++++++++++++++++-----
1 file changed, 26 insertions(+), 5 deletions(-)
diff --git a/test/sparseqr.cpp b/test/sparseqr.cpp
index 3ffe62314..3576cc626 100644
--- a/test/sparseqr.cpp
+++ b/test/sparseqr.cpp
@@ -43,6 +43,7 @@ int generate_sparse_rectangular_problem(MatrixType& A, DenseMat& dA, int maxRows
template<typename Scalar> void test_sparseqr_scalar()
{
+ typedef typename NumTraits<Scalar>::Real RealScalar;
typedef SparseMatrix<Scalar,ColMajor> MatrixType;
typedef Matrix<Scalar,Dynamic,Dynamic> DenseMat;
typedef Matrix<Scalar,Dynamic,1> DenseVector;
@@ -91,14 +92,34 @@ template<typename Scalar> void test_sparseqr_scalar()
exit(0);
return;
}
-
- VERIFY_IS_APPROX(A * x, b);
-
- //Compare with a dense QR solver
+
+ // Compare with a dense QR solver
ColPivHouseholderQR<DenseMat> dqr(dA);
refX = dqr.solve(b);
- VERIFY_IS_EQUAL(dqr.rank(), solver.rank());
+ bool rank_deficient = A.cols()>A.rows() || dqr.rank()<A.cols();
+ if(rank_deficient)
+ {
+ // rank deficient problem -> we might have to increase the threshold
+ // to get a correct solution.
+ RealScalar th = RealScalar(20)*dA.colwise().norm().maxCoeff()*(A.rows()+A.cols()) * NumTraits<RealScalar>::epsilon();
+ for(Index k=0; (k<16) && !test_isApprox(A*x,b); ++k)
+ {
+ th *= RealScalar(10);
+ solver.setPivotThreshold(th);
+ solver.compute(A);
+ x = solver.solve(b);
+ }
+ }
+
+ VERIFY_IS_APPROX(A * x, b);
+
+ // For rank deficient problem, the estimated rank might
+ // be slightly off, so let's only raise a warning in such cases.
+ if(rank_deficient) ++g_test_level;
+ VERIFY_IS_EQUAL(solver.rank(), dqr.rank());
+ if(rank_deficient) --g_test_level;
+
if(solver.rank()==A.cols()) // full rank
VERIFY_IS_APPROX(x, refX);
// else
--
GitLab

56
eigen3.changes
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@ -1,9 +1,63 @@
-------------------------------------------------------------------
Tue Dec 8 19:27:09 UTC 2020 - Atri Bhattacharya <badshah400@gmail.com>
- Update to version 3.3.9:
* Introduce rendering Doxygen math formulas with MathJax and the
option EIGEN_DOC_USE_MATHJAX to control this.
* Issue 1746: Removed implementation of standard
copy-constructor and standard copy-assign-operator from
PermutationMatrix and Transpositions to allow malloc-less
std::move.
* Issue 2036: Make sure the
find_standard_math_library_test_program compiles and doesn't
optimize away functions we try to test for.
* Issue 2046: Rename test/array.cpp to test/array_cwise.cpp to
fix an issue with the C++ standard library header "array"
* Issue 2040: Fix an issue in test/ctorleak that occured when
disabling exceptions.
* Issue 2011: Remove error counting in OpenMP parallel section
in Eigen's GEMM parallelizing logic.
* Issue 2012: Define coeff-wise binary array operators for base
class to fix an issue when using Eigen with C++20
* Fix an issue with Intel® MKL PARDISO support.
- Drop Remove-error-counting-in-OpenMP-parallelize_gemm.patch:
incorporated upstream.
- Add patches to fix building and running tests:
* eigen3-failtests-handling.patch: Simplify handling of tests
that must fail to compile; upstream commit: 72c0bbe.
* eigen3-make-sparseqr-unit-test-stable.patch: Make sparseqr
test more stable to prevent random failures; patch taken from
upstream commit
[https://gitlab.com/libeigen/eigen/-/issues/899].
* eigen3-googlehash-detection.patch: GoogleHash needs C++11 std
to compile test code and be succesfully detected.
* eigen3-fix-forward_adolc-unit-test.patch: Prevent conflict of
std::min/max with eigen's macros by importing eigen
test-suite's main.h header only after all system headers have
been included.
- Setup but don't run tests due to random errors in test-suite
itself
* Pass EIGEN_TEST_CXX11:Bool=ON and EIGEN_TEST_OPENMP:Bool=ON to
cmake to enable building c++11 and openmp tests.
* export EIGEN_SEED=100 to build with fixed seed (see
https://gitlab.com/libeigen/eigen/-/issues/2088).
* export EIGEN_REPEAT=1 to run each test only once (default 10)
to save time and since we use a fixed seed anyway.
* Disable for non-86_64 archs as some unsupported tests fail for
the others (for i586 some supported tests too, see
https://gitlab.com/libeigen/eigen/-/issues/2092).
- Pass CMAKE_SKIP_RPATH:BOOL=OFF and
CMAKE_SKIP_INSTALL_RPATH:BOOL=ON to cmake to fix rpath handling
in Leap 15.2's cmake macros (doesn't hurt generally).
- Change CMAKE_BUILD_TYPE from Release to RelWithDebInfo (openSUSE
default).
-------------------------------------------------------------------
Wed Nov 4 13:27:10 UTC 2020 - Atri Bhattacharya <badshah400@gmail.com>
- Drop eigen_pkgconfig.patch: the includedir now needs to be
specified relative to CMAKE_INSTALL_PREFIX, so this patch causes
the includedir in the pkgconfig file to be erroneousi
the includedir in the pkgconfig file to be erroneous
(boo#1178139).
- Use %autosetup to automatically run through patches.

