Hello community,
here is the log from the commit of package sundials for openSUSE:Factory
checked in at 2020-12-17 17:04:00
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Factory/sundials (Old)
and /work/SRC/openSUSE:Factory/.sundials.new.5145 (New)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "sundials"
Thu Dec 17 17:04:00 2020 rev:5 rq:855910 version:5.5.0
Changes:
--------
--- /work/SRC/openSUSE:Factory/sundials/sundials.changes 2020-09-15
16:25:25.258431971 +0200
+++ /work/SRC/openSUSE:Factory/.sundials.new.5145/sundials.changes
2020-12-17 17:08:26.889919825 +0100
@@ -1,0 +2,27 @@
+Wed Dec 2 12:59:07 UTC 2020 - Atri Bhattacharya <badshah...@gmail.com>
+
+- Update to version 5.5.0:
+ * Refactored the SUNDIALS CMake build system to improve build
+ times by as much as 35%.
+ * CMake 3.12.0 or newer is now required.
+ * Users will likely see CMake deprecation warnings, and
+ potentially new errors when incompatible CMake options have
+ been set (previously, these would fail silently).
+ * SUNDIALS now exports CMake targets and installs a
+ SUNDIALSConfig.cmake file.
+ * Added support for SuperLU DIST 6.3.0+.
+- Add sundials-link-pthread.patch: Link against pthread explicitly
+ to fix linking errors when `-Wl,--no-undefined` is added to the
+ linker flags; patch sent upstream.
+- Add BuildRequires: suitesparse-devel and enable KLU solver; pass
+ appropriate options to cmake to make sure the klu library and
+ header is correctly found.
+- Use cmake macros instead of manual cmake commands.
+- Split out new libsundials_generic package with the
+ libsundials_generic shared library.
+- Enable openmpi4 flavour.
+- Run tests except for tests that fail due to floating point
+ errors in the tests themselves.
+- Drop Group tags.
+
+-------------------------------------------------------------------
Old:
----
sundials-5.3.0.tar.gz
New:
----
sundials-5.5.0.tar.gz
sundials-link-pthread.patch
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ sundials.spec ++++++
--- /var/tmp/diff_new_pack.sMANzk/_old 2020-12-17 17:08:27.725920656 +0100
+++ /var/tmp/diff_new_pack.sMANzk/_new 2020-12-17 17:08:27.729920659 +0100
@@ -24,9 +24,11 @@
%undefine DisOMPI1
%undefine DisOMPI2
%undefine DisOMPI3
+%undefine DisOMPI4
%else
%define DisOMPI1 ExclusiveArch: do_not_build
%define DisOMPI3 ExclusiveArch: do_not_build
+%define DisOMPI4 ExclusiveArch: do_not_build
%undefine DisOMPI2
%endif
@@ -61,6 +63,12 @@
%{?DisOMPI3}
%endif
+%if "%{flavor}" == "openmpi4"
+%global mpi_flavor openmpi
+%define mpi_vers 4
+%{?DisOMPI4}
+%endif
+
%{?mpi_flavor:%{bcond_without mpi}}%{!?mpi_flavor:%{bcond_with mpi}}
%{?with_mpi:%{!?mpi_flavor:error "No MPI family specified!"}}
@@ -90,26 +98,29 @@
%define shlib_arkode libsundials_arkode4%{?my_suffix}
%define shlib_cvode libsundials_cvode5%{?my_suffix}
%define shlib_cvodes libsundials_cvodes5%{?my_suffix}
+%define shlib_generic libsundials_generic5%{?my_suffix}
%define shlib_ida libsundials_ida5%{?my_suffix}
%define shlib_idas libsundials_idas4%{?my_suffix}
%define shlib_kinsol libsundials_kinsol5%{?my_suffix}
%define shlib_nvec libsundials_nvec5%{?my_suffix}
Name: %{package_name}
-Version: 5.3.0
+Version: 5.5.0
Release: 0
Summary: Suite of nonlinear solvers
# SUNDIALS is licensed under BSD with some additional (but unrestrictive)
clauses.
