Hello community, here is the log from the commit of package lammps for openSUSE:Factory checked in at 2020-09-25 16:34:12 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/lammps (Old) and /work/SRC/openSUSE:Factory/.lammps.new.4249 (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "lammps" Fri Sep 25 16:34:12 2020 rev:18 rq:836169 version:20200918 Changes: -------- --- /work/SRC/openSUSE:Factory/lammps/lammps.changes 2020-06-15 20:31:21.310549879 +0200 +++ /work/SRC/openSUSE:Factory/.lammps.new.4249/lammps.changes 2020-09-25 16:35:25.728097769 +0200 @@ -1,0 +2,112 @@ +Sun Sep 20 14:56:09 UTC 2020 - Christoph Junghans <[email protected]> + +- dropped disable_noopt.patch, merged upstream +- added 9cdde97863825e4fdce449920d39b25414b2b0b3.patch from + https://github.com/lammps/lammps/pull/2381 fix a failing test +- added 61ce73273b3290083c01e6a2fadfb3db0889b9ba.patch from + https://github.com/lammps/lammps/pull/2381 fix another failing test +- bump version to 20200918 (patch) + - New fix pafi to perform langevin or brownian dynamics time + integration constrained to a potential hyperplane. Intended to + be coupled to the PAFI C++ code (Thomas Swinburne, CNRS /CINaM + Marseille and Mihai-Cosmin Marinica, SRMP/CEA Saclay) PR + [gh#lammps/lammps#1472] + - Update of the Kokkos library to version 3.2 (Stand Moore, SNL + and the Kokkos developers), PR [gh#lammps/lammps#2311] + - Updates to KOKKOS package to improve usability with the HIP + backend for AMD GPUs (Nick Curtis) PR [gh#lammps/lammps#2371] + - Update of the USER-COLVARS package to version 2020-09-17 + (Giacomo Fiorin, NIH and other Colvars developers) PR + [gh#lammps/lammps#2356], PR [gh#lammps/lammps#2376] + - Change behavior of fix bond/react to update all charges by + default which is the more intuitive behavior. Keywords have + been updated to be more intuitive as well (Jake Gissinger, U + Colorado) PR [gh#lammps/lammps#2368] + - Update of dump styles in the COMPRESS package to be consistent + with recent changes elsewhere, added support for Zstd + compression and the option to set the compression level (Richard + Berger, Temple U), PR [gh#lammps/lammps#2331] + - Use eigensolver contributed to USER-REACTION package to + replace the old "jacobi" function to avoid licensing issues. + Implement wrapper functions around templated implementation + (Andrew Jewett, Scripps), PR [gh#lammps/lammps#2347] + - Small refactor of fix qeq/reax and its USER-OMP and KOKKOS + variants to reduce code replication and allow to add features + (Stan Moore, SNL) PR [gh#lammps/lammps#2354] + - Replace the use of the C-style NULL with the C++11 nullptr + keyword, where meaningful. (E. Anne Gunn, Sheridan College) PR + [gh#lammps/lammps#2358] + - Replace numeric constants in Atom and AtomVec classes by + symbolic ones via enumerators (Axel Kohlmeyer, Temple U) PR + [gh#lammps/lammps#2360] + - Bugfixes for the GPU package and related CMake/make files + (Vsevolod Nikolskiy, HSE University Moscow and Trung Nguyen, + Northwestern U), PR [gh#lammps/lammps#2307], PR + [gh#lammps/lammps#2313], PR [gh#lammps/lammps#2322], PR + [gh#lammps/lammps#2326] + - Bugfix for Langevin thermostatting inside of multiple fix + rigid variants (Trung Nguyen, Northwestern U) PR + [gh#lammps/lammps#2367] + - Refactoring of the C library interface and the Python wrapper + for consistency and maintainability, unit test support for the + interfaces, decoration of library functions with Doxygen comments + for semi-automatic documentation in the manual (Axel Kohlmeyer and + Richard Berger, Temple U) PR [gh#lammps/lammps#2310], PR + [gh#lammps/lammps#2318], PR [gh#lammps/lammps#2320], PR + [gh#lammps/lammps#2357], PR [gh#lammps/lammps#2359], PR + [gh#lammps/lammps#2362] + - Update of documentation build system to include Doxygen + processing and integration of that output via the "breathe" + Sphinx extension inclusion of the Developer Guide in the + manual, update and corrections to the CMake support (Axel + Kohlmeyer and Richard Berger, Temple