43
eigen3.spec
View File

@ -20,6 +20,12 @@
%global pkgname eigen3
%global srcname eigen
# The OpenGL support test fails
%bcond_with opengl_test
# Tests fail for different reasons within the test-suite itself; disable for now
# See e.g. https://gitlab.com/libeigen/eigen/-/issues/2088, https://gitlab.com/libeigen/eigen/-/issues/2092
# Also balloons the resources required: > 32 GiB disk space + >= 12 GiB memory
%bcond_with tests
%if "%{flavor}" == "docs"
@ -27,7 +33,7 @@
%endif
Name: eigen3%{?pkgsuffix}
Version: 3.3.8
Version: 3.3.9
Release: 0
Summary: C++ Template Library for Linear Algebra
License: MPL-2.0 AND LGPL-2.1-only AND LGPL-2.1-or-later AND BSD-3-Clause
@ -41,8 +47,18 @@ Patch3: 01_install_FindEigen3.patch
Patch4: eigen3-3.3.1-fixcmake.patch
# PATCH-FIX-UPSTREAM eigen3-CastXML-support-for-aarch64.patch badshah400@gmail.com -- Add CastXML support for ARM aarch64 [https://gitlab.com/libeigen/eigen/-/issues/1979]
Patch5: eigen3-CastXML-support-for-aarch64.patch
# PATCH-FIX-UPSTREAM -- https://gitlab.com/libeigen/eigen/-/merge_requests/232
Patch6: Remove-error-counting-in-OpenMP-parallelize_gemm.patch
%if %{with tests}
# SECTION Patches to fix tests
# PATCH-FIX-UPSTREAM https://gitlab.com/libeigen/eigen/-/commit/72c0bbe2bd1c49c75b6efdb81d0558f8b62578d1
Patch7: eigen3-failtests-handling.patch
# PATCH-FIX-UPSTREAM eigen3-make-sparseqr-unit-test-stable.patch https://gitlab.com/libeigen/eigen/-/issues/899 badshah400@gmail.com -- Make sparseqr test more stable to prevent random failures; patch taken from upstream commit
Patch8: eigen3-make-sparseqr-unit-test-stable.patch
# PATCH-FIX-UPSTREAM eigen3-googlehash-detection.patch badshah400@gmail.com -- GoogleHash needs C++11 std to compile test code and be succesfully detected
Patch9: eigen3-googlehash-detection.patch
# PATCH-FIX-UPSTREAM eigen3-fix-forward_adolc-unit-test.patch badshah400@gmail -- Prevent conflict of std::min/max with eigen's macros by importing eigen test-suite's main.h header only after all system headers have been included
Patch10: eigen3-fix-forward_adolc-unit-test.patch
# /SECTION
%endif
BuildRequires: adolc-devel
BuildRequires: cmake
BuildRequires: fftw3-devel
@ -66,7 +82,7 @@ BuildRequires: texlive-dvips
BuildRequires: texlive-latex
BuildRequires: tex(newunicodechar.sty)
%endif
%if %{with tests}
%if %{with opengl_test}
BuildRequires: freeglut-devel
BuildRequires: glew-devel
BuildRequires: pkgconfig(gl)
@ -106,12 +122,14 @@ echo "HTML_TIMESTAMP = NO" >> doc/Doxyfile.in
%build
%cmake \
-DCMAKE_BUILD_TYPE=Release \
-DINCLUDE_INSTALL_DIR=include/eigen3 \
-DGOOGLEHASH_INCLUDES=%{_includedir}
-DCMAKE_SKIP_RPATH:BOOL=OFF \
-DCMAKE_SKIP_INSTALL_RPATH:BOOL=ON \
-DEIGEN_TEST_CXX11:Bool=%{?with_tests:ON}%{!?with_tests:OFF} \
-DEIGEN_TEST_OPENMP:Bool=%{?with_tests:ON}%{!?with_tests:OFF}
%if "%{flavor}" == ""
make %{?_smp_mflags} all
make %{?_smp_mflags} all %{?with_tests:buildtests}
%else
make %{?_smp_mflags} doc
%endif
@ -126,6 +144,17 @@ find doc -name _formulas.log -print -delete
%fdupes -s build/doc/html/
%endif
%if "%{flavor}" == ""
%if %{with tests}
%check
# Run with a fixed seed to prevent random failures: https://gitlab.com/libeigen/eigen/-/issues/2088
export EIGEN_SEED=100
# Repeat each test once to reduce time spent, since we use a fixed seed anyway
export EIGEN_REPEAT=1
%ctest
%endif
%endif
%if "%{flavor}" == "docs"
%files
%doc build/doc/html/