# Check the file 'LICENSE' for details.
License: BSD-3-Clause
-Group: System/Libraries
URL: https://computation.llnl.gov/projects/sundials/
Source0:
https://computation.llnl.gov/projects/sundials/download/%{pname}-%{version}.tar.gz
+# PATCH-FIX-UPSTREAM sundials-link-pthread.patch badshah...@gmail.com --
Explicitly link against pthread to fix linking errors when `-Wl,--no-undefined`
is added to the linker flags
+Patch0: sundials-link-pthread.patch
BuildRequires: blas-devel
-BuildRequires: cmake
+BuildRequires: cmake >= 3.12
BuildRequires: fdupes
BuildRequires: gcc-fortran
BuildRequires: lapack-devel
+BuildRequires: suitesparse-devel
%if %{with mpi}
BuildRequires: %{mpi_flavor}%{?mpi_ext}-devel
%if 0%{?suse_version} >= 1550 && %{flavor} != "mvapich2"
@@ -131,10 +142,10 @@
%package devel
Summary: Suite of nonlinear solvers (developer files)
-Group: Development/Libraries/C and C++
Requires: %{shlib_arkode} = %{version}
Requires: %{shlib_cvodes} = %{version}
Requires: %{shlib_cvode} = %{version}
+Requires: %{shlib_generic} = %{version}
Requires: %{shlib_idas} = %{version}
Requires: %{shlib_ida} = %{version}
Requires: %{shlib_kinsol} = %{version}
@@ -149,7 +160,6 @@
%package doc
Summary: Suite of nonlinear solvers (documentation)
-Group: Documentation/Other
%description doc
SUNDIALS is a SUite of Non-linear DIfferential/ALgebraic equation Solvers
@@ -159,7 +169,6 @@
%package -n %{shlib_main}
Summary: Suite of nonlinear solvers - main shared libraries
-Group: Productivity/Scientific/Math
%description -n %{shlib_main}
SUNDIALS is a SUite of Non-linear DIfferential/ALgebraic equation Solvers
@@ -169,7 +178,6 @@
%package -n %{shlib_arkode}
Summary: Suite of nonlinear solvers - arkode shared libraries
-Group: Productivity/Scientific/Math
%description -n %{shlib_arkode}
SUNDIALS is a SUite of Non-linear DIfferential/ALgebraic equation Solvers
@@ -179,7 +187,6 @@
%package -n %{shlib_cvode}
Summary: Suite of nonlinear solvers - cvode shared libraries
-Group: Productivity/Scientific/Math
%description -n %{shlib_cvode}
SUNDIALS is a SUite of Non-linear DIfferential/ALgebraic equation Solvers
@@ -189,7 +196,6 @@
%package -n %{shlib_cvodes}
Summary: Suite of nonlinear solvers - cvodes shared libraries
-Group: Productivity/Scientific/Math
%description -n %{shlib_cvodes}
SUNDIALS is a SUite of Non-linear DIfferential/ALgebraic equation Solvers
@@ -197,9 +203,17 @@
This package provides the shared libraries for SUNDIALS' cvodes solver.
+%package -n %{shlib_generic}
+Summary: Suite of nonlinear solvers - generic shared libraries
+
+%description -n %{shlib_generic}
+SUNDIALS is a SUite of Non-linear DIfferential/ALgebraic equation Solvers
+for use in writing mathematical software.
+
+This package provides the shared libraries for SUNDIALS' generic solver.