U) PR + [gh#lammps/lammps#2309], PR [gh#lammps/lammps#2312], PR + [gh#lammps/lammps#2327] + - Update headers in the documentation of LAMMPS style commands + to be more compact and check for missing index entries + (Richard Berger, Temple U) PR [gh#lammps/lammps#2335] + - Update the compilation related documentation to use the + sphinx-tabs extension (in HTML mode only) to make it more + compact (Axel Kohlmeyer, Temple U) PR [gh#lammps/lammps#2348] + - Revised internal and external links in the documentation (Matt + Mansell and others) PR [gh#lammps/lammps#2341] + - Move more convenience functions from classes to the utils + namespace, update the code to consistently use the new + versions and remove the old, update the manual to include the + documentation of those APIs into the developer guide (Axel + Kohlmeyer, Temple U) PR [gh#lammps/lammps#2319], PR + [gh#lammps/lammps#2349] + - Start of a new (and "official") Fortran library interface and + corresponding sphinx API documentation in the programmer guide + plus unit tests for implemented APIs (Axel Kohlmeyer, Temple U) PR + [gh#lammps/lammps#2325] + - Update include file conventions and update lists of include + files accordingly, add make iwyu target to run the + include-what-you-use tool (Axel Kohlmeyer, Temple U) PR + [gh#lammps/lammps#2338] + - Make internal memory usage reporting consistently use the same + data type (Axel Kohlmeyer, Temple U) PR + [gh#lammps/lammps#2363] + - Add support to call reset_mol_ids internally from fix + bond/react (Jake Gissinger, U Colorado), PR + [gh#lammps/lammps#2240] + - Add RMSD based constraint to fix bond/react (Jake Gissinger, U + Collorado, and Andrew Jewett, Scripps, and Yuya Kurebayashi, + Tohoku U) PR [gh#lammps/lammps#2314] + - Refactor of USER-BOCS code to fix memory leaks and memory + access issues (E. Anne Gunn, Sheridan College) PR + [gh#lammps/lammps#2274] + - Implementation of force history for Mindlin variants of the + granular pair style (Jibril B. Coulibaly, Northwestern U), PR + [gh#lammps/lammps#2196] + - Updated singularity container description files to better + support the upcoming stable release (Richard Berger, Temple U) + PR [gh#lammps/lammps#2340] + - Various small updates and corrections (multiple authors) PR + [gh#lammps/lammps#2315], PR [gh#lammps/lammps#2317], PR + [gh#lammps/lammps#2336], PR [gh#lammps/lammps#2344], PR + [gh#lammps/lammps#2353], PR [gh#lammps/lammps#2364], PR + [gh#lammps/lammps#2366], PR [gh#lammps/lammps#2373], PR + [gh#lammps/lammps#2369], PR [gh#lammps/lammps#2375] + +------------------------------------------------------------------- Old: ---- disable_noopt.patch lammps-patch_5May2020.tar.gz lammps-testing-patch_5May2020.tar.gz New: ---- 61ce73273b3290083c01e6a2fadfb3db0889b9ba.patch 9cdde97863825e4fdce449920d39b25414b2b0b3.patch lammps-patch_18Sep2020.tar.gz release-1.10.0.tar.gz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ lammps.spec ++++++ --- /var/tmp/diff_new_pack.Hv3zAE/_old 2020-09-25 16:35:27.808099615 +0200 +++ /var/tmp/diff_new_pack.Hv3zAE/_new 2020-09-25 16:35:27.812099620 +0200 @@ -33,17 +33,19 @@ %endif Name: lammps -Version: 20200505 +Version: 20200918 Release: 0 -%define uversion patch_5May2020 +%define uversion patch_18Sep2020 Summary: Molecular Dynamics Simulator License: GPL-2.0-only AND GPL-3.0-or-later Group: Productivity/Scientific/Chemistry URL: https://lammps.sandia.gov Source0: https://github.com/lammps/lammps/archive/%{uversion}.tar.gz#/%{name}-%{uversion}.tar.gz -Source1: https://github.com/lammps/lammps-testing/archive/%{uversion}.tar.gz#/%{name}-testing-%{uversion}.tar.gz -# PATCH-FIX-UPSTREAM disable_noopt.patch, gcc flags a false positive [gh#lammps/lammps#2078] -Patch0: disable_noopt.patch +Source1: https://github.com/google/googletest/archive/release-1.10.0.tar.gz +# PATCH-FIX-UPSTREAM 9cdde97863825e4fdce449920d39b25414b2b0b3.patch from https://github.com/lammps/lammps/pull/2381 fix a failing test +Patch0: 9cdde97863825e4fdce449920d39b25414b2b0b3.patch +# PATCH-FIX-UPSTREAM 