+
%package -n %{shlib_ida}
Summary: Suite of nonlinear solvers - ida shared libraries
-Group: Productivity/Scientific/Math
%description -n %{shlib_ida}
SUNDIALS is a SUite of Non-linear DIfferential/ALgebraic equation Solvers
@@ -209,7 +223,6 @@
%package -n %{shlib_idas}
Summary: Suite of nonlinear solvers - idas shared libraries
-Group: Productivity/Scientific/Math
%description -n %{shlib_idas}
SUNDIALS is a SUite of Non-linear DIfferential/ALgebraic equation Solvers
@@ -219,7 +232,6 @@
%package -n %{shlib_kinsol}
Summary: Suite of nonlinear solvers - kinsol shared libraries
-Group: Productivity/Scientific/Math
%description -n %{shlib_kinsol}
SUNDIALS is a SUite of Non-linear DIfferential/ALgebraic equation Solvers
@@ -229,7 +241,6 @@
%package -n %{shlib_nvec}
Summary: Suite of nonlinear solvers - nvec shared libraries
-Group: Productivity/Scientific/Math
%description -n %{shlib_nvec}
SUNDIALS is a SUite of Non-linear DIfferential/ALgebraic equation Solvers
@@ -238,40 +249,29 @@
This package provides the shared libraries for SUNDIALS' nvec solvers.
%prep
-%setup -q -n %{pname}-%{version}
+%autosetup -p1 -n %{pname}-%{version}
%build
-# CAN'T DIRECTLY USE %%cmake MACRO SINCE CUSTOM CMAKE_INSTALL_PREFIX IS NEEDED
-mkdir -p build
-pushd build
-cmake .. \
+%cmake \
-DCMAKE_INSTALL_PREFIX=%{my_prefix} \
- -DCMAKE_BUILD_TYPE=RelWithDebInfo \
- -DCMAKE_C_FLAGS="${CFLAGS:-%optflags} -DNDEBUG" \
- -DCMAKE_CXX_FLAGS="${CXXFLAGS:-%optflags} -DNDEBUG" \
- -DCMAKE_Fortran_FLAGS="${FFLAGS:-%optflags%{?_fmoddir: -I%_fmoddir}}
-DNDEBUG" \
- -DCMAKE_EXE_LINKER_FLAGS="-Wl,--as-needed -Wl,--no-undefined
-Wl,-z,now" \
- -DCMAKE_MODULE_LINKER_FLAGS="-Wl,--as-needed" \
- -DCMAKE_SHARED_LINKER_FLAGS="-Wl,--as-needed -Wl,--no-undefined
-Wl,-z,now" \
+ -DCMAKE_INSTALL_LIBDIR=%{my_libdir} \
%if "%{?_lib}" == "lib64"
-DLIB_SUFFIX=64 \
%endif
- -DCMAKE_SKIP_RPATH:BOOL=ON \
- -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \
- -DBUILD_SHARED_LIBS:BOOL=ON \
- -DBUILD_STATIC_LIBS:BOOL=OFF \
- -DCMAKE_COLOR_MAKEFILE:BOOL=OFF \
- -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF \
- -DBLAS_ENABLE:BOOL=ON \
- -DLAPACK_ENABLE:BOOL=ON \
- -DPTHREAD_ENABLE:BOOL=ON \
+ -DCMAKE_SKIP_RPATH:BOOL=OFF \
+ -DCMAKE_SKIP_INSTALL_RPATH:BOOL=ON \
+ -DENABLE_LAPACK:BOOL=ON \
+ -DENABLE_PTHREAD:BOOL=ON \
+ -DENABLE_KLU:BOOL=ON \
+ -DKLU_INCLUDE_DIR:PATH=%{_includedir}/suitesparse \
+ -DKLU_LIBRARY_DIR:PATH=%{_libdir} \
-DSUNDIALS_BUILD_WITH_MONITORING:BOOL=ON \
%if %{without mpi}
-DEXAMPLES_INSTALL_PATH=%{_docdir}/%{name}/examples \
- -DMPI_ENABLE:BOOL=OFF
+ -DENABLE_MPI:BOOL=OFF
%else
-DEXAMPLES_INSTALL:BOOL=OFF \
- -DMPI_ENABLE:BOOL=ON \
+ -DENABLE_MPI:BOOL=ON \
-DMPI_C_COMPILER=%{my_bindir}/mpicc \
-DMPI_CXX_COMPILER=%{my_bindir}/mpicxx \
-DMPI_Fortran_COMPILER=%{my_bindir}/mpif90 \
@@ -279,16 +279,25 @@
%endif
%cmake_build
-popd
%install
-# SUNDIALS does not support the 'DESTDIR' method, hence:
%cmake_install
rm %{buildroot}%{my_incdir}/sundials/{NOTICE,LICENSE}
%fdupes %{buildroot}
+%check
+# Send extremely verbose output to a log file instead of printing to screen to
avoid build log bloat
+# Disable the sunlinsol tests which fail apparently due to minor floating pt
issues
+# On 32-bit, also disable the sunmatrix tests which fail due to minor floating
pt issues
+export LD_LIBRARY_PATH=%{my_libdir}
+%ifarch %ix86
+%ctest --quiet --output-log test-output.log --exclude-regex
"test_(sunlinsol_lapack|sunmatrix_sparse)*" || ( grep "Fail" test-output.log;
exit 1 )
+%else
+%ctest --quiet --output-log test-output.log --exclude-regex
"test_sunlinsol_lapack*" || ( grep "Fail" test-output.log; exit 1; )
+%endif
+
%post -n %{shlib_main} -p /sbin/ldconfig
%postun -n %{shlib_main} -p /sbin/ldconfig
@@ -301,6 +310,9 @@
%post -n %{shlib_cvodes} -p /sbin/ldconfig
%postun -n %{shlib_cvodes} -p /sbin/ldconfig
+%post -n %{shlib_generic} -p /sbin/ldconfig
+%postun -n %{shlib_generic} -p /sbin/ldconfig
+
%post -n %{shlib_ida} -p /sbin/ldconfig
%postun -n %{shlib_ida} -p /sbin/ldconfig
@@ -331,6 +343,10 @@
%doc README.md CONTRIBUTING.md NOTICE
%{my_libdir}/*.so
%{my_incdir}/*
+%if %{with mpi}
+%dir %{my_libdir}/cmake
+%endif
+%{my_libdir}/cmake/sundials/
%files -n %{shlib_main}
%{my_libdir}/libsundials_sun*.so.*
@@ -346,6 +362,9 @@
%files -n %{shlib_cvodes}
%{my_libdir}/libsundials_cvodes.so.*
+%files -n %{shlib_generic}
+%{my_libdir}/libsundials_generic.so.*
+
%files -n %{shlib_ida}
%{my_libdir}/libsundials_ida.so.*
++++++ _multibuild ++++++
--- /var/tmp/diff_new_pack.sMANzk/_old 2020-12-17 17:08:27.757920687 +0100
+++ /var/tmp/diff_new_pack.sMANzk/_new 2020-12-17 17:08:27.761920690 +0100
@@ -3,5 +3,6 @@
<package>openmpi1</package>
<package>openmpi2</package>
<package>openmpi3</package>
+ <package>openmpi4</package>
<package>mvapich2</package>
</multibuild>
++++++ sundials-5.3.0.tar.gz -> sundials-5.5.0.tar.gz ++++++
/work/SRC/openSUSE:Factory/sundials/sundials-5.3.0.tar.gz
/work/SRC/openSUSE:Factory/.sundials.new.5145/sundials-5.5.0.tar.gz differ:
char 5, line 1
++++++ sundials-link-pthread.patch ++++++
Index: sundials-5.5.0/src/nvector/pthreads/CMakeLists.txt
===================================================================
--- sundials-5.5.0.orig/src/nvector/pthreads/CMakeLists.txt
+++ sundials-5.5.0/src/nvector/pthreads/CMakeLists.txt
@@ -27,6 +27,8 @@ sundials_add_library(sundials_nvecpthrea
nvector_pthreads.c
OBJECT_LIBRARIES
sundials_generic_obj
+ LINK_LIBRARIES
+ PRIVATE pthread
OUTPUT_NAME
sundials_nvecpthreads
VERSION
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