61ce73273b3290083c01e6a2fadfb3db0889b9ba.patch from https://github.com/lammps/lammps/pull/2381 fix another failing test +Patch1: 61ce73273b3290083c01e6a2fadfb3db0889b9ba.patch BuildRequires: %{mpiver} BuildRequires: %{mpiver}-devel BuildRequires: cmake @@ -53,6 +55,8 @@ BuildRequires: gcc-fortran BuildRequires: gsl-devel BuildRequires: kim-api-devel >= 2.1 +# for testing +BuildRequires: kim-api-examples BuildRequires: libjpeg-devel BuildRequires: libpng-devel BuildRequires: ocl-icd-devel @@ -62,7 +66,7 @@ BuildRequires: zlib-devel %ifnarch ppc64 %ix86 %global with_kokkos 1 -BuildRequires: kokkos-devel >= 3.1 +BuildRequires: kokkos-devel >= 3.2 %endif Requires: %{name}-data BuildRoot: %{_tmppath}/%{name}-%{version}-build @@ -164,11 +168,7 @@ %prep %setup -a 1 -q -n %{name}-%{uversion} %patch0 -p1 -# see [gh#lammps/lammps#2079], this is a bug in older version -# of the ocl package, compare [GCC#58241] -%ifarch ppc64le -sed -i '/CMAKE_CXX_EXTENSIONS/s/OFF/ON/' cmake/CMakeLists.txt -%endif +%patch1 -p1 %build source %{_libdir}/mpi/gcc/%{mpiver}/bin/mpivars.sh @@ -176,19 +176,24 @@ %{cmake} \ -C ../cmake/presets/all_on.cmake \ -C ../cmake/presets/nolib.cmake \ - -DCMAKE_Fortran_COMPILER="$(type -p gfortran)" \ - -DCMAKE_TUNE_FLAGS='' \ + -DCMAKE_TUNE_FLAGS='%{?tune_flags}' \ -DBUILD_TOOLS=ON \ -DBUILD_OMP=ON \ %{?with_kokkos:-DPKG_KOKKOS=ON -DEXTERNAL_KOKKOS=ON} \ - -DBUILD_MPI=ON -DPKG_PYTHON=ON \ - -DPKG_KIM=ON -DENABLE_TESTING=ON -DPKG_VORONOI=ON \ - -DPKG_GPU=ON -DGPU_API=OpenCL -DFFT=FFTW3 \ - -DPYTHON_INSTDIR=%{python_sitearch} -DCMAKE_INSTALL_SYSCONFDIR=/etc \ -%ifnarch x86_64 i586 + -DBUILD_MPI=ON \ + -DPKG_PYTHON=ON \ + -DPKG_KIM=ON \ + -DPKG_VORONOI=ON \ + -DPKG_GPU=ON -DGPU_API=OpenCL \ + -DFFT=FFTW3 \ + -DPYTHON_INSTDIR=%{python_sitearch} \ + -DCMAKE_INSTALL_SYSCONFDIR=/etc \ +%ifnarch x86_64 %ix86 -DPKG_USER-INTEL=OFF \ %endif - -DLAMMPS_TESTING_SOURCE_DIR=$(echo $PWD/../lammps-testing-*) ../cmake + -DENABLE_TESTING=ON \ + -DGTEST_URL=%{S:1} \ + ../cmake %cmake_build %install @@ -196,7 +201,13 @@ %check export LD_LIBRARY_PATH='%{buildroot}%{_libdir}:%{_libdir}/mpi/gcc/%{mpiver}/%{_lib}' -%ctest + +# https://github.com/lammps/lammps/issues/2383, inject -msse2 on %ix86 to make test pass +%ifarch %ix86 +%global testargs --exclude-regex AtomStyle +%endif + +%ctest %{?testargs} %post -n liblammps0 -p /sbin/ldconfig %postun -n liblammps0 -p /sbin/ldconfig ++++++ 61ce73273b3290083c01e6a2fadfb3db0889b9ba.patch ++++++ >From 61ce73273b3290083c01e6a2fadfb3db0889b9ba Mon Sep 17 00:00:00 2001 From: Richard Berger <[email protected]> Date: Sat, 19 Sep 2020 22:27:21 -0400 Subject: [PATCH] Add missing -u flag for unbuffered PyLammps tests Addresses issue #2380 --- unittest/python/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/unittest/python/CMakeLists.txt b/unittest/python/CMakeLists.txt index 6082eb99b1..490314ca9d 100644 --- a/unittest/python/CMakeLists.txt +++ b/unittest/python/CMakeLists.txt @@ -37,7 +37,7 @@ if (Python_EXECUTABLE) set(PYTHON_TEST_RUNNER ${Python_EXECUTABLE} -u) endif() else() - set(PYTHON_TEST_RUNNER ${Python_EXECUTABLE}) + set(PYTHON_TEST_RUNNER ${Python_EXECUTABLE} -u) endif() add_test(NAME PythonOpen ++++++ 9cdde97863825e4fdce449920d39b25414b2b0b3.patch ++++++ >From 9cdde97863825e4fdce449920d39b25414b2b0b3 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer <[email protected]> Date: Fri, 18 Sep 2020 22:36:05 -0400 Subject: [PATCH] correct test logic --- unittest/c-library/test_library_properties.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/unittest/c-library/test_library_properties.cpp b/unittest/c-library/test_library_properties.cpp index 11bdc28552..2f8724e325 100644 --- a/unittest/c-library/test_library_properties.cpp +++ b/unittest/c-library/test_library_properties.cpp @@ -53,7 +53,7 @@ class LibraryProperties : public ::testing::Test { TEST_F(LibraryProperties, version) { - EXPECT_GE(20200824, lammps_version(lmp)); + EXPECT_LT(20200917, lammps_version(lmp)); }; TEST_F(LibraryProperties, memory_usage)
